query stringlengths 7 33.1k | document stringlengths 7 335k | metadata dict | negatives listlengths 3 101 | negative_scores listlengths 3 101 | document_score stringlengths 3 10 | document_rank stringclasses 102
values |
|---|---|---|---|---|---|---|
Total Product in Cart | @ModelAttribute("TotalProduct")
public int totalProduct(Authentication authentication){
int total = 0;
if (authentication != null){
String emailName = authentication.getName();
User user = userService.getUserFindByEmail(emailName);
List<Cart> listCart = user.getListCart();
for(int i = 0; i < listCart.size(); i++){
total = total + listCart.get(i).getQuantity();
}
}
return total;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"private double totalPrice(){\n\n double sum = 0;\n\n for (CarComponent carComponent : componentsCart) {\n sum += (carComponent.getCompPrice() * carComponent.getCompQuantity()) ;\n }\n return sum;\n }",
"void calculateTotalPrice(){\n totalPrice = 0;\n cartCo... | [
"0.78003865",
"0.7727704",
"0.7620494",
"0.751521",
"0.75042367",
"0.74948335",
"0.7493079",
"0.72967637",
"0.7269469",
"0.7253282",
"0.7207012",
"0.71750164",
"0.71462995",
"0.70980275",
"0.7075874",
"0.7040019",
"0.69911265",
"0.6968401",
"0.6947225",
"0.69389665",
"0.68920... | 0.72894627 | 8 |
constructor which initializes the words | public Removalstops()
{
stopWords.add("am");
stopWords.add("my");
stopWords.add("at");
stopWords.add("a");
stopWords.add("i");
stopWords.add("is");
stopWords.add("of");
stopWords.add("have");
stopWords.add("--");
stopWords.add("do");
stopWords.add("the");
stopWords.add("was");
stopWords.add("iam");
stopWords.add("there");
stopWords.add("what");
stopWords.add("for");
stopWords.add("in");
stopWords.add("very");
stopWords.add("and");
stopWords.add("to");
stopWords.add("often");
stopWords.add("because");
stopWords.add("in");
stopWords.add("an");
stopWords.add("can");
stopWords.add("via");
stopWords.add("even");
stopWords.add("as");
stopWords.add("best");
stopWords.add("been");
stopWords.add("into");
stopWords.add("by");
stopWords.add("around");
stopWords.add("being");
stopWords.add("from");
stopWords.add("etc");
stopWords.add("his");
stopWords.add("do");
stopWords.add("have");
stopWords.add("had");
stopWords.add("able");
stopWords.add("about");
stopWords.add("above");
stopWords.add("abroad");
stopWords.add("according");
stopWords.add("accordingly");
stopWords.add("across");
stopWords.add("actually");
stopWords.add("adj");
stopWords.add("after");
stopWords.add("afterwards");
stopWords.add("again");
stopWords.add("against");
stopWords.add("ago");
stopWords.add("ahead");
stopWords.add("ain't");
stopWords.add("all");
stopWords.add("allow");
stopWords.add("allows");
stopWords.add("almost");
stopWords.add("alone");
stopWords.add("along");
stopWords.add("alongside");
stopWords.add("already");
stopWords.add("also");
stopWords.add("although");
stopWords.add("always");
stopWords.add("am");
stopWords.add("amid");
stopWords.add("amidst");
stopWords.add("among");
stopWords.add("amongst");
stopWords.add("an");
stopWords.add("and");
stopWords.add("another");
stopWords.add("any");
stopWords.add("anybody");
stopWords.add("anyhow");
stopWords.add("anyone");
stopWords.add("anything");
stopWords.add("anyway");
stopWords.add("anyways");
stopWords.add("anywhere");
stopWords.add("apart");
stopWords.add("appear");
stopWords.add("appreciate");
stopWords.add("appropriate");
stopWords.add("are");
stopWords.add("aren't");
stopWords.add("around");
stopWords.add("as");
stopWords.add("a's");
stopWords.add("aside");
stopWords.add("ask");
stopWords.add("asking");
stopWords.add("associated");
stopWords.add("at");
stopWords.add("available");
stopWords.add("away");
stopWords.add("awfully");
stopWords.add("back");
stopWords.add("backward");
stopWords.add("backwards");
stopWords.add("be");
stopWords.add("became");
stopWords.add("beacause");
stopWords.add("become");
stopWords.add("becomes");
stopWords.add("becoming");
stopWords.add("been");
stopWords.add("before");
stopWords.add("beforehand");
stopWords.add("begin");
stopWords.add("behind");
stopWords.add("being");
stopWords.add("believe");
stopWords.add("below");
stopWords.add("beside");
stopWords.add("besides");
stopWords.add("best");
stopWords.add("better");
stopWords.add("between");
stopWords.add("beyond");
stopWords.add("both");
stopWords.add("brief");
stopWords.add("but");
stopWords.add("by");
stopWords.add("came");
stopWords.add("can");
stopWords.add("cannot");
stopWords.add("cant");
stopWords.add("can't");
stopWords.add("caption");
stopWords.add("cause");
stopWords.add("causes");
stopWords.add("certain");
stopWords.add("cetrainly");
stopWords.add("changes");
stopWords.add("clearly");
stopWords.add("c'mon");
stopWords.add("co");
stopWords.add("co.");
stopWords.add("com");
stopWords.add("come");
stopWords.add("comes");
stopWords.add("concerning");
stopWords.add("consequently");
stopWords.add("consider");
stopWords.add("considering");
stopWords.add("could");
stopWords.add("couldn't");
stopWords.add("c's");
stopWords.add("currently");
stopWords.add("dare");
stopWords.add("daren't");
stopWords.add("definitely");
stopWords.add("described");
stopWords.add("despite");
stopWords.add("did");
stopWords.add("didn't");
stopWords.add("different");
stopWords.add("directly");
stopWords.add("do");
stopWords.add("does");
stopWords.add("doesn't");
stopWords.add("doing");
stopWords.add("done");
stopWords.add("don't");
stopWords.add("down");
stopWords.add("downwards");
stopWords.add("during");
stopWords.add("each");
stopWords.add("edu");
stopWords.add("eg");
stopWords.add("eight");
stopWords.add("eighty");
stopWords.add("either");
stopWords.add("else");
stopWords.add("elsewhere");
stopWords.add("end");
stopWords.add("ending");
stopWords.add("enough");
stopWords.add("entirely");
stopWords.add("especially");
stopWords.add("et");
stopWords.add("etc");
stopWords.add("even");
stopWords.add("evenmore");
stopWords.add("every");
stopWords.add("everybody");
stopWords.add("everyone");
stopWords.add("everything");
stopWords.add("everywhere");
stopWords.add("ex");
stopWords.add("exactly");
stopWords.add("example");
stopWords.add("except");
stopWords.add("fairly");
stopWords.add("far");
stopWords.add("farhter");
stopWords.add("few");
stopWords.add("fewer");
stopWords.add("fifth");
stopWords.add("first");
stopWords.add("five");
stopWords.add("followed");
stopWords.add("following");
stopWords.add("follows");
stopWords.add("for");
stopWords.add("forever");
stopWords.add("former");
stopWords.add("formerly");
stopWords.add("forth");
stopWords.add("forward");
stopWords.add("found");
stopWords.add("four");
stopWords.add("from");
stopWords.add("further");
stopWords.add("furthermore");
stopWords.add("get");
stopWords.add("gets");
stopWords.add("getting");
stopWords.add("given");
stopWords.add("gives");
stopWords.add("go");
stopWords.add("goes");
stopWords.add("going");
stopWords.add("gone");
stopWords.add("got");
stopWords.add("gotten");
stopWords.add("greetings");
stopWords.add("had");
stopWords.add("hadn't");
stopWords.add("half");
stopWords.add("happens");
stopWords.add("hardly");
stopWords.add("has");
stopWords.add("hasn't");
stopWords.add("have");
stopWords.add("haven't");
stopWords.add("having");
stopWords.add("he");
stopWords.add("he'd");
stopWords.add("he'll");
stopWords.add("hello");
stopWords.add("help");
stopWords.add("hence");
stopWords.add("her");
stopWords.add("here");
stopWords.add("hereafter");
stopWords.add("hereby");
stopWords.add("herein");
stopWords.add("here's");
stopWords.add("hereupon");
stopWords.add("hers");
stopWords.add("herself");
stopWords.add("he's");
stopWords.add("hi");
stopWords.add("him");
stopWords.add("himself");
stopWords.add("his");
stopWords.add("hither");
stopWords.add("hopefully");
stopWords.add("how");
stopWords.add("howbeit");
stopWords.add("however");
stopWords.add("however");
stopWords.add("hundred");
stopWords.add("i'd");
stopWords.add("ie");
stopWords.add("if");
stopWords.add("ignored");
stopWords.add("i'll");
stopWords.add("i'm");
stopWords.add("immediate");
stopWords.add("in");
stopWords.add("iansmuch");
stopWords.add("inc");
stopWords.add("inc.");
stopWords.add("indeed");
stopWords.add("indicate");
stopWords.add("indicated");
stopWords.add("indicates");
stopWords.add("inner");
stopWords.add("inside");
stopWords.add("insofar");
stopWords.add("into");
stopWords.add("inward");
stopWords.add("is");
stopWords.add("isn't");
stopWords.add("it");
stopWords.add("it'd");
stopWords.add("it'll");
stopWords.add("its");
stopWords.add("it's");
stopWords.add("itself");
stopWords.add("i've");
stopWords.add("just");
stopWords.add("k");
stopWords.add("keep");
stopWords.add("keeps");
stopWords.add("kept");
stopWords.add("know");
stopWords.add("knows");
stopWords.add("known");
stopWords.add("last");
stopWords.add("lately");
stopWords.add("later");
stopWords.add("latter");
stopWords.add("latterly");
stopWords.add("least");
stopWords.add("less");
stopWords.add("let");
stopWords.add("let's");
stopWords.add("like");
stopWords.add("liked");
stopWords.add("likely");
stopWords.add("likewise");
stopWords.add("little");
stopWords.add("look");
stopWords.add("looks");
stopWords.add("low");
stopWords.add("lower");
stopWords.add("ltd");
stopWords.add("made");
stopWords.add("mainly");
stopWords.add("make");
stopWords.add("makes");
stopWords.add("many");
stopWords.add("may");
stopWords.add("maybe");
stopWords.add("mayn't");
stopWords.add("me");
stopWords.add("mean");
stopWords.add("meanwhile");
stopWords.add("merely");
stopWords.add("might");
stopWords.add("mightn't");
stopWords.add("mine");
stopWords.add("minus");
stopWords.add("miss");
stopWords.add("more");
stopWords.add("moreover");
stopWords.add("most");
stopWords.add("mostly");
stopWords.add("mr");
stopWords.add("mrs");
stopWords.add("much");
stopWords.add("must");
stopWords.add("mustn't");
stopWords.add("my");
stopWords.add("myself");
stopWords.add("name");
stopWords.add("namely");
stopWords.add("nd");
stopWords.add("near");
stopWords.add("nearly");
stopWords.add("necessary");
stopWords.add("need");
stopWords.add("needn't");
stopWords.add("needs");
stopWords.add("neither");
stopWords.add("never");
stopWords.add("neverf");
stopWords.add("neverless");
stopWords.add("nevertheless");
stopWords.add("new");
stopWords.add("next");
stopWords.add("nine");
stopWords.add("ninety");
stopWords.add("no");
stopWords.add("nobody");
stopWords.add("non");
stopWords.add("none");
stopWords.add("nonetheless");
stopWords.add("noone");
stopWords.add("no-one");
stopWords.add("nor");
stopWords.add("normally");
stopWords.add("not");
stopWords.add("nothing");
stopWords.add("notwithstanding");
stopWords.add("novel");
stopWords.add("now");
stopWords.add("nowwhere");
stopWords.add("obviously");
stopWords.add("of");
stopWords.add("off");
stopWords.add("often");
stopWords.add("oh");
stopWords.add("ok");
stopWords.add("okay");
stopWords.add("old");
stopWords.add("on");
stopWords.add("once");
stopWords.add("one");
stopWords.add("ones");
stopWords.add("one's");
stopWords.add("only");
stopWords.add("onto");
stopWords.add("opposite");
stopWords.add("or");
stopWords.add("other");
stopWords.add("others");
stopWords.add("otherwise");
stopWords.add("ought");
stopWords.add("oughtn't");
stopWords.add("our");
stopWords.add("ourselves");
stopWords.add("out");
stopWords.add("outside");
stopWords.add("over");
stopWords.add("overall");
stopWords.add("own");
stopWords.add("particular");
stopWords.add("particularly");
stopWords.add("past");
stopWords.add("per");
stopWords.add("perhaps");
stopWords.add("placed");
stopWords.add("please");
stopWords.add("plus");
stopWords.add("possible");
stopWords.add("presumably");
stopWords.add("probably");
stopWords.add("provided");
stopWords.add("provides");
stopWords.add("que");
stopWords.add("quite");
stopWords.add("qv");
stopWords.add("rather");
stopWords.add("rd");
stopWords.add("re");
stopWords.add("really");
stopWords.add("reasonably");
stopWords.add("recent");
stopWords.add("recently");
stopWords.add("regarding");
stopWords.add("regardless");
stopWords.add("regards");
stopWords.add("relatively");
stopWords.add("respectively");
stopWords.add("right");
stopWords.add("round");
stopWords.add("said");
stopWords.add("same");
stopWords.add("saw");
stopWords.add("say");
stopWords.add("saying");
stopWords.add("says");
stopWords.add("second");
stopWords.add("secondly");
stopWords.add("see");
stopWords.add("seeing");
stopWords.add("seem");
stopWords.add("seemed");
stopWords.add("seeming");
stopWords.add("seems");
stopWords.add("seen");
stopWords.add("self");
stopWords.add("selves");
stopWords.add("sensible");
stopWords.add("sent");
stopWords.add("serious");
stopWords.add("seriously");
stopWords.add("seven");
stopWords.add("several");
stopWords.add("shall");
stopWords.add("shan't");
stopWords.add("she");
stopWords.add("she'd");
stopWords.add("she'll");
stopWords.add("she's");
stopWords.add("should");
stopWords.add("shouldn't");
stopWords.add("since");
stopWords.add("six");
stopWords.add("so");
stopWords.add("some");
stopWords.add("somebody");
stopWords.add("someday");
stopWords.add("somehow");
stopWords.add("someone");
stopWords.add("something");
stopWords.add("sometime");
stopWords.add("sometimes");
stopWords.add("somewhat");
stopWords.add("somewhere");
stopWords.add("soon");
stopWords.add("sorry");
stopWords.add("specified");
stopWords.add("specify");
stopWords.add("specifying");
stopWords.add("still");
stopWords.add("sub");
stopWords.add("such");
stopWords.add("sup");
stopWords.add("sure");
stopWords.add("take");
stopWords.add("taken");
stopWords.add("taking");
stopWords.add("tell");
stopWords.add("tends");
stopWords.add("th");
stopWords.add("than");
stopWords.add("thank");
stopWords.add("thanks");
stopWords.add("thanx");
stopWords.add("that");
stopWords.add("that'll");
stopWords.add("thats");
stopWords.add("that've");
stopWords.add("the");
stopWords.add("their");
stopWords.add("theirs");
stopWords.add("them");
stopWords.add("themselves");
stopWords.add("then");
stopWords.add("thence");
stopWords.add("there");
stopWords.add("thereafter");
stopWords.add("thereby");
stopWords.add("there'd");
stopWords.add("therefore");
stopWords.add("therein");
stopWords.add("ther'll");
stopWords.add("there're");
stopWords.add("theres");
stopWords.add("there's");
stopWords.add("thereupon");
stopWords.add("there've");
stopWords.add("these");
stopWords.add("they");
stopWords.add("they'd");
stopWords.add("they'll");
stopWords.add("they're");
stopWords.add("they've");
stopWords.add("thing");
stopWords.add("things");
stopWords.add("think");
stopWords.add("third");
stopWords.add("thirty");
stopWords.add("this");
stopWords.add("thorough");
stopWords.add("thoroughly");
stopWords.add("those");
stopWords.add("though");
stopWords.add("throughout");
stopWords.add("thru");
stopWords.add("thus");
stopWords.add("till");
stopWords.add("to");
stopWords.add("together");
stopWords.add("too");
stopWords.add("took");
stopWords.add("toward");
stopWords.add("towards");
stopWords.add("tried");
stopWords.add("tries");
stopWords.add("truly");
stopWords.add("try");
stopWords.add("trying");
stopWords.add("t's");
stopWords.add("twice");
stopWords.add("two");
stopWords.add("un");
stopWords.add("under");
stopWords.add("underneath");
stopWords.add("undoing");
stopWords.add("unfortunately");
stopWords.add("unless");
stopWords.add("unlike");
stopWords.add("unlikely");
stopWords.add("untill");
stopWords.add("unto");
stopWords.add("up");
stopWords.add("upon");
stopWords.add("upwards");
stopWords.add("us");
stopWords.add("use");
stopWords.add("used");
stopWords.add("useful");
stopWords.add("uses");
stopWords.add("using");
stopWords.add("usually");
stopWords.add("v");
stopWords.add("value");
stopWords.add("various");
stopWords.add("versus");
stopWords.add("very");
stopWords.add("via");
stopWords.add("viz");
stopWords.add("vs");
stopWords.add("want");
stopWords.add("wants");
stopWords.add("was");
stopWords.add("wasn't");
stopWords.add("way");
stopWords.add("we");
stopWords.add("we'd");
stopWords.add("welcome");
stopWords.add("well");
stopWords.add("we'll");
stopWords.add("went");
stopWords.add("were");
stopWords.add("we're");
stopWords.add("weren't");
stopWords.add("we've");
stopWords.add("what");
stopWords.add("whatever");
stopWords.add("what'll");
stopWords.add("what's");
stopWords.add("what've");
stopWords.add("when");
stopWords.add("whence");
stopWords.add("whenever");
stopWords.add("where");
stopWords.add("whereafter");
stopWords.add("whereas");
stopWords.add("whereby");
stopWords.add("wherein");
stopWords.add("where's");
stopWords.add("whereupon");
stopWords.add("whereever");
stopWords.add("whether");
stopWords.add("which");
stopWords.add("whichever");
stopWords.add("while");
stopWords.add("whilst");
stopWords.add("whither");
stopWords.add("who");
stopWords.add("who'd");
stopWords.add("whoever");
stopWords.add("whole");
stopWords.add("who'll");
stopWords.add("whom");
stopWords.add("whomever");
stopWords.add("who's");
stopWords.add("whose");
stopWords.add("why");
stopWords.add("will");
stopWords.add("willing");
stopWords.add("wish");
stopWords.add("with");
stopWords.add("within");
stopWords.add("without");
stopWords.add("wonder");
stopWords.add("won't");
stopWords.add("would");
stopWords.add("wouldn't");
stopWords.add("yes");
stopWords.add("yet");
stopWords.add("you");
stopWords.add("you'd");
stopWords.add("you'll");
stopWords.add("your");
stopWords.add("you're");
stopWords.add("yours");
stopWords.add("yourself");
stopWords.add("you've");
stopWords.add("zero");
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public WordGenerator()\n {\n adjective1a = new ArrayList<String>();\n adjective1b = new ArrayList<String>();\n adjective1c = new ArrayList<String>();\n adjective2a = new ArrayList<String>();\n adjective2b = new ArrayList<String>();\n adjective2c = new ArrayList<String>();\n fillAdjectives();\... | [
"0.76317644",
"0.7545281",
"0.7545281",
"0.7545281",
"0.752353",
"0.74651843",
"0.74460554",
"0.74453956",
"0.74395007",
"0.743902",
"0.74243635",
"0.74038893",
"0.7381507",
"0.73439866",
"0.7340342",
"0.72289604",
"0.7189924",
"0.7045309",
"0.701709",
"0.6976395",
"0.6968872... | 0.60988116 | 88 |
contans method of collection list will be called to check for possible presence of the String s | public int removings(String s)
{
if(stopWords.contains(s))
{
return 1;
}
else
{
return 0;
}
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"private boolean stringContainsList(String s, ArrayList<String> list){\n\t\tboolean flag = true;\n\t\tfor(String temp : list){\n\t\t\tif(!s.contains(temp)){\n\t\t\t\tflag = false;\n\t\t\t\treturn flag;\n\t\t\t}\n\t\t}\n\t\treturn flag;\n\t}",
"public boolean containsCaseInsensitive(String s, List<String> l) {\n\t... | [
"0.68409455",
"0.6215611",
"0.6161457",
"0.6133119",
"0.6133119",
"0.6133119",
"0.59894645",
"0.59720945",
"0.59363633",
"0.5933077",
"0.5824974",
"0.58187085",
"0.58100516",
"0.5793222",
"0.5773933",
"0.57527435",
"0.5740498",
"0.5738124",
"0.57380855",
"0.57257605",
"0.5725... | 0.0 | -1 |
Inflate the menu; this adds items to the action bar if it is present. | @Override
public boolean onCreateOptionsMenu(Menu menu) {
getMenuInflater().inflate(R.menu.menu_set_location, menu);
return true;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\n public boolean onCreateOptionsMenu(Menu menu) {\n \tMenuInflater inflater = getMenuInflater();\n \tinflater.inflate(R.menu.main_activity_actions, menu);\n \treturn super.onCreateOptionsMenu(menu);\n }",
"@Override\n public void onCreateOptionsMenu(Menu menu, MenuInflater inflater) {... | [
"0.7246102",
"0.7201358",
"0.7194834",
"0.7176498",
"0.71066517",
"0.7039537",
"0.7037961",
"0.70112145",
"0.70094734",
"0.69807225",
"0.6944953",
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"0.6916928",
"0.6891486",
"0.68831646",
"0.68754137",
"0.68745375",
"0.68621665",
"0.6862... | 0.0 | -1 |
Create a method that will accept a String ArrayList and return the largest Palindrome String from it => Assume there is no Strings with the same length and there will be at least one element > "dad" "abcab", "racecar","cat" | public static void main(String[] args) {
ArrayList<String> list = new ArrayList<>(Arrays.asList("racecar","dad","abcab","cat","level","Kayak"));
System.out.println(largestPalindrome(list));
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public static String maxString(ArrayList<String> array){\n \n String max = \"\";\n for(String s:array){\n \n if(s.length() > max.length()){\n max = s;\n }\n }\n return max;\n }",
"public String longestPalindrome(String s) {\n ... | [
"0.73311",
"0.7234848",
"0.6996195",
"0.6908244",
"0.6871052",
"0.68420386",
"0.6692585",
"0.6675967",
"0.6605912",
"0.6585878",
"0.65284854",
"0.65213156",
"0.64810216",
"0.6410742",
"0.6385728",
"0.6380318",
"0.6301657",
"0.62989426",
"0.6273812",
"0.61934704",
"0.6188538",... | 0.7626517 | 0 |
It is not permitted to access localStorage from data URLs in WebKit, that is why a standalone page must be used. | @Override
protected void doEnsureSettingHasValue(Boolean value) throws Throwable {
loadUrlSyncByContent(mXWalkContent, client,
UrlUtils.getTestFileUrl("xwalkview/localStorage.html"));
assertEquals(
value == ENABLED ? HAS_LOCAL_STORAGE : NO_LOCAL_STORAGE,
client.getChangedTitle());
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public void loadFromLocalStorage() {\n\t\t\n\t}",
"public boolean isLocalStorageOnly() {\n\t\treturn this.localStorageOnly;\n\t}",
"@Test\n public void deleteCertainLocalStorageEntry() {\n assertThat(localStorage.isItemPresentInLocalStorage(\"logged-in\"), is(true));\n\n // delete certain loca... | [
"0.6432849",
"0.563519",
"0.52302235",
"0.5143447",
"0.51386887",
"0.51223695",
"0.507356",
"0.49503624",
"0.49393168",
"0.48246297",
"0.48144436",
"0.4808502",
"0.47672898",
"0.47575352",
"0.4743501",
"0.47149423",
"0.46926126",
"0.4687224",
"0.4677675",
"0.46204713",
"0.461... | 0.46467233 | 19 |
Verifies the following statements about a setting: initially, the setting has a default value; the setting can be switched to an alternate value and back; switching a setting in the first XWalkView doesn't affect the setting state in the second XWalkView and vice versa. | private void runPerViewSettingsTest(XWalkViewSettingsTestHelper helper0,
XWalkViewSettingsTestHelper helper1) throws Throwable {
helper0.ensureSettingHasInitialValue();
helper1.ensureSettingHasInitialValue();
helper1.setAlteredSettingValue();
helper0.ensureSettingHasInitialValue();
helper1.ensureSettingHasAlteredValue();
helper1.setInitialSettingValue();
helper0.ensureSettingHasInitialValue();
helper1.ensureSettingHasInitialValue();
helper0.setAlteredSettingValue();
helper0.ensureSettingHasAlteredValue();
helper1.ensureSettingHasInitialValue();
helper0.setInitialSettingValue();
helper0.ensureSettingHasInitialValue();
helper1.ensureSettingHasInitialValue();
helper0.setAlteredSettingValue();
helper0.ensureSettingHasAlteredValue();
helper1.ensureSettingHasInitialValue();
helper1.setAlteredSettingValue();
helper0.ensureSettingHasAlteredValue();
helper1.ensureSettingHasAlteredValue();
helper0.setInitialSettingValue();
helper0.ensureSettingHasInitialValue();
helper1.ensureSettingHasAlteredValue();
helper1.setInitialSettingValue();
helper0.ensureSettingHasInitialValue();
helper1.ensureSettingHasInitialValue();
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\n protected void doEnsureSettingHasValue(Boolean value) throws Throwable {\n loadUrlSyncByContent(mXWalkContent, client,\n UrlUtils.getTestFileUrl(\"xwalkview/localStorage.html\"));\n assertEquals(\n value == ENABLED ? HAS_LOCAL_STORAGE : NO_... | [
"0.6471014",
"0.5850698",
"0.5757064",
"0.5640055",
"0.5640055",
"0.563485",
"0.55121064",
"0.5422894",
"0.54154885",
"0.5399301",
"0.5397221",
"0.5386553",
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"0.53643787",
"0.53518915",
"0.535105",
"0.53484994",
"0.5329194",
"0.53243345",
"0.5268838",
"0.5268826",... | 0.5963632 | 1 |
Returns the jobs that need to be finished before this job can start. | public List<IJob> getDependentJobs(); | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public String[] getJobsWaiting();",
"protected boolean isAllJobsFinished() {\r\n \tIterator<Progress> jobsIterator = JobManager.iterator();\r\n \twhile (jobsIterator.hasNext()) {\r\n \t\tProgress job = jobsIterator.next();\r\n\t\t\tif (!job.isFinished()) {\r\n\t\t\t\treturn false;\r\n\t\t\t}\r\n\t\t}\r\... | [
"0.7177362",
"0.6680803",
"0.6514374",
"0.6335534",
"0.631715",
"0.62728906",
"0.61331886",
"0.60892916",
"0.6070152",
"0.6033269",
"0.60328674",
"0.60278535",
"0.59960884",
"0.5992463",
"0.59590894",
"0.5931089",
"0.59040964",
"0.5878783",
"0.5874314",
"0.5851098",
"0.584157... | 0.60402524 | 9 |
Adds a job that needs to finish before this job may start. | public void addDependentJob(IJob job); | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public void addJob(Job job) {\n try {\n JobWrapper jobWrapper = new JobWrapper(agentManager, job);\n this.runningPool.execute(jobWrapper);\n JobWrapper jobWrapperRet = jobs.putIfAbsent(jobWrapper.getJob().getJobInstanceId(), jobWrapper);\n if (jobWrapperRet != nul... | [
"0.6681832",
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"0.6150569",
"0.614364",
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"0.5644586",
"0.5557729",
"0.55552304",
"0.55129915",
"0.5477491",
"0.5385164... | 0.691167 | 0 |
Check whether this job depends upon completion of a given job. | public boolean dependsOn(IJob job); | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public boolean isComplete() {\n return addedFrontWork.size() == 0 && addedBackWork.size() == 0 && sawAllDone.get();\n }",
"boolean hasIsComplete();",
"boolean hasIsComplete();",
"public boolean isComplete();",
"boolean isComplete();",
"boolean isComplete();",
"public abstract boolean isComplete();"... | [
"0.6515193",
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"0.6494356",
"0.6476991",
"0.64670855",
"0.64670855",
"0.6427258",
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"0.63819104",
"0.63627076",
"0.6221201",
"0.6208649",
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"0.6183525",
"0.61722565",
"0.616471",
"0.6161818",
"0.6160164",
"0.6139201",
"0.6132365",
"0.6131907"... | 0.72251797 | 0 |
Sets this job's status. | public void setStatus(JobStatus status); | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public JobBuilder status(String status) {\r\n job.setStatus(status);\r\n return this;\r\n }",
"@Override\n\tpublic void setJobStatus(int jobStatus) {\n\t\tmodel.setJobStatus(jobStatus);\n\t}",
"public void setJobStatus(Integer jobStatus) {\n this.jobStatus = jobStatus;\n }",
"publi... | [
"0.7566642",
"0.7523746",
"0.7373603",
"0.7284003",
"0.7245662",
"0.7223006",
"0.7223006",
"0.7209716",
"0.7155464",
"0.7128999",
"0.7082381",
"0.70809084",
"0.70809084",
"0.70809084",
"0.70809084",
"0.707594",
"0.7059714",
"0.69968605",
"0.6987676",
"0.6956856",
"0.6944969",... | 0.79965407 | 0 |
Returns this job's status. | public JobStatus getStatus(); | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public String getJobStatus() {\n return this.jobStatus;\n }",
"public String getJobStatus() {\n return this.jobStatus;\n }",
"public Integer getJobStatus() {\n return jobStatus;\n }",
"@Override\n\tpublic int getJobStatus() {\n\t\treturn model.getJobStatus();\n\t}",
"public Ba... | [
"0.85423046",
"0.85423046",
"0.85340554",
"0.8388121",
"0.77300495",
"0.7728615",
"0.77193755",
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"0.7669666",
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"0.7632721",
"0.7632721",
"0.7632721",
"0.76322865",
"0.76175785",
"0.7615849",
"0.76158... | 0.8664146 | 0 |
Tests whether this job has a given status. | public boolean hasStatus(JobStatus... s); | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"boolean hasStatus();",
"boolean hasStatus();",
"boolean hasStatus();",
"boolean hasStatus();",
"boolean hasStatus();",
"boolean hasStatus();",
"boolean hasStatus();",
"boolean hasStatus();",
"boolean hasStatus();",
"boolean hasStatus();",
"boolean hasStatus();",
"boolean hasStatus();",
"boo... | [
"0.7572556",
"0.7572556",
"0.7572556",
"0.7572556",
"0.7572556",
"0.7572556",
"0.7572556",
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"0.7572556",
"0.7572556",
"0.7572556",
"0.7572556",
"0.7572556",
"0.7572556",
"0.7572556",
"... | 0.74003917 | 22 |
Sets the starting date for this job. This method may only be invoked on simple jobs (since complex ones have a derived starting date). | public void setStartDate(Date s); | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public void setJobStartDate(java.util.Calendar jobStartDate)\r\n {\r\n synchronized (monitor())\r\n {\r\n check_orphaned();\r\n org.apache.xmlbeans.SimpleValue target = null;\r\n target = (org.apache.xmlbeans.SimpleValue)get_store().find_element_user(JOBSTARTDATE$0... | [
"0.7128164",
"0.7120039",
"0.70592314",
"0.7015252",
"0.6966485",
"0.6948013",
"0.69434994",
"0.6930108",
"0.6904005",
"0.6814306",
"0.6814306",
"0.6814241",
"0.6814241",
"0.6799098",
"0.6799098",
"0.67974377",
"0.6786373",
"0.67416805",
"0.67416805",
"0.67410254",
"0.6741025... | 0.676667 | 17 |
Returns the date range this job covers. | public DateRange getDateRange(); | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public RangeDate<Vente> getDateRange() {\n return dateRange;\n }",
"public Range<LocalDate> getWorkingRange() {\n return Range.closedOpen(effectDate, endDate.plusDays(1));\n }",
"public java.lang.String CC_GetCurrentJobsInRange(java.lang.String accessToken, java.lang.String CCCode, java.uti... | [
"0.6521775",
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"0.5695888",
"0.5667368",
"0.5574338",
"0.55228627",
"0.55228627",
"0.55085593",
"0.5499656",
"0.5499656",
"0.54893124",
"0.548804",
"0.5463102",
"0.543574",
"0.5417771",
"0.5417771",
"0.5341884",
"0.53298444",
"0.5317034",... | 0.6972046 | 0 |
Returns the earliest starting date of this job. For simple jobs, this is their assigned start date , for complex jobs this is the latest earliest finishing date of all jobs this job depends on. | public Date getEarliestStartDate(); | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public java.util.Calendar getJobStartDate()\r\n {\r\n synchronized (monitor())\r\n {\r\n check_orphaned();\r\n org.apache.xmlbeans.SimpleValue target = null;\r\n target = (org.apache.xmlbeans.SimpleValue)get_store().find_element_user(JOBSTARTDATE$0, 0);\r\n ... | [
"0.71748835",
"0.7101853",
"0.69593406",
"0.69235456",
"0.66323185",
"0.6450474",
"0.6437956",
"0.64069664",
"0.63922244",
"0.63773495",
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"0.6316887",
"0.6291536",
"0.62790215",
"0.62682396",
"0.62682396",
"0.61... | 0.7219706 | 0 |
Returns the earliest finishing date of this job. For simple jobs, this is always ( startDate + duration ) , for complex jobs this is the latest earliest finishing date of all jobs this job depends on plus the duration of THIS job. | public Date getEarliestFinishingDate(); | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public java.util.Calendar getJobStartDate()\r\n {\r\n synchronized (monitor())\r\n {\r\n check_orphaned();\r\n org.apache.xmlbeans.SimpleValue target = null;\r\n target = (org.apache.xmlbeans.SimpleValue)get_store().find_element_user(JOBSTARTDATE$0, 0);\r\n ... | [
"0.58967966",
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"0.5677016",
"0.5606714",
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"0.5102433",
"0.5097567",
"0.5088494",
"0.50677425",
"0.505639... | 0.691803 | 0 |
Returns the starting date for this job. For simple jobs, this method returns the assigned starting date. For complex jobs, this method returns the latest earliest finishing date of all jobs this job depends on. | public Date getStartDate(); | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public java.util.Calendar getJobStartDate()\r\n {\r\n synchronized (monitor())\r\n {\r\n check_orphaned();\r\n org.apache.xmlbeans.SimpleValue target = null;\r\n target = (org.apache.xmlbeans.SimpleValue)get_store().find_element_user(JOBSTARTDATE$0, 0);\r\n ... | [
"0.71367854",
"0.69423455",
"0.6853797",
"0.6602818",
"0.6580886",
"0.6521579",
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"0.62584823",
"0.62584823",
"0.62584823",
"0.6256979",
"0.62000024",
"0.616883",... | 0.6125648 | 25 |
Returns the end date of this job. | public Date getEndDate(); | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public Date get_end() {\n\t\treturn this.end;\n\t}",
"public Date getEND_DATE() {\n return END_DATE;\n }",
"public java.util.Date getEndDateTime() {\n return this.endDateTime;\n }",
"public Date getDtEnd() {\r\n return dtEnd;\r\n }",
"Date getEndDate();",
"Date getEndDate();... | [
"0.7988641",
"0.78171223",
"0.76322806",
"0.7603597",
"0.7599495",
"0.7599495",
"0.7536575",
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"0.7529459",
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"0.7515679",
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"0.7491063",
"0.7472225",
"0.7472225",
"0.74268705",
"0.74069047",
"0.74069047",
"0.74013... | 0.728668 | 42 |
Returns the duration left for this job after a given date. this.earliestFinishingDate startDate: Duration.ZERO this.earliestStartDate | public Duration getDurationFrom(Date startDate); | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public Date getEarliestFinishingDate();",
"private long remainingTime() {\n final long remainingTime = this.designatedEnd - System.currentTimeMillis();\n return remainingTime >= 0 ? remainingTime : 0L;\n }",
"public double getTimeRemaining() {\n\t\treturn (startingTime + duration) - System.cur... | [
"0.6189672",
"0.591915",
"0.5728432",
"0.5676512",
"0.5625077",
"0.5553205",
"0.5509251",
"0.5464718",
"0.5409707",
"0.5394465",
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"0.5212036",
"0.519653",
"0.5191852",
"0.51477927",
"0.5143422",
"0.5143386",
... | 0.60969573 | 1 |
Returns the amount of time this job will be running within a given date range. | public Duration getDurationWithin(Date startDate,Date endDate); | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"private int jobLength(){\n LocalDate completedLocalDate = LocalDate.of(this.dateCompleted.getYear(), \n this.dateCompleted.getMonth(), this.dateCompleted.getDay());\n \n LocalDate startedLocalDate = LocalDate.of(this.dateStarted.getYear(), \n this.dateStarted.getM... | [
"0.7275362",
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"0.60793304",
"0.60449994",
"0.58706474",
"0.58270323",
"0.5705635",
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"0.5659141",
"0.56532675",
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"0.5603532",
"0.55935585",
"0.557757",
"0.5564722",
"0.5564722",
"0.5564722",
"0.55563... | 0.56277126 | 14 |
Sets the number of runs for this job. | public void setRuns(int runs); | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public static void setNumIterations(long aNumIterations) {\n\t\tnumIterations = aNumIterations;\n\t}",
"public void setNumberOfThreads(java.lang.Integer value) {\n __getInternalInterface().setFieldValue(NUMBEROFTHREADS_PROP.get(), value);\n }",
"public void setCount(int value) {\n this.count = v... | [
"0.6583286",
"0.6467417",
"0.6464881",
"0.6464881",
"0.6464881",
"0.645911",
"0.642307",
"0.640822",
"0.62286115",
"0.62242293",
"0.62103945",
"0.6174532",
"0.6142292",
"0.6119449",
"0.6118695",
"0.610326",
"0.60732037",
"0.6004384",
"0.59584045",
"0.5957794",
"0.5955126",
... | 0.75171363 | 0 |
Returns the number of runs for this job. | public int getRuns(); | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public int getRunCount() {\n return runCount;\n }",
"public int getRuns() {\n return runs;\n }",
"int getJobsCount();",
"int getJobsCount();",
"int getJobsCount();",
"public int getRunningCount() {\r\n return root.getRunningCount();\r\n }",
"public int getJobsCount() {\n if... | [
"0.7970634",
"0.72963554",
"0.7231412",
"0.7231412",
"0.7231412",
"0.7177844",
"0.7152409",
"0.71466005",
"0.69840825",
"0.68992156",
"0.689172",
"0.6858557",
"0.6839551",
"0.6834342",
"0.6828573",
"0.6678514",
"0.66291076",
"0.65926707",
"0.6563525",
"0.65588313",
"0.6553389... | 0.6873773 | 11 |
Check whether this job runs at a given date. | public boolean runsAt(Date date); | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public boolean runsOn( GTFSDate date ) {\n\t\tif( date.before( this.start_date) ) {\n\t\t\tthrow new DateOutOfBoundsException( date+\" is before period start \"+this.start_date );\n\t\t}\n\t\tif( date.after( this.end_date) ) {\n\t\t\tthrow new DateOutOfBoundsException( date+\" is after period end \"+this.end_date ... | [
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"0.6079819",
"0.6049049",
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"0.5982598",
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"0.57784724",
"0.5776476",
"0.57750404",
"0.57750404... | 0.75699353 | 0 |
Snackbar.make(view, "Replace with your own action", Snackbar.LENGTH_LONG) .setAction("Action", null).show(); | @Override
public void onClick(View view) {
finish();
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\n public void onClick(View v) {\n Snackbar.make(v, \"I'm dead! =(\", Snackbar.LENGTH_LONG)\n .setAction(\"Action\", null).show();\n }",
"private void showSnackbarMessage(String message){\n if(view != null){\n Snackbar.make(view, message, Sna... | [
"0.77849233",
"0.73431313",
"0.7312924",
"0.7308021",
"0.71119523",
"0.70179576",
"0.6977823",
"0.693279",
"0.6817242",
"0.67794555",
"0.6773066",
"0.6769153",
"0.66969097",
"0.66901416",
"0.6535203",
"0.6526453",
"0.6526107",
"0.64990896",
"0.64981586",
"0.64537144",
"0.6414... | 0.0 | -1 |
lay thong tin nhap vao | protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
String Name = request.getParameter("name");
String Sign = request.getParameter("message");
Connection c = null;
try
{
String url = "jdbc:mysql://localhost/web";//tên cơ sở dữ liệu
String username = "root";
String password = "1234";
String sql = "insert into member (name,sign) values (?,?)";
c = DriverManager.getConnection(url, username, password);
PreparedStatement pstmt = c.prepareStatement(sql);
pstmt.setString(1, Name);
pstmt.setString(2, Sign);
//Thực thi câu lenh
pstmt.executeUpdate();
}
catch(SQLException e)
{
throw new ServletException(e);
}
finally
{
//đóng connection
try
{
if(c != null) c.close();
}
catch(SQLException e)
{
throw new ServletException(e);
}
}
request.getRequestDispatcher("Members").forward(request, response);
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\r\n public void prenderVehiculo() {\r\n System.out.println(\"___________________________________________________\");\r\n System.out.println(\"prender Jet\");\r\n }",
"protected String elaboraTemplateAvviso() {\n String testo = VUOTA;\n String dataCorrente = date.get()... | [
"0.63565624",
"0.610558",
"0.59946495",
"0.5911207",
"0.5875492",
"0.58704853",
"0.58654654",
"0.58617264",
"0.5850475",
"0.5835929",
"0.58347154",
"0.5799119",
"0.5796253",
"0.57574797",
"0.57555",
"0.573677",
"0.57272094",
"0.572118",
"0.5696788",
"0.5689428",
"0.5674572",
... | 0.0 | -1 |
Created by huhui on 2017/12/4. | public interface BodyChangeDao {
BodyChange insert(BodyChange item);
List<BodyChange> query(BodyChange item);
void update(BodyChange item);
void delete(BodyChange item);
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\n public void perish() {\n \n }",
"private stendhal() {\n\t}",
"@Override\n\tpublic void grabar() {\n\t\t\n\t}",
"@Override\r\n\tpublic void bicar() {\n\t\t\r\n\t}",
"@Override\r\n\tpublic void bicar() {\n\t\t\r\n\t}",
"@Override\n\tpublic void comer() {\n\t\t\n\t}",
"private sta... | [
"0.61636144",
"0.6075055",
"0.5863244",
"0.5862687",
"0.5862687",
"0.5858016",
"0.5852642",
"0.57735246",
"0.57511383",
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"0.57013124",
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"0.5658032",
"0.5657187",
"0.56427747",
"0.5640243",
"0.5638284",
"0.56135803",
"0.5594748... | 0.0 | -1 |
/ working ?? need to explore more | private void deleteFun() throws IOException {
String jsonObject = "{\"age\":10,\"dateOfBirth\":1471455886564,\"fullName\":\"Johan Doe\"}";
IndexRequest indexRequest = new IndexRequest("people");
indexRequest.source(jsonObject, XContentType.JSON);
IndexResponse response = client.index(indexRequest, RequestOptions.DEFAULT);
String id = response.getId();
System.out.println("id = " + id);
GetRequest getRequest = new GetRequest("people");
getRequest.id(id);
GetResponse getResponse = client.get(getRequest, RequestOptions.DEFAULT);
System.out.println(getResponse.getSourceAsString());
DeleteRequest deleteRequest = new DeleteRequest("people");
deleteRequest.id(id);
DeleteResponse deleteResponse = client.delete(deleteRequest, RequestOptions.DEFAULT);
System.out.println("deleteResponse = " + deleteResponse.toString());
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"private static void cajas() {\n\t\t\n\t}",
"public void gored() {\n\t\t\n\t}",
"private void strin() {\n\n\t}",
"public void mo38117a() {\n }",
"private void kk12() {\n\n\t}",
"public void mo4359a() {\n }",
"public static void listing5_14() {\n }",
"public void verliesLeven() {\r\n\t... | [
"0.5930778",
"0.5622956",
"0.55912006",
"0.5532744",
"0.5530062",
"0.5493049",
"0.54592973",
"0.54320073",
"0.54135466",
"0.5406912",
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"0.53475296",
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"0.53123367",
"0.53123367",
"0.53123367",
"0.53123367",
"0.53123367",
"0.5... | 0.0 | -1 |
protected boolean encrypted = false; | public Delivery(Signer from, Signer to, ItemComponent[] payload) {
super(from, to, payload);
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public void setEncrypted(Boolean encrypted) {\n this.encrypted = encrypted;\n }",
"@Override\n\tpublic boolean isEncrypted() {\n\t\treturn encrypted;\n\t}",
"public Boolean getEncrypted() {\n return this.encrypted;\n }",
"public Boolean isEncrypted() {\n return this.isEncrypted;\n ... | [
"0.79655135",
"0.7954927",
"0.78772014",
"0.77222955",
"0.7679619",
"0.7623316",
"0.73567635",
"0.7292949",
"0.72892237",
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"0.6928598",
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"0.66835177",
"0.6633175",
"0.66237795",
"0.6605209",
"0.65588653",
"0.65438503",
"0.64788747",
"0.6... | 0.0 | -1 |
Called when connection has been established. | default void onConnect(SessionID sessionID) {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"protected void connectionEstablished() {}",
"void connectionCreated();",
"@Override\n\tpublic void connectionReady() {\n\t}",
"void handleConnectionOpened();",
"protected void onConnect() {}",
"@Override\n protected void connectionEstablished()\n {\n peer.resetConnectionClosed();\n\n ... | [
"0.8492044",
"0.7516248",
"0.74815464",
"0.738944",
"0.71728647",
"0.7161124",
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"0.66802084",
"0.6622446",
"0.6601249",
"0.6594747",
"0.6526734",
"0.651439... | 0.0 | -1 |
Called when Exception occurs during connection establishment. | default void onConnectException(SessionID sessionID, Exception exception) {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"protected void connectionException(Exception exception) {}",
"protected void onConnectionError() {\n\t}",
"public void onConnectionError()\n\t\t{\n\t\t}",
"protected void connectionEstablished() {}",
"@Override\n \tpublic void reconnectionFailed(Exception arg0) {\n \t}",
"@Override\n public void onCon... | [
"0.7931323",
"0.75646573",
"0.74903196",
"0.710404",
"0.6930894",
"0.69232786",
"0.68617195",
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"0.68196",
"0.68081343",
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"0.68050885",
"0.67966354",
"0.67800575",
"0.67800575",
"0.6777934",
"0.6776461",
"0.6773717",
"0.6742876"... | 0.7039803 | 4 |
Called when connection has been disconnected. | default void onDisconnect(SessionID sessionID) {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"abstract protected void onDisconnection();",
"@Override\r\n\t\tpublic void onDisconnect(Connection connection) {\n\r\n\t\t}",
"public void onDisconnected() {\n\t\t\r\n\t}",
"protected void connectionClosed() {}",
"@Override\n\t\tpublic void disconnected() {\n\t\t\tsuper.disconnected();\n\t\t}",
"protecte... | [
"0.78942424",
"0.7806365",
"0.7796237",
"0.7784061",
"0.77489716",
"0.77020174",
"0.7673925",
"0.76683074",
"0.75618285",
"0.7477465",
"0.7468693",
"0.7401639",
"0.73988926",
"0.73829365",
"0.7375514",
"0.73417044",
"0.73417044",
"0.73417044",
"0.73257524",
"0.7310935",
"0.73... | 0.6755317 | 94 |
Called when session has been logged on. | default void onLogon(SessionID sessionID) {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"private void loggedInUser() {\n\t\t\n\t}",
"@Override\n public void onLoggedIn() {\n\n }",
"public void sessionStarted() {\n\t\t\r\n\t}",
"@Override\n\tpublic void onExpiration(Session session) {\n\t\tlogger.info(\"onExpiration session created:id= {}, begin at {}\", session.getId(), session.getStartTim... | [
"0.761498",
"0.7499068",
"0.7459579",
"0.723292",
"0.72292686",
"0.72271913",
"0.7035033",
"0.6963756",
"0.67983747",
"0.6776629",
"0.67624533",
"0.67376614",
"0.67230266",
"0.6697242",
"0.66916513",
"0.6673581",
"0.6632087",
"0.661402",
"0.6610933",
"0.66074634",
"0.65772814... | 0.7152776 | 6 |
Called when session has been logged out. | default void onLogout(SessionID sessionID) {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public void onLogout() {\n ParseUser.logOut();\n\n promptForLogin();\n }",
"@Override\n public void Logout() {\n\t \n }",
"protected void userLoggedOut() {\n\t\tRuvego.userLoggedOut();\n\t\tResultsActivityMenu.userLoggedOut();\n\t\tHistory.newItem(\"homePage\");\n\t}",
"public void ... | [
"0.7863422",
"0.78321195",
"0.7819526",
"0.777534",
"0.7723557",
"0.7705316",
"0.7665859",
"0.762099",
"0.76110315",
"0.7600107",
"0.75988626",
"0.75864846",
"0.7561399",
"0.749089",
"0.7467234",
"0.7465573",
"0.74619097",
"0.7413564",
"0.73517054",
"0.7349272",
"0.7333487",
... | 0.7647458 | 7 |
Called when message store gets reset. | default void onReset(SessionID sessionID) {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"protected void onReset() {\n\t\t\n\t}",
"protected void onReset() {\n // Do nothing.\n }",
"void resetMessageCounter();",
"public abstract void onReset();",
"protected void reset() {\n\t\t}",
"public synchronized void reset() {\n }",
"public void reset() {\n mNewNotificationCount.setV... | [
"0.73435986",
"0.71965784",
"0.71077156",
"0.70964855",
"0.7094889",
"0.70941925",
"0.6976226",
"0.6936676",
"0.6930406",
"0.6929767",
"0.6928396",
"0.6927588",
"0.6907409",
"0.68977255",
"0.6895859",
"0.6866112",
"0.68589467",
"0.68529665",
"0.6851944",
"0.6851944",
"0.68519... | 0.0 | -1 |
Called when message store gets refreshed on Logon. | default void onRefresh(SessionID sessionID) {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\r\n\t\t\t\t\tpublic void onLoginedNotify() {\n\t\t\t\t\t\tTypeSDKLogger.d( \"onLoginedNotify\");\r\n\t\t\t\t\t\thaimaLogout();\r\n\t\t\t\t\t\thaimaLogin();\r\n\t\t\t\t\t}",
"@Override\n public void onRefresh() {\n getUserOnlineStatus();\n }",
"@Override\n publi... | [
"0.68171227",
"0.65946573",
"0.6466719",
"0.6415033",
"0.6374217",
"0.6288839",
"0.6264505",
"0.6260454",
"0.6258225",
"0.62326914",
"0.621107",
"0.61946577",
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"0.61468905",
"0.6141279",
"0.6134784",
"0.60604376",
"0.6022782",
"0.6020633",
"0.59928197",
"0.596053... | 0.65825117 | 2 |
Called when TestRequest is sent out due to missed Heartbeat. | default void onMissedHeartBeat(SessionID sessionID) {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"private void clearHeartBeatReq() {\n if (reqCase_ == 5) {\n reqCase_ = 0;\n req_ = null;\n }\n }",
"private void onResponseTimerTick()\r\n {\r\n EneterTrace aTrace = EneterTrace.entering();\r\n try\r\n {\r\n cleanAfterConnection(true, true);\r\n ... | [
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"0.55673945",
"0.5557639",
"0.5521713",
"0.55182457",
"0.549323",
"0.545842... | 0.63578284 | 0 |
Called when Heartbeat timeout has been detected. | default void onHeartBeatTimeout(SessionID sessionID) {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"protected void onTimeout() {\n }",
"public abstract void onTimeout();",
"public void onTimeout();",
"public void handleTimeout();",
"protected void pktTimeout() {}",
"public void onSupperTimeout() {\r\n }",
"public void handleScreenOnTimeout() {\n this.mTimeoutSummary = getTimeoutSumma... | [
"0.7574952",
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"0.6142469",
"0.6142045",
"0.61108047",
"0.610466",
"0.6100311",
... | 0.726559 | 1 |
Called when ResendRequest has been sent out. | default void onResendRequestSent(SessionID sessionID, int beginSeqNo, int endSeqNo, int currentEndSeqNo) {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"protected void onEndRequest()\n\t{\n\t}",
"default void onResendRequestSatisfied(SessionID sessionID, int beginSeqNo, int endSeqNo) {\n }",
"private void resendWorkaround() {\r\n synchronized(waiters) {\r\n if(waiters.size() > 0 && lastResponseNumber == responseNumber && System.currentTimeMillis... | [
"0.7494426",
"0.69340855",
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"0.57939965",
"0.57657737",
"0.5744126",
"0.5724585",
"0.572200... | 0.7323159 | 1 |
Called when SequenceReset has been received. | default void onSequenceResetReceived(SessionID sessionID, int newSeqNo, boolean gapFillFlag) {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"protected void onReset() {\n\t\t\n\t}",
"public abstract void onReset();",
"@Override\n public void onSequenceFinish() {\n // Yay\n }",
"protected void reset()\n {\n super.reset();\n m_seqNum = 1;\n }",
"protected void resetSe... | [
"0.7212865",
"0.70500946",
"0.686983",
"0.6777949",
"0.67389596",
"0.6730774",
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"0.6014019",
"0.5991097",
"0.5990774",
"0.59222627",
"0.5910617",
"0.5908760... | 0.7918256 | 0 |
Called when a received ResendRequest has been satisfied. | default void onResendRequestSatisfied(SessionID sessionID, int beginSeqNo, int endSeqNo) {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"default void onResendRequestSent(SessionID sessionID, int beginSeqNo, int endSeqNo, int currentEndSeqNo) {\n }",
"protected void onEndRequest()\n\t{\n\t}",
"@Override\n\t\t\t\tpublic void onResponseReceived(Request request, Response response) {\n\t\t\t\t\t\n\t\t\t\t}",
"@Override\n public void onFinish... | [
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"0.5596914",
"0.5576879",
"0.55618... | 0.7655993 | 0 |
By default Espresso Intents does not stub any Intents. Stubbing needs to be setup before every test run. In this case all external Intents will be blocked. | @Before
public void stubAllExternalIntents() {
intending(not(isInternal())).respondWith(new Instrumentation.ActivityResult(Activity.RESULT_OK, null));
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Before\n public void stubAllExternalIntents() {\n intending(not(isInternal()))\n .respondWith(new Instrumentation.ActivityResult(Activity.RESULT_OK, null));\n }",
"@Before\n public void stubAllExternalIntents() {\n intending(not(isInternal()))\n .respondWith(... | [
"0.81117827",
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"0.6145095",
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"0.59386116",
"0.5927704",
"0.5915789",
"0.5896742",
"0.5865364",
"0.5837744"... | 0.80530494 | 2 |
Invoked from the GUI because it's easier this way | public void executeFromGui(Player target) {
removeTrail(target);
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\n\tpublic void guiTinNhan() {\n\n\t}",
"private void updateGUIStatus() {\r\n\r\n }",
"@Override\n\tprotected void UpdateUI() {\n\t\t\n\t}",
"@Override\n\tprotected void UpdateUI() {\n\t\t\n\t}",
"@Override\n public void initGUI() {\n\n }",
"private static void initAndShowGUI() {\n }",... | [
"0.7137828",
"0.6982397",
"0.6875956",
"0.6875956",
"0.68629676",
"0.6733807",
"0.67165023",
"0.6637292",
"0.657599",
"0.65426123",
"0.6537203",
"0.64637744",
"0.6425565",
"0.6419065",
"0.6382768",
"0.6288481",
"0.6284301",
"0.62749976",
"0.62614256",
"0.62571895",
"0.6257189... | 0.0 | -1 |
TODO Autogenerated method stub | @Override
protected void onCreate(Bundle savedInstanceState) {
super.onCreate(savedInstanceState);
setContentView(R.layout.view_activity);
btn = (Button)findViewById(R.id.btnid2) ;
btn.setOnClickListener(new OnClickListener() {
@Override
public void onClick(View v) {
Intent intent = new Intent(getBaseContext(), MainActivity.class) ;
startActivity(intent);
}
});
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\r\n\tpublic void comer() \r\n\t{\n\t\t\r\n\t}",
"@Override\n\tpublic void comer() {\n\t\t\n\t}",
"@Override\n public void perish() {\n \n }",
"@Override\r\n\t\t\tpublic void annadir() {\n\r\n\t\t\t}",
"@Override\n\tpublic void anular() {\n\n\t}",
"@Override\n\tprotected void getExr... | [
"0.6671074",
"0.6567672",
"0.6523024",
"0.6481211",
"0.6477082",
"0.64591026",
"0.64127725",
"0.63762105",
"0.6276059",
"0.6254286",
"0.623686",
"0.6223679",
"0.6201336",
"0.61950207",
"0.61950207",
"0.61922914",
"0.6186996",
"0.6173591",
"0.61327106",
"0.61285484",
"0.608016... | 0.0 | -1 |
Used when created from Mule flow from XPATH where all incoming data is strings. | public FilterParameters(String filterAvregOrsak, String filterSekretessMarkering, String senasteAndringFBF) {
this.filterSekretessMarkering = (filterSekretessMarkering != null && filterSekretessMarkering != "") ? JaNejTYPE.valueOf(filterSekretessMarkering) : null;
this.filterAvregOrsak = (filterAvregOrsak != null) ? filterAvregOrsak : null;
this.filterSenasteAndringFBF = senasteAndringFBF != null && !senasteAndringFBF.equals("") ? senasteAndringFBF : null;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\n\tpublic Object fromXMLString(String arg0) {\n\t\treturn null;\n\t}",
"@Test\n public void testGetXmlPayload() {\n System.out.println(\"getXmlPayload\");\n String expResult = \"<?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?><json xmlns=\\\"uk.nhs.digital.mait.tkwx.jsonconverter.Jso... | [
"0.57119626",
"0.53346527",
"0.5231553",
"0.51885176",
"0.5175024",
"0.51178914",
"0.5063916",
"0.50568926",
"0.50511104",
"0.5049206",
"0.5048258",
"0.5042182",
"0.49916545",
"0.49903318",
"0.49786225",
"0.49782532",
"0.49416155",
"0.4937257",
"0.49325275",
"0.49163878",
"0.... | 0.0 | -1 |
Creates new form MainFrame | public MainFrame() {
initComponents();
java.net.URL imgURL = getClass().getResource("/pkg4seqgui/images/dna.png");
ImageIcon image = new ImageIcon(imgURL);
DefaultTreeCellRenderer renderer =(DefaultTreeCellRenderer) AnalysisTree.getCellRenderer();
renderer.setLeafIcon(image);
imgURL = getClass().getResource("/pkg4seqgui/images/dna1.png");
ImageIcon image2 = new ImageIcon(imgURL);
renderer.setOpenIcon(image2);
expandAllNodes(AnalysisTree, 0, AnalysisTree.getRowCount());
//JTREE MULTIPLEFILE
//adding here all the textarea that must be maneged with right button mouse
//vRNAPanel
contextMenu.add(vThreadText);
contextMenu.add(vAdapter5Text);
contextMenu.add(vAdapter3Text);
contextMenu.add(vMinLengthText);
contextMenu.add(vOrganismText);
//indexingSTARPanel
contextMenu.add(iThreadText);
contextMenu.add(iGenomeURLText);
contextMenu.add(iGTFURLText);
//miRNAPanel
contextMenu.add(mmiRBaseText);
//PCA
contextMenu.add(pComponent1Text);
contextMenu.add(pComponent2Text);
//DES
contextMenu.add(dLog2fcText);
contextMenu.add(dFDRText);
//indexingBW
contextMenu.add(iThreadBText);
contextMenu.add(iGenomeURLBText);
//indexingSalmonPanel
contextMenu.add(iThreadSText);
contextMenu.add(iGenomeURLSText);
contextMenu.add(iGTFURLSText);
//countingSalmon
contextMenu.add(cThreadText);
contextMenu.add(cAdapter5Text);
contextMenu.add(cAdapter3Text);
contextMenu.add(cMinLengthText);
//filterCount
contextMenu.add(fFPKMfileText);
contextMenu.add(fOutputFolderText);
FPKMFileTable.getColumn("Folder").setPreferredWidth(1000);
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
String HorSplPan = getPreferences().get("4SeqGUI_HorizontalSplitPanel", null);
if (HorSplPan!=null){
HorizontalSplitPanel.setDividerLocation(Integer.valueOf(HorSplPan));
}
else{
HorizontalSplitPanel.setDividerLocation(screenSize.height*3/10);
}
String VerSplPan = getPreferences().get("4SeqGUI_VerticalSplitPanel", null);
if (VerSplPan!=null){
VerticalSplitPanel.setDividerLocation(Integer.valueOf(VerSplPan));
}
else {
VerticalSplitPanel.setDividerLocation(screenSize.height*7/10);
}
String WindowWidth= getPreferences().get("4SeqGUI_WindowWidth", null);
String WindowHeight= getPreferences().get("4SeqGUI_WindowHeight", null);
if ((WindowWidth!=null)&&(WindowHeight!=null)){
setSize(Integer.valueOf(WindowWidth),Integer.valueOf(WindowHeight));
}
else{
setSize(screenSize.width*95/100,screenSize.height*95/100);
}
//OUTPUT FRAME
int OutputframeWidth= Integer.valueOf(getPreferences().get("4SeqGUI_WindowOutputWidth", "0"));
int OutputframeHeight= Integer.valueOf(getPreferences().get("4SeqGUI_WindowOutputHeight", "0"));
if ((OutputframeWidth==0)||(OutputframeHeight==0)){
OutputframeWidth=screenSize.width*4/100;
OutputframeHeight=screenSize.height*5/100;
}
OutputFrame.setSize(OutputframeWidth,OutputframeHeight);
int DownloadframeWidth= Integer.valueOf(getPreferences().get("4SeqGUI_WindowDownloadWidth", "0"));
int DownloadframeHeight= Integer.valueOf(getPreferences().get("4SeqGUI_WindowDownloadHeight", "0"));
if ((DownloadframeWidth==0)||(DownloadframeHeight==0)){
DownloadframeWidth=screenSize.width*4/100;
DownloadframeHeight=screenSize.height*5/100;
}
DownloadFrame.setSize(DownloadframeWidth,DownloadframeHeight);
String WidthGroup = getPreferences().get("4SeqGUI_GroupCellWidth", null);
String WidthBatch = getPreferences().get("4SeqGUI_BatchCellWidth", null);
String WidthFolder = getPreferences().get("4SeqGUI_FolderCellWidth", null);
if ((WidthGroup!=null)&&(WidthBatch!=null)&&(WidthFolder!=null)){
FPKMFileTable.getColumnModel().getColumn(1).setPreferredWidth(Integer.valueOf(WidthGroup));
FPKMFileTable.getColumnModel().getColumn(2).setPreferredWidth(Integer.valueOf(WidthBatch));
FPKMFileTable.getColumnModel().getColumn(0).setPreferredWidth(Integer.valueOf(WidthFolder));
}
else
FPKMFileTable.getColumnModel().getColumn(1).setPreferredWidth(FPKMFileTable.getWidth()*10/100);
String WidthGroup1 = getPreferences().get("4SeqGUI_Group1CellWidth", null);
String WidthBatch1 = getPreferences().get("4SeqGUI_Batch1CellWidth", null);
String WidthHeader = getPreferences().get("4SeqGUI_HeaderCellWidth", null);
if ((WidthGroup1!=null)&&(WidthBatch1!=null)&&(WidthHeader!=null)){
CCountHeaderTable.getColumnModel().getColumn(1).setPreferredWidth(Integer.valueOf(WidthGroup1));
CCountHeaderTable.getColumnModel().getColumn(2).setPreferredWidth(Integer.valueOf(WidthBatch1));
CCountHeaderTable.getColumnModel().getColumn(0).setPreferredWidth(Integer.valueOf(WidthHeader));
}
else
CCountHeaderTable.getColumnModel().getColumn(1).setPreferredWidth(CCountHeaderTable.getWidth()*10/100);
setLocationRelativeTo(null);
invalidate();
doLayout();
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public static void createMainframe()\n\t{\n\t\t//Creates the frame\n\t\tJFrame foodFrame = new JFrame(\"USDA Food Database\");\n\t\t//Sets up the frame\n\t\tfoodFrame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);\n\t\tfoodFrame.setSize(1000,750);\n\t\tfoodFrame.setResizable(false);\n\t\tfoodFrame.setIconImage(ic... | [
"0.7865973",
"0.7794478",
"0.772496",
"0.7702068",
"0.7677763",
"0.7677763",
"0.7677763",
"0.7677763",
"0.7677763",
"0.7677763",
"0.7677763",
"0.7677763",
"0.7677763",
"0.7677763",
"0.7677763",
"0.7677763",
"0.7630447",
"0.7617989",
"0.7527141",
"0.749589",
"0.730413",
"0.7... | 0.0 | -1 |
This method is called from within the constructor to initialize the form. WARNING: Do NOT modify this code. The content of this method is always regenerated by the Form Editor. | @SuppressWarnings("unchecked")
// <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
private void initComponents() {
java.awt.GridBagConstraints gridBagConstraints;
jMenu1 = new javax.swing.JMenu();
jMenu2 = new javax.swing.JMenu();
vExecution = new javax.swing.ButtonGroup();
vSeq = new javax.swing.ButtonGroup();
Strand = new javax.swing.ButtonGroup();
Truncating = new javax.swing.ButtonGroup();
Annotation = new javax.swing.ButtonGroup();
mExecution = new javax.swing.ButtonGroup();
mDownload = new javax.swing.ButtonGroup();
mTrimmed = new javax.swing.ButtonGroup();
OutputFrame = new javax.swing.JFrame();
jScrollPane3 = new javax.swing.JScrollPane();
OutputText = new javax.swing.JTextArea();
CloseOutput = new javax.swing.JToggleButton();
ReloadOutput = new javax.swing.JToggleButton();
RemoveOutput = new javax.swing.JButton();
DlogButton = new javax.swing.JButton();
IExecutionStarRSEM = new javax.swing.ButtonGroup();
ConfigurationFrame = new javax.swing.JFrame();
jLabel18 = new javax.swing.JLabel();
ParallelTextField = new javax.swing.JTextField();
jLabel19 = new javax.swing.JLabel();
ThreadTextField = new javax.swing.JTextField();
jLabel21 = new javax.swing.JLabel();
Adapter5TextField = new javax.swing.JTextField();
jLabel22 = new javax.swing.JLabel();
Adapter3TextField = new javax.swing.JTextField();
ConfCancell = new javax.swing.JButton();
jButton10 = new javax.swing.JButton();
jButton11 = new javax.swing.JButton();
jMenuItem5 = new javax.swing.JMenuItem();
CovComboBox = new javax.swing.JComboBox<>();
DataType = new javax.swing.ButtonGroup();
Covariates = new javax.swing.ButtonGroup();
DEStype = new javax.swing.ButtonGroup();
buttonGroup1 = new javax.swing.ButtonGroup();
IExecutionBWA = new javax.swing.ButtonGroup();
GATK = new javax.swing.ButtonGroup();
jRadioButton1 = new javax.swing.JRadioButton();
MExecution = new javax.swing.ButtonGroup();
MSeq = new javax.swing.ButtonGroup();
MRemoveDuplicates = new javax.swing.ButtonGroup();
MAdapter = new javax.swing.ButtonGroup();
BatchComboBox = new javax.swing.JComboBox<>();
DESBatch = new javax.swing.ButtonGroup();
DownloadFrame = new javax.swing.JFrame();
jButton31 = new javax.swing.JButton();
jButton32 = new javax.swing.JButton();
jPanel1 = new javax.swing.JPanel();
jLabel12 = new javax.swing.JLabel();
jButton33 = new javax.swing.JButton();
jButton34 = new javax.swing.JButton();
Downloadtext = new javax.swing.JTextField();
About4SeqGUIFrame = new javax.swing.JFrame();
jLabel96 = new javax.swing.JLabel();
jLabel100 = new javax.swing.JLabel();
jLabel101 = new javax.swing.JLabel();
jButton36 = new javax.swing.JButton();
jLabel99 = new javax.swing.JLabel();
jLabel102 = new javax.swing.JLabel();
IExecutionSalmon = new javax.swing.ButtonGroup();
cExecutiionSalmon = new javax.swing.ButtonGroup();
cSeq = new javax.swing.ButtonGroup();
cStrand = new javax.swing.ButtonGroup();
DataFilter = new javax.swing.ButtonGroup();
jToolBar1 = new javax.swing.JToolBar();
jButton1 = new javax.swing.JButton();
jButton2 = new javax.swing.JButton();
jToggleButton11 = new javax.swing.JToggleButton();
jButton9 = new javax.swing.JButton();
jButton26 = new javax.swing.JButton();
jButton35 = new javax.swing.JButton();
VerticalSplitPanel = new javax.swing.JSplitPane();
BottomPanel = new javax.swing.JPanel();
jScrollPane4 = new javax.swing.JScrollPane();
ProcStatusPanel = new javax.swing.JPanel();
jScrollPane2 = new javax.swing.JScrollPane();
ProcList = new javax.swing.JList<>();
HorizontalSplitPanel = new javax.swing.JSplitPane();
MainPanel = new javax.swing.JPanel();
Empty = new javax.swing.JScrollPane();
EmptyPanel = new javax.swing.JPanel();
jLabel24 = new javax.swing.JLabel();
IndexingStarRSEM = new javax.swing.JScrollPane();
IndexingStarRSEMPanel = new javax.swing.JPanel();
iCloseButton = new javax.swing.JButton();
jButton12 = new javax.swing.JButton();
iResetButton = new javax.swing.JButton();
jButton14 = new javax.swing.JButton();
jPanel13 = new javax.swing.JPanel();
jLabel28 = new javax.swing.JLabel();
iGenomeFolderText = new javax.swing.JTextField();
jToggleButton15 = new javax.swing.JToggleButton();
jToggleButton16 = new javax.swing.JToggleButton();
jLabel30 = new javax.swing.JLabel();
iGenomeURLText = new javax.swing.JTextField();
jLabel33 = new javax.swing.JLabel();
iGTFURLText = new javax.swing.JTextField();
jPanel14 = new javax.swing.JPanel();
jLabel31 = new javax.swing.JLabel();
iSudoRadioButton = new javax.swing.JRadioButton();
iDockerRadioButton = new javax.swing.JRadioButton();
jLabel32 = new javax.swing.JLabel();
iThreadText = new javax.swing.JTextField();
mRNA = new javax.swing.JScrollPane();
mRNAPanel = new javax.swing.JPanel();
jButton6 = new javax.swing.JButton();
jButton8 = new javax.swing.JButton();
jButton7 = new javax.swing.JButton();
vCloseButton1 = new javax.swing.JButton();
jPanel9 = new javax.swing.JPanel();
jLabel17 = new javax.swing.JLabel();
mmiRBaseText = new javax.swing.JTextField();
jLabel20 = new javax.swing.JLabel();
mDTrueRadioButton = new javax.swing.JRadioButton();
mDFalseRadioButton = new javax.swing.JRadioButton();
jLabel23 = new javax.swing.JLabel();
mANEBRadioButton = new javax.swing.JRadioButton();
mAILLUMINARadioButton = new javax.swing.JRadioButton();
jLabel25 = new javax.swing.JLabel();
mTTrueRadioButton = new javax.swing.JRadioButton();
mTFalseRadioButton = new javax.swing.JRadioButton();
jPanel8 = new javax.swing.JPanel();
jLabel15 = new javax.swing.JLabel();
mFastQFolderText = new javax.swing.JTextField();
jToggleButton8 = new javax.swing.JToggleButton();
jToggleButton7 = new javax.swing.JToggleButton();
mOutputFolderText = new javax.swing.JTextField();
jToggleButton9 = new javax.swing.JToggleButton();
jToggleButton10 = new javax.swing.JToggleButton();
jLabel16 = new javax.swing.JLabel();
jPanel7 = new javax.swing.JPanel();
jLabel14 = new javax.swing.JLabel();
mSudoRadioButton = new javax.swing.JRadioButton();
mDockerRadioButton = new javax.swing.JRadioButton();
FPKM = new javax.swing.JScrollPane();
FPKMPanel = new javax.swing.JPanel();
jPanel4 = new javax.swing.JPanel();
jScrollPane6 = new javax.swing.JScrollPane();
FPKMFileTable = new javax.swing.JTable();
FAddFile = new javax.swing.JButton();
jButton13 = new javax.swing.JButton();
jLabel26 = new javax.swing.JLabel();
FtypesComboBox = new javax.swing.JComboBox<>();
jLabel27 = new javax.swing.JLabel();
FOutputFolderText = new javax.swing.JTextField();
Fbrowes = new javax.swing.JButton();
Fcancel = new javax.swing.JButton();
FExecuteButton = new javax.swing.JButton();
FSaveButton = new javax.swing.JButton();
FResetButton = new javax.swing.JButton();
FCloseButton = new javax.swing.JButton();
vmRNA = new javax.swing.JScrollPane();
vmRNAPanel = new javax.swing.JPanel();
vCloseButton = new javax.swing.JButton();
jButton4 = new javax.swing.JButton();
jButton5 = new javax.swing.JButton();
jButton3 = new javax.swing.JButton();
jPanel2 = new javax.swing.JPanel();
jLabel2 = new javax.swing.JLabel();
vFastQFolderText = new javax.swing.JTextField();
jToggleButton2 = new javax.swing.JToggleButton();
jToggleButton1 = new javax.swing.JToggleButton();
jLabel3 = new javax.swing.JLabel();
vOutputFolderText = new javax.swing.JTextField();
jToggleButton4 = new javax.swing.JToggleButton();
jToggleButton3 = new javax.swing.JToggleButton();
jLabel9 = new javax.swing.JLabel();
vGenomeFolderText = new javax.swing.JTextField();
jToggleButton5 = new javax.swing.JToggleButton();
jToggleButton6 = new javax.swing.JToggleButton();
jPanel3 = new javax.swing.JPanel();
jLabel1 = new javax.swing.JLabel();
vSudoRadioButton = new javax.swing.JRadioButton();
vDockerRadioButton = new javax.swing.JRadioButton();
jLabel4 = new javax.swing.JLabel();
vThreadText = new javax.swing.JTextField();
jPanel6 = new javax.swing.JPanel();
vAdapter5Text = new javax.swing.JTextField();
jLabel5 = new javax.swing.JLabel();
jLabel6 = new javax.swing.JLabel();
vAdapter3Text = new javax.swing.JTextField();
vPeRadioButton = new javax.swing.JRadioButton();
vSeRadioButton = new javax.swing.JRadioButton();
jLabel7 = new javax.swing.JLabel();
jLabel8 = new javax.swing.JLabel();
vMinLengthText = new javax.swing.JTextField();
jLabel10 = new javax.swing.JLabel();
vSNoneRadioButton = new javax.swing.JRadioButton();
vSForwardRadioButton = new javax.swing.JRadioButton();
vSReverseRadioButton = new javax.swing.JRadioButton();
vOrganismText = new javax.swing.JTextField();
jLabel11 = new javax.swing.JLabel();
jLabel13 = new javax.swing.JLabel();
vBAMyesRadioButton = new javax.swing.JRadioButton();
vBAMnoLRadioButton = new javax.swing.JRadioButton();
PCA = new javax.swing.JScrollPane();
PCAPanel = new javax.swing.JPanel();
vCloseButton2 = new javax.swing.JButton();
jButton15 = new javax.swing.JButton();
jButton16 = new javax.swing.JButton();
jButton17 = new javax.swing.JButton();
jPanel5 = new javax.swing.JPanel();
jLabel29 = new javax.swing.JLabel();
pFPKMfileText = new javax.swing.JTextField();
jToggleButton12 = new javax.swing.JToggleButton();
fCancelButton = new javax.swing.JToggleButton();
jLabel34 = new javax.swing.JLabel();
pOutputFolderText = new javax.swing.JTextField();
jToggleButton13 = new javax.swing.JToggleButton();
fCancelButton1 = new javax.swing.JToggleButton();
jPanel11 = new javax.swing.JPanel();
pComponent1Text = new javax.swing.JTextField();
jLabel38 = new javax.swing.JLabel();
jLabel39 = new javax.swing.JLabel();
pComponent2Text = new javax.swing.JTextField();
jLabel42 = new javax.swing.JLabel();
pCountsRadioButton = new javax.swing.JRadioButton();
pFPKMRadioButton = new javax.swing.JRadioButton();
pTPMRadioButton = new javax.swing.JRadioButton();
jLabel43 = new javax.swing.JLabel();
jLabel44 = new javax.swing.JLabel();
pCovYesRadioButton = new javax.swing.JRadioButton();
pCovNoRadioButton = new javax.swing.JRadioButton();
pLegendComboBox = new javax.swing.JComboBox<>();
DES = new javax.swing.JScrollPane();
DESPanel = new javax.swing.JPanel();
vCloseButton3 = new javax.swing.JButton();
jButton18 = new javax.swing.JButton();
jButton19 = new javax.swing.JButton();
jButton20 = new javax.swing.JButton();
jPanel10 = new javax.swing.JPanel();
jLabel35 = new javax.swing.JLabel();
dFPKMfileText = new javax.swing.JTextField();
jToggleButton14 = new javax.swing.JToggleButton();
fCancelButton2 = new javax.swing.JToggleButton();
jLabel36 = new javax.swing.JLabel();
dOutputFolderText = new javax.swing.JTextField();
jToggleButton17 = new javax.swing.JToggleButton();
fCancelButton3 = new javax.swing.JToggleButton();
jPanel12 = new javax.swing.JPanel();
dLog2fcText = new javax.swing.JTextField();
jLabel40 = new javax.swing.JLabel();
jLabel41 = new javax.swing.JLabel();
dFDRText = new javax.swing.JTextField();
jLabel45 = new javax.swing.JLabel();
dGeneRadioButton = new javax.swing.JRadioButton();
jLabel47 = new javax.swing.JLabel();
dCovComboBox = new javax.swing.JComboBox<>();
dmiRNARadioButton = new javax.swing.JRadioButton();
jLabel58 = new javax.swing.JLabel();
jLabel59 = new javax.swing.JLabel();
dIsoformRadioButton = new javax.swing.JRadioButton();
jLabel62 = new javax.swing.JLabel();
dBatchesTrue = new javax.swing.JRadioButton();
DBatchesFalse = new javax.swing.JRadioButton();
IndexingBWA = new javax.swing.JScrollPane();
IndexingBWAPanel = new javax.swing.JPanel();
iCloseButton1 = new javax.swing.JButton();
jButton21 = new javax.swing.JButton();
iResetButton1 = new javax.swing.JButton();
jButton22 = new javax.swing.JButton();
jPanel15 = new javax.swing.JPanel();
jLabel37 = new javax.swing.JLabel();
iGenomeFolderBText = new javax.swing.JTextField();
jToggleButton18 = new javax.swing.JToggleButton();
jToggleButton19 = new javax.swing.JToggleButton();
jLabel46 = new javax.swing.JLabel();
iGenomeURLBText = new javax.swing.JTextField();
jLabel48 = new javax.swing.JLabel();
idbSPNText = new javax.swing.JTextField();
jLabel51 = new javax.swing.JLabel();
iBTrueRadioButton = new javax.swing.JRadioButton();
iBFalseRadioButton = new javax.swing.JRadioButton();
i1000GenomeText = new javax.swing.JTextField();
jLabel52 = new javax.swing.JLabel();
i1000BrowseButton = new javax.swing.JToggleButton();
i1000CancelButton = new javax.swing.JToggleButton();
idbSPNBrowseButton = new javax.swing.JToggleButton();
idbSPNCancelButton = new javax.swing.JToggleButton();
jPanel16 = new javax.swing.JPanel();
jLabel49 = new javax.swing.JLabel();
iSudoBRadioButton = new javax.swing.JRadioButton();
iDockerBRadioButton = new javax.swing.JRadioButton();
jLabel50 = new javax.swing.JLabel();
iThreadBText = new javax.swing.JTextField();
MACS = new javax.swing.JScrollPane();
MACSPanel = new javax.swing.JPanel();
vCloseButton4 = new javax.swing.JButton();
jButton23 = new javax.swing.JButton();
jButton24 = new javax.swing.JButton();
jButton25 = new javax.swing.JButton();
jPanel17 = new javax.swing.JPanel();
jLabel53 = new javax.swing.JLabel();
MOutputFolderText = new javax.swing.JTextField();
jToggleButton20 = new javax.swing.JToggleButton();
jToggleButton21 = new javax.swing.JToggleButton();
jLabel54 = new javax.swing.JLabel();
MScratchFolderText = new javax.swing.JTextField();
jToggleButton22 = new javax.swing.JToggleButton();
jToggleButton23 = new javax.swing.JToggleButton();
jLabel55 = new javax.swing.JLabel();
MMockFolderText = new javax.swing.JTextField();
jToggleButton24 = new javax.swing.JToggleButton();
jToggleButton25 = new javax.swing.JToggleButton();
MGenomeFolderText = new javax.swing.JTextField();
jToggleButton26 = new javax.swing.JToggleButton();
jToggleButton27 = new javax.swing.JToggleButton();
jLabel60 = new javax.swing.JLabel();
jLabel67 = new javax.swing.JLabel();
MTestFolderText = new javax.swing.JTextField();
jToggleButton28 = new javax.swing.JToggleButton();
jToggleButton29 = new javax.swing.JToggleButton();
jPanel18 = new javax.swing.JPanel();
jLabel56 = new javax.swing.JLabel();
MSudoRadioButton = new javax.swing.JRadioButton();
MDockerRadioButton = new javax.swing.JRadioButton();
jLabel57 = new javax.swing.JLabel();
MThreadText = new javax.swing.JTextField();
jLabel61 = new javax.swing.JLabel();
jPanel19 = new javax.swing.JPanel();
jLabel63 = new javax.swing.JLabel();
MToolComboBox = new javax.swing.JComboBox<>();
Tool = new javax.swing.JPanel();
jPanel22 = new javax.swing.JPanel();
jLabel78 = new javax.swing.JLabel();
MMaxmfoldText = new javax.swing.JTextField();
jLabel79 = new javax.swing.JLabel();
jLabel82 = new javax.swing.JLabel();
MMinmfoldText = new javax.swing.JTextField();
MMpvalueText = new javax.swing.JTextField();
jPanel23 = new javax.swing.JPanel();
jLabel80 = new javax.swing.JLabel();
MSgsizeText = new javax.swing.JTextField();
jLabel81 = new javax.swing.JLabel();
jLabel83 = new javax.swing.JLabel();
MSWindowsText = new javax.swing.JTextField();
MSFDRText = new javax.swing.JTextField();
jPanel20 = new javax.swing.JPanel();
MAdapter5Text = new javax.swing.JTextField();
jLabel68 = new javax.swing.JLabel();
jLabel69 = new javax.swing.JLabel();
MAdapter3Text = new javax.swing.JTextField();
jLabel70 = new javax.swing.JLabel();
MTTSText = new javax.swing.JTextField();
jLabel71 = new javax.swing.JLabel();
jLabel72 = new javax.swing.JLabel();
jLabel73 = new javax.swing.JLabel();
MRyesRadioButton = new javax.swing.JRadioButton();
MRnoRadioButton = new javax.swing.JRadioButton();
jLabel74 = new javax.swing.JLabel();
MOrgComboBox = new javax.swing.JComboBox<>();
MMinLengthText = new javax.swing.JTextField();
MMaxUpstreamText = new javax.swing.JTextField();
jLabel75 = new javax.swing.JLabel();
jLabel76 = new javax.swing.JLabel();
MReadLengthTextField = new javax.swing.JTextField();
SampleSize = new javax.swing.JScrollPane();
SampleSizePanel = new javax.swing.JPanel();
jPanel21 = new javax.swing.JPanel();
jLabel64 = new javax.swing.JLabel();
SSOutputFolderText = new javax.swing.JTextField();
SSbrowes = new javax.swing.JButton();
SScancel = new javax.swing.JButton();
jLabel65 = new javax.swing.JLabel();
jLabel66 = new javax.swing.JLabel();
SSCountTableText = new javax.swing.JTextField();
jButton27 = new javax.swing.JButton();
jButton28 = new javax.swing.JButton();
SSExecuteButton = new javax.swing.JButton();
SSSaveButton = new javax.swing.JButton();
SSResetButton = new javax.swing.JButton();
SSCloseButton = new javax.swing.JButton();
jPanel24 = new javax.swing.JPanel();
jLabel77 = new javax.swing.JLabel();
jLabel84 = new javax.swing.JLabel();
jLabel85 = new javax.swing.JLabel();
jLabel86 = new javax.swing.JLabel();
SSPowerText = new javax.swing.JTextField();
SSGeneText = new javax.swing.JTextField();
SSlog2Text = new javax.swing.JTextField();
jLabel87 = new javax.swing.JLabel();
SSFDRtext = new javax.swing.JTextField();
ExperimentPower = new javax.swing.JScrollPane();
ExperimentPowerPanel = new javax.swing.JPanel();
jPanel25 = new javax.swing.JPanel();
jLabel88 = new javax.swing.JLabel();
EPOutputFolderText = new javax.swing.JTextField();
SSbrowes1 = new javax.swing.JButton();
SScancel1 = new javax.swing.JButton();
jLabel89 = new javax.swing.JLabel();
jLabel90 = new javax.swing.JLabel();
EPCountTableText = new javax.swing.JTextField();
jButton29 = new javax.swing.JButton();
jButton30 = new javax.swing.JButton();
EPExecuteButton1 = new javax.swing.JButton();
EPSaveButton = new javax.swing.JButton();
EPResetButton = new javax.swing.JButton();
EPCloseButton = new javax.swing.JButton();
jPanel26 = new javax.swing.JPanel();
jLabel91 = new javax.swing.JLabel();
jLabel92 = new javax.swing.JLabel();
jLabel93 = new javax.swing.JLabel();
jLabel94 = new javax.swing.JLabel();
EPSampleText = new javax.swing.JTextField();
EPGeneText = new javax.swing.JTextField();
EPlog2Text = new javax.swing.JTextField();
jLabel95 = new javax.swing.JLabel();
EPFDRtext = new javax.swing.JTextField();
mRNABatch = new javax.swing.JScrollPane();
mRNABatchPanel = new javax.swing.JPanel();
jPanel27 = new javax.swing.JPanel();
jScrollPane7 = new javax.swing.JScrollPane();
CCountHeaderTable = new javax.swing.JTable();
CCovInputFileText = new javax.swing.JTextField();
Cinbrowes = new javax.swing.JButton();
Cincancel = new javax.swing.JButton();
jLabel98 = new javax.swing.JLabel();
jLabel97 = new javax.swing.JLabel();
COutputFolderText = new javax.swing.JTextField();
Coutbrowes = new javax.swing.JButton();
Coutcancel = new javax.swing.JButton();
FExecuteButton1 = new javax.swing.JButton();
FSaveButton1 = new javax.swing.JButton();
CResetButton1 = new javax.swing.JButton();
CCloseButton1 = new javax.swing.JButton();
IndexingSalmon = new javax.swing.JScrollPane();
IndexingSalmonPanel = new javax.swing.JPanel();
iCloseButton2 = new javax.swing.JButton();
jButton37 = new javax.swing.JButton();
iResetButton2 = new javax.swing.JButton();
jButton38 = new javax.swing.JButton();
jPanel28 = new javax.swing.JPanel();
jLabel103 = new javax.swing.JLabel();
iGenomeFolderSText = new javax.swing.JTextField();
jToggleButton30 = new javax.swing.JToggleButton();
jToggleButton31 = new javax.swing.JToggleButton();
jLabel104 = new javax.swing.JLabel();
iGenomeURLSText = new javax.swing.JTextField();
jLabel105 = new javax.swing.JLabel();
iGTFURLSText = new javax.swing.JTextField();
iKmerSText = new javax.swing.JTextField();
jLabel108 = new javax.swing.JLabel();
jLabel109 = new javax.swing.JLabel();
jPanel29 = new javax.swing.JPanel();
jLabel106 = new javax.swing.JLabel();
iSudoRadioSButton = new javax.swing.JRadioButton();
iDockerRadioSButton = new javax.swing.JRadioButton();
jLabel107 = new javax.swing.JLabel();
iThreadSText = new javax.swing.JTextField();
CountingSalmon = new javax.swing.JScrollPane();
CountingSalmonPanel = new javax.swing.JPanel();
vCloseButton5 = new javax.swing.JButton();
jButton39 = new javax.swing.JButton();
jButton40 = new javax.swing.JButton();
jButton41 = new javax.swing.JButton();
jPanel30 = new javax.swing.JPanel();
jLabel110 = new javax.swing.JLabel();
cFastQFolderText = new javax.swing.JTextField();
jToggleButton32 = new javax.swing.JToggleButton();
jToggleButton33 = new javax.swing.JToggleButton();
jLabel111 = new javax.swing.JLabel();
cOutputFolderText = new javax.swing.JTextField();
jToggleButton34 = new javax.swing.JToggleButton();
jToggleButton35 = new javax.swing.JToggleButton();
jLabel112 = new javax.swing.JLabel();
cGenomeFolderText = new javax.swing.JTextField();
jToggleButton36 = new javax.swing.JToggleButton();
jToggleButton37 = new javax.swing.JToggleButton();
jPanel31 = new javax.swing.JPanel();
jLabel113 = new javax.swing.JLabel();
cSudoRadioButton = new javax.swing.JRadioButton();
cDockerRadioButton = new javax.swing.JRadioButton();
jLabel114 = new javax.swing.JLabel();
cThreadText = new javax.swing.JTextField();
jPanel32 = new javax.swing.JPanel();
cAdapter5Text = new javax.swing.JTextField();
jLabel115 = new javax.swing.JLabel();
jLabel116 = new javax.swing.JLabel();
cAdapter3Text = new javax.swing.JTextField();
cPeRadioButton = new javax.swing.JRadioButton();
cSeRadioButton = new javax.swing.JRadioButton();
jLabel117 = new javax.swing.JLabel();
jLabel118 = new javax.swing.JLabel();
cMinLengthText = new javax.swing.JTextField();
jLabel119 = new javax.swing.JLabel();
cSNoneRadioButton = new javax.swing.JRadioButton();
cSForwardRadioButton = new javax.swing.JRadioButton();
cSReverseRadioButton = new javax.swing.JRadioButton();
filterCounts = new javax.swing.JScrollPane();
filterCountsPanel = new javax.swing.JPanel();
vCloseButton6 = new javax.swing.JButton();
jButton42 = new javax.swing.JButton();
jButton43 = new javax.swing.JButton();
jButton44 = new javax.swing.JButton();
jPanel33 = new javax.swing.JPanel();
jLabel120 = new javax.swing.JLabel();
fFPKMfileText = new javax.swing.JTextField();
jToggleButton38 = new javax.swing.JToggleButton();
fCancelButton4 = new javax.swing.JToggleButton();
jLabel121 = new javax.swing.JLabel();
fOutputFolderText = new javax.swing.JTextField();
jToggleButton39 = new javax.swing.JToggleButton();
fCancelButton5 = new javax.swing.JToggleButton();
jPanel34 = new javax.swing.JPanel();
jLabel124 = new javax.swing.JLabel();
fgeneRadioButton = new javax.swing.JRadioButton();
fisoformRadioButton = new javax.swing.JRadioButton();
fmirnaRadioButton = new javax.swing.JRadioButton();
LeftPanel = new javax.swing.JPanel();
jScrollPane1 = new javax.swing.JScrollPane();
AnalysisTree = new javax.swing.JTree();
jMenuBar1 = new javax.swing.JMenuBar();
jMenu3 = new javax.swing.JMenu();
jMenuItem3 = new javax.swing.JMenuItem();
jMenuItem4 = new javax.swing.JMenuItem();
jMenuItem6 = new javax.swing.JMenuItem();
jMenu4 = new javax.swing.JMenu();
jMenuItem1 = new javax.swing.JMenuItem();
jMenuItem8 = new javax.swing.JMenuItem();
jMenuItem2 = new javax.swing.JMenuItem();
jMenu5 = new javax.swing.JMenu();
jMenuItem7 = new javax.swing.JMenuItem();
jMenu1.setText("jMenu1");
jMenu2.setText("jMenu2");
OutputFrame.setTitle("Process Output");
OutputFrame.setLocation(new java.awt.Point(100, 100));
OutputFrame.addWindowListener(new java.awt.event.WindowAdapter() {
public void windowClosing(java.awt.event.WindowEvent evt) {
OutputFrameWindowClosing(evt);
}
});
OutputFrame.getContentPane().setLayout(new java.awt.GridBagLayout());
OutputText.setEditable(false);
OutputText.setColumns(20);
OutputText.setRows(5);
jScrollPane3.setViewportView(OutputText);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 6;
gridBagConstraints.gridheight = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
gridBagConstraints.weightx = 0.2;
gridBagConstraints.weighty = 0.2;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
OutputFrame.getContentPane().add(jScrollPane3, gridBagConstraints);
CloseOutput.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
CloseOutput.setText("Close");
CloseOutput.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
CloseOutputActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 5;
gridBagConstraints.gridy = 5;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
OutputFrame.getContentPane().add(CloseOutput, gridBagConstraints);
ReloadOutput.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/reset.png"))); // NOI18N
ReloadOutput.setText("Reload");
ReloadOutput.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
ReloadOutputActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 5;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
OutputFrame.getContentPane().add(ReloadOutput, gridBagConstraints);
RemoveOutput.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/remove.png"))); // NOI18N
RemoveOutput.setText("RemoveEntry");
RemoveOutput.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
RemoveOutputActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 4;
gridBagConstraints.gridy = 5;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
OutputFrame.getContentPane().add(RemoveOutput, gridBagConstraints);
DlogButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/log.png"))); // NOI18N
DlogButton.setText("Docker Logs");
DlogButton.setEnabled(false);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 5;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_END;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
OutputFrame.getContentPane().add(DlogButton, gridBagConstraints);
ConfigurationFrame.setTitle("Configuration");
ConfigurationFrame.setLocation(new java.awt.Point(200, 200));
ConfigurationFrame.setName("ConfigurationFrame"); // NOI18N
ConfigurationFrame.setResizable(false);
jLabel18.setText("Maximum number of parallel proceses:");
jLabel19.setText("Maximum number of threads for process:");
jLabel21.setText("Default adapter 5':");
jLabel22.setText("Default adapter 3':");
ConfCancell.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
ConfCancell.setText("Cancel");
ConfCancell.setToolTipText("");
ConfCancell.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
ConfCancellActionPerformed(evt);
}
});
jButton10.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/86b.png"))); // NOI18N
jButton10.setText("Save&Close");
jButton10.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton10ActionPerformed(evt);
}
});
jButton11.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/reset.png"))); // NOI18N
jButton11.setText("Reset");
jButton11.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton11ActionPerformed(evt);
}
});
javax.swing.GroupLayout ConfigurationFrameLayout = new javax.swing.GroupLayout(ConfigurationFrame.getContentPane());
ConfigurationFrame.getContentPane().setLayout(ConfigurationFrameLayout);
ConfigurationFrameLayout.setHorizontalGroup(
ConfigurationFrameLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(ConfigurationFrameLayout.createSequentialGroup()
.addContainerGap()
.addGroup(ConfigurationFrameLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(ConfigurationFrameLayout.createSequentialGroup()
.addGroup(ConfigurationFrameLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(ConfigurationFrameLayout.createSequentialGroup()
.addComponent(jLabel18, javax.swing.GroupLayout.PREFERRED_SIZE, 297, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(ParallelTextField, javax.swing.GroupLayout.DEFAULT_SIZE, 114, Short.MAX_VALUE))
.addGroup(ConfigurationFrameLayout.createSequentialGroup()
.addComponent(jLabel19, javax.swing.GroupLayout.PREFERRED_SIZE, 297, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(ThreadTextField)))
.addGap(627, 627, 627))
.addGroup(ConfigurationFrameLayout.createSequentialGroup()
.addComponent(jLabel21, javax.swing.GroupLayout.PREFERRED_SIZE, 297, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(Adapter5TextField)
.addContainerGap())
.addGroup(ConfigurationFrameLayout.createSequentialGroup()
.addComponent(jLabel22, javax.swing.GroupLayout.PREFERRED_SIZE, 297, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(Adapter3TextField)
.addContainerGap())))
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, ConfigurationFrameLayout.createSequentialGroup()
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(jButton11)
.addGap(18, 18, 18)
.addComponent(jButton10)
.addGap(18, 18, 18)
.addComponent(ConfCancell)
.addContainerGap())
);
ConfigurationFrameLayout.setVerticalGroup(
ConfigurationFrameLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(ConfigurationFrameLayout.createSequentialGroup()
.addContainerGap()
.addGroup(ConfigurationFrameLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jLabel18)
.addComponent(ParallelTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGap(18, 18, 18)
.addGroup(ConfigurationFrameLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jLabel19)
.addComponent(ThreadTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGap(18, 18, 18)
.addGroup(ConfigurationFrameLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jLabel21)
.addComponent(Adapter5TextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGap(18, 18, 18)
.addGroup(ConfigurationFrameLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jLabel22)
.addComponent(Adapter3TextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 14, Short.MAX_VALUE)
.addGroup(ConfigurationFrameLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(ConfCancell)
.addComponent(jButton10)
.addComponent(jButton11))
.addContainerGap())
);
jMenuItem5.setText("jMenuItem5");
CovComboBox.setModel(new javax.swing.DefaultComboBoxModel<>(new String[] { "Cov.1", "Cov.2", "Cov.3", "Cov.4", "Cov.5", "Cov.6", "Cov.7", "Cov.8", "Cov.9", "Cov.10", "Cov.11", "Cov.12", "Cov.13", "Cov.14", "Cov.15", "Cov.16", "Cov.17", "Cov.18", "Cov.19", "Cov.20", "Cov.21", "Cov.22", "Cov.23", "Cov.24", "Cov.25", "Cov.26", "Cov.27", "Cov.28", "Cov.29", "Cov.30" }));
jRadioButton1.setText("jRadioButton1");
BatchComboBox.setModel(new javax.swing.DefaultComboBoxModel<>(new String[] { "Batch1", "Batch2", "Batch3", "Batch4", "Batch5", "Batch6", "Batch7", "Batch8", "Batch9", "Batch10", "Batch11", "Batch12", "Batch13", "Batch14", "Batch15", "Batch16", "Batch17", "Batch18", "Batch19", "Batch20" }));
DownloadFrame.setTitle("Download Docker imges");
DownloadFrame.getContentPane().setLayout(new java.awt.GridBagLayout());
jButton31.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/close.png"))); // NOI18N
jButton31.setText("Cancel");
jButton31.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton31ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 8);
DownloadFrame.getContentPane().add(jButton31, gridBagConstraints);
jButton32.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/downloadb.png"))); // NOI18N
jButton32.setText("Download");
jButton32.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton32ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
DownloadFrame.getContentPane().add(jButton32, gridBagConstraints);
jPanel1.setBackground(new java.awt.Color(194, 238, 194));
jPanel1.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "Select a subset of Images (Optional)", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("Dialog", 1, 12), new java.awt.Color(0, 102, 51))); // NOI18N
jPanel1.setLayout(new java.awt.GridBagLayout());
jLabel12.setText("Container list file: ");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.insets = new java.awt.Insets(15, 10, 10, 10);
jPanel1.add(jLabel12, gridBagConstraints);
jButton33.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
jButton33.setText("Cancel");
jButton33.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton33ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 8;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel1.add(jButton33, gridBagConstraints);
jButton34.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/fileb.png"))); // NOI18N
jButton34.setText("Browse ");
jButton34.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton34ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel1.add(jButton34, gridBagConstraints);
Downloadtext.setEditable(false);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.weightx = 5.0;
gridBagConstraints.insets = new java.awt.Insets(15, 10, 10, 10);
jPanel1.add(Downloadtext, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 3;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 0, 10);
DownloadFrame.getContentPane().add(jPanel1, gridBagConstraints);
About4SeqGUIFrame.setTitle("About 4SeqGUI");
About4SeqGUIFrame.setResizable(false);
About4SeqGUIFrame.getContentPane().setLayout(new java.awt.GridBagLayout());
jLabel96.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/4SeqGUI.png"))); // NOI18N
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.weightx = 0.01;
gridBagConstraints.insets = new java.awt.Insets(10, 1, 10, 1);
About4SeqGUIFrame.getContentPane().add(jLabel96, gridBagConstraints);
jLabel100.setFont(new java.awt.Font("Dialog", 1, 14)); // NOI18N
jLabel100.setText("Version 1.2.1");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.insets = new java.awt.Insets(1, 1, 1, 1);
About4SeqGUIFrame.getContentPane().add(jLabel100, gridBagConstraints);
jLabel101.setFont(new java.awt.Font("Dialog", 1, 10)); // NOI18N
jLabel101.setText("Copyright © January 2017");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.insets = new java.awt.Insets(10, 0, 10, 0);
About4SeqGUIFrame.getContentPane().add(jLabel101, gridBagConstraints);
jButton36.setText("OK");
jButton36.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton36ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 4;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_END;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
About4SeqGUIFrame.getContentPane().add(jButton36, gridBagConstraints);
jLabel99.setFont(jLabel99.getFont());
jLabel99.setText("M. Beccuti, R. Calogero and F. Cordero");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 3;
gridBagConstraints.insets = new java.awt.Insets(5, 20, 10, 20);
About4SeqGUIFrame.getContentPane().add(jLabel99, gridBagConstraints);
About4SeqGUIFrame.getContentPane().add(jLabel102, new java.awt.GridBagConstraints());
setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
setTitle("4SeqGUI");
addWindowListener(new java.awt.event.WindowAdapter() {
public void windowClosing(java.awt.event.WindowEvent evt) {
formWindowClosing(evt);
}
});
jToolBar1.setBackground(new java.awt.Color(237, 237, 237));
jToolBar1.setBorder(javax.swing.BorderFactory.createEtchedBorder());
jToolBar1.setRollover(true);
jButton1.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52.png"))); // NOI18N
jButton1.setToolTipText("Open a previous execution");
jButton1.setBorder(javax.swing.BorderFactory.createEmptyBorder(5, 10, 5, 5));
jButton1.setFocusable(false);
jButton1.setHorizontalTextPosition(javax.swing.SwingConstants.CENTER);
jButton1.setVerticalTextPosition(javax.swing.SwingConstants.BOTTOM);
jButton1.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton1ActionPerformed(evt);
}
});
jToolBar1.add(jButton1);
jButton2.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/86.png"))); // NOI18N
jButton2.setToolTipText("Save current executions");
jButton2.setBorder(javax.swing.BorderFactory.createEmptyBorder(5, 5, 5, 5));
jButton2.setFocusable(false);
jButton2.setHorizontalTextPosition(javax.swing.SwingConstants.CENTER);
jButton2.setVerticalTextPosition(javax.swing.SwingConstants.BOTTOM);
jButton2.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton2ActionPerformed(evt);
}
});
jToolBar1.add(jButton2);
jToggleButton11.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/preference.png"))); // NOI18N
jToggleButton11.setToolTipText("Configure 4SeqGUI");
jToggleButton11.setBorder(javax.swing.BorderFactory.createEmptyBorder(5, 15, 5, 15));
jToggleButton11.setFocusable(false);
jToggleButton11.setHorizontalTextPosition(javax.swing.SwingConstants.CENTER);
jToggleButton11.setVerticalTextPosition(javax.swing.SwingConstants.BOTTOM);
jToggleButton11.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton11ActionPerformed(evt);
}
});
jToolBar1.add(jToggleButton11);
jButton9.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/docker.png"))); // NOI18N
jButton9.setToolTipText("Remove docker containers");
jButton9.setBorder(javax.swing.BorderFactory.createEmptyBorder(5, 5, 5, 5));
jButton9.setFocusable(false);
jButton9.setHorizontalTextPosition(javax.swing.SwingConstants.CENTER);
jButton9.setVerticalTextPosition(javax.swing.SwingConstants.BOTTOM);
jButton9.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton9ActionPerformed(evt);
}
});
jToolBar1.add(jButton9);
jButton26.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/download.png"))); // NOI18N
jButton26.setToolTipText("Download docker images");
jButton26.setBorder(javax.swing.BorderFactory.createEmptyBorder(5, 5, 5, 5));
jButton26.setFocusable(false);
jButton26.setHorizontalTextPosition(javax.swing.SwingConstants.CENTER);
jButton26.setMargin(new java.awt.Insets(2, 140, 2, 140));
jButton26.setVerticalTextPosition(javax.swing.SwingConstants.BOTTOM);
jButton26.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton26ActionPerformed(evt);
}
});
jToolBar1.add(jButton26);
jButton35.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/iconDNA-small.png"))); // NOI18N
jButton35.setToolTipText("About 4SeqGUI");
jButton35.setBorder(javax.swing.BorderFactory.createEmptyBorder(5, 15, 5, 15));
jButton35.setFocusable(false);
jButton35.setHorizontalTextPosition(javax.swing.SwingConstants.CENTER);
jButton35.setVerticalTextPosition(javax.swing.SwingConstants.BOTTOM);
jButton35.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton35ActionPerformed(evt);
}
});
jToolBar1.add(jButton35);
getContentPane().add(jToolBar1, java.awt.BorderLayout.NORTH);
VerticalSplitPanel.setOrientation(javax.swing.JSplitPane.VERTICAL_SPLIT);
BottomPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
BottomPanel.setLayout(new java.awt.GridBagLayout());
jScrollPane4.setToolTipText("");
ProcStatusPanel.setLayout(new java.awt.GridBagLayout());
ProcList.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "Process status", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("Dialog", 1, 14), new java.awt.Color(0, 82, 150))); // NOI18N
ProcList.setSelectionMode(javax.swing.ListSelectionModel.SINGLE_SELECTION);
ProcList.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseClicked(java.awt.event.MouseEvent evt) {
ProcListMouseClicked(evt);
}
});
ProcList.addListSelectionListener(new javax.swing.event.ListSelectionListener() {
public void valueChanged(javax.swing.event.ListSelectionEvent evt) {
ProcListValueChanged(evt);
}
});
jScrollPane2.setViewportView(ProcList);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.weighty = 0.1;
ProcStatusPanel.add(jScrollPane2, gridBagConstraints);
jScrollPane4.setViewportView(ProcStatusPanel);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.weighty = 0.1;
BottomPanel.add(jScrollPane4, gridBagConstraints);
VerticalSplitPanel.setBottomComponent(BottomPanel);
HorizontalSplitPanel.setBorder(null);
MainPanel.setBackground(new java.awt.Color(255, 255, 255));
MainPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
MainPanel.setLayout(new java.awt.CardLayout());
EmptyPanel.setBackground(new java.awt.Color(255, 255, 255));
EmptyPanel.setLayout(new java.awt.GridBagLayout());
jLabel24.setBackground(new java.awt.Color(255, 255, 255));
jLabel24.setHorizontalAlignment(javax.swing.SwingConstants.CENTER);
jLabel24.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/background.png"))); // NOI18N
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.insets = new java.awt.Insets(12, 12, 12, 12);
EmptyPanel.add(jLabel24, gridBagConstraints);
Empty.setViewportView(EmptyPanel);
MainPanel.add(Empty, "Empty");
IndexingStarRSEMPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "Genome indexing STAR-RSEM", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("Dialog", 1, 14), new java.awt.Color(0, 102, 102))); // NOI18N
IndexingStarRSEMPanel.setToolTipText("");
IndexingStarRSEMPanel.setLayout(new java.awt.GridBagLayout());
iCloseButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/close.png"))); // NOI18N
iCloseButton.setText("Close");
iCloseButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
iCloseButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
IndexingStarRSEMPanel.add(iCloseButton, gridBagConstraints);
jButton12.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/exec.png"))); // NOI18N
jButton12.setText("Execute");
jButton12.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton12ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weightx = 0.3;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
IndexingStarRSEMPanel.add(jButton12, gridBagConstraints);
iResetButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/reset.png"))); // NOI18N
iResetButton.setText("Reset");
iResetButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
iResetButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
IndexingStarRSEMPanel.add(iResetButton, gridBagConstraints);
jButton14.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/86b.png"))); // NOI18N
jButton14.setText("Save conf.");
jButton14.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton14ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
IndexingStarRSEMPanel.add(jButton14, gridBagConstraints);
jPanel13.setBackground(new java.awt.Color(230, 235, 235));
jPanel13.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel13.setLayout(new java.awt.GridBagLayout());
jLabel28.setText("Genome folder:");
jLabel28.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel13.add(jLabel28, gridBagConstraints);
iGenomeFolderText.setEditable(false);
iGenomeFolderText.setToolTipText("The folder that will contain the indexed genome.");
iGenomeFolderText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
iGenomeFolderTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE;
gridBagConstraints.weightx = 0.2;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel13.add(iGenomeFolderText, gridBagConstraints);
jToggleButton15.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
jToggleButton15.setText("Browse");
jToggleButton15.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton15ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 5;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel13.add(jToggleButton15, gridBagConstraints);
jToggleButton16.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
jToggleButton16.setText("Cancel");
jToggleButton16.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton16ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel13.add(jToggleButton16, gridBagConstraints);
jLabel30.setText("Genome url:");
jLabel30.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel13.add(jLabel30, gridBagConstraints);
iGenomeURLText.setToolTipText("The URL which will be used to download the genome");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 6;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel13.add(iGenomeURLText, gridBagConstraints);
jLabel33.setText("GTF url:");
jLabel33.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel13.add(jLabel33, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 6;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel13.add(iGTFURLText, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
IndexingStarRSEMPanel.add(jPanel13, gridBagConstraints);
jPanel14.setBackground(new java.awt.Color(230, 235, 235));
jPanel14.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel14.setLayout(new java.awt.GridBagLayout());
jLabel31.setText("Execution:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel14.add(jLabel31, gridBagConstraints);
iSudoRadioButton.setBackground(new java.awt.Color(230, 235, 235));
IExecutionStarRSEM.add(iSudoRadioButton);
iSudoRadioButton.setText("sudo");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel14.add(iSudoRadioButton, gridBagConstraints);
iDockerRadioButton.setBackground(new java.awt.Color(230, 235, 235));
IExecutionStarRSEM.add(iDockerRadioButton);
iDockerRadioButton.setSelected(true);
iDockerRadioButton.setText("docker");
iDockerRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
iDockerRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 4;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel14.add(iDockerRadioButton, gridBagConstraints);
jLabel32.setText("Thread number:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel14.add(jLabel32, gridBagConstraints);
iThreadText.setText("8");
iThreadText.setToolTipText("The number of threads which will be used during the computation.");
iThreadText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
iThreadTextFocusLost(evt);
}
});
iThreadText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
iThreadTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel14.add(iThreadText, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
IndexingStarRSEMPanel.add(jPanel14, gridBagConstraints);
IndexingStarRSEM.setViewportView(IndexingStarRSEMPanel);
MainPanel.add(IndexingStarRSEM, "indexing");
mRNA.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "miRNA counting", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("Dialog", 1, 14), new java.awt.Color(153, 0, 0))); // NOI18N
mRNAPanel.setLayout(new java.awt.GridBagLayout());
jButton6.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/exec.png"))); // NOI18N
jButton6.setText("Execute");
jButton6.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton6ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
mRNAPanel.add(jButton6, gridBagConstraints);
jButton8.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/86b.png"))); // NOI18N
jButton8.setText("Save conf.");
jButton8.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton8ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
mRNAPanel.add(jButton8, gridBagConstraints);
jButton7.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/reset.png"))); // NOI18N
jButton7.setText("Reset");
jButton7.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton7ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
mRNAPanel.add(jButton7, gridBagConstraints);
vCloseButton1.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/close.png"))); // NOI18N
vCloseButton1.setText("Close");
vCloseButton1.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vCloseButton1ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
mRNAPanel.add(vCloseButton1, gridBagConstraints);
jPanel9.setBackground(new java.awt.Color(235, 230, 230));
jPanel9.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel9.setLayout(new java.awt.GridBagLayout());
jLabel17.setText("miRBase organism:");
jLabel17.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel9.add(jLabel17, gridBagConstraints);
mmiRBaseText.setText("hsa");
mmiRBaseText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
mmiRBaseTextFocusLost(evt);
}
});
mmiRBaseText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
mmiRBaseTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 9;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel9.add(mmiRBaseText, gridBagConstraints);
jLabel20.setText("mirBase donwload: ");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel9.add(jLabel20, gridBagConstraints);
mDTrueRadioButton.setBackground(new java.awt.Color(235, 230, 230));
mDownload.add(mDTrueRadioButton);
mDTrueRadioButton.setText("True");
mDTrueRadioButton.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel9.add(mDTrueRadioButton, gridBagConstraints);
mDFalseRadioButton.setBackground(new java.awt.Color(235, 230, 230));
mDownload.add(mDFalseRadioButton);
mDFalseRadioButton.setSelected(true);
mDFalseRadioButton.setText("False");
mDFalseRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
mDFalseRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel9.add(mDFalseRadioButton, gridBagConstraints);
jLabel23.setText("Adapter type:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 4;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel9.add(jLabel23, gridBagConstraints);
mANEBRadioButton.setBackground(new java.awt.Color(235, 230, 230));
MAdapter.add(mANEBRadioButton);
mANEBRadioButton.setText("NEB");
mANEBRadioButton.setToolTipText("");
mANEBRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
mANEBRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 3;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel9.add(mANEBRadioButton, gridBagConstraints);
mAILLUMINARadioButton.setBackground(new java.awt.Color(235, 230, 230));
MAdapter.add(mAILLUMINARadioButton);
mAILLUMINARadioButton.setSelected(true);
mAILLUMINARadioButton.setText("ILLUMINA");
mAILLUMINARadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
mAILLUMINARadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 6;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel9.add(mAILLUMINARadioButton, gridBagConstraints);
jLabel25.setText("Save trimmed Fastq:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 6;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel9.add(jLabel25, gridBagConstraints);
mTTrueRadioButton.setBackground(new java.awt.Color(230, 230, 235));
mTrimmed.add(mTTrueRadioButton);
mTTrueRadioButton.setText("True");
mTTrueRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
mTTrueRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 6;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel9.add(mTTrueRadioButton, gridBagConstraints);
mTFalseRadioButton.setBackground(new java.awt.Color(230, 230, 235));
mTrimmed.add(mTFalseRadioButton);
mTFalseRadioButton.setSelected(true);
mTFalseRadioButton.setText("False");
mTFalseRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
mTFalseRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 6;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel9.add(mTFalseRadioButton, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
mRNAPanel.add(jPanel9, gridBagConstraints);
jPanel8.setBackground(new java.awt.Color(235, 230, 230));
jPanel8.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel8.setLayout(new java.awt.GridBagLayout());
jLabel15.setText("FastQ folder:");
jLabel15.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel8.add(jLabel15, gridBagConstraints);
mFastQFolderText.setEditable(false);
mFastQFolderText.setToolTipText("The folder containing the input reads");
mFastQFolderText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
mFastQFolderTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 50, 10, 10);
jPanel8.add(mFastQFolderText, gridBagConstraints);
jToggleButton8.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
jToggleButton8.setText("Browse");
jToggleButton8.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton8ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 5;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_TRAILING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel8.add(jToggleButton8, gridBagConstraints);
jToggleButton7.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
jToggleButton7.setText("Cancel");
jToggleButton7.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton7ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_TRAILING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel8.add(jToggleButton7, gridBagConstraints);
mOutputFolderText.setEditable(false);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 50, 10, 10);
jPanel8.add(mOutputFolderText, gridBagConstraints);
jToggleButton9.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
jToggleButton9.setText("Cancel");
jToggleButton9.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton9ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_TRAILING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel8.add(jToggleButton9, gridBagConstraints);
jToggleButton10.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
jToggleButton10.setText("Browse");
jToggleButton10.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton10ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 5;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_TRAILING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel8.add(jToggleButton10, gridBagConstraints);
jLabel16.setText("Scratch folder:");
jLabel16.setToolTipText("This folder will be mounted in the docker container");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel8.add(jLabel16, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
mRNAPanel.add(jPanel8, gridBagConstraints);
jPanel7.setBackground(new java.awt.Color(235, 230, 230));
jPanel7.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel7.setLayout(new java.awt.GridBagLayout());
jLabel14.setText("Execution:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel7.add(jLabel14, gridBagConstraints);
mSudoRadioButton.setBackground(new java.awt.Color(237, 230, 230));
mExecution.add(mSudoRadioButton);
mSudoRadioButton.setText("sudo");
mSudoRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
mSudoRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 85, 10, 10);
jPanel7.add(mSudoRadioButton, gridBagConstraints);
mDockerRadioButton.setBackground(new java.awt.Color(237, 230, 230));
mExecution.add(mDockerRadioButton);
mDockerRadioButton.setSelected(true);
mDockerRadioButton.setText("docker");
mDockerRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
mDockerRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel7.add(mDockerRadioButton, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
mRNAPanel.add(jPanel7, gridBagConstraints);
mRNA.setViewportView(mRNAPanel);
MainPanel.add(mRNA, "mRNA");
FPKMPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "From samples to experiment", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("Dialog", 1, 14), new java.awt.Color(102, 0, 153))); // NOI18N
FPKMPanel.setLayout(new java.awt.GridBagLayout());
jPanel4.setBackground(new java.awt.Color(232, 232, 242));
jPanel4.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel4.setLayout(new java.awt.GridBagLayout());
FPKMFileTable.setModel(new javax.swing.table.DefaultTableModel(
new Object [][] {
},
new String [] {
"Folder", "Grouping", "Batch"
}
) {
Class[] types = new Class [] {
java.lang.String.class, java.lang.Object.class, java.lang.Object.class
};
public Class getColumnClass(int columnIndex) {
return types [columnIndex];
}
});
FPKMFileTable.setColumnSelectionAllowed(true);
FPKMFileTable.setSelectionMode(javax.swing.ListSelectionModel.SINGLE_SELECTION);
FPKMFileTable.getTableHeader().setReorderingAllowed(false);
jScrollPane6.setViewportView(FPKMFileTable);
FPKMFileTable.getColumnModel().getSelectionModel().setSelectionMode(javax.swing.ListSelectionModel.SINGLE_SELECTION);
if (FPKMFileTable.getColumnModel().getColumnCount() > 0) {
FPKMFileTable.getColumnModel().getColumn(1).setCellEditor(new DefaultCellEditor(CovComboBox));
FPKMFileTable.getColumnModel().getColumn(2).setCellEditor(new DefaultCellEditor(BatchComboBox));
}
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weightx = 1.0;
gridBagConstraints.weighty = 1.0;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel4.add(jScrollPane6, gridBagConstraints);
FAddFile.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/fileb.png"))); // NOI18N
FAddFile.setText("Add");
FAddFile.setToolTipText("");
FAddFile.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
FAddFileActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 1;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel4.add(FAddFile, gridBagConstraints);
jButton13.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/remove.png"))); // NOI18N
jButton13.setText("Remove");
jButton13.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton13ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 4;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel4.add(jButton13, gridBagConstraints);
jLabel26.setText("Biological Types:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 4;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel4.add(jLabel26, gridBagConstraints);
FtypesComboBox.setModel(new javax.swing.DefaultComboBoxModel<>(new String[] { "protein_coding", "unitary_pseudogene", "unprocessed_pseudogene", "processed_pseudogene", "transcribed_unprocessed_pseudogene", "processed_transcript", "antisense", "transcribed_unitary_pseudogene", "polymorphic_pseudogene", "lincRNA", "sense_intronic", "transcribed_processed_pseudogene", "sense_overlapping", "IG_V_pseudogene", "pseudogene", "TR_V_gene", "3prime_overlapping_ncRNA", "IG_V_gene", "bidirectional_promoter_lncRNA", "snRNA", "miRNA", "misc_RNA", "snoRNA", "rRNA", "IG_C_gene", "IG_J_gene", "TR_J_gene", "TR_C_gene", "TR_V_pseudogene", "TR_J_pseudogene", "IG_D_gene", "ribozyme", "IG_C_pseudogene", "TR_D_gene", "TEC", "IG_J_pseudogene", "scRNA", "scaRNA", "vaultRNA", "sRNA", "macro_lncRNA", "non_coding", "IG_pseudogene" }));
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.weightx = 0.2;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel4.add(FtypesComboBox, gridBagConstraints);
jLabel27.setText("Output Folder:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel4.add(jLabel27, gridBagConstraints);
FOutputFolderText.setEditable(false);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.weightx = 0.4;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel4.add(FOutputFolderText, gridBagConstraints);
Fbrowes.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
Fbrowes.setText("Browse");
Fbrowes.setToolTipText("");
Fbrowes.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
FbrowesActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_END;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel4.add(Fbrowes, gridBagConstraints);
Fcancel.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
Fcancel.setText("Cancel");
Fcancel.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
FcancelActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 4;
gridBagConstraints.gridy = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_TRAILING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel4.add(Fcancel, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
FPKMPanel.add(jPanel4, gridBagConstraints);
FExecuteButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/exec.png"))); // NOI18N
FExecuteButton.setText("Execute");
FExecuteButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
FExecuteButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
FPKMPanel.add(FExecuteButton, gridBagConstraints);
FSaveButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/86b.png"))); // NOI18N
FSaveButton.setText("Save conf.");
FSaveButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
FSaveButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
FPKMPanel.add(FSaveButton, gridBagConstraints);
FResetButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/reset.png"))); // NOI18N
FResetButton.setText("Reset");
FResetButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
FResetButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
FPKMPanel.add(FResetButton, gridBagConstraints);
FCloseButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/close.png"))); // NOI18N
FCloseButton.setText("Close");
FCloseButton.setToolTipText("");
FCloseButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
FCloseButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
FPKMPanel.add(FCloseButton, gridBagConstraints);
FPKM.setViewportView(FPKMPanel);
MainPanel.add(FPKM, "FPKMCounting");
vmRNAPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "Genes, isoforms counting RSEM", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("Dialog", 1, 14), new java.awt.Color(0, 102, 102))); // NOI18N
vmRNAPanel.setToolTipText("");
vmRNAPanel.setLayout(new java.awt.GridBagLayout());
vCloseButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/close.png"))); // NOI18N
vCloseButton.setText("Close");
vCloseButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vCloseButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
vmRNAPanel.add(vCloseButton, gridBagConstraints);
jButton4.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/exec.png"))); // NOI18N
jButton4.setText("Execute");
jButton4.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton4ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
vmRNAPanel.add(jButton4, gridBagConstraints);
jButton5.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/reset.png"))); // NOI18N
jButton5.setText("Reset");
jButton5.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton5ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
vmRNAPanel.add(jButton5, gridBagConstraints);
jButton3.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/86b.png"))); // NOI18N
jButton3.setText("Save conf.");
jButton3.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton3ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
vmRNAPanel.add(jButton3, gridBagConstraints);
jPanel2.setBackground(new java.awt.Color(230, 235, 235));
jPanel2.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel2.setLayout(new java.awt.GridBagLayout());
jLabel2.setText("FastQ folder:");
jLabel2.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel2.add(jLabel2, gridBagConstraints);
vFastQFolderText.setEditable(false);
vFastQFolderText.setToolTipText("The folder containing the input reads in FastQ format.");
vFastQFolderText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vFastQFolderTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weightx = 0.2;
gridBagConstraints.insets = new java.awt.Insets(10, 28, 10, 10);
jPanel2.add(vFastQFolderText, gridBagConstraints);
jToggleButton2.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
jToggleButton2.setText("Browse");
jToggleButton2.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton2ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel2.add(jToggleButton2, gridBagConstraints);
jToggleButton1.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
jToggleButton1.setText("Cancel");
jToggleButton1.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton1ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 7;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel2.add(jToggleButton1, gridBagConstraints);
jLabel3.setText("Scratch folder:");
jLabel3.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel2.add(jLabel3, gridBagConstraints);
vOutputFolderText.setEditable(false);
vOutputFolderText.setToolTipText("This folder will be mounted in the docker container.");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weightx = 0.2;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 28, 10, 10);
jPanel2.add(vOutputFolderText, gridBagConstraints);
jToggleButton4.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
jToggleButton4.setText("Browse");
jToggleButton4.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton4ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel2.add(jToggleButton4, gridBagConstraints);
jToggleButton3.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
jToggleButton3.setText("Cancel");
jToggleButton3.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton3ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 7;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel2.add(jToggleButton3, gridBagConstraints);
jLabel9.setText("Genome folder:");
jLabel9.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 1.6;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel2.add(jLabel9, gridBagConstraints);
vGenomeFolderText.setEditable(false);
vGenomeFolderText.setToolTipText("The folder containing the indexed genome.");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weightx = 0.2;
gridBagConstraints.insets = new java.awt.Insets(10, 28, 10, 10);
jPanel2.add(vGenomeFolderText, gridBagConstraints);
jToggleButton5.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
jToggleButton5.setText("Browse");
jToggleButton5.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton5ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel2.add(jToggleButton5, gridBagConstraints);
jToggleButton6.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
jToggleButton6.setText("Cancel");
jToggleButton6.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton6ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 7;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel2.add(jToggleButton6, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
vmRNAPanel.add(jPanel2, gridBagConstraints);
jPanel3.setBackground(new java.awt.Color(230, 235, 235));
jPanel3.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel3.setLayout(new java.awt.GridBagLayout());
jLabel1.setText("Execution:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel3.add(jLabel1, gridBagConstraints);
vSudoRadioButton.setBackground(new java.awt.Color(230, 235, 235));
vExecution.add(vSudoRadioButton);
vSudoRadioButton.setText("sudo");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 28, 10, 10);
jPanel3.add(vSudoRadioButton, gridBagConstraints);
vDockerRadioButton.setBackground(new java.awt.Color(230, 235, 235));
vExecution.add(vDockerRadioButton);
vDockerRadioButton.setSelected(true);
vDockerRadioButton.setText("docker");
vDockerRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vDockerRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 4;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel3.add(vDockerRadioButton, gridBagConstraints);
jLabel4.setText("Thread number:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel3.add(jLabel4, gridBagConstraints);
vThreadText.setText("8");
vThreadText.setToolTipText("The number of threads which will be used during the computation.");
vThreadText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
vThreadTextFocusLost(evt);
}
});
vThreadText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vThreadTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 28, 10, 10);
jPanel3.add(vThreadText, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
vmRNAPanel.add(jPanel3, gridBagConstraints);
jPanel6.setBackground(new java.awt.Color(230, 235, 235));
jPanel6.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel6.setLayout(new java.awt.GridBagLayout());
vAdapter5Text.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
vAdapter5TextFocusLost(evt);
}
});
vAdapter5Text.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vAdapter5TextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 24;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel6.add(vAdapter5Text, gridBagConstraints);
jLabel5.setText("Adapter 5':");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel6.add(jLabel5, gridBagConstraints);
jLabel6.setText("Adapter 3':");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel6.add(jLabel6, gridBagConstraints);
vAdapter3Text.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
vAdapter3TextFocusLost(evt);
}
});
vAdapter3Text.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vAdapter3TextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 24;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel6.add(vAdapter3Text, gridBagConstraints);
vPeRadioButton.setBackground(new java.awt.Color(230, 235, 235));
vSeq.add(vPeRadioButton);
vPeRadioButton.setSelected(true);
vPeRadioButton.setText("paired-end");
vPeRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vPeRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 7;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 7;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel6.add(vPeRadioButton, gridBagConstraints);
vSeRadioButton.setBackground(new java.awt.Color(230, 235, 235));
vSeq.add(vSeRadioButton);
vSeRadioButton.setText("single-end");
vSeRadioButton.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel6.add(vSeRadioButton, gridBagConstraints);
jLabel7.setText("Type of Sequence");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel6.add(jLabel7, gridBagConstraints);
jLabel8.setText("Min length:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 6;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel6.add(jLabel8, gridBagConstraints);
vMinLengthText.setText("40");
vMinLengthText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
vMinLengthTextFocusLost(evt);
}
});
vMinLengthText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vMinLengthTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 6;
gridBagConstraints.gridwidth = 3;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel6.add(vMinLengthText, gridBagConstraints);
jLabel10.setText("Strandness:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 8;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel6.add(jLabel10, gridBagConstraints);
vSNoneRadioButton.setBackground(new java.awt.Color(230, 235, 235));
Strand.add(vSNoneRadioButton);
vSNoneRadioButton.setSelected(true);
vSNoneRadioButton.setText("none");
vSNoneRadioButton.setToolTipText("");
vSNoneRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vSNoneRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 8;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel6.add(vSNoneRadioButton, gridBagConstraints);
vSForwardRadioButton.setBackground(new java.awt.Color(230, 235, 235));
Strand.add(vSForwardRadioButton);
vSForwardRadioButton.setText("forward");
vSForwardRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vSForwardRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 7;
gridBagConstraints.gridy = 8;
gridBagConstraints.gridwidth = 6;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel6.add(vSForwardRadioButton, gridBagConstraints);
vSReverseRadioButton.setBackground(new java.awt.Color(230, 235, 235));
Strand.add(vSReverseRadioButton);
vSReverseRadioButton.setText("reverse");
vSReverseRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vSReverseRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 16;
gridBagConstraints.gridy = 8;
gridBagConstraints.gridwidth = 8;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 1.0;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel6.add(vSReverseRadioButton, gridBagConstraints);
vOrganismText.setText("hg38");
vOrganismText.setToolTipText("");
vOrganismText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
vOrganismTextFocusLost(evt);
}
});
vOrganismText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vOrganismTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 10;
gridBagConstraints.gridwidth = 24;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel6.add(vOrganismText, gridBagConstraints);
jLabel11.setText("Organism:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 10;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel6.add(jLabel11, gridBagConstraints);
jLabel13.setText("Save alignments:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 12;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_TRAILING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel6.add(jLabel13, gridBagConstraints);
vBAMyesRadioButton.setBackground(new java.awt.Color(230, 235, 235));
Annotation.add(vBAMyesRadioButton);
vBAMyesRadioButton.setText("Yes");
vBAMyesRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vBAMyesRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 12;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel6.add(vBAMyesRadioButton, gridBagConstraints);
vBAMnoLRadioButton.setBackground(new java.awt.Color(230, 235, 235));
Annotation.add(vBAMnoLRadioButton);
vBAMnoLRadioButton.setSelected(true);
vBAMnoLRadioButton.setText("No");
vBAMnoLRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vBAMnoLRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 12;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel6.add(vBAMnoLRadioButton, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_START;
gridBagConstraints.weightx = 1.0;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
vmRNAPanel.add(jPanel6, gridBagConstraints);
vmRNA.setViewportView(vmRNAPanel);
MainPanel.add(vmRNA, "vmRNA");
PCAPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "PCA", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("Dialog", 1, 14), new java.awt.Color(204, 102, 0))); // NOI18N
PCAPanel.setToolTipText("");
PCAPanel.setLayout(new java.awt.GridBagLayout());
vCloseButton2.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/close.png"))); // NOI18N
vCloseButton2.setText("Close");
vCloseButton2.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vCloseButton2ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
PCAPanel.add(vCloseButton2, gridBagConstraints);
jButton15.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/exec.png"))); // NOI18N
jButton15.setText("Execute");
jButton15.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton15ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.weighty = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
PCAPanel.add(jButton15, gridBagConstraints);
jButton16.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/reset.png"))); // NOI18N
jButton16.setText("Reset");
jButton16.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton16ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
PCAPanel.add(jButton16, gridBagConstraints);
jButton17.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/86b.png"))); // NOI18N
jButton17.setText("Save conf.");
jButton17.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton17ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
PCAPanel.add(jButton17, gridBagConstraints);
jPanel5.setBackground(new java.awt.Color(250, 241, 233));
jPanel5.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel5.setLayout(new java.awt.GridBagLayout());
jLabel29.setText("Output folders:");
jLabel29.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel5.add(jLabel29, gridBagConstraints);
pFPKMfileText.setEditable(false);
pFPKMfileText.setToolTipText("Input data folder.");
pFPKMfileText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
pFPKMfileTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 20, 10, 10);
jPanel5.add(pFPKMfileText, gridBagConstraints);
jToggleButton12.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/fileb.png"))); // NOI18N
jToggleButton12.setText("Browse");
jToggleButton12.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton12ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel5.add(jToggleButton12, gridBagConstraints);
fCancelButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
fCancelButton.setText("Cancel");
fCancelButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
fCancelButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel5.add(fCancelButton, gridBagConstraints);
jLabel34.setText("FPKM/TPM file:");
jLabel34.setToolTipText("The FPKM or TPM table file name");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel5.add(jLabel34, gridBagConstraints);
pOutputFolderText.setEditable(false);
pOutputFolderText.setToolTipText("Output data folder.");
pOutputFolderText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
pOutputFolderTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 20, 10, 10);
jPanel5.add(pOutputFolderText, gridBagConstraints);
jToggleButton13.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
jToggleButton13.setText("Browse");
jToggleButton13.setEnabled(false);
jToggleButton13.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton13ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel5.add(jToggleButton13, gridBagConstraints);
fCancelButton1.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
fCancelButton1.setText("Cancel");
fCancelButton1.setEnabled(false);
fCancelButton1.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
fCancelButton1ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel5.add(fCancelButton1, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
PCAPanel.add(jPanel5, gridBagConstraints);
jPanel11.setBackground(new java.awt.Color(250, 241, 233));
jPanel11.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel11.setLayout(new java.awt.GridBagLayout());
pComponent1Text.setToolTipText("First component number");
pComponent1Text.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
pComponent1TextFocusLost(evt);
}
});
pComponent1Text.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
pComponent1TextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 0;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel11.add(pComponent1Text, gridBagConstraints);
jLabel38.setText("Component 1:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel11.add(jLabel38, gridBagConstraints);
jLabel39.setText("Component 2:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel11.add(jLabel39, gridBagConstraints);
pComponent2Text.setToolTipText("Second componet number");
pComponent2Text.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
pComponent2TextFocusLost(evt);
}
});
pComponent2Text.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
pComponent2TextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 1;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel11.add(pComponent2Text, gridBagConstraints);
jLabel42.setText("Data type:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel11.add(jLabel42, gridBagConstraints);
pCountsRadioButton.setBackground(new java.awt.Color(250, 241, 233));
DataType.add(pCountsRadioButton);
pCountsRadioButton.setText("counts");
pCountsRadioButton.setToolTipText("");
pCountsRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
pCountsRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel11.add(pCountsRadioButton, gridBagConstraints);
pFPKMRadioButton.setBackground(new java.awt.Color(250, 241, 233));
DataType.add(pFPKMRadioButton);
pFPKMRadioButton.setSelected(true);
pFPKMRadioButton.setText("FPKM");
pFPKMRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
pFPKMRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 4;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 6;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel11.add(pFPKMRadioButton, gridBagConstraints);
pTPMRadioButton.setBackground(new java.awt.Color(250, 241, 233));
DataType.add(pTPMRadioButton);
pTPMRadioButton.setText("TPM");
pTPMRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
pTPMRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 11;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 8;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.3;
gridBagConstraints.weighty = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 25, 10, 10);
jPanel11.add(pTPMRadioButton, gridBagConstraints);
jLabel43.setText("Legend position:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel11.add(jLabel43, gridBagConstraints);
jLabel44.setText("Covariates:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel11.add(jLabel44, gridBagConstraints);
pCovYesRadioButton.setBackground(new java.awt.Color(250, 241, 233));
Covariates.add(pCovYesRadioButton);
pCovYesRadioButton.setSelected(true);
pCovYesRadioButton.setText("yes");
pCovYesRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
pCovYesRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 4;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel11.add(pCovYesRadioButton, gridBagConstraints);
pCovNoRadioButton.setBackground(new java.awt.Color(250, 241, 233));
Covariates.add(pCovNoRadioButton);
pCovNoRadioButton.setText("no");
pCovNoRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
pCovNoRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 4;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weighty = 0.2;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel11.add(pCovNoRadioButton, gridBagConstraints);
pLegendComboBox.setModel(new javax.swing.DefaultComboBoxModel<>(new String[] { "bottom", "bottomleft", "left", "topleft", "top", "topright", "right", "center" }));
pLegendComboBox.setSelectedIndex(1);
pLegendComboBox.setToolTipText("Plot legend position.");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel11.add(pLegendComboBox, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
PCAPanel.add(jPanel11, gridBagConstraints);
PCA.setViewportView(PCAPanel);
MainPanel.add(PCA, "PCA");
DESPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "DESeq2 analysis", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("Dialog", 1, 14), new java.awt.Color(0, 153, 204))); // NOI18N
DESPanel.setToolTipText("");
DESPanel.setLayout(new java.awt.GridBagLayout());
vCloseButton3.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/close.png"))); // NOI18N
vCloseButton3.setText("Close");
vCloseButton3.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vCloseButton3ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
DESPanel.add(vCloseButton3, gridBagConstraints);
jButton18.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/exec.png"))); // NOI18N
jButton18.setText("Execute");
jButton18.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton18ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.weighty = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
DESPanel.add(jButton18, gridBagConstraints);
jButton19.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/reset.png"))); // NOI18N
jButton19.setText("Reset");
jButton19.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton19ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
DESPanel.add(jButton19, gridBagConstraints);
jButton20.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/86b.png"))); // NOI18N
jButton20.setText("Save conf.");
jButton20.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton20ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
DESPanel.add(jButton20, gridBagConstraints);
jPanel10.setBackground(new java.awt.Color(233, 243, 251));
jPanel10.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel10.setLayout(new java.awt.GridBagLayout());
jLabel35.setText("Output folders:");
jLabel35.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel10.add(jLabel35, gridBagConstraints);
dFPKMfileText.setEditable(false);
dFPKMfileText.setToolTipText("Input data folder.");
dFPKMfileText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
dFPKMfileTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 65, 10, 10);
jPanel10.add(dFPKMfileText, gridBagConstraints);
jToggleButton14.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/fileb.png"))); // NOI18N
jToggleButton14.setText("Browse");
jToggleButton14.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton14ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel10.add(jToggleButton14, gridBagConstraints);
fCancelButton2.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
fCancelButton2.setText("Cancel");
fCancelButton2.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
fCancelButton2ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel10.add(fCancelButton2, gridBagConstraints);
jLabel36.setText("Count file:");
jLabel36.setToolTipText("The FPKM or TPM table file nam");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel10.add(jLabel36, gridBagConstraints);
dOutputFolderText.setEditable(false);
dOutputFolderText.setToolTipText("Output data folder.");
dOutputFolderText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
dOutputFolderTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 65, 10, 10);
jPanel10.add(dOutputFolderText, gridBagConstraints);
jToggleButton17.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
jToggleButton17.setText("Browse");
jToggleButton17.setEnabled(false);
jToggleButton17.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton17ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel10.add(jToggleButton17, gridBagConstraints);
fCancelButton3.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
fCancelButton3.setText("Cancel");
fCancelButton3.setEnabled(false);
fCancelButton3.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
fCancelButton3ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel10.add(fCancelButton3, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
DESPanel.add(jPanel10, gridBagConstraints);
jPanel12.setBackground(new java.awt.Color(233, 243, 251));
jPanel12.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel12.setLayout(new java.awt.GridBagLayout());
dLog2fcText.setToolTipText("Log_2 fold change threshold for differetially expressed genes");
dLog2fcText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
dLog2fcTextFocusLost(evt);
}
});
dLog2fcText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
dLog2fcTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel12.add(dLog2fcText, gridBagConstraints);
jLabel40.setText("Log2fc threshold:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel12.add(jLabel40, gridBagConstraints);
jLabel41.setText("adj. p-value threshold:");
jLabel41.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel12.add(jLabel41, gridBagConstraints);
dFDRText.setToolTipText("adjusted p-value threshold");
dFDRText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
dFDRTextFocusLost(evt);
}
});
dFDRText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
dFDRTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel12.add(dFDRText, gridBagConstraints);
jLabel45.setText("Data type:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel12.add(jLabel45, gridBagConstraints);
dGeneRadioButton.setBackground(new java.awt.Color(225, 239, 250));
DEStype.add(dGeneRadioButton);
dGeneRadioButton.setText("gene");
dGeneRadioButton.setToolTipText("");
dGeneRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
dGeneRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel12.add(dGeneRadioButton, gridBagConstraints);
jLabel47.setText("Ref. Covariates:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 3;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel12.add(jLabel47, gridBagConstraints);
dCovComboBox.setModel(new javax.swing.DefaultComboBoxModel<>(new String[] { "Cov.1", "Cov.2", "Cov.3", "Cov.4", "Cov.5", "Cov.6", "Cov.7", "Cov.8", "Cov.9", "Cov.10" }));
dCovComboBox.setToolTipText("Plot legend position.");
dCovComboBox.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
dCovComboBoxActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 3;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel12.add(dCovComboBox, gridBagConstraints);
dmiRNARadioButton.setBackground(new java.awt.Color(225, 239, 250));
DEStype.add(dmiRNARadioButton);
dmiRNARadioButton.setText("miRNA");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 7;
gridBagConstraints.gridy = 2;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel12.add(dmiRNARadioButton, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_START;
gridBagConstraints.weightx = 0.3;
jPanel12.add(jLabel58, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_START;
gridBagConstraints.weightx = 0.3;
jPanel12.add(jLabel59, gridBagConstraints);
dIsoformRadioButton.setBackground(new java.awt.Color(225, 239, 250));
DEStype.add(dIsoformRadioButton);
dIsoformRadioButton.setSelected(true);
dIsoformRadioButton.setText("isoform");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 5;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel12.add(dIsoformRadioButton, gridBagConstraints);
jLabel62.setText("Batches:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 4;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel12.add(jLabel62, gridBagConstraints);
dBatchesTrue.setBackground(new java.awt.Color(225, 239, 250));
DESBatch.add(dBatchesTrue);
dBatchesTrue.setText("TRUE");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 4;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel12.add(dBatchesTrue, gridBagConstraints);
DBatchesFalse.setBackground(new java.awt.Color(225, 239, 250));
DESBatch.add(DBatchesFalse);
DBatchesFalse.setSelected(true);
DBatchesFalse.setText("FALSE");
DBatchesFalse.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
DBatchesFalseActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 5;
gridBagConstraints.gridy = 4;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel12.add(DBatchesFalse, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
DESPanel.add(jPanel12, gridBagConstraints);
DES.setViewportView(DESPanel);
MainPanel.add(DES, "DES");
IndexingBWAPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "Genome indexing BWA", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("Dialog", 1, 14), new java.awt.Color(0, 153, 153))); // NOI18N
IndexingBWAPanel.setToolTipText("");
IndexingBWAPanel.setLayout(new java.awt.GridBagLayout());
iCloseButton1.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/close.png"))); // NOI18N
iCloseButton1.setText("Close");
iCloseButton1.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
iCloseButton1ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
IndexingBWAPanel.add(iCloseButton1, gridBagConstraints);
jButton21.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/exec.png"))); // NOI18N
jButton21.setText("Execute");
jButton21.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton21ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weightx = 0.3;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
IndexingBWAPanel.add(jButton21, gridBagConstraints);
iResetButton1.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/reset.png"))); // NOI18N
iResetButton1.setText("Reset");
iResetButton1.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
iResetButton1ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
IndexingBWAPanel.add(iResetButton1, gridBagConstraints);
jButton22.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/86b.png"))); // NOI18N
jButton22.setText("Save conf.");
jButton22.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton22ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
IndexingBWAPanel.add(jButton22, gridBagConstraints);
jPanel15.setBackground(new java.awt.Color(230, 235, 235));
jPanel15.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel15.setLayout(new java.awt.GridBagLayout());
jLabel37.setText("Genome folder:");
jLabel37.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel15.add(jLabel37, gridBagConstraints);
iGenomeFolderBText.setEditable(false);
iGenomeFolderBText.setToolTipText("The folder that will contain the indexed genome.");
iGenomeFolderBText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
iGenomeFolderBTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE;
gridBagConstraints.weightx = 0.2;
gridBagConstraints.insets = new java.awt.Insets(10, 20, 10, 10);
jPanel15.add(iGenomeFolderBText, gridBagConstraints);
jToggleButton18.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
jToggleButton18.setText("Browse");
jToggleButton18.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton18ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 5;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel15.add(jToggleButton18, gridBagConstraints);
jToggleButton19.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
jToggleButton19.setText("Cancel");
jToggleButton19.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton19ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel15.add(jToggleButton19, gridBagConstraints);
jLabel46.setText("USCS Genome url:");
jLabel46.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel15.add(jLabel46, gridBagConstraints);
iGenomeURLBText.setToolTipText("The URL which will be used to download the genome");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 6;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 20, 10, 10);
jPanel15.add(iGenomeURLBText, gridBagConstraints);
jLabel48.setText("dbSNP VCF file:");
jLabel48.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 4;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel15.add(jLabel48, gridBagConstraints);
idbSPNText.setEditable(false);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.2;
gridBagConstraints.insets = new java.awt.Insets(10, 20, 10, 10);
jPanel15.add(idbSPNText, gridBagConstraints);
jLabel51.setText("GATK:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel15.add(jLabel51, gridBagConstraints);
iBTrueRadioButton.setBackground(new java.awt.Color(230, 235, 235));
GATK.add(iBTrueRadioButton);
iBTrueRadioButton.setText("True");
iBTrueRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
iBTrueRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 20, 10, 10);
jPanel15.add(iBTrueRadioButton, gridBagConstraints);
iBFalseRadioButton.setBackground(new java.awt.Color(230, 235, 235));
GATK.add(iBFalseRadioButton);
iBFalseRadioButton.setSelected(true);
iBFalseRadioButton.setText("False");
iBFalseRadioButton.addChangeListener(new javax.swing.event.ChangeListener() {
public void stateChanged(javax.swing.event.ChangeEvent evt) {
iBFalseRadioButtonStateChanged(evt);
}
});
iBFalseRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
iBFalseRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel15.add(iBFalseRadioButton, gridBagConstraints);
i1000GenomeText.setEditable(false);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 3;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.2;
gridBagConstraints.insets = new java.awt.Insets(10, 20, 10, 10);
jPanel15.add(i1000GenomeText, gridBagConstraints);
jLabel52.setText(" 1000 Genome VCF file:");
jLabel52.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel15.add(jLabel52, gridBagConstraints);
i1000BrowseButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/fileb.png"))); // NOI18N
i1000BrowseButton.setText("Browse");
i1000BrowseButton.setEnabled(false);
i1000BrowseButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
i1000BrowseButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 5;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel15.add(i1000BrowseButton, gridBagConstraints);
i1000CancelButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
i1000CancelButton.setText("Cancel");
i1000CancelButton.setEnabled(false);
i1000CancelButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
i1000CancelButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel15.add(i1000CancelButton, gridBagConstraints);
idbSPNBrowseButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/fileb.png"))); // NOI18N
idbSPNBrowseButton.setText("Browse");
idbSPNBrowseButton.setEnabled(false);
idbSPNBrowseButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
idbSPNBrowseButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 5;
gridBagConstraints.gridy = 4;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel15.add(idbSPNBrowseButton, gridBagConstraints);
idbSPNCancelButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
idbSPNCancelButton.setText("Cancel");
idbSPNCancelButton.setEnabled(false);
idbSPNCancelButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
idbSPNCancelButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 4;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel15.add(idbSPNCancelButton, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
IndexingBWAPanel.add(jPanel15, gridBagConstraints);
jPanel16.setBackground(new java.awt.Color(230, 235, 235));
jPanel16.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel16.setLayout(new java.awt.GridBagLayout());
jLabel49.setText("Execution:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel16.add(jLabel49, gridBagConstraints);
iSudoBRadioButton.setBackground(new java.awt.Color(230, 235, 235));
IExecutionBWA.add(iSudoBRadioButton);
iSudoBRadioButton.setText("sudo");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 70, 10, 10);
jPanel16.add(iSudoBRadioButton, gridBagConstraints);
iDockerBRadioButton.setBackground(new java.awt.Color(230, 235, 235));
IExecutionBWA.add(iDockerBRadioButton);
iDockerBRadioButton.setSelected(true);
iDockerBRadioButton.setText("docker");
iDockerBRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
iDockerBRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 4;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel16.add(iDockerBRadioButton, gridBagConstraints);
jLabel50.setText("Thread number:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel16.add(jLabel50, gridBagConstraints);
iThreadBText.setText("8");
iThreadBText.setToolTipText("The number of threads which will be used during the computation.");
iThreadBText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
iThreadBTextFocusLost(evt);
}
});
iThreadBText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
iThreadBTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 70, 10, 10);
jPanel16.add(iThreadBText, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
IndexingBWAPanel.add(jPanel16, gridBagConstraints);
IndexingBWA.setViewportView(IndexingBWAPanel);
MainPanel.add(IndexingBWA, "indexingB");
MACSPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "MACS & SICER analysis", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("Dialog", 1, 14), new java.awt.Color(51, 153, 0))); // NOI18N
MACSPanel.setToolTipText("");
MACSPanel.setLayout(new java.awt.GridBagLayout());
vCloseButton4.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/close.png"))); // NOI18N
vCloseButton4.setText("Close");
vCloseButton4.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vCloseButton4ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 4;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
MACSPanel.add(vCloseButton4, gridBagConstraints);
jButton23.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/exec.png"))); // NOI18N
jButton23.setText("Execute");
jButton23.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton23ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 4;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
MACSPanel.add(jButton23, gridBagConstraints);
jButton24.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/reset.png"))); // NOI18N
jButton24.setText("Reset");
jButton24.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton24ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 4;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
MACSPanel.add(jButton24, gridBagConstraints);
jButton25.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/86b.png"))); // NOI18N
jButton25.setText("Save conf.");
jButton25.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton25ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 4;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
MACSPanel.add(jButton25, gridBagConstraints);
jPanel17.setBackground(new java.awt.Color(230, 240, 230));
jPanel17.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel17.setLayout(new java.awt.GridBagLayout());
jLabel53.setText("Output folder:");
jLabel53.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel17.add(jLabel53, gridBagConstraints);
MOutputFolderText.setEditable(false);
MOutputFolderText.setToolTipText("The ouput folder, where the data will be saved.");
MOutputFolderText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
MOutputFolderTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 7;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weightx = 0.5;
gridBagConstraints.insets = new java.awt.Insets(10, 35, 10, 10);
jPanel17.add(MOutputFolderText, gridBagConstraints);
jToggleButton20.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
jToggleButton20.setText("Browse");
jToggleButton20.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton20ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 8;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel17.add(jToggleButton20, gridBagConstraints);
jToggleButton21.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
jToggleButton21.setText("Cancel");
jToggleButton21.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton21ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 9;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel17.add(jToggleButton21, gridBagConstraints);
jLabel54.setText("Scratch folder:");
jLabel54.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel17.add(jLabel54, gridBagConstraints);
MScratchFolderText.setEditable(false);
MScratchFolderText.setToolTipText("This folder will be mounted in the docker container.");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 7;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weightx = 0.5;
gridBagConstraints.insets = new java.awt.Insets(10, 35, 10, 10);
jPanel17.add(MScratchFolderText, gridBagConstraints);
jToggleButton22.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
jToggleButton22.setText("Browse");
jToggleButton22.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton22ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 8;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel17.add(jToggleButton22, gridBagConstraints);
jToggleButton23.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
jToggleButton23.setText("Cancel");
jToggleButton23.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton23ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 9;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel17.add(jToggleButton23, gridBagConstraints);
jLabel55.setText("Mock folder:");
jLabel55.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 4;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel17.add(jLabel55, gridBagConstraints);
MMockFolderText.setEditable(false);
MMockFolderText.setToolTipText("The folder containing the indexed genome.");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 7;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weightx = 0.2;
gridBagConstraints.insets = new java.awt.Insets(10, 35, 10, 10);
jPanel17.add(MMockFolderText, gridBagConstraints);
jToggleButton24.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
jToggleButton24.setText("Browse");
jToggleButton24.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton24ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 8;
gridBagConstraints.gridy = 4;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel17.add(jToggleButton24, gridBagConstraints);
jToggleButton25.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
jToggleButton25.setText("Cancel");
jToggleButton25.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton25ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 9;
gridBagConstraints.gridy = 4;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel17.add(jToggleButton25, gridBagConstraints);
MGenomeFolderText.setEditable(false);
MGenomeFolderText.setToolTipText("The folder containing the indexed genome.");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 7;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weightx = 0.2;
gridBagConstraints.insets = new java.awt.Insets(10, 35, 10, 10);
jPanel17.add(MGenomeFolderText, gridBagConstraints);
jToggleButton26.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
jToggleButton26.setText("Browse");
jToggleButton26.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton26ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 8;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel17.add(jToggleButton26, gridBagConstraints);
jToggleButton27.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
jToggleButton27.setText("Cancel");
jToggleButton27.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton27ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 9;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel17.add(jToggleButton27, gridBagConstraints);
jLabel60.setText("Genome folder:");
jLabel60.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel17.add(jLabel60, gridBagConstraints);
jLabel67.setText("Test folder:");
jLabel67.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel17.add(jLabel67, gridBagConstraints);
MTestFolderText.setEditable(false);
MTestFolderText.setToolTipText("The folder containing the indexed genome.");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 3;
gridBagConstraints.gridwidth = 7;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weightx = 0.2;
gridBagConstraints.insets = new java.awt.Insets(10, 35, 10, 10);
jPanel17.add(MTestFolderText, gridBagConstraints);
jToggleButton28.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
jToggleButton28.setText("Browse");
jToggleButton28.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton28ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 8;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel17.add(jToggleButton28, gridBagConstraints);
jToggleButton29.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
jToggleButton29.setText("Cancel");
jToggleButton29.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton29ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 9;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel17.add(jToggleButton29, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
MACSPanel.add(jPanel17, gridBagConstraints);
jPanel18.setBackground(new java.awt.Color(230, 240, 230));
jPanel18.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel18.setLayout(new java.awt.GridBagLayout());
jLabel56.setText("Execution:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = java.awt.GridBagConstraints.RELATIVE;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel18.add(jLabel56, gridBagConstraints);
MSudoRadioButton.setBackground(new java.awt.Color(230, 240, 230));
MExecution.add(MSudoRadioButton);
MSudoRadioButton.setText("sudo");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = java.awt.GridBagConstraints.RELATIVE;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 35, 10, 10);
jPanel18.add(MSudoRadioButton, gridBagConstraints);
MDockerRadioButton.setBackground(new java.awt.Color(230, 240, 230));
MExecution.add(MDockerRadioButton);
MDockerRadioButton.setSelected(true);
MDockerRadioButton.setText("docker");
MDockerRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
MDockerRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = java.awt.GridBagConstraints.RELATIVE;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel18.add(MDockerRadioButton, gridBagConstraints);
jLabel57.setText("Thread number:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 5;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = java.awt.GridBagConstraints.RELATIVE;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel18.add(jLabel57, gridBagConstraints);
MThreadText.setText("8");
MThreadText.setToolTipText("The number of threads which will be used during the computation.");
MThreadText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
MThreadTextFocusLost(evt);
}
});
MThreadText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
MThreadTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 3;
gridBagConstraints.gridheight = java.awt.GridBagConstraints.RELATIVE;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weightx = 0.05;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel18.add(MThreadText, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 9;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.weightx = 1.0;
jPanel18.add(jLabel61, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
MACSPanel.add(jPanel18, gridBagConstraints);
jPanel19.setBackground(new java.awt.Color(230, 240, 230));
jPanel19.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel19.setLayout(new java.awt.GridBagLayout());
jLabel63.setText("Tool selection:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel19.add(jLabel63, gridBagConstraints);
MToolComboBox.setModel(new javax.swing.DefaultComboBoxModel<>(new String[] { "macs", "sicer" }));
MToolComboBox.setToolTipText("");
MToolComboBox.addItemListener(new java.awt.event.ItemListener() {
public void itemStateChanged(java.awt.event.ItemEvent evt) {
MToolComboBoxItemStateChanged(evt);
}
});
MToolComboBox.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
MToolComboBoxActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 40, 10, 10);
jPanel19.add(MToolComboBox, gridBagConstraints);
Tool.setLayout(new java.awt.CardLayout());
jPanel22.setBackground(new java.awt.Color(230, 240, 230));
jPanel22.setLayout(new java.awt.GridBagLayout());
jLabel78.setText("MACS min. mfold:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel22.add(jLabel78, gridBagConstraints);
MMaxmfoldText.setText("30");
MMaxmfoldText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
MMaxmfoldTextFocusLost(evt);
}
});
MMaxmfoldText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
MMaxmfoldTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 8;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 20, 10, 10);
jPanel22.add(MMaxmfoldText, gridBagConstraints);
jLabel79.setText("MACS p-value:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 12;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel22.add(jLabel79, gridBagConstraints);
jLabel82.setText("MACS max. mfold:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 7;
gridBagConstraints.gridy = 0;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel22.add(jLabel82, gridBagConstraints);
MMinmfoldText.setText("10");
MMinmfoldText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
MMinmfoldTextFocusLost(evt);
}
});
MMinmfoldText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
MMinmfoldTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 20, 10, 10);
jPanel22.add(MMinmfoldText, gridBagConstraints);
MMpvalueText.setText("1e-5");
MMpvalueText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
MMpvalueTextFocusLost(evt);
}
});
MMpvalueText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
MMpvalueTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 13;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 20, 10, 10);
jPanel22.add(MMpvalueText, gridBagConstraints);
Tool.add(jPanel22, "MACS");
jPanel23.setBackground(new java.awt.Color(230, 240, 230));
jPanel23.setLayout(new java.awt.GridBagLayout());
jLabel80.setText("SICER windows:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel23.add(jLabel80, gridBagConstraints);
MSgsizeText.setText("200");
MSgsizeText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
MSgsizeTextFocusLost(evt);
}
});
MSgsizeText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
MSgsizeTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 8;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 20, 10, 10);
jPanel23.add(MSgsizeText, gridBagConstraints);
jLabel81.setText("SICER FDR:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 12;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel23.add(jLabel81, gridBagConstraints);
jLabel83.setText("SICER gsize:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 7;
gridBagConstraints.gridy = 0;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel23.add(jLabel83, gridBagConstraints);
MSWindowsText.setText("200");
MSWindowsText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
MSWindowsTextFocusLost(evt);
}
});
MSWindowsText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
MSWindowsTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 30, 10, 10);
jPanel23.add(MSWindowsText, gridBagConstraints);
MSFDRText.setText("0.1");
MSFDRText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
MSFDRTextFocusLost(evt);
}
});
MSFDRText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
MSFDRTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 13;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 20, 10, 10);
jPanel23.add(MSFDRText, gridBagConstraints);
Tool.add(jPanel23, "SICER");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.weightx = 0.2;
jPanel19.add(Tool, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 3;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.PAGE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
MACSPanel.add(jPanel19, gridBagConstraints);
jPanel20.setBackground(new java.awt.Color(230, 240, 230));
jPanel20.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel20.setLayout(new java.awt.GridBagLayout());
MAdapter5Text.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
MAdapter5TextFocusLost(evt);
}
});
MAdapter5Text.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
MAdapter5TextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 27;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel20.add(MAdapter5Text, gridBagConstraints);
jLabel68.setText("Adapter 5':");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel20.add(jLabel68, gridBagConstraints);
jLabel69.setText("Adapter 3':");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel20.add(jLabel69, gridBagConstraints);
MAdapter3Text.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
MAdapter3TextFocusLost(evt);
}
});
MAdapter3Text.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
MAdapter3TextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 27;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel20.add(MAdapter3Text, gridBagConstraints);
jLabel70.setText("Min length:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel20.add(jLabel70, gridBagConstraints);
MTTSText.setText("0");
MTTSText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
MTTSTextFocusLost(evt);
}
});
MTTSText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
MTTSTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 15;
gridBagConstraints.gridy = 5;
gridBagConstraints.gridwidth = 6;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.2;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel20.add(MTTSText, gridBagConstraints);
jLabel71.setText("Max. upstream distance:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 9;
gridBagConstraints.gridy = 5;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel20.add(jLabel71, gridBagConstraints);
jLabel72.setText("Organism:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 14;
gridBagConstraints.gridy = 4;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel20.add(jLabel72, gridBagConstraints);
jLabel73.setText("Remove duplicates:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 5;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel20.add(jLabel73, gridBagConstraints);
MRyesRadioButton.setBackground(new java.awt.Color(230, 240, 230));
MRemoveDuplicates.add(MRyesRadioButton);
MRyesRadioButton.setText("yes");
MRyesRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
MRyesRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 5;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel20.add(MRyesRadioButton, gridBagConstraints);
MRnoRadioButton.setBackground(new java.awt.Color(230, 240, 230));
MRemoveDuplicates.add(MRnoRadioButton);
MRnoRadioButton.setSelected(true);
MRnoRadioButton.setText("no");
MRnoRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
MRnoRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 4;
gridBagConstraints.gridy = 5;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel20.add(MRnoRadioButton, gridBagConstraints);
jLabel74.setText("Read length:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 9;
gridBagConstraints.gridy = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel20.add(jLabel74, gridBagConstraints);
MOrgComboBox.setModel(new javax.swing.DefaultComboBoxModel<>(new String[] { "hg19", "hg38", "mm9", "mm10" }));
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 15;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 3;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel20.add(MOrgComboBox, gridBagConstraints);
MMinLengthText.setText("30");
MMinLengthText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
MMinLengthTextFocusLost(evt);
}
});
MMinLengthText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
MMinLengthTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 6;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel20.add(MMinLengthText, gridBagConstraints);
MMaxUpstreamText.setText("10000");
MMaxUpstreamText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
MMaxUpstreamTextFocusLost(evt);
}
});
MMaxUpstreamText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
MMaxUpstreamTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 10;
gridBagConstraints.gridy = 5;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.2;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel20.add(MMaxUpstreamText, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 21;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 3;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.weightx = 0.5;
jPanel20.add(jLabel75, gridBagConstraints);
jLabel76.setText("TTS distance:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 14;
gridBagConstraints.gridy = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel20.add(jLabel76, gridBagConstraints);
MReadLengthTextField.setText("50");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 10;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel20.add(MReadLengthTextField, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.PAGE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
MACSPanel.add(jPanel20, gridBagConstraints);
MACS.setViewportView(MACSPanel);
MainPanel.add(MACS, "MACS");
SampleSizePanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "Sample size estimator", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("Dialog", 1, 14), new java.awt.Color(218, 174, 0))); // NOI18N
SampleSizePanel.setLayout(new java.awt.GridBagLayout());
jPanel21.setBackground(new java.awt.Color(249, 248, 235));
jPanel21.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel21.setLayout(new java.awt.GridBagLayout());
jLabel64.setText("Output Folder:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel21.add(jLabel64, gridBagConstraints);
SSOutputFolderText.setEditable(false);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.weightx = 0.4;
gridBagConstraints.insets = new java.awt.Insets(10, 48, 10, 10);
jPanel21.add(SSOutputFolderText, gridBagConstraints);
SSbrowes.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
SSbrowes.setText("Browse");
SSbrowes.setToolTipText("");
SSbrowes.setEnabled(false);
SSbrowes.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
SSbrowesActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_END;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel21.add(SSbrowes, gridBagConstraints);
SScancel.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
SScancel.setText("Cancel");
SScancel.setEnabled(false);
SScancel.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
SScancelActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 4;
gridBagConstraints.gridy = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_TRAILING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel21.add(SScancel, gridBagConstraints);
jPanel21.add(jLabel65, new java.awt.GridBagConstraints());
jLabel66.setText("Count table file:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel21.add(jLabel66, gridBagConstraints);
SSCountTableText.setEditable(false);
SSCountTableText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
SSCountTableTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.insets = new java.awt.Insets(10, 48, 10, 10);
jPanel21.add(SSCountTableText, gridBagConstraints);
jButton27.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/fileb.png"))); // NOI18N
jButton27.setText("Browse");
jButton27.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton27ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 0;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel21.add(jButton27, gridBagConstraints);
jButton28.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
jButton28.setText("Cancel");
jButton28.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton28ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 4;
gridBagConstraints.gridy = 0;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel21.add(jButton28, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
SampleSizePanel.add(jPanel21, gridBagConstraints);
SSExecuteButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/exec.png"))); // NOI18N
SSExecuteButton.setText("Execute");
SSExecuteButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
SSExecuteButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
SampleSizePanel.add(SSExecuteButton, gridBagConstraints);
SSSaveButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/86b.png"))); // NOI18N
SSSaveButton.setText("Save conf.");
SSSaveButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
SSSaveButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
SampleSizePanel.add(SSSaveButton, gridBagConstraints);
SSResetButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/reset.png"))); // NOI18N
SSResetButton.setText("Reset");
SSResetButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
SSResetButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
SampleSizePanel.add(SSResetButton, gridBagConstraints);
SSCloseButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/close.png"))); // NOI18N
SSCloseButton.setText("Close");
SSCloseButton.setToolTipText("");
SSCloseButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
SSCloseButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
SampleSizePanel.add(SSCloseButton, gridBagConstraints);
jPanel24.setBackground(new java.awt.Color(249, 248, 235));
jPanel24.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel24.setLayout(new java.awt.GridBagLayout());
jLabel77.setText("Log2 fold change:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel24.add(jLabel77, gridBagConstraints);
jLabel84.setText("#gene for dispertion:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel24.add(jLabel84, gridBagConstraints);
jPanel24.add(jLabel85, new java.awt.GridBagConstraints());
jLabel86.setText("Statistical power:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel24.add(jLabel86, gridBagConstraints);
SSPowerText.setText("0.8");
SSPowerText.setToolTipText("expected statistical power required to detect prognostic genes");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel24.add(SSPowerText, gridBagConstraints);
SSGeneText.setText("200");
SSGeneText.setToolTipText(" an integer indicating the number of genes used in estimation of read counts and dispersion distribution");
SSGeneText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
SSGeneTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.weightx = 0.4;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel24.add(SSGeneText, gridBagConstraints);
SSlog2Text.setText("1");
SSlog2Text.setToolTipText("an integer indicating the minimum log2 fold change for prognostic genes between two group");
SSlog2Text.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
SSlog2TextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel24.add(SSlog2Text, gridBagConstraints);
jLabel87.setText("False discovery rate:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 6;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel24.add(jLabel87, gridBagConstraints);
SSFDRtext.setText("0.1");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 6;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel24.add(SSFDRtext, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
SampleSizePanel.add(jPanel24, gridBagConstraints);
SampleSize.setViewportView(SampleSizePanel);
MainPanel.add(SampleSize, "SampleSize");
ExperimentPowerPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "Experiment power", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("Dialog", 1, 14), new java.awt.Color(0, 51, 102))); // NOI18N
ExperimentPowerPanel.setLayout(new java.awt.GridBagLayout());
jPanel25.setBackground(new java.awt.Color(233, 242, 250));
jPanel25.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel25.setLayout(new java.awt.GridBagLayout());
jLabel88.setText("Output Folder:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel25.add(jLabel88, gridBagConstraints);
EPOutputFolderText.setEditable(false);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.weightx = 0.4;
gridBagConstraints.insets = new java.awt.Insets(10, 48, 10, 10);
jPanel25.add(EPOutputFolderText, gridBagConstraints);
SSbrowes1.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
SSbrowes1.setText("Browse");
SSbrowes1.setToolTipText("");
SSbrowes1.setEnabled(false);
SSbrowes1.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
SSbrowes1ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_END;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel25.add(SSbrowes1, gridBagConstraints);
SScancel1.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
SScancel1.setText("Cancel");
SScancel1.setEnabled(false);
SScancel1.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
SScancel1ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 4;
gridBagConstraints.gridy = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_TRAILING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel25.add(SScancel1, gridBagConstraints);
jPanel25.add(jLabel89, new java.awt.GridBagConstraints());
jLabel90.setText("Count table file:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel25.add(jLabel90, gridBagConstraints);
EPCountTableText.setEditable(false);
EPCountTableText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
EPCountTableTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.insets = new java.awt.Insets(10, 48, 10, 10);
jPanel25.add(EPCountTableText, gridBagConstraints);
jButton29.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/fileb.png"))); // NOI18N
jButton29.setText("Browse");
jButton29.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton29ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 0;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel25.add(jButton29, gridBagConstraints);
jButton30.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
jButton30.setText("Cancel");
jButton30.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton30ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 4;
gridBagConstraints.gridy = 0;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel25.add(jButton30, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
ExperimentPowerPanel.add(jPanel25, gridBagConstraints);
EPExecuteButton1.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/exec.png"))); // NOI18N
EPExecuteButton1.setText("Execute");
EPExecuteButton1.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
EPExecuteButton1ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
ExperimentPowerPanel.add(EPExecuteButton1, gridBagConstraints);
EPSaveButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/86b.png"))); // NOI18N
EPSaveButton.setText("Save conf.");
EPSaveButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
EPSaveButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
ExperimentPowerPanel.add(EPSaveButton, gridBagConstraints);
EPResetButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/reset.png"))); // NOI18N
EPResetButton.setText("Reset");
EPResetButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
EPResetButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
ExperimentPowerPanel.add(EPResetButton, gridBagConstraints);
EPCloseButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/close.png"))); // NOI18N
EPCloseButton.setText("Close");
EPCloseButton.setToolTipText("");
EPCloseButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
EPCloseButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
ExperimentPowerPanel.add(EPCloseButton, gridBagConstraints);
jPanel26.setBackground(new java.awt.Color(233, 242, 250));
jPanel26.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel26.setLayout(new java.awt.GridBagLayout());
jLabel91.setText("Log2 fold change:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel26.add(jLabel91, gridBagConstraints);
jLabel92.setText("#gene for dispertion:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel26.add(jLabel92, gridBagConstraints);
jPanel26.add(jLabel93, new java.awt.GridBagConstraints());
jLabel94.setText("Number of samples:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel26.add(jLabel94, gridBagConstraints);
EPSampleText.setText("3");
EPSampleText.setToolTipText("the number of samples in each group");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel26.add(EPSampleText, gridBagConstraints);
EPGeneText.setText("200");
EPGeneText.setToolTipText(" an integer indicating the number of genes used in estimation of read counts and dispersion distribution");
EPGeneText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
EPGeneTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.weightx = 0.4;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel26.add(EPGeneText, gridBagConstraints);
EPlog2Text.setText("1");
EPlog2Text.setToolTipText("an integer indicating the minimum log2 fold change for prognostic genes between two group");
EPlog2Text.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
EPlog2TextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel26.add(EPlog2Text, gridBagConstraints);
jLabel95.setText("False discovery rate:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 6;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel26.add(jLabel95, gridBagConstraints);
EPFDRtext.setText("0.1");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 6;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel26.add(EPFDRtext, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
ExperimentPowerPanel.add(jPanel26, gridBagConstraints);
ExperimentPower.setViewportView(ExperimentPowerPanel);
MainPanel.add(ExperimentPower, "ExperimentPower");
mRNABatchPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "Adding covariates and batch information", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("Dialog", 1, 14), new java.awt.Color(0, 153, 153))); // NOI18N
mRNABatchPanel.setLayout(new java.awt.GridBagLayout());
jPanel27.setBackground(new java.awt.Color(238, 250, 247));
jPanel27.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel27.setToolTipText("the all.counts.txt file generated from miRNAseq step");
jPanel27.setLayout(new java.awt.GridBagLayout());
CCountHeaderTable.setModel(new javax.swing.table.DefaultTableModel(
new Object [][] {
},
new String [] {
"Count Header", "Grouping", "Batch"
}
) {
Class[] types = new Class [] {
java.lang.String.class, java.lang.Object.class, java.lang.Object.class
};
public Class getColumnClass(int columnIndex) {
return types [columnIndex];
}
});
CCountHeaderTable.setSelectionMode(javax.swing.ListSelectionModel.SINGLE_SELECTION);
CCountHeaderTable.getTableHeader().setReorderingAllowed(false);
jScrollPane7.setViewportView(CCountHeaderTable);
CCountHeaderTable.getColumnModel().getSelectionModel().setSelectionMode(javax.swing.ListSelectionModel.SINGLE_SELECTION);
if (CCountHeaderTable.getColumnModel().getColumnCount() > 0) {
CCountHeaderTable.getColumnModel().getColumn(1).setCellEditor(new DefaultCellEditor(CovComboBox));
CCountHeaderTable.getColumnModel().getColumn(2).setCellEditor(new DefaultCellEditor(BatchComboBox));
}
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weightx = 1.0;
gridBagConstraints.weighty = 1.0;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel27.add(jScrollPane7, gridBagConstraints);
CCovInputFileText.setEditable(false);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel27.add(CCovInputFileText, gridBagConstraints);
Cinbrowes.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/fileb.png"))); // NOI18N
Cinbrowes.setText("Browse");
Cinbrowes.setToolTipText("");
Cinbrowes.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
CinbrowesActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 0;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel27.add(Cinbrowes, gridBagConstraints);
Cincancel.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
Cincancel.setText("Cancel");
Cincancel.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
CincancelActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 4;
gridBagConstraints.gridy = 0;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel27.add(Cincancel, gridBagConstraints);
jLabel98.setText("Output Folder:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel27.add(jLabel98, gridBagConstraints);
jLabel97.setText("Count file:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel27.add(jLabel97, gridBagConstraints);
COutputFolderText.setEditable(false);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 3;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.weightx = 0.4;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel27.add(COutputFolderText, gridBagConstraints);
Coutbrowes.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
Coutbrowes.setText("Browse");
Coutbrowes.setToolTipText("");
Coutbrowes.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
CoutbrowesActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_END;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel27.add(Coutbrowes, gridBagConstraints);
Coutcancel.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
Coutcancel.setText("Cancel");
Coutcancel.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
CoutcancelActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 4;
gridBagConstraints.gridy = 3;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_TRAILING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel27.add(Coutcancel, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
mRNABatchPanel.add(jPanel27, gridBagConstraints);
FExecuteButton1.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/exec.png"))); // NOI18N
FExecuteButton1.setText("Execute");
FExecuteButton1.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
FExecuteButton1ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
mRNABatchPanel.add(FExecuteButton1, gridBagConstraints);
FSaveButton1.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/86b.png"))); // NOI18N
FSaveButton1.setText("Save conf.");
FSaveButton1.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
FSaveButton1ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
mRNABatchPanel.add(FSaveButton1, gridBagConstraints);
CResetButton1.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/reset.png"))); // NOI18N
CResetButton1.setText("Reset");
CResetButton1.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
CResetButton1ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
mRNABatchPanel.add(CResetButton1, gridBagConstraints);
CCloseButton1.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/close.png"))); // NOI18N
CCloseButton1.setText("Close");
CCloseButton1.setToolTipText("");
CCloseButton1.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
CCloseButton1ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_END;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
mRNABatchPanel.add(CCloseButton1, gridBagConstraints);
mRNABatch.setViewportView(mRNABatchPanel);
MainPanel.add(mRNABatch, "AddingCovmRNA");
IndexingSalmonPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "Transcriptome pseudo-reference building with Salmon\n", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("Dialog", 1, 14), new java.awt.Color(255, 102, 102))); // NOI18N
IndexingSalmonPanel.setToolTipText("");
IndexingSalmonPanel.setLayout(new java.awt.GridBagLayout());
iCloseButton2.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/close.png"))); // NOI18N
iCloseButton2.setText("Close");
iCloseButton2.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
iCloseButton2ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
IndexingSalmonPanel.add(iCloseButton2, gridBagConstraints);
jButton37.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/exec.png"))); // NOI18N
jButton37.setText("Execute");
jButton37.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton37ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weightx = 0.3;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
IndexingSalmonPanel.add(jButton37, gridBagConstraints);
iResetButton2.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/reset.png"))); // NOI18N
iResetButton2.setText("Reset");
iResetButton2.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
iResetButton2ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
IndexingSalmonPanel.add(iResetButton2, gridBagConstraints);
jButton38.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/86b.png"))); // NOI18N
jButton38.setText("Save conf.");
jButton38.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton38ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
IndexingSalmonPanel.add(jButton38, gridBagConstraints);
jPanel28.setBackground(new java.awt.Color(253, 232, 232));
jPanel28.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel28.setLayout(new java.awt.GridBagLayout());
jLabel103.setText("Genome folder:");
jLabel103.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel28.add(jLabel103, gridBagConstraints);
iGenomeFolderSText.setEditable(false);
iGenomeFolderSText.setToolTipText("The folder that will contain the indexed genome.");
iGenomeFolderSText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
iGenomeFolderSTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE;
gridBagConstraints.weightx = 0.2;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel28.add(iGenomeFolderSText, gridBagConstraints);
jToggleButton30.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
jToggleButton30.setText("Browse");
jToggleButton30.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton30ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 5;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel28.add(jToggleButton30, gridBagConstraints);
jToggleButton31.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
jToggleButton31.setText("Cancel");
jToggleButton31.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton31ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel28.add(jToggleButton31, gridBagConstraints);
jLabel104.setText("Genome url:");
jLabel104.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel28.add(jLabel104, gridBagConstraints);
iGenomeURLSText.setToolTipText("The URL which will be used to download the genome");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 6;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel28.add(iGenomeURLSText, gridBagConstraints);
jLabel105.setText("GTF url:");
jLabel105.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel28.add(jLabel105, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 6;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel28.add(iGTFURLSText, gridBagConstraints);
iKmerSText.setText("31");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 3;
gridBagConstraints.gridwidth = 3;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_START;
gridBagConstraints.weightx = 0.05;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel28.add(iKmerSText, gridBagConstraints);
jLabel108.setText("K-mer size:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel28.add(jLabel108, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 4;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_START;
gridBagConstraints.weightx = 0.2;
jPanel28.add(jLabel109, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
IndexingSalmonPanel.add(jPanel28, gridBagConstraints);
jPanel29.setBackground(new java.awt.Color(253, 232, 232));
jPanel29.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel29.setLayout(new java.awt.GridBagLayout());
jLabel106.setText("Execution:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel29.add(jLabel106, gridBagConstraints);
iSudoRadioSButton.setBackground(new java.awt.Color(253, 232, 232));
IExecutionSalmon.add(iSudoRadioSButton);
iSudoRadioSButton.setText("sudo");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel29.add(iSudoRadioSButton, gridBagConstraints);
iDockerRadioSButton.setBackground(new java.awt.Color(253, 232, 232));
IExecutionSalmon.add(iDockerRadioSButton);
iDockerRadioSButton.setSelected(true);
iDockerRadioSButton.setText("docker");
iDockerRadioSButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
iDockerRadioSButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 4;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel29.add(iDockerRadioSButton, gridBagConstraints);
jLabel107.setText("Thread number:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel29.add(jLabel107, gridBagConstraints);
iThreadSText.setText("8");
iThreadSText.setToolTipText("The number of threads which will be used during the computation.");
iThreadSText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
iThreadSTextFocusLost(evt);
}
});
iThreadSText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
iThreadSTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.ABOVE_BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel29.add(iThreadSText, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
IndexingSalmonPanel.add(jPanel29, gridBagConstraints);
IndexingSalmon.setViewportView(IndexingSalmonPanel);
MainPanel.add(IndexingSalmon, "indexingSalmon");
CountingSalmonPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "Transcripts and genes counting with Salmon ", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("Dialog", 1, 14), new java.awt.Color(255, 102, 102))); // NOI18N
CountingSalmonPanel.setToolTipText("");
CountingSalmonPanel.setLayout(new java.awt.GridBagLayout());
vCloseButton5.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/close.png"))); // NOI18N
vCloseButton5.setText("Close");
vCloseButton5.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vCloseButton5ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
CountingSalmonPanel.add(vCloseButton5, gridBagConstraints);
jButton39.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/exec.png"))); // NOI18N
jButton39.setText("Execute");
jButton39.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton39ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
CountingSalmonPanel.add(jButton39, gridBagConstraints);
jButton40.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/reset.png"))); // NOI18N
jButton40.setText("Reset");
jButton40.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton40ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
CountingSalmonPanel.add(jButton40, gridBagConstraints);
jButton41.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/86b.png"))); // NOI18N
jButton41.setText("Save conf.");
jButton41.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton41ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
CountingSalmonPanel.add(jButton41, gridBagConstraints);
jPanel30.setBackground(new java.awt.Color(253, 232, 232));
jPanel30.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel30.setToolTipText("");
jPanel30.setLayout(new java.awt.GridBagLayout());
jLabel110.setText("FastQ folder:");
jLabel110.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel30.add(jLabel110, gridBagConstraints);
cFastQFolderText.setEditable(false);
cFastQFolderText.setToolTipText("The folder containing the input reads in FastQ format.");
cFastQFolderText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
cFastQFolderTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weightx = 0.2;
gridBagConstraints.insets = new java.awt.Insets(10, 28, 10, 10);
jPanel30.add(cFastQFolderText, gridBagConstraints);
jToggleButton32.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
jToggleButton32.setText("Browse");
jToggleButton32.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton32ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel30.add(jToggleButton32, gridBagConstraints);
jToggleButton33.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
jToggleButton33.setText("Cancel");
jToggleButton33.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton33ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 7;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel30.add(jToggleButton33, gridBagConstraints);
jLabel111.setText("Scratch folder:");
jLabel111.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel30.add(jLabel111, gridBagConstraints);
cOutputFolderText.setEditable(false);
cOutputFolderText.setToolTipText("This folder will be mounted in the docker container.");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weightx = 0.2;
gridBagConstraints.weighty = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 28, 10, 10);
jPanel30.add(cOutputFolderText, gridBagConstraints);
jToggleButton34.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
jToggleButton34.setText("Browse");
jToggleButton34.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton34ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel30.add(jToggleButton34, gridBagConstraints);
jToggleButton35.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
jToggleButton35.setText("Cancel");
jToggleButton35.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton35ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 7;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel30.add(jToggleButton35, gridBagConstraints);
jLabel112.setText("Genome folder:");
jLabel112.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 1.6;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel30.add(jLabel112, gridBagConstraints);
cGenomeFolderText.setEditable(false);
cGenomeFolderText.setToolTipText("The folder containing the indexed genome.");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weightx = 0.2;
gridBagConstraints.insets = new java.awt.Insets(10, 28, 10, 10);
jPanel30.add(cGenomeFolderText, gridBagConstraints);
jToggleButton36.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
jToggleButton36.setText("Browse");
jToggleButton36.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton36ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 6;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel30.add(jToggleButton36, gridBagConstraints);
jToggleButton37.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
jToggleButton37.setText("Cancel");
jToggleButton37.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton37ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 7;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel30.add(jToggleButton37, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
CountingSalmonPanel.add(jPanel30, gridBagConstraints);
jPanel31.setBackground(new java.awt.Color(253, 232, 232));
jPanel31.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel31.setToolTipText("");
jPanel31.setLayout(new java.awt.GridBagLayout());
jLabel113.setText("Execution:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel31.add(jLabel113, gridBagConstraints);
cSudoRadioButton.setBackground(new java.awt.Color(253, 232, 232));
cExecutiionSalmon.add(cSudoRadioButton);
cSudoRadioButton.setText("sudo");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 28, 10, 10);
jPanel31.add(cSudoRadioButton, gridBagConstraints);
cDockerRadioButton.setBackground(new java.awt.Color(253, 232, 232));
cExecutiionSalmon.add(cDockerRadioButton);
cDockerRadioButton.setSelected(true);
cDockerRadioButton.setText("docker");
cDockerRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
cDockerRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 4;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel31.add(cDockerRadioButton, gridBagConstraints);
jLabel114.setText("Thread number:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel31.add(jLabel114, gridBagConstraints);
cThreadText.setText("8");
cThreadText.setToolTipText("The number of threads which will be used during the computation.");
cThreadText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
cThreadTextFocusLost(evt);
}
});
cThreadText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
cThreadTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 28, 10, 10);
jPanel31.add(cThreadText, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
CountingSalmonPanel.add(jPanel31, gridBagConstraints);
jPanel32.setBackground(new java.awt.Color(253, 232, 232));
jPanel32.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel32.setLayout(new java.awt.GridBagLayout());
cAdapter5Text.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
cAdapter5TextFocusLost(evt);
}
});
cAdapter5Text.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
cAdapter5TextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 24;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel32.add(cAdapter5Text, gridBagConstraints);
jLabel115.setText("Adapter 5':");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel32.add(jLabel115, gridBagConstraints);
jLabel116.setText("Adapter 3':");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel32.add(jLabel116, gridBagConstraints);
cAdapter3Text.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
cAdapter3TextFocusLost(evt);
}
});
cAdapter3Text.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
cAdapter3TextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 24;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel32.add(cAdapter3Text, gridBagConstraints);
cPeRadioButton.setBackground(new java.awt.Color(253, 232, 232));
cSeq.add(cPeRadioButton);
cPeRadioButton.setSelected(true);
cPeRadioButton.setText("paired-end");
cPeRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
cPeRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 7;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 7;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel32.add(cPeRadioButton, gridBagConstraints);
cSeRadioButton.setBackground(new java.awt.Color(253, 232, 232));
cSeq.add(cSeRadioButton);
cSeRadioButton.setText("single-end");
cSeRadioButton.setToolTipText("");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 5;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel32.add(cSeRadioButton, gridBagConstraints);
jLabel117.setText("Type of Sequence");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 4;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel32.add(jLabel117, gridBagConstraints);
jLabel118.setText("Min length:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 6;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel32.add(jLabel118, gridBagConstraints);
cMinLengthText.setText("40");
cMinLengthText.addFocusListener(new java.awt.event.FocusAdapter() {
public void focusLost(java.awt.event.FocusEvent evt) {
cMinLengthTextFocusLost(evt);
}
});
cMinLengthText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
cMinLengthTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 6;
gridBagConstraints.gridwidth = 3;
gridBagConstraints.gridheight = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel32.add(cMinLengthText, gridBagConstraints);
jLabel119.setText("Strandness:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 8;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel32.add(jLabel119, gridBagConstraints);
cSNoneRadioButton.setBackground(new java.awt.Color(253, 232, 232));
cStrand.add(cSNoneRadioButton);
cSNoneRadioButton.setSelected(true);
cSNoneRadioButton.setText("none");
cSNoneRadioButton.setToolTipText("");
cSNoneRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
cSNoneRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 8;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel32.add(cSNoneRadioButton, gridBagConstraints);
cSForwardRadioButton.setBackground(new java.awt.Color(253, 232, 232));
cStrand.add(cSForwardRadioButton);
cSForwardRadioButton.setText("forward");
cSForwardRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
cSForwardRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 7;
gridBagConstraints.gridy = 8;
gridBagConstraints.gridwidth = 6;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel32.add(cSForwardRadioButton, gridBagConstraints);
cSReverseRadioButton.setBackground(new java.awt.Color(253, 232, 232));
cStrand.add(cSReverseRadioButton);
cSReverseRadioButton.setText("reverse");
cSReverseRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
cSReverseRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 16;
gridBagConstraints.gridy = 8;
gridBagConstraints.gridwidth = 8;
gridBagConstraints.gridheight = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 1.0;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel32.add(cSReverseRadioButton, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.PAGE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
CountingSalmonPanel.add(jPanel32, gridBagConstraints);
CountingSalmon.setViewportView(CountingSalmonPanel);
MainPanel.add(CountingSalmon, "countingSalmon");
filterCountsPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "Filter Counts", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("Dialog", 1, 14), new java.awt.Color(255, 51, 51))); // NOI18N
filterCountsPanel.setToolTipText("");
filterCountsPanel.setLayout(new java.awt.GridBagLayout());
vCloseButton6.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/close.png"))); // NOI18N
vCloseButton6.setText("Close");
vCloseButton6.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
vCloseButton6ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 3;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
filterCountsPanel.add(vCloseButton6, gridBagConstraints);
jButton42.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/exec.png"))); // NOI18N
jButton42.setText("Execute");
jButton42.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton42ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.weighty = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
filterCountsPanel.add(jButton42, gridBagConstraints);
jButton43.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/reset.png"))); // NOI18N
jButton43.setText("Reset");
jButton43.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton43ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
filterCountsPanel.add(jButton43, gridBagConstraints);
jButton44.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/86b.png"))); // NOI18N
jButton44.setText("Save conf.");
jButton44.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButton44ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weighty = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
filterCountsPanel.add(jButton44, gridBagConstraints);
jPanel33.setBackground(new java.awt.Color(250, 231, 225));
jPanel33.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel33.setLayout(new java.awt.GridBagLayout());
jLabel120.setText("Output folder:");
jLabel120.setToolTipText("Output folder");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel33.add(jLabel120, gridBagConstraints);
fFPKMfileText.setEditable(false);
fFPKMfileText.setToolTipText("Input data folder.");
fFPKMfileText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
fFPKMfileTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 0;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 20, 10, 10);
jPanel33.add(fFPKMfileText, gridBagConstraints);
jToggleButton38.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/fileb.png"))); // NOI18N
jToggleButton38.setText("Browse");
jToggleButton38.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton38ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel33.add(jToggleButton38, gridBagConstraints);
fCancelButton4.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
fCancelButton4.setText("Cancel");
fCancelButton4.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
fCancelButton4ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel33.add(fCancelButton4, gridBagConstraints);
jLabel121.setText("Input folder:");
jLabel121.setToolTipText("The folder containing FPKM or TPM table files");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel33.add(jLabel121, gridBagConstraints);
fOutputFolderText.setEditable(false);
fOutputFolderText.setToolTipText("Output data folder.");
fOutputFolderText.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
fOutputFolderTextActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 20, 10, 10);
jPanel33.add(fOutputFolderText, gridBagConstraints);
jToggleButton39.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52b.png"))); // NOI18N
jToggleButton39.setText("Browse");
jToggleButton39.setEnabled(false);
jToggleButton39.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jToggleButton39ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.weightx = 0.1;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel33.add(jToggleButton39, gridBagConstraints);
fCancelButton5.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33b.png"))); // NOI18N
fCancelButton5.setText("Cancel");
fCancelButton5.setEnabled(false);
fCancelButton5.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
fCancelButton5ActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel33.add(fCancelButton5, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
filterCountsPanel.add(jPanel33, gridBagConstraints);
jPanel34.setBackground(new java.awt.Color(250, 231, 225));
jPanel34.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
jPanel34.setLayout(new java.awt.GridBagLayout());
jLabel124.setText("Data type:");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel34.add(jLabel124, gridBagConstraints);
fgeneRadioButton.setBackground(new java.awt.Color(250, 231, 225));
DataFilter.add(fgeneRadioButton);
fgeneRadioButton.setText("gene");
fgeneRadioButton.setToolTipText("");
fgeneRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
fgeneRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel34.add(fgeneRadioButton, gridBagConstraints);
fisoformRadioButton.setBackground(new java.awt.Color(250, 231, 225));
DataFilter.add(fisoformRadioButton);
fisoformRadioButton.setSelected(true);
fisoformRadioButton.setText("isoform");
fisoformRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
fisoformRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 4;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 6;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
jPanel34.add(fisoformRadioButton, gridBagConstraints);
fmirnaRadioButton.setBackground(new java.awt.Color(250, 231, 225));
DataFilter.add(fmirnaRadioButton);
fmirnaRadioButton.setText("mirna");
fmirnaRadioButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
fmirnaRadioButtonActionPerformed(evt);
}
});
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 11;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 8;
gridBagConstraints.anchor = java.awt.GridBagConstraints.BASELINE_LEADING;
gridBagConstraints.weightx = 0.3;
gridBagConstraints.weighty = 0.3;
gridBagConstraints.insets = new java.awt.Insets(10, 25, 10, 10);
jPanel34.add(fmirnaRadioButton, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 2;
gridBagConstraints.gridwidth = 4;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_START;
gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
filterCountsPanel.add(jPanel34, gridBagConstraints);
filterCounts.setViewportView(filterCountsPanel);
MainPanel.add(filterCounts, "filtercounts");
HorizontalSplitPanel.setRightComponent(MainPanel);
LeftPanel.setBackground(new java.awt.Color(255, 255, 255));
LeftPanel.setLayout(new java.awt.GridBagLayout());
jScrollPane1.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
javax.swing.tree.DefaultMutableTreeNode treeNode1 = new javax.swing.tree.DefaultMutableTreeNode("SeqBox");
javax.swing.tree.DefaultMutableTreeNode treeNode2 = new javax.swing.tree.DefaultMutableTreeNode("RNAseq Workflow");
javax.swing.tree.DefaultMutableTreeNode treeNode3 = new javax.swing.tree.DefaultMutableTreeNode("Genome indexing STAR-RSEM");
treeNode2.add(treeNode3);
treeNode3 = new javax.swing.tree.DefaultMutableTreeNode("Genes, isoforms counting RSEM");
treeNode2.add(treeNode3);
treeNode3 = new javax.swing.tree.DefaultMutableTreeNode("Transcriptome pseudo-reference building with Salmon");
treeNode2.add(treeNode3);
treeNode3 = new javax.swing.tree.DefaultMutableTreeNode("Transcripts and genes counting with Salmon");
treeNode2.add(treeNode3);
treeNode3 = new javax.swing.tree.DefaultMutableTreeNode("From samples to experiment");
treeNode2.add(treeNode3);
treeNode3 = new javax.swing.tree.DefaultMutableTreeNode("PCA");
treeNode2.add(treeNode3);
treeNode3 = new javax.swing.tree.DefaultMutableTreeNode("Sample size estimator");
treeNode2.add(treeNode3);
treeNode3 = new javax.swing.tree.DefaultMutableTreeNode("Experiment stat. Power");
treeNode2.add(treeNode3);
treeNode3 = new javax.swing.tree.DefaultMutableTreeNode("DESeq2 analysis");
treeNode2.add(treeNode3);
treeNode3 = new javax.swing.tree.DefaultMutableTreeNode("Count Filter");
treeNode2.add(treeNode3);
treeNode1.add(treeNode2);
treeNode2 = new javax.swing.tree.DefaultMutableTreeNode("miRNA workflow");
treeNode3 = new javax.swing.tree.DefaultMutableTreeNode("miRNA counting");
treeNode2.add(treeNode3);
treeNode3 = new javax.swing.tree.DefaultMutableTreeNode("Adding covariates and batchs");
treeNode2.add(treeNode3);
treeNode3 = new javax.swing.tree.DefaultMutableTreeNode("PCA");
treeNode2.add(treeNode3);
treeNode3 = new javax.swing.tree.DefaultMutableTreeNode("Sample size estimator");
treeNode2.add(treeNode3);
treeNode3 = new javax.swing.tree.DefaultMutableTreeNode("Experiment stat. Power");
treeNode2.add(treeNode3);
treeNode3 = new javax.swing.tree.DefaultMutableTreeNode("DESeq2 analysis");
treeNode2.add(treeNode3);
treeNode3 = new javax.swing.tree.DefaultMutableTreeNode("Count Filter");
treeNode2.add(treeNode3);
treeNode1.add(treeNode2);
treeNode2 = new javax.swing.tree.DefaultMutableTreeNode("Chipseq workflow");
treeNode3 = new javax.swing.tree.DefaultMutableTreeNode("Genome indexing BWA");
treeNode2.add(treeNode3);
treeNode3 = new javax.swing.tree.DefaultMutableTreeNode("MACS & SICER analysis");
treeNode2.add(treeNode3);
treeNode1.add(treeNode2);
AnalysisTree.setModel(new javax.swing.tree.DefaultTreeModel(treeNode1));
AnalysisTree.addTreeSelectionListener(new javax.swing.event.TreeSelectionListener() {
public void valueChanged(javax.swing.event.TreeSelectionEvent evt) {
AnalysisTreeValueChanged(evt);
}
});
jScrollPane1.setViewportView(AnalysisTree);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
gridBagConstraints.weightx = 1.0;
gridBagConstraints.weighty = 1.0;
LeftPanel.add(jScrollPane1, gridBagConstraints);
HorizontalSplitPanel.setLeftComponent(LeftPanel);
VerticalSplitPanel.setTopComponent(HorizontalSplitPanel);
getContentPane().add(VerticalSplitPanel, java.awt.BorderLayout.CENTER);
jMenuBar1.setBorder(javax.swing.BorderFactory.createCompoundBorder());
jMenu3.setText("File");
jMenuItem3.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_O, java.awt.event.InputEvent.CTRL_MASK));
jMenuItem3.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/52.png"))); // NOI18N
jMenuItem3.setText("Open");
jMenuItem3.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jMenuItem3ActionPerformed(evt);
}
});
jMenu3.add(jMenuItem3);
jMenuItem4.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_S, java.awt.event.InputEvent.CTRL_MASK));
jMenuItem4.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/86.png"))); // NOI18N
jMenuItem4.setText("Save");
jMenuItem4.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jMenuItem4ActionPerformed(evt);
}
});
jMenu3.add(jMenuItem4);
jMenuItem6.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_X, java.awt.event.InputEvent.CTRL_MASK));
jMenuItem6.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/33.png"))); // NOI18N
jMenuItem6.setText("Exit");
jMenuItem6.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jMenuItem6ActionPerformed(evt);
}
});
jMenu3.add(jMenuItem6);
jMenuBar1.add(jMenu3);
jMenu4.setText("Edit");
jMenuItem1.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_F, java.awt.event.InputEvent.CTRL_MASK));
jMenuItem1.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/preference.png"))); // NOI18N
jMenuItem1.setText("Configure 4SeqGUI");
jMenuItem1.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jMenuItem1ActionPerformed(evt);
}
});
jMenu4.add(jMenuItem1);
jMenuItem8.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_I, java.awt.event.InputEvent.CTRL_MASK));
jMenuItem8.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/download.png"))); // NOI18N
jMenuItem8.setText("Download Docker Images");
jMenuItem8.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jMenuItem8ActionPerformed(evt);
}
});
jMenu4.add(jMenuItem8);
jMenuItem2.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_D, java.awt.event.InputEvent.CTRL_MASK));
jMenuItem2.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/docker.png"))); // NOI18N
jMenuItem2.setText("Remove Docker Containers");
jMenuItem2.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jMenuItem2ActionPerformed(evt);
}
});
jMenu4.add(jMenuItem2);
jMenuBar1.add(jMenu4);
jMenu5.setText("?");
jMenu5.setToolTipText("");
jMenuItem7.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_A, java.awt.event.InputEvent.CTRL_MASK));
jMenuItem7.setIcon(new javax.swing.ImageIcon(getClass().getResource("/pkg4seqgui/images/iconDNA-small.png"))); // NOI18N
jMenuItem7.setText("About 4SeqGUI");
jMenuItem7.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jMenuItem7ActionPerformed(evt);
}
});
jMenu5.add(jMenuItem7);
jMenuBar1.add(jMenu5);
setJMenuBar(jMenuBar1);
pack();
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public Form() {\n initComponents();\n }",
"public MainForm() {\n initComponents();\n }",
"public MainForm() {\n initComponents();\n }",
"public MainForm() {\n initComponents();\n }",
"public frmRectangulo() {\n initComponents();\n }",
"public form() {\n ... | [
"0.73206544",
"0.7291311",
"0.7291311",
"0.7291311",
"0.7286492",
"0.7249181",
"0.7213362",
"0.72085494",
"0.71965617",
"0.7190475",
"0.7184897",
"0.7159234",
"0.71483016",
"0.7094075",
"0.7081491",
"0.70579433",
"0.6987627",
"0.69776064",
"0.69552463",
"0.69549114",
"0.69453... | 0.0 | -1 |
Creates or finds a ApplicationGatewayClientRevocationOptions from its string representation. | @JsonCreator
public static ApplicationGatewayClientRevocationOptions fromString(String name) {
return fromString(name, ApplicationGatewayClientRevocationOptions.class);
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public static Collection<ApplicationGatewayClientRevocationOptions> values() {\n return values(ApplicationGatewayClientRevocationOptions.class);\n }",
"public static AriVersion fromVersionString( String version ) throws ARIException {\n\n for ( AriVersion av: AriVersion.values() ) {\n ... | [
"0.4941495",
"0.4572294",
"0.43942514",
"0.43191925",
"0.42136732",
"0.41573447",
"0.40876588",
"0.40069035",
"0.3995727",
"0.3992638",
"0.3981743",
"0.39636934",
"0.39408314",
"0.39393333",
"0.3900779",
"0.38973048",
"0.38785267",
"0.3866078",
"0.3853994",
"0.3852275",
"0.38... | 0.75945157 | 0 |
Gets known ApplicationGatewayClientRevocationOptions values. | public static Collection<ApplicationGatewayClientRevocationOptions> values() {
return values(ApplicationGatewayClientRevocationOptions.class);
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public List<VpnClientRevokedCertificateInner> vpnClientRevokedCertificates() {\n return this.vpnClientRevokedCertificates;\n }",
"@JsonCreator\n public static ApplicationGatewayClientRevocationOptions fromString(String name) {\n return fromString(name, ApplicationGatewayClientRevocationOption... | [
"0.6032188",
"0.5610515",
"0.5341461",
"0.5081167",
"0.50512993",
"0.5001583",
"0.49807373",
"0.49655548",
"0.49156734",
"0.48575735",
"0.48484132",
"0.48462686",
"0.48214015",
"0.48139942",
"0.47971487",
"0.47772297",
"0.4776363",
"0.47735626",
"0.47638845",
"0.4708615",
"0.... | 0.8349333 | 0 |
/ Getters / Setters | public String getProduct() {
return product;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"protected abstract Set method_1559();",
"@Override\r\n\tpublic void get() {\n\t\t\r\n\t}",
"@Override\n public void get() {}",
"@Override\n\tprotected void getData() {\n\t\t\n\t}",
"public void get() {\n }",
"public void setdat()\n {\n }",
"@Override\n\tpublic void getData() {\n\t\t\n\t}",
... | [
"0.68003595",
"0.6558789",
"0.6552484",
"0.64120036",
"0.62294185",
"0.6210205",
"0.61401826",
"0.61208946",
"0.6081686",
"0.6043031",
"0.5965628",
"0.5945217",
"0.59434736",
"0.5939926",
"0.5920166",
"0.5899987",
"0.5898689",
"0.58881354",
"0.5869365",
"0.5869247",
"0.583858... | 0.0 | -1 |
/ Constructor Default constructor | public DescriptorImpl() {
super();
load();
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public Constructor(){\n\t\t\n\t}",
"Constructor() {\r\n\t\t \r\n\t }",
"defaultConstructor(){}",
"void DefaultConstructor(){}",
"@SuppressWarnings(\"unused\")\n public NoConstructor() {\n // Empty\n }",
"ConstructorPractice () {\n\t\tSystem.out.println(\"Default Constructor\");\n... | [
"0.83749145",
"0.8343262",
"0.7992264",
"0.78817445",
"0.7779739",
"0.77190185",
"0.75351423",
"0.74882823",
"0.7461926",
"0.74335325",
"0.7425329",
"0.73703325",
"0.7352034",
"0.73460907",
"0.7344312",
"0.733987",
"0.7333713",
"0.73313683",
"0.73140347",
"0.72804683",
"0.727... | 0.0 | -1 |
/ Getters / Setters | public String getServiceUrl() {
return serviceUrl;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"protected abstract Set method_1559();",
"@Override\r\n\tpublic void get() {\n\t\t\r\n\t}",
"@Override\n public void get() {}",
"@Override\n\tprotected void getData() {\n\t\t\n\t}",
"public void get() {\n }",
"public void setdat()\n {\n }",
"@Override\n\tpublic void getData() {\n\t\t\n\t}",
... | [
"0.68003595",
"0.6558789",
"0.6552484",
"0.64120036",
"0.62294185",
"0.6210205",
"0.61401826",
"0.61208946",
"0.6081686",
"0.6043031",
"0.5965628",
"0.5945217",
"0.59434736",
"0.5939926",
"0.5920166",
"0.5899987",
"0.5898689",
"0.58881354",
"0.5869365",
"0.5869247",
"0.583858... | 0.0 | -1 |
/ Overridden methods Fires step right after build job ends | @Override
public Void run() throws Exception {
TaskListener listener = getContext().get(TaskListener.class);
assert listener != null;
PrintStream logger = listener.getLogger();
logger.println(Constants.UPDATING_WHITESOURCE);
Run run = getContext().get(Run.class);
WhiteSourceStep whiteSourceStep = new WhiteSourceStep(step, new WhiteSourceDescriptor((DescriptorImpl) step.getDescriptor()));
// make sure we have an organization token
if (StringUtils.isBlank(Secret.toString(whiteSourceStep.getJobApiToken()))) {
logger.println(Constants.INVALID_API_TOKEN);
return null;
}
FilePath workspace = getContext().get(FilePath.class);
Collection<AgentProjectInfo> projectInfos = whiteSourceStep.getProjectInfos(run, listener, workspace, true);
// if (projectInfos == null) {
// whiteSourceStep.stopBuild(run, listener, "Unrecognized build type " + run.getClass().getName());
// return null;
// } else
if (projectInfos.isEmpty()) {
logger.println(Constants.OSS_INFO_NOT_FOUND);
} else {
whiteSourceStep.update(run, listener, projectInfos);
}
return null;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"protected void runAfterStep() {}",
"@Override\n protected void finished(StepContext context) throws Exception {\n boolean finished = false;\n while (!finished) {\n List<String> log = context.get(Run.class).getLog(100);\n for (String s : log) {\n ... | [
"0.7585181",
"0.71707237",
"0.6864101",
"0.68379956",
"0.6597854",
"0.65855366",
"0.64448154",
"0.6431088",
"0.6408814",
"0.6350777",
"0.6350777",
"0.6315343",
"0.6313897",
"0.6306966",
"0.63016474",
"0.62472326",
"0.6229074",
"0.6200591",
"0.6200591",
"0.617306",
"0.617306",... | 0.0 | -1 |
TODO Autogenerated method stub | public Iterator iterator() {
return new IteratorLinkedList<T>(cabeza);
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\r\n\tpublic void comer() \r\n\t{\n\t\t\r\n\t}",
"@Override\n\tpublic void comer() {\n\t\t\n\t}",
"@Override\n public void perish() {\n \n }",
"@Override\r\n\t\t\tpublic void annadir() {\n\r\n\t\t\t}",
"@Override\n\tpublic void anular() {\n\n\t}",
"@Override\n\tprotected void getExr... | [
"0.66713095",
"0.6567948",
"0.652319",
"0.648097",
"0.64770466",
"0.64586824",
"0.64132667",
"0.6376419",
"0.62759",
"0.62545097",
"0.62371093",
"0.62237984",
"0.6201738",
"0.619477",
"0.619477",
"0.61924416",
"0.61872935",
"0.6173417",
"0.613289",
"0.6127952",
"0.6080854",
... | 0.0 | -1 |
check wether to pokemon have same information | static boolean pokemonEq(Pokemon a, Pokemon b) {
if (a == null || b == null) {
System.out.println("null error");
return false;
}
String aStr = a.getName();
String bStr = b.getName();
if (aStr == null || !aStr.equals(bStr)) {
System.out.print("name not match: ");
System.out.print(aStr);
System.out.println(bStr);
return false;
}
aStr = a.getType1();
bStr = b.getType1();
if (aStr == null || !aStr.equals(bStr)) {
System.out.print("type1 not match: ");
System.out.print(aStr);
System.out.println(bStr);
return false;
}
aStr = a.getType2();
bStr = b.getType2();
if (aStr == null || !aStr.equals(bStr)) {
System.out.print("type2 not match: ");
System.out.print(aStr);
System.out.println(bStr);
return false;
}
if (a.getHp() != b.getHp()) {
System.out.println("hp not match");
return false;
}
if (a.getAttack() != b.getAttack()) {
System.out.println("attack not match");
return false;
}
if (a.getDefense() != b.getDefense()) {
System.out.println("defense not match");
return false;
}
if (a.getSpAttack() != b.getSpAttack()) {
System.out.println("SpAttack not match");
return false;
}
if (a.getSpDefense() != b.getSpDefense()) {
System.out.println("SpDefense not match");
return false;
}
if (a.getSpeed() != b.getSpeed()) {
System.out.println("speed not match");
return false;
}
if (a.isLegendary() != b.isLegendary()) {
System.out.println("legendary not match");
return false;
}
return true;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\r\n public boolean equals(Object obj) {\r\n if (obj instanceof Pokemon) {\r\n Pokemon objOne = (Pokemon) obj;\r\n return objOne.number == this.number;\r\n// return objOne.hashCode() == this.hashCode();\r\n } else {\r\n return false;\r\n ... | [
"0.7002782",
"0.67708236",
"0.6770135",
"0.67612106",
"0.6719853",
"0.65481055",
"0.6430279",
"0.63853246",
"0.613073",
"0.61185795",
"0.6081182",
"0.60203964",
"0.59712934",
"0.59595937",
"0.5959333",
"0.592369",
"0.59055054",
"0.58921796",
"0.5872973",
"0.5869204",
"0.58595... | 0.67782605 | 1 |
test the loading of the data from csv file | public static boolean testLoading() {
Data instance = new Data();
Pokemon[] list;
try {
instance.update();
list = instance.getPokemonList();
int cnt = 0;
while (cnt < list.length && list[cnt] != null)
cnt++;
if (cnt != 799) {
System.out.print("Pokemon num incorrect: ");
System.out.println(cnt - 1);
return false;
}
} catch (IOException e) {
e.printStackTrace();
System.out.println("fall the test in exception");
return false;
}
for (int i = 0; i < 6; i++) {
if (!pokemonEq(testList[i], list[indices[i]])) {
System.out.print("fail the test in check element ");
System.out.println(i);
return false;
}
}
return true;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"private void testDataReader() {\n File csv = new File(pathTest);\n try (FileReader fr = new FileReader(csv); BufferedReader bfr = new BufferedReader(fr)) {\n Logger.printInfo(\"Reading test data\");\n for (String line; (line = bfr.readLine()) != null; ) {\n String... | [
"0.747721",
"0.7334183",
"0.7175028",
"0.7116729",
"0.71098155",
"0.6912641",
"0.6911568",
"0.6890037",
"0.6876813",
"0.6668234",
"0.66560537",
"0.66379565",
"0.6632718",
"0.6600711",
"0.6584993",
"0.65764576",
"0.6570389",
"0.65689397",
"0.6520383",
"0.6514191",
"0.64873403"... | 0.0 | -1 |
test the getter and setter of Pokemom class | public static boolean testPokemomGetSet() {
Pokemon inst = new Pokemon("name", "type1", "type2", 2, 3, 4, 5, 6, 7, 8, false, false);
if (!Objects.equals(inst.getName(), "name") || !Objects.equals(inst.getType1(), "type1")
|| !Objects.equals(inst.getType2(), "type2") || !Objects.equals(inst.getHp(), 2)
|| !Objects.equals(inst.getAttack(), 3) || !Objects.equals(inst.getDefense(), 4)
|| !Objects.equals(inst.getSpAttack(), 5) || !Objects.equals(inst.getSpDefense(), 6)
|| !Objects.equals(inst.getSpeed(), 7) || !Objects.equals(inst.getTotal(), 8)
|| !Objects.equals(inst.isLegendary(), false) || !Objects
.equals(inst.getFavorite(), false)) {
return false;
}
inst.setName("sName");
inst.setType1("ttype1");
inst.setType2("ttype2");
inst.setHp(11);
inst.setAttack(10);
inst.setDefense(33);
inst.setSpAttack(44);
inst.setSpDefense(41);
inst.setSpeed(1);
inst.setTotal(222);
inst.setLegendary(true);
inst.setFavorite(true);
if (!Objects.equals(inst.getName(), "sName") || !Objects.equals(inst.getType1(), "ttype1")
|| !Objects.equals(inst.getType2(), "ttype2") || !Objects.equals(inst.getHp(), 11)
|| !Objects.equals(inst.getAttack(), 10) || !Objects.equals(inst.getDefense(), 33)
|| !Objects.equals(inst.getSpAttack(), 44) || !Objects.equals(inst.getSpDefense(), 41)
|| !Objects.equals(inst.getSpeed(), 1) || !Objects.equals(inst.getTotal(), 222)
|| !Objects.equals(inst.isLegendary(), true) || !Objects
.equals(inst.getFavorite(), true)) {
return false;
}
return true;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Test\r\n public void testSetMicentro() {\r\n System.out.println(\"setMicentro\");\r\n CentroEcu_Observado micentro = new CentroEcu_Observado();\r\n micentro.setCiudad(\"Loja\");\r\n Servicio_CentroEcu instance = new Servicio_CentroEcu();\r\n instance.setMicentro(micentro);\r\... | [
"0.6696676",
"0.65274096",
"0.64796424",
"0.64533097",
"0.64170593",
"0.64124185",
"0.64024067",
"0.6372416",
"0.63685",
"0.6321013",
"0.6309157",
"0.6297054",
"0.6271117",
"0.6270293",
"0.62689817",
"0.62645537",
"0.6246085",
"0.6228915",
"0.62081546",
"0.61819077",
"0.61714... | 0.65486926 | 1 |
test the get method of hashtable | public static boolean testTableGet() {
try {
for (int i = 0; i < 6; i++) {
if (!pokemonEq(table.get(testList[i].getName()), testList[i]))
return false;
}
} catch (NoSuchElementException e) {
return false;
}
return true;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@org.junit.Test\n public void get() throws Exception {\n assertEquals(null, hashTable.get(\"savon\"));\n assertEquals(\"camp\", hashTable.get(\"math\"));\n hashTable.put(\"math\", \"club\");\n assertEquals(\"club\", hashTable.get(\"math\"));\n }",
"@org.junit.jupiter.api.Test\n ... | [
"0.80471456",
"0.78119123",
"0.7135702",
"0.7004146",
"0.6905201",
"0.68464726",
"0.6624307",
"0.6601733",
"0.6537614",
"0.65327185",
"0.65097535",
"0.63555384",
"0.62959325",
"0.62949365",
"0.628786",
"0.6275381",
"0.62297654",
"0.6214728",
"0.62134874",
"0.61754173",
"0.616... | 0.5908581 | 39 |
test the clean method of hashtable | public static boolean testTableClear() {
table.clear();
if (table.size() != 0)
return false;
return true;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@org.junit.Test\n public void clear() throws Exception {\n hashTable.clear();\n assertEquals(null, hashTable.get(\"Savon\"));\n assertEquals(null, hashTable.get(\"Blue\"));\n assertEquals(null, hashTable.get(\"math\"));\n }",
"@org.junit.jupiter.api.Test\n void dropNormal() {... | [
"0.7238472",
"0.6901835",
"0.6871635",
"0.67790616",
"0.6777133",
"0.67517096",
"0.6748745",
"0.6690692",
"0.6647514",
"0.6571599",
"0.65589106",
"0.65215075",
"0.6519071",
"0.6427396",
"0.6414259",
"0.64103967",
"0.63799524",
"0.6342357",
"0.6320749",
"0.62754905",
"0.626095... | 0.57589704 | 55 |
test the remove method of hashtable | public static boolean testTableRemove(int size) {
for (int i = 0; i < 6; i++) {
if (table.remove(testList[i].getName()) == null)
return false;
if (table.size() != size - 1 - i) {
return false;
}
try {
table.get(testList[i].getName());
} catch (NoSuchElementException e) {
continue;
}
return false;
}
return true;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Test\n public void test007_test_remove() {\n try {\n HashTableADT test = new HashTable<Integer, String>();\n test.insert(1, \"2\");\n if(test.remove(2) != false) {\n fail(\"remove didn't work correctly on value not present.\");\n }\n test.insert(2, \"3\");\n if (test.remov... | [
"0.7952701",
"0.78927976",
"0.7850963",
"0.7599863",
"0.7411369",
"0.74025446",
"0.7315697",
"0.71743536",
"0.7090634",
"0.70486903",
"0.70208484",
"0.6979839",
"0.69792205",
"0.697009",
"0.6966183",
"0.6958399",
"0.694912",
"0.69117",
"0.6891791",
"0.68730086",
"0.6863083",
... | 0.0 | -1 |
test all the sort method in the PokemonList class | public static boolean testSort() {
Manager inst;
try {
inst = new PokemonTable();
} catch (IOException e) {
e.printStackTrace();
return false;
}
LinkedList<Pokemon> list;
list = inst.sortByAttack(true);
for (int i = 1; i < list.size(); i++) {
if (list.get(i - 1).getAttack() < list.get(i).getAttack()) {
System.out.println("attack sort");
return false;
}
}
list = inst.sortByAttack(false);
for (int i = 1; i < list.size(); i++) {
if (list.get(i - 1).getAttack() > list.get(i).getAttack()) {
System.out.println("attack sort");
return false;
}
}
list = inst.sortByDefense(true);
for (int i = 1; i < list.size(); i++) {
if (list.get(i - 1).getDefense() < list.get(i).getDefense()) {
System.out.println("defense sort");
return false;
}
}
list = inst.sortByDefense(false);
for (int i = 1; i < list.size(); i++) {
if (list.get(i - 1).getDefense() > list.get(i).getDefense()) {
System.out.println("defense sort");
return false;
}
}
list = inst.sortByFavorite(true);
for (int i = 1; i < list.size(); i++) {
if (!list.get(i - 1).getFavorite() && list.get(i).getFavorite()) {
System.out.println("favorite sort");
return false;
}
}
list = inst.sortByFavorite(false);
for (int i = 1; i < list.size(); i++) {
if (list.get(i - 1).getFavorite() && !list.get(i).getFavorite()) {
System.out.println("favorite sort");
return false;
}
}
list = inst.sortByHp(true);
for (int i = 1; i < list.size(); i++) {
if (list.get(i - 1).getHp() < list.get(i).getHp()) {
System.out.println("hp sort");
return false;
}
}
list = inst.sortByHp(false);
for (int i = 1; i < list.size(); i++) {
if (list.get(i - 1).getHp() > list.get(i).getHp()) {
System.out.println("hp sort");
return false;
}
}
list = inst.sortByLegendary(true);
for (int i = 1; i < list.size(); i++) {
if (!list.get(i - 1).isLegendary() && list.get(i).isLegendary()) {
System.out.println("legendary sort");
return false;
}
}
list = inst.sortByLegendary(false);
for (int i = 1; i < list.size(); i++) {
if (list.get(i - 1).isLegendary() && !list.get(i).isLegendary()) {
System.out.println("legendary sort");
return false;
}
}
list = inst.sortByName(true);
for (int i = 1; i < list.size(); i++) {
if (list.get(i - 1).getName().compareTo(list.get(i).getName()) > 0) {
System.out.println("name sort");
return false;
}
}
list = inst.sortByName(false);
for (int i = 1; i < list.size(); i++) {
if (list.get(i - 1).getName().compareTo(list.get(i).getName()) < 0) {
System.out.println("name sort");
return false;
}
}
list = inst.sortBySpAttack(true);
for (int i = 1; i < list.size(); i++) {
if (list.get(i - 1).getSpAttack() < list.get(i).getSpAttack()) {
System.out.println("spAttack sort");
return false;
}
}
list = inst.sortBySpAttack(false);
for (int i = 1; i < list.size(); i++) {
if (list.get(i - 1).getSpAttack() > list.get(i).getSpAttack()) {
System.out.println("spAttack sort");
return false;
}
}
list = inst.sortBySpDefense(true);
for (int i = 1; i < list.size(); i++) {
if (list.get(i - 1).getSpDefense() < list.get(i).getSpDefense()) {
System.out.println("spDefense sort");
return false;
}
}
list = inst.sortBySpDefense(false);
for (int i = 1; i < list.size(); i++) {
if (list.get(i - 1).getSpDefense() > list.get(i).getSpDefense()) {
System.out.println("spDefense sort");
return false;
}
}
list = inst.sortBySpeed(true);
for (int i = 1; i < list.size(); i++) {
if (list.get(i - 1).getSpeed() < list.get(i).getSpeed()) {
System.out.println("speed sort");
return false;
}
}
list = inst.sortBySpeed(false);
for (int i = 1; i < list.size(); i++) {
if (list.get(i - 1).getSpeed() > list.get(i).getSpeed()) {
System.out.println("speed sort");
return false;
}
}
return true;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Test\n public void testSort() {\n initialize();\n var realList = new HighScoreList();\n realList.setList(list);\n realList.sort();\n\n assertEquals(300, realList.getList().get(0).getScore());\n assertEquals(200, realList.getList().get(1).getScore());\n assertEqu... | [
"0.71821016",
"0.7106772",
"0.68959653",
"0.68799037",
"0.6852728",
"0.68094736",
"0.67511743",
"0.6748985",
"0.6719028",
"0.67124665",
"0.6630915",
"0.65899247",
"0.65722275",
"0.6568198",
"0.65383536",
"0.65012056",
"0.64990884",
"0.646551",
"0.64600027",
"0.6448262",
"0.64... | 0.8275229 | 0 |
test getAll method of PokemonTable | public static boolean testPokemonTableGetAll() throws IOException {
PokemonTable inst = new PokemonTable(10);
for (Pokemon item : testList) {
inst.put(item.getName(), item);
}
LinkedList<Pokemon> list = inst.getAll();
if (list.size() != 6)
return false;
for (Pokemon item : testList) {
if (!list.contains(item)) {
return false;
}
}
return true;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public void getAll() {\n\n PokeStubDTOWrapper wrappedPokemonStubs = restTemplate.getForObject(\"https://pokeapi.co/api/v2/pokemon?limit=1118\", PokeStubDTOWrapper.class);\n List<PokeStubDTO> pokemonStubList = wrappedPokemonStubs.getDTOs();\n\n for (PokeStubDTO pokeStub: pokemonStubList) {\n ... | [
"0.72386414",
"0.694306",
"0.6808518",
"0.67976576",
"0.67762655",
"0.66386616",
"0.6634246",
"0.6574191",
"0.65366185",
"0.65336645",
"0.6532274",
"0.65219814",
"0.65073097",
"0.646391",
"0.6458405",
"0.6420743",
"0.6413674",
"0.63976467",
"0.6365871",
"0.636511",
"0.6354707... | 0.72560996 | 0 |
test getAll method of MyFAvorite | public static boolean testMyFavoriteGetAll() {
MyFavorite inst = new MyFavorite(10);
for (Pokemon item : testList) {
inst.put(item.getName(), item);
}
LinkedList<Pokemon> list = inst.getAll();
if (list.size() != 6)
return false;
for (Pokemon item : testList) {
if (!list.contains(item)) {
return false;
}
}
return true;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Test\n public void test_getAll_1() throws Exception {\n clearDB();\n\n List<User> res = instance.getAll();\n\n assertEquals(\"'getAll' should be correct.\", 0, res.size());\n }",
"@Test\r\n public void testGetAllFestivities() {\r\n System.out.println(\"getAllFestivities\");\... | [
"0.7307322",
"0.7281958",
"0.72077614",
"0.7098412",
"0.7086062",
"0.7061438",
"0.70499283",
"0.6972562",
"0.69680583",
"0.6958603",
"0.69467336",
"0.6942246",
"0.6926916",
"0.6918179",
"0.68978554",
"0.6896326",
"0.68924105",
"0.68805003",
"0.6868507",
"0.68615294",
"0.68540... | 0.0 | -1 |
Loads a File as a resource (/reference/pos/). | public List<String> loadFile(String filename) {
List<String> patterns = new ArrayList<>();
String resourceFilename = (filename.indexOf('/') == 0) ? filename : "/reference/pos/" + filename;
URL url = getClass().getResource(resourceFilename);
if(url == null) {
throw new IllegalArgumentException("Could not load resource: \"" + resourceFilename + "\"");
}
try(InputStream stream = url.openStream()) {
byte[] bytes = stream.readAllBytes();
StringBuilder sb = new StringBuilder();
for(byte b : bytes) {
sb.append((char)b);
}
String s = sb.toString();
String[] lines = s.split("\\R"); // Unicode linebreak sequence
sb = new StringBuilder();
for(String line : lines) {
if(line.startsWith("//"))
continue;
if(line.endsWith("+")) {
sb.append(line.substring(0, line.length() - 1));
}
else if(sb.length() > 0 ) {
sb.append(line);
patterns.add(sb.toString());
sb = new StringBuilder();
}
else
patterns.add(line);
}
}
catch(Exception e) {
System.err.println("Could not load " + resourceFilename + " " + e.toString());
}
return patterns;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"void load(File file);",
"public Resource load(IFile f);",
"public void load (File file) throws Exception;",
"public void loadFile(File p_file) throws IOException;",
"public void load(File source);",
"public void load (IFile file) throws Exception;",
"public Resource load(String filename) throws Malform... | [
"0.6879736",
"0.6836283",
"0.6812924",
"0.67571604",
"0.65720564",
"0.6477276",
"0.63755125",
"0.62875056",
"0.6215614",
"0.61116403",
"0.60517144",
"0.601107",
"0.5939912",
"0.59121263",
"0.5901732",
"0.5895235",
"0.5865389",
"0.58428127",
"0.5823698",
"0.5809551",
"0.580599... | 0.0 | -1 |
browser for launch the chrome | public void browser() {
System.setProperty("webdriver.chrome.driver", "src/test/resources/Driver/chromedriver.exe");
driver = new ChromeDriver();
driver.manage().window().maximize();// maximize the window
driver.manage().timeouts().implicitlyWait(50, TimeUnit.SECONDS);
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Given(\"^launch an chrome browser$\")\r\n\tpublic void launch_an_chrome_browser() throws Throwable {\n\t sign.url();\r\n\t\t\r\n\t}",
"public void openBrowser() {\n ResourceBundle config = ResourceBundle.getBundle(\"config\");\n\n config.getString(\"browser\").equalsIgnoreCase(\"Chrome\");\n ... | [
"0.8038407",
"0.7950652",
"0.7891193",
"0.7848332",
"0.78119135",
"0.78086716",
"0.7728446",
"0.77096385",
"0.76261765",
"0.75986034",
"0.7519608",
"0.7516424",
"0.7480884",
"0.74300736",
"0.7423203",
"0.73936015",
"0.7375536",
"0.7272167",
"0.7229791",
"0.71411127",
"0.71249... | 0.72292215 | 19 |
Persist from Account Activity | private void setupUI() {
String status_value = getIntent().getStringExtra("status_value");
String display_name_value = getIntent().getStringExtra("display_name_value");
mStatus.getEditText().setHint(status_value);
mName.getEditText().setHint(display_name_value);
mSaveChanges.setOnClickListener(new View.OnClickListener() {
@Override
public void onClick(View v) {
Log.d(TAG, "onClick: ");
mRegProgress = new ProgressDialog(SettingsActivity.this);
mRegProgress.setTitle("Saving changes");
mRegProgress.setMessage("Please wait while we save the changes");
mRegProgress.setCanceledOnTouchOutside(false);
mRegProgress.show();
String status_v = mStatus.getEditText().getText().toString();
String name_v = mName.getEditText().getText().toString();
if (!TextUtils.isEmpty(status_v)) {
presenter.getmUserDatabase().child(presenter.getMcurrent_user_id())
.child("status").setValue(status_v).addOnCompleteListener(new OnCompleteListener<Void>() {
@Override
public void onComplete(@NonNull Task<Void> task) {
Log.d(TAG, "onComplete: Status update");
if (task.isSuccessful()) {
Log.d(TAG, "Status update: is Sucessfull");
mRegProgress.dismiss();
} else {
Log.d(TAG, "Status update: is not sucessfull");
mRegProgress.hide();
Toast.makeText(SettingsActivity.this, "Error saving changes", Toast.LENGTH_LONG).show();
}
}
});
}
if (!TextUtils.isEmpty(name_v)) {
presenter.getmUserDatabase().child(presenter.getMcurrent_user_id())
.child("name").setValue(name_v).addOnCompleteListener(new OnCompleteListener<Void>() {
@Override
public void onComplete(@NonNull Task<Void> task) {
Log.d(TAG, "onComplete: Display Name update");
if (task.isSuccessful()) {
Log.d(TAG, "Display Name update: is Sucessfull");
mRegProgress.dismiss();
} else {
Log.d(TAG, "Display Name update: is not sucessfull");
mRegProgress.hide();
Toast.makeText(SettingsActivity.this,
"Error saving changes", Toast.LENGTH_LONG).show();
}
}
});
}
}
});
mChangeImage.setOnClickListener(new View.OnClickListener() {
@Override
public void onClick(View v) {
//option 1
// this will direct user to the Gallery chooser (the library to choose images)
Intent intent = new Intent();
intent.setType("image/*");
intent.setAction(Intent.ACTION_GET_CONTENT);
startActivityForResult(Intent.createChooser(intent, "SELECT IMAGE"), GALLERY_PICK);
}
});
rewardClaim.setOnClickListener(new View.OnClickListener() {
@Override
public void onClick(View v) {
AlertDialog.Builder builder = new AlertDialog.Builder(SettingsActivity.this);
builder.setTitle("Rewards Coming Soon");
builder.setMessage("We are planning some cool rewards just for you. \nPlease look forward to it!");
builder.create().show();
}
});
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"void save(Account account);",
"private void writeAccount() {\n SharedPreferences pref = getSharedPreferences(\"ACCOUNT\", Context.MODE_PRIVATE);\n SharedPreferences.Editor edt = pref.edit();\n\n edt.putString(\"email\", Me.getInstance().getEmail());\n edt.putString(\"password\", txtPa... | [
"0.743104",
"0.7423402",
"0.7219852",
"0.70818704",
"0.6967659",
"0.6936646",
"0.68820655",
"0.6849296",
"0.66436535",
"0.64427716",
"0.63861364",
"0.63587326",
"0.6340396",
"0.6339273",
"0.63241094",
"0.63132024",
"0.6304263",
"0.62997204",
"0.6178042",
"0.61621296",
"0.6144... | 0.0 | -1 |
option 1 this will direct user to the Gallery chooser (the library to choose images) | @Override
public void onClick(View v) {
Intent intent = new Intent();
intent.setType("image/*");
intent.setAction(Intent.ACTION_GET_CONTENT);
startActivityForResult(Intent.createChooser(intent, "SELECT IMAGE"), GALLERY_PICK);
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"private void showGalleryChooser() {\n Intent intent = new Intent();\n intent.setType(\"image/*\");\n intent.setAction(Intent.ACTION_GET_CONTENT);\n startActivityForResult(Intent.createChooser(intent, \"Select Picture\"), PICK_IMAGE_REQUEST);\n }",
"public void opengallery() {\n ... | [
"0.81329393",
"0.77003354",
"0.7594392",
"0.75814134",
"0.7570556",
"0.7545307",
"0.75446993",
"0.750812",
"0.7428125",
"0.7420231",
"0.7415804",
"0.74147236",
"0.74122936",
"0.7389019",
"0.73697525",
"0.7365792",
"0.735613",
"0.73462605",
"0.7324593",
"0.7324593",
"0.7318692... | 0.7316323 | 21 |
no Default value for abstract class | public void setValue(double newV) { // assuming REST API update at instantiation - must be a Set method to prevent access to a variable directly
this.Value=newV;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"_ExtendsNotAbstract() {\n super(\"s\"); // needs this if not default ctor;\n }",
"abstract public E addDefault();",
"private Default()\n {}",
"protected abstract S createDefault();",
"public boolean isAbstract()\n/* */ {\n/* 146 */ return false;\n/* */ }",
"public Abstrac... | [
"0.68132573",
"0.68090284",
"0.67346877",
"0.65186554",
"0.65073425",
"0.6496769",
"0.64761543",
"0.6438699",
"0.6384692",
"0.6342669",
"0.62743247",
"0.62705344",
"0.62625784",
"0.6250656",
"0.6229109",
"0.62091",
"0.6204166",
"0.6197535",
"0.6150971",
"0.61393064",
"0.61387... | 0.0 | -1 |
Constructor that executes the model. | public DummyGuiController(SoundModelInterface model) {
this.model = model;
view = new DummyGui(model);
this.runModel();
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"private Model(){}",
"public Model() {\n\t}",
"public Model() {\n\t}",
"Build_Model() {\n\n }",
"public Model() {\n }",
"public Model() {\n }",
"public Model() {\n }",
"public Model() {\n\n }",
"private MainModel() {\n jsonManager = new JsonManager(this);\n }",
"public Mod... | [
"0.68681985",
"0.67714924",
"0.67714924",
"0.6600522",
"0.6489119",
"0.6489119",
"0.6489119",
"0.63778096",
"0.63103455",
"0.62959003",
"0.6277168",
"0.6266339",
"0.6260668",
"0.62131894",
"0.6180988",
"0.6157176",
"0.6157176",
"0.6150261",
"0.6136161",
"0.61339444",
"0.61124... | 0.0 | -1 |
Helper method to convert degrees to polar axes | private static int convertDegreesToPolar(int degrees) {
switch (degrees) {
case -90:
return 270;
case -60:
return 300;
case -30:
return 330;
default:
return degrees;
}
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public String asPolar(){\n// return \"<\" + this.getR() + \", ∠\" + this.getTheta() + \">\";\n return String.format(POLAR_FORMAT, this.getR(), this.getTheta());\n }",
"public Vector2D toPolar()\n {\n return new Vector2D(Math.sqrt(this.x * this.x + this.y * this.y), Math.atan2(t... | [
"0.6879271",
"0.66870767",
"0.635012",
"0.61972696",
"0.60721236",
"0.6061659",
"0.60205394",
"0.6008466",
"0.60012615",
"0.59841067",
"0.5981148",
"0.5981148",
"0.5981148",
"0.5980086",
"0.5980086",
"0.5967167",
"0.5964533",
"0.59636277",
"0.5961871",
"0.5959913",
"0.5953464... | 0.7493267 | 0 |
Method to select input layer type of model based on model type. | public InputLayer selectInputLayer(ModelInputTypes m) {
switch(m) {
case GENERATEDSIN:
return new SoundGeneration(log, model.getDegrees());
case PRECORDEDHRIR:
return new SoundFromFile(log, convertDegreesToPolar(model.getDegrees()));
default:
throw new IllegalArgumentException("No Model Input Type Found.");
}
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"void modelType(Class<?> modelType);",
"public IInputType getInputTypeById(String id);",
"public InputType getOutputType(InputType... inputType) throws InvalidKerasConfigurationException {\n if (inputType.length > 1)\n throw new InvalidKerasConfigurationException(\n \"Keras ... | [
"0.5769398",
"0.5672151",
"0.56395155",
"0.5595773",
"0.55046487",
"0.5373475",
"0.52889615",
"0.52371347",
"0.52125895",
"0.51671135",
"0.51048416",
"0.50707126",
"0.5048714",
"0.50302255",
"0.5029941",
"0.49580818",
"0.49497417",
"0.4926942",
"0.49112985",
"0.4905777",
"0.4... | 0.71754545 | 0 |
Uneeded method stubs from interface, ignored if called in model. Only want to print the required log output. | @Override
public void settings() {
// TODO Auto-generated method stub
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\n public void log()\n {\n }",
"public void interfaceMethod() {\n\t\tSystem.out.println(\"overriden method from interface\");\t\t\r\n\t}",
"@Override\n public void logs() {\n \n }",
"public void doLog() {\n SelfInvokeTestService self = (SelfInvokeTestService)context.... | [
"0.67438924",
"0.66074175",
"0.6353931",
"0.63251364",
"0.6234315",
"0.6200449",
"0.61851203",
"0.613724",
"0.607611",
"0.6051734",
"0.60394895",
"0.60072255",
"0.5980029",
"0.5977749",
"0.59423083",
"0.59255004",
"0.59249693",
"0.5921157",
"0.59200186",
"0.5909829",
"0.59090... | 0.0 | -1 |
TODO Autogenerated method stub | @Override
public void logs() {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\r\n\tpublic void comer() \r\n\t{\n\t\t\r\n\t}",
"@Override\n\tpublic void comer() {\n\t\t\n\t}",
"@Override\n public void perish() {\n \n }",
"@Override\r\n\t\t\tpublic void annadir() {\n\r\n\t\t\t}",
"@Override\n\tpublic void anular() {\n\n\t}",
"@Override\n\tprotected void getExr... | [
"0.6671074",
"0.6567672",
"0.6523024",
"0.6481211",
"0.6477082",
"0.64591026",
"0.64127725",
"0.63762105",
"0.6276059",
"0.6254286",
"0.623686",
"0.6223679",
"0.6201336",
"0.61950207",
"0.61950207",
"0.61922914",
"0.6186996",
"0.6173591",
"0.61327106",
"0.61285484",
"0.608016... | 0.0 | -1 |
TODO Autogenerated method stub | @Override
public void inputTypeChange(ModelInputTypes m) {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\r\n\tpublic void comer() \r\n\t{\n\t\t\r\n\t}",
"@Override\n\tpublic void comer() {\n\t\t\n\t}",
"@Override\n public void perish() {\n \n }",
"@Override\r\n\t\t\tpublic void annadir() {\n\r\n\t\t\t}",
"@Override\n\tpublic void anular() {\n\n\t}",
"@Override\n\tprotected void getExr... | [
"0.66713095",
"0.6567948",
"0.652319",
"0.648097",
"0.64770466",
"0.64586824",
"0.64132667",
"0.6376419",
"0.62759",
"0.62545097",
"0.62371093",
"0.62237984",
"0.6201738",
"0.619477",
"0.619477",
"0.61924416",
"0.61872935",
"0.6173417",
"0.613289",
"0.6127952",
"0.6080854",
... | 0.0 | -1 |
TODO Autogenerated method stub | @Override
public void setFile(File f) {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\r\n\tpublic void comer() \r\n\t{\n\t\t\r\n\t}",
"@Override\n\tpublic void comer() {\n\t\t\n\t}",
"@Override\n public void perish() {\n \n }",
"@Override\r\n\t\t\tpublic void annadir() {\n\r\n\t\t\t}",
"@Override\n\tpublic void anular() {\n\n\t}",
"@Override\n\tprotected void getExr... | [
"0.6671074",
"0.6567672",
"0.6523024",
"0.6481211",
"0.6477082",
"0.64591026",
"0.64127725",
"0.63762105",
"0.6276059",
"0.6254286",
"0.623686",
"0.6223679",
"0.6201336",
"0.61950207",
"0.61950207",
"0.61922914",
"0.6186996",
"0.6173591",
"0.61327106",
"0.61285484",
"0.608016... | 0.0 | -1 |
TODO Autogenerated method stub | @Override
public void closeWindow() {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\r\n\tpublic void comer() \r\n\t{\n\t\t\r\n\t}",
"@Override\n\tpublic void comer() {\n\t\t\n\t}",
"@Override\n public void perish() {\n \n }",
"@Override\r\n\t\t\tpublic void annadir() {\n\r\n\t\t\t}",
"@Override\n\tpublic void anular() {\n\n\t}",
"@Override\n\tprotected void getExr... | [
"0.6671074",
"0.6567672",
"0.6523024",
"0.6481211",
"0.6477082",
"0.64591026",
"0.64127725",
"0.63762105",
"0.6276059",
"0.6254286",
"0.623686",
"0.6223679",
"0.6201336",
"0.61950207",
"0.61950207",
"0.61922914",
"0.6186996",
"0.6173591",
"0.61327106",
"0.61285484",
"0.608016... | 0.0 | -1 |
TODO Autogenerated method stub | @Override
public void soundSourceDegreesUpdate(int selectedItem) {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\r\n\tpublic void comer() \r\n\t{\n\t\t\r\n\t}",
"@Override\n\tpublic void comer() {\n\t\t\n\t}",
"@Override\n public void perish() {\n \n }",
"@Override\r\n\t\t\tpublic void annadir() {\n\r\n\t\t\t}",
"@Override\n\tpublic void anular() {\n\n\t}",
"@Override\n\tprotected void getExr... | [
"0.6671074",
"0.6567672",
"0.6523024",
"0.6481211",
"0.6477082",
"0.64591026",
"0.64127725",
"0.63762105",
"0.6276059",
"0.6254286",
"0.623686",
"0.6223679",
"0.6201336",
"0.61950207",
"0.61950207",
"0.61922914",
"0.6186996",
"0.6173591",
"0.61327106",
"0.61285484",
"0.608016... | 0.0 | -1 |
TODO Autogenerated method stub | @Override
public void closeSettings() {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\r\n\tpublic void comer() \r\n\t{\n\t\t\r\n\t}",
"@Override\n\tpublic void comer() {\n\t\t\n\t}",
"@Override\n public void perish() {\n \n }",
"@Override\r\n\t\t\tpublic void annadir() {\n\r\n\t\t\t}",
"@Override\n\tpublic void anular() {\n\n\t}",
"@Override\n\tprotected void getExr... | [
"0.66713095",
"0.6567948",
"0.652319",
"0.648097",
"0.64770466",
"0.64586824",
"0.64132667",
"0.6376419",
"0.62759",
"0.62545097",
"0.62371093",
"0.62237984",
"0.6201738",
"0.619477",
"0.619477",
"0.61924416",
"0.61872935",
"0.6173417",
"0.613289",
"0.6127952",
"0.6080854",
... | 0.0 | -1 |
TODO Autogenerated method stub | @Override
public void terminateProgram() {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\r\n\tpublic void comer() \r\n\t{\n\t\t\r\n\t}",
"@Override\n\tpublic void comer() {\n\t\t\n\t}",
"@Override\n public void perish() {\n \n }",
"@Override\r\n\t\t\tpublic void annadir() {\n\r\n\t\t\t}",
"@Override\n\tpublic void anular() {\n\n\t}",
"@Override\n\tprotected void getExr... | [
"0.6671074",
"0.6567672",
"0.6523024",
"0.6481211",
"0.6477082",
"0.64591026",
"0.64127725",
"0.63762105",
"0.6276059",
"0.6254286",
"0.623686",
"0.6223679",
"0.6201336",
"0.61950207",
"0.61950207",
"0.61922914",
"0.6186996",
"0.6173591",
"0.61327106",
"0.61285484",
"0.608016... | 0.0 | -1 |
TODO Autogenerated method stub | @Override
public void closeLog() {
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\r\n\tpublic void comer() \r\n\t{\n\t\t\r\n\t}",
"@Override\n\tpublic void comer() {\n\t\t\n\t}",
"@Override\n public void perish() {\n \n }",
"@Override\r\n\t\t\tpublic void annadir() {\n\r\n\t\t\t}",
"@Override\n\tpublic void anular() {\n\n\t}",
"@Override\n\tprotected void getExr... | [
"0.6671074",
"0.6567672",
"0.6523024",
"0.6481211",
"0.6477082",
"0.64591026",
"0.64127725",
"0.63762105",
"0.6276059",
"0.6254286",
"0.623686",
"0.6223679",
"0.6201336",
"0.61950207",
"0.61950207",
"0.61922914",
"0.6186996",
"0.6173591",
"0.61327106",
"0.61285484",
"0.608016... | 0.0 | -1 |
Helper method which creates three tabs, one for basic test parameter, one for the standard output and one for standard error. | protected String createBasicTestData() {
BaseSignatureTestData baseData = baseTestInfo.getBaseTestData();
String basicParameterBody = createBasicParameterRepresentation(baseData);
StringBuilder basicTestDataPanel = new StringBuilder();
basicTestDataPanel
.append("<ul id=\"tabs\" class=\"nav nav-tabs\" data-tabs=\"tabs\">");
basicTestDataPanel
.append("<li class=\"active\"><a href=\"#basic-parameters\" "
+ "data-toggle=\"tab\">Basic parameters</a></li>");
basicTestDataPanel
.append("<li><a href=\"#std-out\" data-toggle=\"tab\">Standard output</a></li>");
basicTestDataPanel
.append("<li><a href=\"#std-err\" data-toggle=\"tab\">Standard error</a></li>");
basicTestDataPanel.append("</ul>");
basicTestDataPanel
.append("<div id=\"my-tab-content\" class=\"tab-content\">");
basicTestDataPanel
.append("<div class=\"tab-pane active\" id=\"basic-parameters\">");
basicTestDataPanel.append(basicParameterBody);
basicTestDataPanel.append("</div>");
basicTestDataPanel.append("<div class=\"tab-pane\" id=\"std-out\">");
basicTestDataPanel.append("<pre class=\"pre-scrollable\">"
+ baseTestInfo.getStdOut() + "</pre>");
basicTestDataPanel.append("</div>");
basicTestDataPanel.append("<div class=\"tab-pane\" id=\"std-err\">");
basicTestDataPanel.append("<pre class=\"pre-scrollable\">"
+ baseTestInfo.getStdErr() + "</pre>");
basicTestDataPanel.append("</div>");
basicTestDataPanel.append("</div>");
return basicTestDataPanel.toString();
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"private void printTestList()\n {\n print(\"\");\n print(SECTION_DIVIDER);\n print(\"Press <1> to Display Main Video Output Port\");\n print(\"Press <2> to Display All Video Output Configurations\");\n print(\"Press <3> to Change Main Video Configuration with Listener\");\n ... | [
"0.6011908",
"0.5943823",
"0.59088093",
"0.5903437",
"0.57228804",
"0.56666213",
"0.55975366",
"0.5546945",
"0.5521844",
"0.5501088",
"0.5483233",
"0.54654545",
"0.5414279",
"0.5414279",
"0.5397168",
"0.53902984",
"0.5384834",
"0.53815854",
"0.537168",
"0.53533965",
"0.531441... | 0.63344115 | 0 |
This method creates a definition list for basic parameters of a test. | private String createBasicParameterRepresentation(
BaseSignatureTestData baseData) {
StringBuilder sb = new StringBuilder();
sb.append("<dl>");
sb.append(createDescription("Input file", baseData.getPdfFile()));
sb.append(createDescription("Output file", baseData.getOutputFile()));
sb.append(createDescription("Signature profile", baseData.getProfilID()));
sb.append(createDescription("Connector Type", baseData
.getConnectorData().getConnectorType()));
if (baseData.getConnectorData().getConnectorParameters().size() > 0) {
StringBuilder connectorParameters = new StringBuilder();
connectorParameters.append("<dl class=\"dl-horizontal\">");
for (Entry<String, String> e : baseData.getConnectorData()
.getConnectorParameters().entrySet())
connectorParameters.append(createDescription(e.getKey(),
e.getValue()));
connectorParameters.append("</dl>");
sb.append(createDescription("Connector Parameters",
connectorParameters.toString()));
}
sb.append(createDescription("Test Type", getTestType()));
sb.append("</dl>");
return sb.toString();
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"private static final List<ParameterImpl> createParameters() {\n\t\tParameterImpl initialize = new ParameterImpl.Builder()\n\t\t\t\t.setLabel(\"Initialize\") // FIXME: STRING: srogers\n\t\t\t\t.setName(\"INITIALIZE\") // FIXME: STRING: srogers\n\t\t\t\t.setType(\"checkbox\")\n\t\t\t\t.setDefaultValue(\"true\")\n\t\... | [
"0.67591256",
"0.6552651",
"0.61794",
"0.59798074",
"0.59052205",
"0.58970296",
"0.5838607",
"0.5822234",
"0.5725039",
"0.5700755",
"0.5691132",
"0.56633306",
"0.5630281",
"0.56206924",
"0.56114864",
"0.5607805",
"0.5590776",
"0.55161613",
"0.5472492",
"0.54442483",
"0.542394... | 0.5315463 | 29 |
Helper for writing a bootstrap panel with some title and content. | protected void writePanel(PrintWriter pw, String panelTitle,
String panelBody) {
pw.println("<div class=\"panel panel-default\">");
pw.println(" <div class=\"panel-heading\">");
pw.println("<h3 class=\"panel-title\">" + panelTitle + "</h3>");
pw.println("</div>");
pw.println("<div class=\"panel-body\">");
pw.println(panelBody);
pw.println("</div>");
pw.println("</div>");
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"private JPanel createPanel(String title) {\n\t\tJPanel panel = new JPanel();\n\t\tpanel.setLayout(new GridLayout(0, 1));\n\t\tpanel.setBorder(new TitledBorder(new EtchedBorder(), title));\n\t\treturn panel;\n\t}",
"public JPanel titlePanel() {\n\t\tJPanel tpanel = new JPanel(null);\n\t\ttpanel.setBounds(0, 0, 70... | [
"0.624205",
"0.62049097",
"0.61960065",
"0.61744535",
"0.61065316",
"0.6076346",
"0.60488683",
"0.60349035",
"0.60104066",
"0.57800174",
"0.5776584",
"0.57494146",
"0.57140857",
"0.56950766",
"0.56933165",
"0.5686599",
"0.5645",
"0.5631966",
"0.5631697",
"0.5609937",
"0.56056... | 0.6581012 | 0 |
This method creates a HTMLrepresentation for data contained in a throwable. | protected String createExceptionDataString(Throwable t) {
StringBuilder exceptionData = new StringBuilder();
exceptionData.append("<dl class=\"dl-horizontal\">");
exceptionData.append(createDescription("Cause", t.toString()));
StringWriter sw = new StringWriter();
PrintWriter pw = new PrintWriter(sw);
t.printStackTrace(pw);
exceptionData.append(createDescription("Stacktrace", sw.toString()));
exceptionData.append("</dl>");
return exceptionData.toString();
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"HTML createHTML();",
"private void createExpectionalClassDiv(BufferedWriter writer,\r\n\t\t\tResultTable table) throws IOException {\r\n\t\tMap<String, String> data = table.getExpectionMessageData();\r\n\t\tint size = table.getExpectionMessageData().size();\r\n\r\n\t\tif (size != 0) {\r\n\t\t\tint height = ((siz... | [
"0.5838296",
"0.57824105",
"0.5695664",
"0.5463029",
"0.5386494",
"0.5361801",
"0.53563213",
"0.5321104",
"0.52983963",
"0.523672",
"0.521912",
"0.5191349",
"0.5173647",
"0.5160959",
"0.5155068",
"0.51471555",
"0.5133961",
"0.51159686",
"0.509706",
"0.50955766",
"0.50862545",... | 0.60091394 | 0 |
Helper method for creating an item of a definition list. | protected String createDescription(String term, String definition) {
return String.format("<dt>%s</dt><dd>%s</dd>%n", term, definition);
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"ListItem createListItem();",
"String createListItem(String list, int accountId);",
"@Override\n public void definitionListItem_()\n {\n }",
"Definition createDefinition();",
"protected abstract void makeItem();",
"public static ItemDefinition itemDef(int i, ItemDefinition itemDef) {\n voi... | [
"0.7278509",
"0.64813167",
"0.640983",
"0.63264364",
"0.63200605",
"0.62338835",
"0.62210894",
"0.6187449",
"0.6128837",
"0.6068515",
"0.6027648",
"0.599945",
"0.5992944",
"0.59538907",
"0.589062",
"0.5839782",
"0.5786914",
"0.5765489",
"0.57215923",
"0.57192516",
"0.5671121"... | 0.5071699 | 80 |
&9674;&9674;&9674; Running methods for this specific subchapter &9674;&9674;&9674; | public static void main(String[] args) {
System.out.println("Chapter 3 - 3.3. Reduction Operations Using Reduce");
System.out.println();
// *** Reduction Operations on IntStream ***
reductionOperationsOnIntStream();
System.out.println();
// *** Summing Numbers Using reduce() ***
summingNumbersUsingReduce();
System.out.println();
// *** Perform reduce with a BinaryOperator ***
performReduceWithABinaryOperator();
System.out.println();
// *** Using a Collector ***
usingACollector();
System.out.println();
// *** Accumulating Books into a Map ***
new Recipe_3_3_Reduction_Operations_Using_Reduce().accumulatingBooksIntoAMap();
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public void sub() {\n\t\tSystem.out.println(\"I am from substraion method\");\n\t\t\n\t}",
"private void sub() {\n\n\t}",
"public static void doExercise1() {\n // TODO: Complete Exercise 1 Below\n\n }",
"public static void displaySubTitles()\r\n {\n }",
"public static void doExer... | [
"0.6270567",
"0.6148319",
"0.6082356",
"0.60158455",
"0.59423697",
"0.5866581",
"0.5858166",
"0.5824626",
"0.5821499",
"0.57685095",
"0.5713671",
"0.57085985",
"0.5703779",
"0.5677934",
"0.56326306",
"0.56241",
"0.5580282",
"0.5464723",
"0.5437662",
"0.54234195",
"0.54229647"... | 0.0 | -1 |
&9674;&9674;&9674; Perform reduce with a BinaryOperator &9674;&9674;&9674; Integer sum = Stream.of(1, 2, 3, 4, 5).reduce(0, Integer::sum); Integer minValue = Stream.of(5, 4, 9, 2, 1).reduce(Integer.MIN_VALUE, Integer::max); String concatenation = Stream.of("str ", "= ", "alt ", "string") the first parameter becomes the target of the concat method and the second one is the argument to concat the target, the parameter and the result are of the same type and this can be considered a binary operator for the reduce method .reduce("", String::concat); | protected static void performReduceWithABinaryOperator() {
Integer sum = Stream.of(1, 2, 3, 4, 5).reduce(0, Integer::sum);
Integer minValue = Stream.of(5, 4, 9, 2, 1).reduce(Integer.MIN_VALUE, Integer::max);
String concatenation = Stream.of("str ", "= ", "alt ", "string")
// the first parameter becomes the target of the concat method and the second one is the argument to concat
// the target, the parameter and the result are of the same type and this can be considered a binary
// operator for the reduce method
.reduce("", String::concat);
System.out.println(concatenation);
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public static void main(String[] args){\n int result = Stream.of(1,2,3,4,5,6,7,8,9,10)\n .reduce(0,Integer::sum);//metodo referenciado\n// .reduce(0, (acumulador, elemento) -> acumulador+elemento);\n System.out.println(result);\n\n // Obtener lenguajes separados p... | [
"0.6804598",
"0.6361666",
"0.6318965",
"0.629476",
"0.6183886",
"0.61270314",
"0.601953",
"0.5833654",
"0.5789548",
"0.5765127",
"0.5702013",
"0.5680815",
"0.56807727",
"0.56799304",
"0.56371665",
"0.56291014",
"0.5623535",
"0.55686975",
"0.5566753",
"0.55563873",
"0.55563873... | 0.86688364 | 0 |
&9674;&9674;&9674; Using a Collector &9674;&9674;&9674; String string = Stream.of("this", "is", "a", "list") .collect(() &62; new StringBuilder(), // result Supplier (sb, str) &62; sb.append(str), // add a single value to the result (sb1, sb2) &62; sb1.append(sb2)) // combine two results .toString(); Using method reference string = Stream.of("this", "is", "a", "list") .collect(StringBuilder::new, // result Supplier StringBuilder::append, // add a single value to the result StringBuilder::append) // combine two results .toString(); Using joining method string = Stream.of("this", "is", "a", "list").collect(Collectors.joining()); | protected static void usingACollector() {
String string = Stream.of("this", "is", "a", "list")
.collect(() -> new StringBuilder(), // result Supplier
(sb, str) -> sb.append(str), // add a single value to the result
(sb1, sb2) -> sb1.append(sb2)) // combine two results
.toString();
// Using method reference
string = Stream.of("this", "is", "a", "list")
.collect(StringBuilder::new, // result Supplier
StringBuilder::append, // add a single value to the result
StringBuilder::append) // combine two results
.toString();
// Using joining method
string = Stream.of("this", "is", "a", "list").collect(Collectors.joining());
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Test\n void testCollect() {\n List<Integer> numbers = Stream.of(1, 2, 3, 4)\n .collect(Collectors.toList());\n assertEquals(List.of(1, 2, 3, 4), numbers);\n\n // collect to a Set\n numbers = List.of(1, 1, 2, 2);\n Set<Integer> unique = numbers.stream()\n ... | [
"0.661547",
"0.5992544",
"0.58088976",
"0.56335676",
"0.5590958",
"0.5575294",
"0.5502463",
"0.54817724",
"0.54658216",
"0.52960473",
"0.528896",
"0.5288502",
"0.52402323",
"0.5214799",
"0.5193282",
"0.5176596",
"0.51547414",
"0.51262873",
"0.5105088",
"0.5083788",
"0.5078233... | 0.8403388 | 0 |
map method that performs framing the initial key value pairs | public void map(LongWritable key, Text value, OutputCollector<Text, Text> output, Reporter reporter) throws IOException
{
// get filename to send it as key for sorting.
FileSplit fileSplit = (FileSplit)reporter.getInputSplit();
String k = fileSplit.getPath().getName();
//taking one line at a time
String line = value.toString();
// get the position of the meaningful character
int pos = lineno % 40;
// get the character from the string
String character = Character.toString(line.charAt(pos));
// convert pipe symbol to next line
if(character.charAt(0) == '|')
character = "\n";
// sending to output collector which in turn passes the same to reducer
output.collect(new Text(k), new Text(character));
lineno++;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"private void mapValues() {\n\t\tmap.put(1, \"I\");\r\n\t\tmap.put(5, \"V\");\r\n\t\tmap.put(10, \"X\");\r\n\t\tmap.put(50, \"L\");\r\n\t\tmap.put(100, \"C\");\r\n\t\tmap.put(500, \"D\");\r\n\t\tmap.put(1000, \"M\");\r\n\t}",
"private void mapSetUp() {\n\t\tfor (int i = 0; i < allChar.length; i++) {\n\t\t\tmap.p... | [
"0.62421185",
"0.62368387",
"0.6085258",
"0.6016183",
"0.58868283",
"0.58526075",
"0.58426756",
"0.5801066",
"0.57975245",
"0.5777039",
"0.5687637",
"0.56268007",
"0.55681163",
"0.5560662",
"0.55564296",
"0.55561155",
"0.5532598",
"0.5489588",
"0.54504323",
"0.54378396",
"0.5... | 0.0 | -1 |
get employee by id | @Override
@Transactional
public Employee getEmployeeByID(int employeeID) {
Optional<Employee> empData = employeeRepository.findById(employeeID);
return empData.get();
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\r\n\tpublic Employee getEmployee(int id) {\n\t\treturn employees.stream().filter(emp -> emp.getEmpId()==(id)).findFirst().get();\r\n\t}",
"public Employee findEmployee(Long id);",
"public Employee getEmployeeByID(int id) {\n\t\t\r\n\t\ttry {\r\n\t\t\tEmployee f = temp.queryForObject(\"Select * from ... | [
"0.86086214",
"0.85512394",
"0.8549764",
"0.84169763",
"0.83048487",
"0.83011305",
"0.82647115",
"0.8263107",
"0.8204168",
"0.81955457",
"0.81941897",
"0.8164265",
"0.81237817",
"0.81236064",
"0.8116296",
"0.8113932",
"0.8107287",
"0.809597",
"0.80562675",
"0.8052791",
"0.804... | 0.7197161 | 98 |
update employee by id | @Override
@Transactional
public void updateEmp(int employeeID, Employee employee) {
Optional<Employee> empData = employeeRepository.findById(employeeID);
if(empData.isPresent()) {
Employee emp = empData.get();
emp.setFirstName(employee.getFirstName());
emp.setLastName(employee.getLastName());
emp.setEmail(employee.getEmail());
emp.setPhone(employee.getPhone());
employeeRepository.save(emp);
}
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\r\n\tpublic void updateEmployee(long employeeId, Employee updateEmployee) {\n\t\t\r\n\t}",
"public abstract void updateEmployee(int id, Employee emp) throws DatabaseExeption;",
"@PutMapping(\"/updateEmployee/{id}\")\n\tpublic ResponseEntity<Employee> updateEmployee(@PathVariable Long id, @RequestBody... | [
"0.80955666",
"0.80815214",
"0.796134",
"0.79336005",
"0.79218996",
"0.7919036",
"0.784482",
"0.7842039",
"0.7773386",
"0.77396435",
"0.7729171",
"0.77229476",
"0.7681702",
"0.76616937",
"0.762941",
"0.75956357",
"0.75750667",
"0.75279206",
"0.7524372",
"0.7510149",
"0.750220... | 0.7289456 | 28 |
delete employee by id | @Override
public void deleteEmpByID(int employeeID) {
employeeRepository.deleteById(employeeID);
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\n\tpublic void deleteEmployeeById(int id) {\n\t\t\n\t}",
"public void deleteEmployee(Long id) {\n employeeRepository.deleteById(id);\n }",
"@Override\r\n\tpublic void deleteEmployee(int id) {\n\t\ttry {\r\n\t DirectlyDatabase.update(PropertyManager.getProperty(\"db_employee_delete\")... | [
"0.8837166",
"0.8720212",
"0.8622953",
"0.8616821",
"0.8494361",
"0.8474979",
"0.84199214",
"0.8366706",
"0.83481956",
"0.8315401",
"0.8306215",
"0.8273694",
"0.8258912",
"0.82516634",
"0.8250484",
"0.8231417",
"0.81776434",
"0.81551236",
"0.8153424",
"0.81365126",
"0.8068093... | 0.7433418 | 73 |
TODO Autogenerated method stub read in files from DIRECTORY | public static void main(String[] args) {
File txtFiles = new File(DIRECTORY);
TextReader reader = new TextReader();
// read words from each file
for(File f : txtFiles.listFiles()) {
System.out.println("Reading from: " + f.getName());
try {
Scanner s = new Scanner(f);
reader.readWords(s);
s.close();
}
catch(FileNotFoundException e) {
System.out.println("Cannot find file named: " + f.getName());
}
}
// sort words
System.out.println("\n\n\nSorting words\n\n\n");
reader.sortByCount();
//Find 20 most used
System.out.println("Top "+TOPCOUNT+" Words by Count");
for(int i = 0; i < TOPCOUNT; i++) {
System.out.println((i+1) + " : \t" + reader.words.get(i).word + "\t\t" + reader.words.get(i).count);
}
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"private void getDirectoryContents() {\n\t File directory = Utilities.prepareDirectory(\"Filtering\");\n\t if(directory.exists()) {\n\t FilenameFilter filter = new FilenameFilter() {\n\t public boolean accept(File dir, String filename) {\n\t return filename.contains(\".pcm\") ... | [
"0.6341431",
"0.60737014",
"0.6072154",
"0.592309",
"0.58828056",
"0.5814533",
"0.5807407",
"0.5806722",
"0.5804307",
"0.58017695",
"0.57906914",
"0.5788179",
"0.577763",
"0.57751393",
"0.57717395",
"0.5720293",
"0.57141995",
"0.5710712",
"0.56606305",
"0.5648825",
"0.5648303... | 0.0 | -1 |
TODO Autogenerated method stub | @Override
protected void onCreate(Bundle savedInstanceState) {
super.onCreate(savedInstanceState);
GLSurfaceView cubeGL = new GLSurfaceView(this);
requestWindowFeature(Window.FEATURE_CUSTOM_TITLE);
render = new OpenGL3DRenderer(this);
cubeGL.setZOrderOnTop(true);
cubeGL.setEGLConfigChooser(8, 8, 8, 8, 16, 0);
cubeGL.getHolder().setFormat(PixelFormat.TRANSLUCENT);
cubeGL.setBackgroundDrawable(getResources().getDrawable(R.drawable.snowflower));
cubeGL.setRenderer(render);
setContentView(cubeGL);
getWindow().setFeatureInt(Window.FEATURE_CUSTOM_TITLE , R.layout.inc_app_title);
Toast.makeText(OpenGLActivity.this, "zhe", Toast.LENGTH_LONG).show();
LoadingAllVideos();
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"@Override\r\n\tpublic void comer() \r\n\t{\n\t\t\r\n\t}",
"@Override\n\tpublic void comer() {\n\t\t\n\t}",
"@Override\n public void perish() {\n \n }",
"@Override\r\n\t\t\tpublic void annadir() {\n\r\n\t\t\t}",
"@Override\n\tpublic void anular() {\n\n\t}",
"@Override\n\tprotected void getExr... | [
"0.66713095",
"0.6567948",
"0.652319",
"0.648097",
"0.64770466",
"0.64586824",
"0.64132667",
"0.6376419",
"0.62759",
"0.62545097",
"0.62371093",
"0.62237984",
"0.6201738",
"0.619477",
"0.619477",
"0.61924416",
"0.61872935",
"0.6173417",
"0.613289",
"0.6127952",
"0.6080854",
... | 0.0 | -1 |
if beginning character is before ending character for example beginning A ending D >>ABCD if beginning character is after ending character for example beginning D, ending A>>DCBA | public static void printAlphabetInRange(char beginning, char ending ){
if(beginning<ending){
System.out.println("we need to increment from " + beginning+" till "+ending);
for (char i = beginning; i <=ending ; i++) {
System.out.print(i+" ");
}
System.out.println();
}else if (beginning>ending){
System.out.println("we need to decrement from " + beginning+" till "+ending);
for (char i = beginning; i >=ending ; i--) {
System.out.print(i+" ");
}
System.out.println();
}else{
System.out.println("They are same character");
}
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public abstract boolean isStarterChar(char c);",
"public boolean mixStart(String str) {\n if (str.length() < 3) return false;\n return (str.substring(1,3).equals(\"ix\"));\n}",
"public String startOz(String str) {\n String result = \"\";\n \n if (str.length() >= 1 && str.charAt(0)=='o') {\n result = re... | [
"0.61711496",
"0.5852385",
"0.5822357",
"0.58060604",
"0.5732902",
"0.5712352",
"0.56610763",
"0.56505096",
"0.5614374",
"0.56021833",
"0.55982894",
"0.5551565",
"0.55331266",
"0.5518255",
"0.5517471",
"0.5463878",
"0.5461288",
"0.546012",
"0.5427803",
"0.5389526",
"0.5385263... | 0.5520232 | 13 |
printAtoZ create a method that has no parameter and print AZ in one line | public static void printAtoZ(){
for (char i = 'A'; i <= 'Z'; i++) {
System.out.print(i + " ");
}
System.out.println();
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public String print();",
"public void print(){\n System.out.println(\"(\"+a.getAbsis()+\"_a,\"+a.getOrdinat()+\"_a)\");\n System.out.println(\"(\"+b.getAbsis()+\"_b,\"+b.getOrdinat()+\"_b)\");\n System.out.println(\"(\"+c.getAbsis()+\"_b,\"+c.getOrdinat()+\"_c)\");\n }",
"public static ... | [
"0.59672874",
"0.59554493",
"0.5746995",
"0.5736258",
"0.5667017",
"0.5648505",
"0.5608034",
"0.55979025",
"0.55966073",
"0.5577973",
"0.5577973",
"0.5577973",
"0.5577973",
"0.5575206",
"0.556547",
"0.5564069",
"0.5549883",
"0.55432975",
"0.55323935",
"0.54847956",
"0.5480065... | 0.6749977 | 0 |
Remove a bunch of mr files from a directory. Will print a line mentioning the delete for each entry. Assumes standard naming scheme for entries as usual. | public static boolean removeMRFiles( String dir, ArrayList entries_todelete ) {
for (Iterator i=entries_todelete.iterator(); i.hasNext();) {
String entry_code = (String) i.next();
String fname = dir + File.separator + entry_code + ".mr";
File f = new File(fname);
if ( ! f.delete() ) {
General.showError("in MRAnnotate.removeMRFiles found:");
General.showError("Deleting the annotated MR file ["+fname+"]");
return false;
} else {
General.showOutput("Deleted the annotated MR file for entry: ["+entry_code+"]");
}
}
return true;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public static boolean removeMRFilesInteractively( String dir, ArrayList entries_todelete ) {\n \n// String reply = \"bogus\";\n boolean status;\n \n General.showOutput(\"Entries to delete: [\" + entries_todelete.size() + \"]\");\n General.showOutput(\"Entries to... | [
"0.6904569",
"0.6298582",
"0.61524844",
"0.6036331",
"0.58612734",
"0.58301485",
"0.55347544",
"0.5473984",
"0.54402566",
"0.5438012",
"0.5419862",
"0.54151565",
"0.5379606",
"0.53553206",
"0.53075516",
"0.5292611",
"0.52825284",
"0.52797264",
"0.52605766",
"0.52464396",
"0.5... | 0.72239256 | 0 |
Remove a bunch of mr files from the database. Will print a line mentioning the delete for each entry. Assumes standard naming scheme for entries as usual meaning that the mrfiles should have the detail value set to: FILE_DETAIL_CLASSIFIED | public static boolean removeMRFilesFromDB( ArrayList entries_todelete ) {
boolean status = sql_epiII.deleteMRFilesByPDBIdsByDetail(
entries_todelete, SQL_Episode_II.FILE_DETAIL_CLASSIFIED );
if ( ! status ) {
General.showError("in MRAnnotate.removeMRFilesFromDB found:");
General.showError("Deleting the annotated MR files:" + entries_todelete);
return false;
} else {
General.showOutput("Deleted the annotated MR files:" + entries_todelete);
}
return true;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public static boolean removeMRFilesInteractivelyFromDB( ArrayList entries_todelete ) {\n \n// String reply = \"bogus\";\n boolean status;\n \n General.showOutput(\"Entries to delete: [\" + entries_todelete.size() + \"]\");\n General.showOutput(\"Entries to delet... | [
"0.6837551",
"0.6678123",
"0.6480665",
"0.63786113",
"0.59105545",
"0.588921",
"0.58596396",
"0.57717115",
"0.57018614",
"0.5667201",
"0.5655033",
"0.5568618",
"0.55619884",
"0.5533611",
"0.552242",
"0.5503438",
"0.5497736",
"0.549146",
"0.54884857",
"0.5473593",
"0.543588",
... | 0.67580724 | 1 |
Uses removeMRFiles but will first list the files to be deleted and will then ask for conformation. | public static boolean removeMRFilesInteractively( String dir, ArrayList entries_todelete ) {
// String reply = "bogus";
boolean status;
General.showOutput("Entries to delete: [" + entries_todelete.size() + "]");
General.showOutput("Entries to delete: " + entries_todelete.toString() );
General.showWarning("answering yes to the following question will lead to");
General.showWarning("deleting work that might not be recovered!");
String prompt = "Delete ALL the MR files for the above entries from the directory:"+dir+"?";
if ( Strings.getInputBoolean( in, prompt ) ) {
General.showOutput("Deleting the annotated MR files listed above.");
status = removeMRFiles( dir, entries_todelete );
if ( ! status ) {
General.showError("in MRAnnotate.removeMRFilesInteractively found:");
General.showError("Deleting the annotated MR files failed.");
return false;
}
}
return true;
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public static boolean removeMRFilesInteractivelyFromDB( ArrayList entries_todelete ) {\n \n// String reply = \"bogus\";\n boolean status;\n \n General.showOutput(\"Entries to delete: [\" + entries_todelete.size() + \"]\");\n General.showOutput(\"Entries to delet... | [
"0.6377288",
"0.63531566",
"0.6049497",
"0.597395",
"0.5945102",
"0.5919864",
"0.59126216",
"0.5748056",
"0.571043",
"0.57100207",
"0.56559867",
"0.56547457",
"0.56454474",
"0.5640663",
"0.5629563",
"0.56154644",
"0.5615269",
"0.561321",
"0.5607183",
"0.5605126",
"0.55934715"... | 0.6539396 | 0 |
Will look for all mrfiles in the database that have the standard details: mrfile.details = SQL_Episode_II.FILE_DETAIL_CLASSIFIED | public static ArrayList getEntriesFromClassifiedMRFilesNewerThanDays( int max_days ) {
ArrayList entries = sql_epiII.getPDBIdFromMRFileByDetailNewerThanDays(
SQL_Episode_II.FILE_DETAIL_CLASSIFIED, max_days );
if (entries == null) {
General.showError("getting entry codes from the db.");
return (entries);
}
Collections.sort(entries);
return (entries);
} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"public static ArrayList getEntriesFromClassifiedMRFiles() {\n \n ArrayList entries = sql_epiII.getPDBIdFromMRFileByDetail( SQL_Episode_II.FILE_DETAIL_CLASSIFIED );\n \n if (entries == null) {\n General.showError(\"getting entry codes from the db.\");\n return (entr... | [
"0.586193",
"0.5650874",
"0.5439893",
"0.52184105",
"0.51727515",
"0.50775486",
"0.50757295",
"0.5037671",
"0.49760124",
"0.49760124",
"0.49604475",
"0.48777038",
"0.4877627",
"0.48600304",
"0.48305312",
"0.48153985",
"0.47890744",
"0.47831324",
"0.4780414",
"0.4745086",
"0.4... | 0.46474296 | 34 |
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