repo stringlengths 7 58 | path stringlengths 12 218 | func_name stringlengths 3 140 | original_string stringlengths 73 34.1k | language stringclasses 1
value | code stringlengths 73 34.1k | code_tokens list | docstring stringlengths 3 16k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 105 339 | partition stringclasses 1
value |
|---|---|---|---|---|---|---|---|---|---|---|---|
BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/model/TableCandidate.java | TableCandidate.setHighLevelMeta | public void setHighLevelMeta(int i) {
String meta = "<Table>\n";
meta = meta + "<pageNumInDoc>" + (i + 1) + "</pageNumInDoc>\n";
m_caption = replaceAllSpecialChracters(m_caption);
meta = meta + "<TableCaption>" + m_caption + "</TableCaption>\n";
String location = "";
if (m_topCaptionLocation)
location = "top";
else
location = "below";
location = replaceAllSpecialChracters(location);
meta = meta + "<CaptionLocation>" + location + "</CaptionLocation>\n";
m_metadata_HighLevel = replaceAllSpecialChracters(m_metadata_HighLevel);
meta = meta + "<dataHighLevel>" + m_metadata_HighLevel
+ "</dataHighLevel>\n";
this.setMetadataHighLevel(meta);
} | java | public void setHighLevelMeta(int i) {
String meta = "<Table>\n";
meta = meta + "<pageNumInDoc>" + (i + 1) + "</pageNumInDoc>\n";
m_caption = replaceAllSpecialChracters(m_caption);
meta = meta + "<TableCaption>" + m_caption + "</TableCaption>\n";
String location = "";
if (m_topCaptionLocation)
location = "top";
else
location = "below";
location = replaceAllSpecialChracters(location);
meta = meta + "<CaptionLocation>" + location + "</CaptionLocation>\n";
m_metadata_HighLevel = replaceAllSpecialChracters(m_metadata_HighLevel);
meta = meta + "<dataHighLevel>" + m_metadata_HighLevel
+ "</dataHighLevel>\n";
this.setMetadataHighLevel(meta);
} | [
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@param i
the total number of pages of the document | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/model/TableCandidate.java#L446-L462 | train |
BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/model/TableCandidate.java | TableCandidate.setEmptyMetadataStructureLevel | public void setEmptyMetadataStructureLevel(int YNum, int cc,
List<TextPiece> wordsOfAPage, DocInfo m_docInfo) {
String meta = "";
meta = "<TableColumnHeading>\n" + "</TableColumnHeading>"
+ "\n";
meta = meta + "<TableContent>\n";
meta = meta + "</TableContent>" + "\n";
meta = meta + "<TableRowHeading>"
+ "</TableRowHeading>" + "\n";
meta = meta + "<TableFootnote>";
meta = meta + "... </TableFootnote>" + "\n";
meta = meta + "<ColumnNum>" + "</ColumnNum>"
+ "\n";
meta = meta + "<RowNum>" + "</RowNum>" + "\n";
meta = meta + "<ColumnCoordinates>"
+ "</ColumnCoordinates>" + "\n";
meta = meta + "<TableHeight>"
+ "</TableHeight>" + "\n";
meta = meta + "<TableWidth>"
+ "</TableWidth>" + "\n";
meta = meta + "<isWideTable>" + m_WideTable
+ "</isWideTable>\n";
m_referenceText = replaceAllSpecialChracters(m_referenceText);
meta = meta + "<TableReferenceText>"
+ m_referenceText + "</TableReferenceText>" + "\n";
meta = meta + "</Table>" + "\n";
setMetadataStructureLevel(meta);
int tableNum = m_docInfo.getTableNum();
} | java | public void setEmptyMetadataStructureLevel(int YNum, int cc,
List<TextPiece> wordsOfAPage, DocInfo m_docInfo) {
String meta = "";
meta = "<TableColumnHeading>\n" + "</TableColumnHeading>"
+ "\n";
meta = meta + "<TableContent>\n";
meta = meta + "</TableContent>" + "\n";
meta = meta + "<TableRowHeading>"
+ "</TableRowHeading>" + "\n";
meta = meta + "<TableFootnote>";
meta = meta + "... </TableFootnote>" + "\n";
meta = meta + "<ColumnNum>" + "</ColumnNum>"
+ "\n";
meta = meta + "<RowNum>" + "</RowNum>" + "\n";
meta = meta + "<ColumnCoordinates>"
+ "</ColumnCoordinates>" + "\n";
meta = meta + "<TableHeight>"
+ "</TableHeight>" + "\n";
meta = meta + "<TableWidth>"
+ "</TableWidth>" + "\n";
meta = meta + "<isWideTable>" + m_WideTable
+ "</isWideTable>\n";
m_referenceText = replaceAllSpecialChracters(m_referenceText);
meta = meta + "<TableReferenceText>"
+ m_referenceText + "</TableReferenceText>" + "\n";
meta = meta + "</Table>" + "\n";
setMetadataStructureLevel(meta);
int tableNum = m_docInfo.getTableNum();
} | [
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... | Sets an empty metadata file
@param YNum
the total number of table lines including footnote
@param cc
the total number of table columns
@param wordsOfAPage
the list of words in a document page
@param m_docInfo
an object of DocInfo | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/model/TableCandidate.java#L612-L646 | train |
BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/model/TableCandidate.java | TableCandidate.replaceAllSpecialChracters | public static String replaceAllSpecialChracters(String toBeReplaced) {
toBeReplaced = toBeReplaced.replaceAll("&", "&");
toBeReplaced = toBeReplaced.replaceAll("<", "<");
toBeReplaced = toBeReplaced.replaceAll(">", ">");
toBeReplaced = toBeReplaced.replaceAll("\"", """);
toBeReplaced = toBeReplaced.replaceAll("'", "'");
// toBeReplaced = toBeReplaced.replace("^", "&circ");
// toBeReplaced = toBeReplaced.replaceAll("0xb", "");
int len = toBeReplaced.length();
char[] temp = toBeReplaced.toCharArray();
for (int i = 0; i < len; i++) {
char xCode = temp[i];
if ((xCode > '\u0000' && xCode <= '\u0020') || (xCode == '\u0026')
|| (xCode == '\u0022') || (xCode == '\u02C6')
|| (xCode == '\u201C') || (xCode == '\u201D')
|| (xCode == '\u201E')) {
String sub1 = toBeReplaced.substring(0, i);
String sub2 = toBeReplaced.substring(i + 1, len);
String replacement = "";
if ((xCode > '\u0000' && xCode <= '\u0020'))
replacement = " ";
if (xCode == '\u0026')
replacement = " ";
if (xCode == '\u0022')
replacement = " ";
if (xCode == '\u02C6')
replacement = " ";
if (xCode == '\u201C')
replacement = " ";
if (xCode == '\u201D')
replacement = " ";
if (xCode == '\u201E')
replacement = " ";
toBeReplaced = sub1 + replacement + sub2;
}
len = toBeReplaced.length();
temp = toBeReplaced.toCharArray();
}
return (toBeReplaced);
} | java | public static String replaceAllSpecialChracters(String toBeReplaced) {
toBeReplaced = toBeReplaced.replaceAll("&", "&");
toBeReplaced = toBeReplaced.replaceAll("<", "<");
toBeReplaced = toBeReplaced.replaceAll(">", ">");
toBeReplaced = toBeReplaced.replaceAll("\"", """);
toBeReplaced = toBeReplaced.replaceAll("'", "'");
// toBeReplaced = toBeReplaced.replace("^", "&circ");
// toBeReplaced = toBeReplaced.replaceAll("0xb", "");
int len = toBeReplaced.length();
char[] temp = toBeReplaced.toCharArray();
for (int i = 0; i < len; i++) {
char xCode = temp[i];
if ((xCode > '\u0000' && xCode <= '\u0020') || (xCode == '\u0026')
|| (xCode == '\u0022') || (xCode == '\u02C6')
|| (xCode == '\u201C') || (xCode == '\u201D')
|| (xCode == '\u201E')) {
String sub1 = toBeReplaced.substring(0, i);
String sub2 = toBeReplaced.substring(i + 1, len);
String replacement = "";
if ((xCode > '\u0000' && xCode <= '\u0020'))
replacement = " ";
if (xCode == '\u0026')
replacement = " ";
if (xCode == '\u0022')
replacement = " ";
if (xCode == '\u02C6')
replacement = " ";
if (xCode == '\u201C')
replacement = " ";
if (xCode == '\u201D')
replacement = " ";
if (xCode == '\u201E')
replacement = " ";
toBeReplaced = sub1 + replacement + sub2;
}
len = toBeReplaced.length();
temp = toBeReplaced.toCharArray();
}
return (toBeReplaced);
} | [
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@param toBeReplaced
The string to be replaced
@return the string after the replace | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/model/TableCandidate.java#L680-L722 | train |
BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/parser/Parse.java | Parse.addPreviousPunctuation | public void addPreviousPunctuation(Parse punct) {
if (this.prevPunctSet == null) {
this.prevPunctSet = new LinkedHashSet();
}
prevPunctSet.add(punct);
} | java | public void addPreviousPunctuation(Parse punct) {
if (this.prevPunctSet == null) {
this.prevPunctSet = new LinkedHashSet();
}
prevPunctSet.add(punct);
} | [
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@param punct The punctuation. | [
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BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/parser/Parse.java | Parse.addNextPunctuation | public void addNextPunctuation(Parse punct) {
if (this.nextPunctSet == null) {
this.nextPunctSet = new LinkedHashSet();
}
nextPunctSet.add(punct);
} | java | public void addNextPunctuation(Parse punct) {
if (this.nextPunctSet == null) {
this.nextPunctSet = new LinkedHashSet();
}
nextPunctSet.add(punct);
} | [
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@param punct The punctuation set. | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/parser/Parse.java#L148-L153 | train |
BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/parser/Parse.java | Parse.insert | public void insert(final Parse constituent) {
Span ic = constituent.span;
if (span.contains(ic)) {
//double oprob=c.prob;
int pi=0;
int pn = parts.size();
for (; pi < pn; pi++) {
Parse subPart = (Parse) parts.get(pi);
//System.err.println("Parse.insert:con="+constituent+" sp["+pi+"] "+subPart+" "+subPart.getType());
Span sp = subPart.span;
if (sp.getStart() >= ic.getEnd()) {
break;
}
// constituent contains subPart
else if (ic.contains(sp)) {
//System.err.println("Parse.insert:con contains subPart");
parts.remove(pi);
pi--;
constituent.parts.add(subPart);
subPart.setParent(constituent);
//System.err.println("Parse.insert: "+subPart.hashCode()+" -> "+subPart.getParent().hashCode());
pn = parts.size();
}
else if (sp.contains(ic)) {
//System.err.println("Parse.insert:subPart contains con");
subPart.insert(constituent);
return;
}
}
//System.err.println("Parse.insert:adding con="+constituent+" to "+this);
parts.add(pi, constituent);
constituent.setParent(this);
//System.err.println("Parse.insert: "+constituent.hashCode()+" -> "+constituent.getParent().hashCode());
}
else {
throw (new InternalError("Inserting constituent not contained in the sentence!"));
}
} | java | public void insert(final Parse constituent) {
Span ic = constituent.span;
if (span.contains(ic)) {
//double oprob=c.prob;
int pi=0;
int pn = parts.size();
for (; pi < pn; pi++) {
Parse subPart = (Parse) parts.get(pi);
//System.err.println("Parse.insert:con="+constituent+" sp["+pi+"] "+subPart+" "+subPart.getType());
Span sp = subPart.span;
if (sp.getStart() >= ic.getEnd()) {
break;
}
// constituent contains subPart
else if (ic.contains(sp)) {
//System.err.println("Parse.insert:con contains subPart");
parts.remove(pi);
pi--;
constituent.parts.add(subPart);
subPart.setParent(constituent);
//System.err.println("Parse.insert: "+subPart.hashCode()+" -> "+subPart.getParent().hashCode());
pn = parts.size();
}
else if (sp.contains(ic)) {
//System.err.println("Parse.insert:subPart contains con");
subPart.insert(constituent);
return;
}
}
//System.err.println("Parse.insert:adding con="+constituent+" to "+this);
parts.add(pi, constituent);
constituent.setParent(this);
//System.err.println("Parse.insert: "+constituent.hashCode()+" -> "+constituent.getParent().hashCode());
}
else {
throw (new InternalError("Inserting constituent not contained in the sentence!"));
}
} | [
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@param constituent The constituent to be inserted. | [
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BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/parser/Parse.java | Parse.getTagSequenceProb | public double getTagSequenceProb() {
//System.err.println("Parse.getTagSequenceProb: "+type+" "+this);
if (parts.size() == 1 && ((Parse) parts.get(0)).type.equals(ParserME.TOK_NODE)) {
//System.err.println(this+" "+prob);
return (Math.log(prob));
}
else if (parts.size() == 0) {
System.err.println("Parse.getTagSequenceProb: Wrong base case!");
return (0.0);
}
else {
double sum = 0.0;
for (Iterator pi = parts.iterator(); pi.hasNext();) {
sum += ((Parse) pi.next()).getTagSequenceProb();
}
return (sum);
}
} | java | public double getTagSequenceProb() {
//System.err.println("Parse.getTagSequenceProb: "+type+" "+this);
if (parts.size() == 1 && ((Parse) parts.get(0)).type.equals(ParserME.TOK_NODE)) {
//System.err.println(this+" "+prob);
return (Math.log(prob));
}
else if (parts.size() == 0) {
System.err.println("Parse.getTagSequenceProb: Wrong base case!");
return (0.0);
}
else {
double sum = 0.0;
for (Iterator pi = parts.iterator(); pi.hasNext();) {
sum += ((Parse) pi.next()).getTagSequenceProb();
}
return (sum);
}
} | [
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@return The probability associed with the pos-tag sequence assigned to this parse. | [
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BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/parser/Parse.java | Parse.updateHeads | public void updateHeads(HeadRules rules) {
if (parts != null && parts.size() != 0) {
for (int pi=0,pn=parts.size();pi<pn;pi++) {
Parse c = (Parse) parts.get(pi);
c.updateHeads(rules);
}
this.head = rules.getHead((Parse[]) parts.toArray(new Parse[parts.size()]), type);
if (head == null) {
head = this;
}
}
else {
this.head = this;
}
} | java | public void updateHeads(HeadRules rules) {
if (parts != null && parts.size() != 0) {
for (int pi=0,pn=parts.size();pi<pn;pi++) {
Parse c = (Parse) parts.get(pi);
c.updateHeads(rules);
}
this.head = rules.getHead((Parse[]) parts.toArray(new Parse[parts.size()]), type);
if (head == null) {
head = this;
}
}
else {
this.head = this;
}
} | [
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@param rules The head rules which determine how the head of the parse is computed. | [
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BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/parser/Parse.java | Parse.isPosTag | public boolean isPosTag() {
return (parts.size() == 1 && ((Parse) parts.get(0)).getType().equals(ParserME.TOK_NODE));
} | java | public boolean isPosTag() {
return (parts.size() == 1 && ((Parse) parts.get(0)).getType().equals(ParserME.TOK_NODE));
} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/parser/Parse.java#L523-L525 | train |
BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/parser/Parse.java | Parse.getCommonParent | public Parse getCommonParent(Parse node) {
if (this == node) {
return parent;
}
Set parents = new HashSet();
Parse cparent = this;
while(cparent != null) {
parents.add(cparent);
cparent = cparent.getParent();
}
while (node != null) {
if (parents.contains(node)) {
return node;
}
node = node.getParent();
}
return null;
} | java | public Parse getCommonParent(Parse node) {
if (this == node) {
return parent;
}
Set parents = new HashSet();
Parse cparent = this;
while(cparent != null) {
parents.add(cparent);
cparent = cparent.getParent();
}
while (node != null) {
if (parents.contains(node)) {
return node;
}
node = node.getParent();
}
return null;
} | [
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/Blocker.java | Blocker.countCorrectPairs | protected int countCorrectPairs(MatchData data)
{
// count the number of times each id appears in each source */
Map counter = new HashMap();
for (int i=0; i<data.numSources(); i++) {
String src = data.getSource(i);
for (int j=0; j<data.numInstances(src); j++){
String id = data.getInstance(src, j).getId();
if (id!=null) {
IdKey key = new IdKey(id,src);
Integer c = (Integer)counter.get(key);
counter.put( key, (c==null ? new Integer(1) : new Integer(c.intValue()+1)) );
}
}
}
/*
// show the counter
for (Iterator i=counter.keySet().iterator(); i.hasNext(); ) {
IdKey key = (IdKey) i.next();
System.out.println( key.src+"#"+key.id+" = "+counter.get(key) );
}
*/
// count the number of correct pairs
int numCorrectPairs = 0;
Set idsInSrc1 = new HashSet();
for (int i=0; i<data.numSources(); i++) {
String src1 = data.getSource(i);
idsInSrc1.clear();
for (int j=0; j<data.numInstances(src1);j++) {
String id = data.getInstance(src1, j).getId();
idsInSrc1.add(id);
for (int k=i+1; k<data.numSources(); k++) {
String src2 = data.getSource(k);
Integer cInteger = (Integer) counter.get( new IdKey(id,src2) );
if (cInteger!=null) {
numCorrectPairs += cInteger.intValue();
}
//System.out.println( "src1:"+src1+" id:"+id+" src2:"+src2+" c:"+cInteger);
}
}
if (clusterMode) {
// count how often something in src1 can be matched correctly with something
// else in src1
for (Iterator j=idsInSrc1.iterator(); j.hasNext(); ) {
String id = (String)j.next();
Integer cInteger = (Integer) counter.get( new IdKey(id,src1) );
int c = cInteger.intValue();
numCorrectPairs += c*(c-1)/2;
}
}
}
return numCorrectPairs;
} | java | protected int countCorrectPairs(MatchData data)
{
// count the number of times each id appears in each source */
Map counter = new HashMap();
for (int i=0; i<data.numSources(); i++) {
String src = data.getSource(i);
for (int j=0; j<data.numInstances(src); j++){
String id = data.getInstance(src, j).getId();
if (id!=null) {
IdKey key = new IdKey(id,src);
Integer c = (Integer)counter.get(key);
counter.put( key, (c==null ? new Integer(1) : new Integer(c.intValue()+1)) );
}
}
}
/*
// show the counter
for (Iterator i=counter.keySet().iterator(); i.hasNext(); ) {
IdKey key = (IdKey) i.next();
System.out.println( key.src+"#"+key.id+" = "+counter.get(key) );
}
*/
// count the number of correct pairs
int numCorrectPairs = 0;
Set idsInSrc1 = new HashSet();
for (int i=0; i<data.numSources(); i++) {
String src1 = data.getSource(i);
idsInSrc1.clear();
for (int j=0; j<data.numInstances(src1);j++) {
String id = data.getInstance(src1, j).getId();
idsInSrc1.add(id);
for (int k=i+1; k<data.numSources(); k++) {
String src2 = data.getSource(k);
Integer cInteger = (Integer) counter.get( new IdKey(id,src2) );
if (cInteger!=null) {
numCorrectPairs += cInteger.intValue();
}
//System.out.println( "src1:"+src1+" id:"+id+" src2:"+src2+" c:"+cInteger);
}
}
if (clusterMode) {
// count how often something in src1 can be matched correctly with something
// else in src1
for (Iterator j=idsInSrc1.iterator(); j.hasNext(); ) {
String id = (String)j.next();
Integer cInteger = (Integer) counter.get( new IdKey(id,src1) );
int c = cInteger.intValue();
numCorrectPairs += c*(c-1)/2;
}
}
}
return numCorrectPairs;
} | [
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BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/ngram/Dictionary.java | Dictionary.loadGrams | protected void loadGrams(DataInputStream input) throws IOException {
gramSet = new HashSet();
try {
while(true) {
int gramLength=input.readInt();
int[] words = new int[gramLength];
for (int wi=0;wi<gramLength;wi++) {
words[wi]=input.readInt();
}
gramSet.add(new NGram(words));
}
}
catch(EOFException e) {
}
} | java | protected void loadGrams(DataInputStream input) throws IOException {
gramSet = new HashSet();
try {
while(true) {
int gramLength=input.readInt();
int[] words = new int[gramLength];
for (int wi=0;wi<gramLength;wi++) {
words[wi]=input.readInt();
}
gramSet.add(new NGram(words));
}
}
catch(EOFException e) {
}
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BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/ngram/Dictionary.java | Dictionary.contains | public boolean contains(String[] words) {
if (words.length == 1) {
return wordMap.contains(words[0]);
}
else {
NGram ngram = nGramFactory.createNGram(words);
if (ngram == null) {
return false;
}
else {
return gramSet.contains(ngram);
}
}
} | java | public boolean contains(String[] words) {
if (words.length == 1) {
return wordMap.contains(words[0]);
}
else {
NGram ngram = nGramFactory.createNGram(words);
if (ngram == null) {
return false;
}
else {
return gramSet.contains(ngram);
}
}
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BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/ngram/Dictionary.java | Dictionary.main | public static void main(String[] args) throws IOException {
if (args.length == 0) {
System.err.println("Usage: Dictionary dictionary_file");
System.exit(0);
}
Dictionary dict = new Dictionary(args[0]);
BufferedReader in = new BufferedReader(new InputStreamReader(System.in));
String line;
while (null != (line = in.readLine())) {
String[] words = line.split(" ");
if (dict.contains(words)) {
System.out.println("Dictionary contains: "+line);
}
else {
System.out.println("Dictionary does not contain: "+line);
}
}
/*
for (Iterator di = dict.iterator();di.hasNext();) {
System.out.println(di.next());
}
*/
} | java | public static void main(String[] args) throws IOException {
if (args.length == 0) {
System.err.println("Usage: Dictionary dictionary_file");
System.exit(0);
}
Dictionary dict = new Dictionary(args[0]);
BufferedReader in = new BufferedReader(new InputStreamReader(System.in));
String line;
while (null != (line = in.readLine())) {
String[] words = line.split(" ");
if (dict.contains(words)) {
System.out.println("Dictionary contains: "+line);
}
else {
System.out.println("Dictionary does not contain: "+line);
}
}
/*
for (Iterator di = dict.iterator();di.hasNext();) {
System.out.println(di.next());
}
*/
} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Section.java | Section.getSectionHeading | public Title getSectionHeading() {
if (Section_Type.featOkTst && ((Section_Type)jcasType).casFeat_sectionHeading == null)
jcasType.jcas.throwFeatMissing("sectionHeading", "de.julielab.jules.types.Section");
return (Title)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((Section_Type)jcasType).casFeatCode_sectionHeading)));} | java | public Title getSectionHeading() {
if (Section_Type.featOkTst && ((Section_Type)jcasType).casFeat_sectionHeading == null)
jcasType.jcas.throwFeatMissing("sectionHeading", "de.julielab.jules.types.Section");
return (Title)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((Section_Type)jcasType).casFeatCode_sectionHeading)));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Section.java | Section.setSectionHeading | public void setSectionHeading(Title v) {
if (Section_Type.featOkTst && ((Section_Type)jcasType).casFeat_sectionHeading == null)
jcasType.jcas.throwFeatMissing("sectionHeading", "de.julielab.jules.types.Section");
jcasType.ll_cas.ll_setRefValue(addr, ((Section_Type)jcasType).casFeatCode_sectionHeading, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setSectionHeading(Title v) {
if (Section_Type.featOkTst && ((Section_Type)jcasType).casFeat_sectionHeading == null)
jcasType.jcas.throwFeatMissing("sectionHeading", "de.julielab.jules.types.Section");
jcasType.ll_cas.ll_setRefValue(addr, ((Section_Type)jcasType).casFeatCode_sectionHeading, jcasType.ll_cas.ll_getFSRef(v));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Section.java | Section.getSectionId | public String getSectionId() {
if (Section_Type.featOkTst && ((Section_Type)jcasType).casFeat_sectionId == null)
jcasType.jcas.throwFeatMissing("sectionId", "de.julielab.jules.types.Section");
return jcasType.ll_cas.ll_getStringValue(addr, ((Section_Type)jcasType).casFeatCode_sectionId);} | java | public String getSectionId() {
if (Section_Type.featOkTst && ((Section_Type)jcasType).casFeat_sectionId == null)
jcasType.jcas.throwFeatMissing("sectionId", "de.julielab.jules.types.Section");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Section.java | Section.setSectionId | public void setSectionId(String v) {
if (Section_Type.featOkTst && ((Section_Type)jcasType).casFeat_sectionId == null)
jcasType.jcas.throwFeatMissing("sectionId", "de.julielab.jules.types.Section");
jcasType.ll_cas.ll_setStringValue(addr, ((Section_Type)jcasType).casFeatCode_sectionId, v);} | java | public void setSectionId(String v) {
if (Section_Type.featOkTst && ((Section_Type)jcasType).casFeat_sectionId == null)
jcasType.jcas.throwFeatMissing("sectionId", "de.julielab.jules.types.Section");
jcasType.ll_cas.ll_setStringValue(addr, ((Section_Type)jcasType).casFeatCode_sectionId, v);} | [
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/JensenShannonDistance.java | JensenShannonDistance.train | final public void train(StringWrapperIterator i)
{
Set seenTokens = new HashSet();
while (i.hasNext()) {
StringWrapper s = (StringWrapper)i.next();
BagOfTokens bag = asBagOfTokens(i.nextStringWrapper());
for (Iterator j=bag.tokenIterator(); j.hasNext(); ) {
Token tokj = (Token)j.next();
totalTokens++;
// increment backgroundFrequency counts
Integer freq = (Integer)backgroundFrequency.get(tokj);
if (freq==null) backgroundFrequency.put(tokj,ONE);
else if (freq==ONE) backgroundFrequency.put(tokj,TWO);
else if (freq==TWO) backgroundFrequency.put(tokj,THREE);
else backgroundFrequency.put(tokj, new Integer(freq.intValue()+1));
}
}
} | java | final public void train(StringWrapperIterator i)
{
Set seenTokens = new HashSet();
while (i.hasNext()) {
StringWrapper s = (StringWrapper)i.next();
BagOfTokens bag = asBagOfTokens(i.nextStringWrapper());
for (Iterator j=bag.tokenIterator(); j.hasNext(); ) {
Token tokj = (Token)j.next();
totalTokens++;
// increment backgroundFrequency counts
Integer freq = (Integer)backgroundFrequency.get(tokj);
if (freq==null) backgroundFrequency.put(tokj,ONE);
else if (freq==ONE) backgroundFrequency.put(tokj,TWO);
else if (freq==TWO) backgroundFrequency.put(tokj,THREE);
else backgroundFrequency.put(tokj, new Integer(freq.intValue()+1));
}
}
} | [
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/JensenShannonDistance.java | JensenShannonDistance.prepare | final public StringWrapper prepare(String s) {
BagOfTokens bag = new BagOfTokens(s, tokenizer.tokenize(s));
double totalWeight = bag.getTotalWeight();
for (Iterator i=bag.tokenIterator(); i.hasNext(); ) {
Token tok = (Token)i.next();
double freq = bag.getWeight(tok);
bag.setWeight( tok, smoothedProbability(tok, freq, totalWeight) );
}
return bag;
} | java | final public StringWrapper prepare(String s) {
BagOfTokens bag = new BagOfTokens(s, tokenizer.tokenize(s));
double totalWeight = bag.getTotalWeight();
for (Iterator i=bag.tokenIterator(); i.hasNext(); ) {
Token tok = (Token)i.next();
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bag.setWeight( tok, smoothedProbability(tok, freq, totalWeight) );
}
return bag;
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/JensenShannonDistance.java | JensenShannonDistance.backgroundProb | protected double backgroundProb(Token tok)
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double freq = freqInteger==null ? 0 : freqInteger.intValue();
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/JensenShannonDistance.java | JensenShannonDistance.score | final public double score(StringWrapper s,StringWrapper t)
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return 0.5*sum/Math.log(2);
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double sum = 0;
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/MultiStringWrapper.java | MultiStringWrapper.prepare | public void prepare(StringDistance[] innerDistances) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/Timex2.java | Timex2.setVal | public void setVal(String v) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/Timex2.java | Timex2.setSet | public void setSet(String v) {
if (Timex2_Type.featOkTst && ((Timex2_Type)jcasType).casFeat_set == null)
jcasType.jcas.throwFeatMissing("set", "de.julielab.jules.types.ace.Timex2");
jcasType.ll_cas.ll_setStringValue(addr, ((Timex2_Type)jcasType).casFeatCode_set, v);} | java | public void setSet(String v) {
if (Timex2_Type.featOkTst && ((Timex2_Type)jcasType).casFeat_set == null)
jcasType.jcas.throwFeatMissing("set", "de.julielab.jules.types.ace.Timex2");
jcasType.ll_cas.ll_setStringValue(addr, ((Timex2_Type)jcasType).casFeatCode_set, v);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/Timex2.java | Timex2.getNon_specific | public String getNon_specific() {
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jcasType.jcas.throwFeatMissing("non_specific", "de.julielab.jules.types.ace.Timex2");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/Timex2.java | Timex2.setNon_specific | public void setNon_specific(String v) {
if (Timex2_Type.featOkTst && ((Timex2_Type)jcasType).casFeat_non_specific == null)
jcasType.jcas.throwFeatMissing("non_specific", "de.julielab.jules.types.ace.Timex2");
jcasType.ll_cas.ll_setStringValue(addr, ((Timex2_Type)jcasType).casFeatCode_non_specific, v);} | java | public void setNon_specific(String v) {
if (Timex2_Type.featOkTst && ((Timex2_Type)jcasType).casFeat_non_specific == null)
jcasType.jcas.throwFeatMissing("non_specific", "de.julielab.jules.types.ace.Timex2");
jcasType.ll_cas.ll_setStringValue(addr, ((Timex2_Type)jcasType).casFeatCode_non_specific, v);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/Timex2.java | Timex2.getAnchor_dir | public String getAnchor_dir() {
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jcasType.jcas.throwFeatMissing("anchor_dir", "de.julielab.jules.types.ace.Timex2");
return jcasType.ll_cas.ll_getStringValue(addr, ((Timex2_Type)jcasType).casFeatCode_anchor_dir);} | java | public String getAnchor_dir() {
if (Timex2_Type.featOkTst && ((Timex2_Type)jcasType).casFeat_anchor_dir == null)
jcasType.jcas.throwFeatMissing("anchor_dir", "de.julielab.jules.types.ace.Timex2");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/Timex2.java | Timex2.setAnchor_dir | public void setAnchor_dir(String v) {
if (Timex2_Type.featOkTst && ((Timex2_Type)jcasType).casFeat_anchor_dir == null)
jcasType.jcas.throwFeatMissing("anchor_dir", "de.julielab.jules.types.ace.Timex2");
jcasType.ll_cas.ll_setStringValue(addr, ((Timex2_Type)jcasType).casFeatCode_anchor_dir, v);} | java | public void setAnchor_dir(String v) {
if (Timex2_Type.featOkTst && ((Timex2_Type)jcasType).casFeat_anchor_dir == null)
jcasType.jcas.throwFeatMissing("anchor_dir", "de.julielab.jules.types.ace.Timex2");
jcasType.ll_cas.ll_setStringValue(addr, ((Timex2_Type)jcasType).casFeatCode_anchor_dir, v);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.getEvent_type | public String getEvent_type() {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_event_type == null)
jcasType.jcas.throwFeatMissing("event_type", "ch.epfl.bbp.uima.genia.Event");
return jcasType.ll_cas.ll_getStringValue(addr, ((Event_Type)jcasType).casFeatCode_event_type);} | java | public String getEvent_type() {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_event_type == null)
jcasType.jcas.throwFeatMissing("event_type", "ch.epfl.bbp.uima.genia.Event");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.setEvent_type | public void setEvent_type(String v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_event_type == null)
jcasType.jcas.throwFeatMissing("event_type", "ch.epfl.bbp.uima.genia.Event");
jcasType.ll_cas.ll_setStringValue(addr, ((Event_Type)jcasType).casFeatCode_event_type, v);} | java | public void setEvent_type(String v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_event_type == null)
jcasType.jcas.throwFeatMissing("event_type", "ch.epfl.bbp.uima.genia.Event");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.getThemes_protein | public FSArray getThemes_protein() {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_themes_protein == null)
jcasType.jcas.throwFeatMissing("themes_protein", "ch.epfl.bbp.uima.genia.Event");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_themes_protein)));} | java | public FSArray getThemes_protein() {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_themes_protein == null)
jcasType.jcas.throwFeatMissing("themes_protein", "ch.epfl.bbp.uima.genia.Event");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.setThemes_protein | public void setThemes_protein(FSArray v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_themes_protein == null)
jcasType.jcas.throwFeatMissing("themes_protein", "ch.epfl.bbp.uima.genia.Event");
jcasType.ll_cas.ll_setRefValue(addr, ((Event_Type)jcasType).casFeatCode_themes_protein, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setThemes_protein(FSArray v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_themes_protein == null)
jcasType.jcas.throwFeatMissing("themes_protein", "ch.epfl.bbp.uima.genia.Event");
jcasType.ll_cas.ll_setRefValue(addr, ((Event_Type)jcasType).casFeatCode_themes_protein, jcasType.ll_cas.ll_getFSRef(v));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.getThemes_protein | public Protein getThemes_protein(int i) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_themes_protein == null)
jcasType.jcas.throwFeatMissing("themes_protein", "ch.epfl.bbp.uima.genia.Event");
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if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_themes_protein == null)
jcasType.jcas.throwFeatMissing("themes_protein", "ch.epfl.bbp.uima.genia.Event");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.setThemes_protein | public void setThemes_protein(int i, Protein v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_themes_protein == null)
jcasType.jcas.throwFeatMissing("themes_protein", "ch.epfl.bbp.uima.genia.Event");
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if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_themes_protein == null)
jcasType.jcas.throwFeatMissing("themes_protein", "ch.epfl.bbp.uima.genia.Event");
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jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_themes_protein), i, jcasType.ll_cas.ll_getFSRef(v));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.getCauses_protein | public FSArray getCauses_protein() {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_causes_protein == null)
jcasType.jcas.throwFeatMissing("causes_protein", "ch.epfl.bbp.uima.genia.Event");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_causes_protein)));} | java | public FSArray getCauses_protein() {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_causes_protein == null)
jcasType.jcas.throwFeatMissing("causes_protein", "ch.epfl.bbp.uima.genia.Event");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.setCauses_protein | public void setCauses_protein(FSArray v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_causes_protein == null)
jcasType.jcas.throwFeatMissing("causes_protein", "ch.epfl.bbp.uima.genia.Event");
jcasType.ll_cas.ll_setRefValue(addr, ((Event_Type)jcasType).casFeatCode_causes_protein, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setCauses_protein(FSArray v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_causes_protein == null)
jcasType.jcas.throwFeatMissing("causes_protein", "ch.epfl.bbp.uima.genia.Event");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.getCauses_protein | public Protein getCauses_protein(int i) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_causes_protein == null)
jcasType.jcas.throwFeatMissing("causes_protein", "ch.epfl.bbp.uima.genia.Event");
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if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_causes_protein == null)
jcasType.jcas.throwFeatMissing("causes_protein", "ch.epfl.bbp.uima.genia.Event");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_causes_protein), i);
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.setCauses_protein | public void setCauses_protein(int i, Protein v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_causes_protein == null)
jcasType.jcas.throwFeatMissing("causes_protein", "ch.epfl.bbp.uima.genia.Event");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_causes_protein), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_causes_protein), i, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setCauses_protein(int i, Protein v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_causes_protein == null)
jcasType.jcas.throwFeatMissing("causes_protein", "ch.epfl.bbp.uima.genia.Event");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_causes_protein), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_causes_protein), i, jcasType.ll_cas.ll_getFSRef(v));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.getSite | public String getSite() {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_site == null)
jcasType.jcas.throwFeatMissing("site", "ch.epfl.bbp.uima.genia.Event");
return jcasType.ll_cas.ll_getStringValue(addr, ((Event_Type)jcasType).casFeatCode_site);} | java | public String getSite() {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_site == null)
jcasType.jcas.throwFeatMissing("site", "ch.epfl.bbp.uima.genia.Event");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.setSite | public void setSite(String v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_site == null)
jcasType.jcas.throwFeatMissing("site", "ch.epfl.bbp.uima.genia.Event");
jcasType.ll_cas.ll_setStringValue(addr, ((Event_Type)jcasType).casFeatCode_site, v);} | java | public void setSite(String v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_site == null)
jcasType.jcas.throwFeatMissing("site", "ch.epfl.bbp.uima.genia.Event");
jcasType.ll_cas.ll_setStringValue(addr, ((Event_Type)jcasType).casFeatCode_site, v);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.getThemes_event | public FSArray getThemes_event() {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_themes_event == null)
jcasType.jcas.throwFeatMissing("themes_event", "ch.epfl.bbp.uima.genia.Event");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_themes_event)));} | java | public FSArray getThemes_event() {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_themes_event == null)
jcasType.jcas.throwFeatMissing("themes_event", "ch.epfl.bbp.uima.genia.Event");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_themes_event)));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.setThemes_event | public void setThemes_event(FSArray v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_themes_event == null)
jcasType.jcas.throwFeatMissing("themes_event", "ch.epfl.bbp.uima.genia.Event");
jcasType.ll_cas.ll_setRefValue(addr, ((Event_Type)jcasType).casFeatCode_themes_event, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setThemes_event(FSArray v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_themes_event == null)
jcasType.jcas.throwFeatMissing("themes_event", "ch.epfl.bbp.uima.genia.Event");
jcasType.ll_cas.ll_setRefValue(addr, ((Event_Type)jcasType).casFeatCode_themes_event, jcasType.ll_cas.ll_getFSRef(v));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.getThemes_event | public Event getThemes_event(int i) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_themes_event == null)
jcasType.jcas.throwFeatMissing("themes_event", "ch.epfl.bbp.uima.genia.Event");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_themes_event), i);
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if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_themes_event == null)
jcasType.jcas.throwFeatMissing("themes_event", "ch.epfl.bbp.uima.genia.Event");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_themes_event), i);
return (Event)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_themes_event), i)));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.setThemes_event | public void setThemes_event(int i, Event v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_themes_event == null)
jcasType.jcas.throwFeatMissing("themes_event", "ch.epfl.bbp.uima.genia.Event");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_themes_event), i);
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if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_themes_event == null)
jcasType.jcas.throwFeatMissing("themes_event", "ch.epfl.bbp.uima.genia.Event");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_themes_event), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_themes_event), i, jcasType.ll_cas.ll_getFSRef(v));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.getCauses_event | public FSArray getCauses_event() {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_causes_event == null)
jcasType.jcas.throwFeatMissing("causes_event", "ch.epfl.bbp.uima.genia.Event");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_causes_event)));} | java | public FSArray getCauses_event() {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_causes_event == null)
jcasType.jcas.throwFeatMissing("causes_event", "ch.epfl.bbp.uima.genia.Event");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_causes_event)));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.setCauses_event | public void setCauses_event(FSArray v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_causes_event == null)
jcasType.jcas.throwFeatMissing("causes_event", "ch.epfl.bbp.uima.genia.Event");
jcasType.ll_cas.ll_setRefValue(addr, ((Event_Type)jcasType).casFeatCode_causes_event, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setCauses_event(FSArray v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_causes_event == null)
jcasType.jcas.throwFeatMissing("causes_event", "ch.epfl.bbp.uima.genia.Event");
jcasType.ll_cas.ll_setRefValue(addr, ((Event_Type)jcasType).casFeatCode_causes_event, jcasType.ll_cas.ll_getFSRef(v));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.getCauses_event | public Event getCauses_event(int i) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_causes_event == null)
jcasType.jcas.throwFeatMissing("causes_event", "ch.epfl.bbp.uima.genia.Event");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_causes_event), i);
return (Event)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_causes_event), i)));} | java | public Event getCauses_event(int i) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_causes_event == null)
jcasType.jcas.throwFeatMissing("causes_event", "ch.epfl.bbp.uima.genia.Event");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_causes_event), i);
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/genia/Event.java | Event.setCauses_event | public void setCauses_event(int i, Event v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_causes_event == null)
jcasType.jcas.throwFeatMissing("causes_event", "ch.epfl.bbp.uima.genia.Event");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_causes_event), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_causes_event), i, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setCauses_event(int i, Event v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_causes_event == null)
jcasType.jcas.throwFeatMissing("causes_event", "ch.epfl.bbp.uima.genia.Event");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_causes_event), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_causes_event), i, jcasType.ll_cas.ll_getFSRef(v));} | [
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BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/parser/BuildContextGenerator.java | BuildContextGenerator.punct | private String punct(Parse punct, int i) {
StringBuffer feat = new StringBuffer(5);
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feat.append(punct.getType());
return (feat.toString());
} | java | private String punct(Parse punct, int i) {
StringBuffer feat = new StringBuffer(5);
feat.append(i).append("=");
feat.append(punct.getType());
return (feat.toString());
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/NounFeats.java | NounFeats.getGender | public String getGender() {
if (NounFeats_Type.featOkTst && ((NounFeats_Type)jcasType).casFeat_gender == null)
jcasType.jcas.throwFeatMissing("gender", "de.julielab.jules.types.NounFeats");
return jcasType.ll_cas.ll_getStringValue(addr, ((NounFeats_Type)jcasType).casFeatCode_gender);} | java | public String getGender() {
if (NounFeats_Type.featOkTst && ((NounFeats_Type)jcasType).casFeat_gender == null)
jcasType.jcas.throwFeatMissing("gender", "de.julielab.jules.types.NounFeats");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EntityMention.java | EntityMention.getLdcatr | public String getLdcatr() {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_ldcatr == null)
jcasType.jcas.throwFeatMissing("ldcatr", "de.julielab.jules.types.ace.EntityMention");
return jcasType.ll_cas.ll_getStringValue(addr, ((EntityMention_Type)jcasType).casFeatCode_ldcatr);} | java | public String getLdcatr() {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_ldcatr == null)
jcasType.jcas.throwFeatMissing("ldcatr", "de.julielab.jules.types.ace.EntityMention");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EntityMention.java | EntityMention.setLdcatr | public void setLdcatr(String v) {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_ldcatr == null)
jcasType.jcas.throwFeatMissing("ldcatr", "de.julielab.jules.types.ace.EntityMention");
jcasType.ll_cas.ll_setStringValue(addr, ((EntityMention_Type)jcasType).casFeatCode_ldcatr, v);} | java | public void setLdcatr(String v) {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_ldcatr == null)
jcasType.jcas.throwFeatMissing("ldcatr", "de.julielab.jules.types.ace.EntityMention");
jcasType.ll_cas.ll_setStringValue(addr, ((EntityMention_Type)jcasType).casFeatCode_ldcatr, v);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EntityMention.java | EntityMention.getRole | public String getRole() {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_role == null)
jcasType.jcas.throwFeatMissing("role", "de.julielab.jules.types.ace.EntityMention");
return jcasType.ll_cas.ll_getStringValue(addr, ((EntityMention_Type)jcasType).casFeatCode_role);} | java | public String getRole() {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_role == null)
jcasType.jcas.throwFeatMissing("role", "de.julielab.jules.types.ace.EntityMention");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EntityMention.java | EntityMention.getMetonymy_mention | public String getMetonymy_mention() {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_metonymy_mention == null)
jcasType.jcas.throwFeatMissing("metonymy_mention", "de.julielab.jules.types.ace.EntityMention");
return jcasType.ll_cas.ll_getStringValue(addr, ((EntityMention_Type)jcasType).casFeatCode_metonymy_mention);} | java | public String getMetonymy_mention() {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_metonymy_mention == null)
jcasType.jcas.throwFeatMissing("metonymy_mention", "de.julielab.jules.types.ace.EntityMention");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EntityMention.java | EntityMention.setMetonymy_mention | public void setMetonymy_mention(String v) {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_metonymy_mention == null)
jcasType.jcas.throwFeatMissing("metonymy_mention", "de.julielab.jules.types.ace.EntityMention");
jcasType.ll_cas.ll_setStringValue(addr, ((EntityMention_Type)jcasType).casFeatCode_metonymy_mention, v);} | java | public void setMetonymy_mention(String v) {
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jcasType.jcas.throwFeatMissing("metonymy_mention", "de.julielab.jules.types.ace.EntityMention");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EntityMention.java | EntityMention.getMention_type | public String getMention_type() {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_mention_type == null)
jcasType.jcas.throwFeatMissing("mention_type", "de.julielab.jules.types.ace.EntityMention");
return jcasType.ll_cas.ll_getStringValue(addr, ((EntityMention_Type)jcasType).casFeatCode_mention_type);} | java | public String getMention_type() {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_mention_type == null)
jcasType.jcas.throwFeatMissing("mention_type", "de.julielab.jules.types.ace.EntityMention");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EntityMention.java | EntityMention.setMention_type | public void setMention_type(String v) {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_mention_type == null)
jcasType.jcas.throwFeatMissing("mention_type", "de.julielab.jules.types.ace.EntityMention");
jcasType.ll_cas.ll_setStringValue(addr, ((EntityMention_Type)jcasType).casFeatCode_mention_type, v);} | java | public void setMention_type(String v) {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_mention_type == null)
jcasType.jcas.throwFeatMissing("mention_type", "de.julielab.jules.types.ace.EntityMention");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EntityMention.java | EntityMention.getMention_ldctype | public String getMention_ldctype() {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_mention_ldctype == null)
jcasType.jcas.throwFeatMissing("mention_ldctype", "de.julielab.jules.types.ace.EntityMention");
return jcasType.ll_cas.ll_getStringValue(addr, ((EntityMention_Type)jcasType).casFeatCode_mention_ldctype);} | java | public String getMention_ldctype() {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_mention_ldctype == null)
jcasType.jcas.throwFeatMissing("mention_ldctype", "de.julielab.jules.types.ace.EntityMention");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EntityMention.java | EntityMention.setMention_ldctype | public void setMention_ldctype(String v) {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_mention_ldctype == null)
jcasType.jcas.throwFeatMissing("mention_ldctype", "de.julielab.jules.types.ace.EntityMention");
jcasType.ll_cas.ll_setStringValue(addr, ((EntityMention_Type)jcasType).casFeatCode_mention_ldctype, v);} | java | public void setMention_ldctype(String v) {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_mention_ldctype == null)
jcasType.jcas.throwFeatMissing("mention_ldctype", "de.julielab.jules.types.ace.EntityMention");
jcasType.ll_cas.ll_setStringValue(addr, ((EntityMention_Type)jcasType).casFeatCode_mention_ldctype, v);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EntityMention.java | EntityMention.getEntity_ref | public Entity getEntity_ref() {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_entity_ref == null)
jcasType.jcas.throwFeatMissing("entity_ref", "de.julielab.jules.types.ace.EntityMention");
return (Entity)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((EntityMention_Type)jcasType).casFeatCode_entity_ref)));} | java | public Entity getEntity_ref() {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_entity_ref == null)
jcasType.jcas.throwFeatMissing("entity_ref", "de.julielab.jules.types.ace.EntityMention");
return (Entity)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((EntityMention_Type)jcasType).casFeatCode_entity_ref)));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EntityMention.java | EntityMention.setEntity_ref | public void setEntity_ref(Entity v) {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_entity_ref == null)
jcasType.jcas.throwFeatMissing("entity_ref", "de.julielab.jules.types.ace.EntityMention");
jcasType.ll_cas.ll_setRefValue(addr, ((EntityMention_Type)jcasType).casFeatCode_entity_ref, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setEntity_ref(Entity v) {
if (EntityMention_Type.featOkTst && ((EntityMention_Type)jcasType).casFeat_entity_ref == null)
jcasType.jcas.throwFeatMissing("entity_ref", "de.julielab.jules.types.ace.EntityMention");
jcasType.ll_cas.ll_setRefValue(addr, ((EntityMention_Type)jcasType).casFeatCode_entity_ref, jcasType.ll_cas.ll_getFSRef(v));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ConceptMention.java | ConceptMention.getSpecificType | public String getSpecificType() {
if (ConceptMention_Type.featOkTst && ((ConceptMention_Type)jcasType).casFeat_specificType == null)
jcasType.jcas.throwFeatMissing("specificType", "de.julielab.jules.types.ConceptMention");
return jcasType.ll_cas.ll_getStringValue(addr, ((ConceptMention_Type)jcasType).casFeatCode_specificType);} | java | public String getSpecificType() {
if (ConceptMention_Type.featOkTst && ((ConceptMention_Type)jcasType).casFeat_specificType == null)
jcasType.jcas.throwFeatMissing("specificType", "de.julielab.jules.types.ConceptMention");
return jcasType.ll_cas.ll_getStringValue(addr, ((ConceptMention_Type)jcasType).casFeatCode_specificType);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ConceptMention.java | ConceptMention.setSpecificType | public void setSpecificType(String v) {
if (ConceptMention_Type.featOkTst && ((ConceptMention_Type)jcasType).casFeat_specificType == null)
jcasType.jcas.throwFeatMissing("specificType", "de.julielab.jules.types.ConceptMention");
jcasType.ll_cas.ll_setStringValue(addr, ((ConceptMention_Type)jcasType).casFeatCode_specificType, v);} | java | public void setSpecificType(String v) {
if (ConceptMention_Type.featOkTst && ((ConceptMention_Type)jcasType).casFeat_specificType == null)
jcasType.jcas.throwFeatMissing("specificType", "de.julielab.jules.types.ConceptMention");
jcasType.ll_cas.ll_setStringValue(addr, ((ConceptMention_Type)jcasType).casFeatCode_specificType, v);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ConceptMention.java | ConceptMention.getRef | public TOP getRef() {
if (ConceptMention_Type.featOkTst && ((ConceptMention_Type)jcasType).casFeat_ref == null)
jcasType.jcas.throwFeatMissing("ref", "de.julielab.jules.types.ConceptMention");
return (TOP)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((ConceptMention_Type)jcasType).casFeatCode_ref)));} | java | public TOP getRef() {
if (ConceptMention_Type.featOkTst && ((ConceptMention_Type)jcasType).casFeat_ref == null)
jcasType.jcas.throwFeatMissing("ref", "de.julielab.jules.types.ConceptMention");
return (TOP)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((ConceptMention_Type)jcasType).casFeatCode_ref)));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ConceptMention.java | ConceptMention.setRef | public void setRef(TOP v) {
if (ConceptMention_Type.featOkTst && ((ConceptMention_Type)jcasType).casFeat_ref == null)
jcasType.jcas.throwFeatMissing("ref", "de.julielab.jules.types.ConceptMention");
jcasType.ll_cas.ll_setRefValue(addr, ((ConceptMention_Type)jcasType).casFeatCode_ref, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setRef(TOP v) {
if (ConceptMention_Type.featOkTst && ((ConceptMention_Type)jcasType).casFeat_ref == null)
jcasType.jcas.throwFeatMissing("ref", "de.julielab.jules.types.ConceptMention");
jcasType.ll_cas.ll_setRefValue(addr, ((ConceptMention_Type)jcasType).casFeatCode_ref, jcasType.ll_cas.ll_getFSRef(v));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ConceptMention.java | ConceptMention.getResourceEntryList | public FSArray getResourceEntryList() {
if (ConceptMention_Type.featOkTst && ((ConceptMention_Type)jcasType).casFeat_resourceEntryList == null)
jcasType.jcas.throwFeatMissing("resourceEntryList", "de.julielab.jules.types.ConceptMention");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((ConceptMention_Type)jcasType).casFeatCode_resourceEntryList)));} | java | public FSArray getResourceEntryList() {
if (ConceptMention_Type.featOkTst && ((ConceptMention_Type)jcasType).casFeat_resourceEntryList == null)
jcasType.jcas.throwFeatMissing("resourceEntryList", "de.julielab.jules.types.ConceptMention");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((ConceptMention_Type)jcasType).casFeatCode_resourceEntryList)));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ConceptMention.java | ConceptMention.setResourceEntryList | public void setResourceEntryList(FSArray v) {
if (ConceptMention_Type.featOkTst && ((ConceptMention_Type)jcasType).casFeat_resourceEntryList == null)
jcasType.jcas.throwFeatMissing("resourceEntryList", "de.julielab.jules.types.ConceptMention");
jcasType.ll_cas.ll_setRefValue(addr, ((ConceptMention_Type)jcasType).casFeatCode_resourceEntryList, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setResourceEntryList(FSArray v) {
if (ConceptMention_Type.featOkTst && ((ConceptMention_Type)jcasType).casFeat_resourceEntryList == null)
jcasType.jcas.throwFeatMissing("resourceEntryList", "de.julielab.jules.types.ConceptMention");
jcasType.ll_cas.ll_setRefValue(addr, ((ConceptMention_Type)jcasType).casFeatCode_resourceEntryList, jcasType.ll_cas.ll_getFSRef(v));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ConceptMention.java | ConceptMention.getResourceEntryList | public ResourceEntry getResourceEntryList(int i) {
if (ConceptMention_Type.featOkTst && ((ConceptMention_Type)jcasType).casFeat_resourceEntryList == null)
jcasType.jcas.throwFeatMissing("resourceEntryList", "de.julielab.jules.types.ConceptMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((ConceptMention_Type)jcasType).casFeatCode_resourceEntryList), i);
return (ResourceEntry)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((ConceptMention_Type)jcasType).casFeatCode_resourceEntryList), i)));} | java | public ResourceEntry getResourceEntryList(int i) {
if (ConceptMention_Type.featOkTst && ((ConceptMention_Type)jcasType).casFeat_resourceEntryList == null)
jcasType.jcas.throwFeatMissing("resourceEntryList", "de.julielab.jules.types.ConceptMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((ConceptMention_Type)jcasType).casFeatCode_resourceEntryList), i);
return (ResourceEntry)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((ConceptMention_Type)jcasType).casFeatCode_resourceEntryList), i)));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ConceptMention.java | ConceptMention.setResourceEntryList | public void setResourceEntryList(int i, ResourceEntry v) {
if (ConceptMention_Type.featOkTst && ((ConceptMention_Type)jcasType).casFeat_resourceEntryList == null)
jcasType.jcas.throwFeatMissing("resourceEntryList", "de.julielab.jules.types.ConceptMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((ConceptMention_Type)jcasType).casFeatCode_resourceEntryList), i);
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if (ConceptMention_Type.featOkTst && ((ConceptMention_Type)jcasType).casFeat_resourceEntryList == null)
jcasType.jcas.throwFeatMissing("resourceEntryList", "de.julielab.jules.types.ConceptMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((ConceptMention_Type)jcasType).casFeatCode_resourceEntryList), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((ConceptMention_Type)jcasType).casFeatCode_resourceEntryList), i, jcasType.ll_cas.ll_getFSRef(v));} | [
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BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/PdfBoxParser.java | PdfBoxParser.getTextPiecesByPage | @SuppressWarnings("unchecked")
public ArrayList<ArrayList<TextPiece>> getTextPiecesByPage(File pdfFile) {
assert (pdfFile.exists()) : "pdfFile does not exist";
m_wordsByPage = new ArrayList<ArrayList<TextPiece>>();
PDDocument document = null;
try {
document = PDDocument.load(pdfFile);
resetEngine();
m_currentPageNo = 0;
// No support for encrypted file in the current version
if (document.isEncrypted()) {
// TODO: log
} else {
ArrayList<PDPage> pages = (ArrayList<PDPage>) document
.getDocumentCatalog().getAllPages();
for (PDPage page : pages) {
m_currentPageNo++;
PDStream contentStream = page.getContents();
if (contentStream != null) {
COSStream contents = contentStream.getStream();
processPage(page, contents);
}
}
}
} catch (Exception e) {
System.out.printf("[Error] Fail to extract words\n");
m_wordsByPage = null;
} catch (OutOfMemoryError e) {
System.out.printf("[Error] Out Of Memory\n");
m_wordsByPage = null;
} finally {
if (document != null) {
try {
document.close();
} catch (IOException e) {
// ignore
}
}
}
return m_wordsByPage;
} | java | @SuppressWarnings("unchecked")
public ArrayList<ArrayList<TextPiece>> getTextPiecesByPage(File pdfFile) {
assert (pdfFile.exists()) : "pdfFile does not exist";
m_wordsByPage = new ArrayList<ArrayList<TextPiece>>();
PDDocument document = null;
try {
document = PDDocument.load(pdfFile);
resetEngine();
m_currentPageNo = 0;
// No support for encrypted file in the current version
if (document.isEncrypted()) {
// TODO: log
} else {
ArrayList<PDPage> pages = (ArrayList<PDPage>) document
.getDocumentCatalog().getAllPages();
for (PDPage page : pages) {
m_currentPageNo++;
PDStream contentStream = page.getContents();
if (contentStream != null) {
COSStream contents = contentStream.getStream();
processPage(page, contents);
}
}
}
} catch (Exception e) {
System.out.printf("[Error] Fail to extract words\n");
m_wordsByPage = null;
} catch (OutOfMemoryError e) {
System.out.printf("[Error] Out Of Memory\n");
m_wordsByPage = null;
} finally {
if (document != null) {
try {
document.close();
} catch (IOException e) {
// ignore
}
}
}
return m_wordsByPage;
} | [
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@return lists of text pieces (one list per page)
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BlueBrain/bluima | modules/bluima_utils/src/main/java/ch/epfl/bbp/uima/utils/SCharsStemmer.java | SCharsStemmer.stem | @Override
public String stem(String token) {
if (token != null && token.length() > 3 && token.endsWith("s")) {
return token.substring(0, token.length() - 1);
}
return token;
} | java | @Override
public String stem(String token) {
if (token != null && token.length() > 3 && token.endsWith("s")) {
return token.substring(0, token.length() - 1);
}
return token;
} | [
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BlueBrain/bluima | modules/bluima_utils/src/main/java/ch/epfl/bbp/uima/uimafit/CpeBuilder.java | CpeBuilder.materializeDescriptor | private static File materializeDescriptor(ResourceSpecifier resource)
throws IOException, SAXException {
File tempDesc = File.createTempFile("desc", ".xml");
// tempDesc.deleteOnExit();
BufferedWriter out = new BufferedWriter(new OutputStreamWriter(
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resource.toXML(out);
out.close();
return tempDesc;
} | java | private static File materializeDescriptor(ResourceSpecifier resource)
throws IOException, SAXException {
File tempDesc = File.createTempFile("desc", ".xml");
// tempDesc.deleteOnExit();
BufferedWriter out = new BufferedWriter(new OutputStreamWriter(
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/CoordinationElement.java | CoordinationElement.getCat | public String getCat() {
if (CoordinationElement_Type.featOkTst && ((CoordinationElement_Type)jcasType).casFeat_cat == null)
jcasType.jcas.throwFeatMissing("cat", "de.julielab.jules.types.CoordinationElement");
return jcasType.ll_cas.ll_getStringValue(addr, ((CoordinationElement_Type)jcasType).casFeatCode_cat);} | java | public String getCat() {
if (CoordinationElement_Type.featOkTst && ((CoordinationElement_Type)jcasType).casFeat_cat == null)
jcasType.jcas.throwFeatMissing("cat", "de.julielab.jules.types.CoordinationElement");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/CoordinationElement.java | CoordinationElement.setCat | public void setCat(String v) {
if (CoordinationElement_Type.featOkTst && ((CoordinationElement_Type)jcasType).casFeat_cat == null)
jcasType.jcas.throwFeatMissing("cat", "de.julielab.jules.types.CoordinationElement");
jcasType.ll_cas.ll_setStringValue(addr, ((CoordinationElement_Type)jcasType).casFeatCode_cat, v);} | java | public void setCat(String v) {
if (CoordinationElement_Type.featOkTst && ((CoordinationElement_Type)jcasType).casFeat_cat == null)
jcasType.jcas.throwFeatMissing("cat", "de.julielab.jules.types.CoordinationElement");
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BlueBrain/bluima | modules/bluima_bbp/src/main/java/ch/epfl/bbp/uima/projects/brainregions/bams/FindSynonyms3.java | FindSynonyms3.getSynonyms | public Set<String> getSynonyms(final String canonical) {
Set<String> syn = Sets.newHashSet();
for (Map<String, Concept> lexica : lexicon) {
for (String lexCanonical : lexica.keySet()) {
Set<String> variants = lexica.get(lexCanonical).getVariants();
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if (canonical.equals(variant)) {
for (String v : variants) {
syn.add(v.toLowerCase());
}
}
}
}
}
return syn;
} | java | public Set<String> getSynonyms(final String canonical) {
Set<String> syn = Sets.newHashSet();
for (Map<String, Concept> lexica : lexicon) {
for (String lexCanonical : lexica.keySet()) {
Set<String> variants = lexica.get(lexCanonical).getVariants();
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}
}
}
return syn;
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BlueBrain/bluima | utils/pdf_glyph_mapping/src/main/java/org/xmlcml/pdf2svg/GlyphCorrector.java | GlyphCorrector.codePointConversion | public int codePointConversion(String fontName, int codePoint) {
NonStandardFontFamily nonStandardFontFamily = get(fontName);
if (nonStandardFontFamily == null)
return codePoint;
CodePointSet codePointSet = nonStandardFontFamily.getCodePointSet();
if (codePointSet == null)
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CodePoint nameCodePoint = codePointSet.getByName(charNameByCodePoint
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if (nameCodePoint != null)
return nameCodePoint.getUnicodeDecimal();
return codePoint;
} | java | public int codePointConversion(String fontName, int codePoint) {
NonStandardFontFamily nonStandardFontFamily = get(fontName);
if (nonStandardFontFamily == null)
return codePoint;
CodePointSet codePointSet = nonStandardFontFamily.getCodePointSet();
if (codePointSet == null)
return codePoint;
CodePoint decimalCodePoint = codePointSet.getByDecimal(codePoint);
if (decimalCodePoint != null)
// Fetches the correct unicode point
return decimalCodePoint.getUnicodeDecimal();
CodePoint nameCodePoint = codePointSet.getByName(charNameByCodePoint
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if (nameCodePoint != null)
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return codePoint;
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/VerbFeats.java | VerbFeats.getPerson | public String getPerson() {
if (VerbFeats_Type.featOkTst && ((VerbFeats_Type)jcasType).casFeat_person == null)
jcasType.jcas.throwFeatMissing("person", "de.julielab.jules.types.VerbFeats");
return jcasType.ll_cas.ll_getStringValue(addr, ((VerbFeats_Type)jcasType).casFeatCode_person);} | java | public String getPerson() {
if (VerbFeats_Type.featOkTst && ((VerbFeats_Type)jcasType).casFeat_person == null)
jcasType.jcas.throwFeatMissing("person", "de.julielab.jules.types.VerbFeats");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/VerbFeats.java | VerbFeats.setPerson | public void setPerson(String v) {
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jcasType.jcas.throwFeatMissing("person", "de.julielab.jules.types.VerbFeats");
jcasType.ll_cas.ll_setStringValue(addr, ((VerbFeats_Type)jcasType).casFeatCode_person, v);} | java | public void setPerson(String v) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/VerbFeats.java | VerbFeats.getVoice | public String getVoice() {
if (VerbFeats_Type.featOkTst && ((VerbFeats_Type)jcasType).casFeat_voice == null)
jcasType.jcas.throwFeatMissing("voice", "de.julielab.jules.types.VerbFeats");
return jcasType.ll_cas.ll_getStringValue(addr, ((VerbFeats_Type)jcasType).casFeatCode_voice);} | java | public String getVoice() {
if (VerbFeats_Type.featOkTst && ((VerbFeats_Type)jcasType).casFeat_voice == null)
jcasType.jcas.throwFeatMissing("voice", "de.julielab.jules.types.VerbFeats");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/VerbFeats.java | VerbFeats.setVoice | public void setVoice(String v) {
if (VerbFeats_Type.featOkTst && ((VerbFeats_Type)jcasType).casFeat_voice == null)
jcasType.jcas.throwFeatMissing("voice", "de.julielab.jules.types.VerbFeats");
jcasType.ll_cas.ll_setStringValue(addr, ((VerbFeats_Type)jcasType).casFeatCode_voice, v);} | java | public void setVoice(String v) {
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jcasType.jcas.throwFeatMissing("voice", "de.julielab.jules.types.VerbFeats");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/VerbFeats.java | VerbFeats.getAspect | public String getAspect() {
if (VerbFeats_Type.featOkTst && ((VerbFeats_Type)jcasType).casFeat_aspect == null)
jcasType.jcas.throwFeatMissing("aspect", "de.julielab.jules.types.VerbFeats");
return jcasType.ll_cas.ll_getStringValue(addr, ((VerbFeats_Type)jcasType).casFeatCode_aspect);} | java | public String getAspect() {
if (VerbFeats_Type.featOkTst && ((VerbFeats_Type)jcasType).casFeat_aspect == null)
jcasType.jcas.throwFeatMissing("aspect", "de.julielab.jules.types.VerbFeats");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/VerbFeats.java | VerbFeats.setAspect | public void setAspect(String v) {
if (VerbFeats_Type.featOkTst && ((VerbFeats_Type)jcasType).casFeat_aspect == null)
jcasType.jcas.throwFeatMissing("aspect", "de.julielab.jules.types.VerbFeats");
jcasType.ll_cas.ll_setStringValue(addr, ((VerbFeats_Type)jcasType).casFeatCode_aspect, v);} | java | public void setAspect(String v) {
if (VerbFeats_Type.featOkTst && ((VerbFeats_Type)jcasType).casFeat_aspect == null)
jcasType.jcas.throwFeatMissing("aspect", "de.julielab.jules.types.VerbFeats");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/FullTextLinkList.java | FullTextLinkList.getFullTextLinks | public FSArray getFullTextLinks() {
if (FullTextLinkList_Type.featOkTst && ((FullTextLinkList_Type)jcasType).casFeat_fullTextLinks == null)
jcasType.jcas.throwFeatMissing("fullTextLinks", "de.julielab.jules.types.FullTextLinkList");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((FullTextLinkList_Type)jcasType).casFeatCode_fullTextLinks)));} | java | public FSArray getFullTextLinks() {
if (FullTextLinkList_Type.featOkTst && ((FullTextLinkList_Type)jcasType).casFeat_fullTextLinks == null)
jcasType.jcas.throwFeatMissing("fullTextLinks", "de.julielab.jules.types.FullTextLinkList");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((FullTextLinkList_Type)jcasType).casFeatCode_fullTextLinks)));} | [
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"throwFeat... | getter for fullTextLinks - gets
@generated
@return value of the feature | [
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"-",
"gets"
] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/FullTextLinkList.java#L86-L89 | train |
BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/FullTextLinkList.java | FullTextLinkList.setFullTextLinks | public void setFullTextLinks(FSArray v) {
if (FullTextLinkList_Type.featOkTst && ((FullTextLinkList_Type)jcasType).casFeat_fullTextLinks == null)
jcasType.jcas.throwFeatMissing("fullTextLinks", "de.julielab.jules.types.FullTextLinkList");
jcasType.ll_cas.ll_setRefValue(addr, ((FullTextLinkList_Type)jcasType).casFeatCode_fullTextLinks, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setFullTextLinks(FSArray v) {
if (FullTextLinkList_Type.featOkTst && ((FullTextLinkList_Type)jcasType).casFeat_fullTextLinks == null)
jcasType.jcas.throwFeatMissing("fullTextLinks", "de.julielab.jules.types.FullTextLinkList");
jcasType.ll_cas.ll_setRefValue(addr, ((FullTextLinkList_Type)jcasType).casFeatCode_fullTextLinks, jcasType.ll_cas.ll_getFSRef(v));} | [
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... | setter for fullTextLinks - sets
@generated
@param v value to set into the feature | [
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"-",
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/FullTextLinkList.java#L95-L98 | train |
BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/FullTextLinkList.java | FullTextLinkList.getFullTextLinks | public FullTextLink getFullTextLinks(int i) {
if (FullTextLinkList_Type.featOkTst && ((FullTextLinkList_Type)jcasType).casFeat_fullTextLinks == null)
jcasType.jcas.throwFeatMissing("fullTextLinks", "de.julielab.jules.types.FullTextLinkList");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((FullTextLinkList_Type)jcasType).casFeatCode_fullTextLinks), i);
return (FullTextLink)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((FullTextLinkList_Type)jcasType).casFeatCode_fullTextLinks), i)));} | java | public FullTextLink getFullTextLinks(int i) {
if (FullTextLinkList_Type.featOkTst && ((FullTextLinkList_Type)jcasType).casFeat_fullTextLinks == null)
jcasType.jcas.throwFeatMissing("fullTextLinks", "de.julielab.jules.types.FullTextLinkList");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((FullTextLinkList_Type)jcasType).casFeatCode_fullTextLinks), i);
return (FullTextLink)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((FullTextLinkList_Type)jcasType).casFeatCode_fullTextLinks), i)));} | [
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"jcas"... | indexed getter for fullTextLinks - gets an indexed value -
@generated
@param i index in the array to get
@return value of the element at index i | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/FullTextLinkList.java#L105-L109 | train |
BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/FullTextLinkList.java | FullTextLinkList.setFullTextLinks | public void setFullTextLinks(int i, FullTextLink v) {
if (FullTextLinkList_Type.featOkTst && ((FullTextLinkList_Type)jcasType).casFeat_fullTextLinks == null)
jcasType.jcas.throwFeatMissing("fullTextLinks", "de.julielab.jules.types.FullTextLinkList");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((FullTextLinkList_Type)jcasType).casFeatCode_fullTextLinks), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((FullTextLinkList_Type)jcasType).casFeatCode_fullTextLinks), i, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setFullTextLinks(int i, FullTextLink v) {
if (FullTextLinkList_Type.featOkTst && ((FullTextLinkList_Type)jcasType).casFeat_fullTextLinks == null)
jcasType.jcas.throwFeatMissing("fullTextLinks", "de.julielab.jules.types.FullTextLinkList");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((FullTextLinkList_Type)jcasType).casFeatCode_fullTextLinks), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((FullTextLinkList_Type)jcasType).casFeatCode_fullTextLinks), i, jcasType.ll_cas.ll_getFSRef(v));} | [
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@generated
@param i index in the array to set
@param v value to set into the array | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/FullTextLinkList.java#L116-L120 | train |
BlueBrain/bluima | modules/bluima_lexica/src/main/java/ch/epfl/bbp/uima/obo/OBOOntology.java | OBOOntology.read | public void read(File f) throws IOException {
FileInputStream fis = new FileInputStream(f);
try {
read(new BufferedReader(new InputStreamReader(fis, "UTF-8")));
} finally {
IOUtils.closeQuietly(fis);
}
} | java | public void read(File f) throws IOException {
FileInputStream fis = new FileInputStream(f);
try {
read(new BufferedReader(new InputStreamReader(fis, "UTF-8")));
} finally {
IOUtils.closeQuietly(fis);
}
} | [
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... | Read a .obo file
@param f
The .obo file to read.
@throws Exception | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_lexica/src/main/java/ch/epfl/bbp/uima/obo/OBOOntology.java#L39-L46 | train |
BlueBrain/bluima | modules/bluima_lexica/src/main/java/ch/epfl/bbp/uima/obo/OBOOntology.java | OBOOntology.addTerm | public void addTerm(OntologyTerm term) {
terms.put(term.getId(), term);
indexTerm(term);
isTypeOfIsBuilt = false;
} | java | public void addTerm(OntologyTerm term) {
terms.put(term.getId(), term);
indexTerm(term);
isTypeOfIsBuilt = false;
} | [
"public",
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] | Add a single OntologyTerm to the ontology.
@param term
The OntologyTerm. | [
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"."
] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_lexica/src/main/java/ch/epfl/bbp/uima/obo/OBOOntology.java#L81-L85 | train |
BlueBrain/bluima | modules/bluima_lexica/src/main/java/ch/epfl/bbp/uima/obo/OBOOntology.java | OBOOntology.addOntology | public void addOntology(OBOOntology ont) {
for (String id : ont.terms.keySet()) {
addTerm(ont.terms.get(id));
}
} | java | public void addOntology(OBOOntology ont) {
for (String id : ont.terms.keySet()) {
addTerm(ont.terms.get(id));
}
} | [
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"}"
] | Merge a whole ontology into the current one.
@param ont
The ontology to merge in. | [
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"a",
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"."
] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_lexica/src/main/java/ch/epfl/bbp/uima/obo/OBOOntology.java#L93-L97 | train |
BlueBrain/bluima | modules/bluima_lexica/src/main/java/ch/epfl/bbp/uima/obo/OBOOntology.java | OBOOntology.writeOntTxt | public void writeOntTxt(PrintWriter pw) {
for (String id : terms.keySet()) {
OntologyTerm term = terms.get(id);
Set<String> synSet = new HashSet<String>();
synSet.add(term.getName());
for (Synonym s : term.getSynonyms()) {
String st = s.getType();
if (id.startsWith("PTCO")
|| (st != null && !st
.matches(".*(InChI|SMILES|FORMULA).*"))) {
String synonym = s.getSyn();
if (!synonym.matches("\\S")) {// reject ontology terms
// consisting of a single
// letter as these produce too
// many false positives
synSet.add(synonym);
}
}
}
pw.println("[" + id + "]");
for (String syn : synSet)
pw.println(syn);
pw.println();
}
pw.flush();
} | java | public void writeOntTxt(PrintWriter pw) {
for (String id : terms.keySet()) {
OntologyTerm term = terms.get(id);
Set<String> synSet = new HashSet<String>();
synSet.add(term.getName());
for (Synonym s : term.getSynonyms()) {
String st = s.getType();
if (id.startsWith("PTCO")
|| (st != null && !st
.matches(".*(InChI|SMILES|FORMULA).*"))) {
String synonym = s.getSyn();
if (!synonym.matches("\\S")) {// reject ontology terms
// consisting of a single
// letter as these produce too
// many false positives
synSet.add(synonym);
}
}
}
pw.println("[" + id + "]");
for (String syn : synSet)
pw.println(syn);
pw.println();
}
pw.flush();
} | [
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@param pw
The PrintWriter to write to. | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_lexica/src/main/java/ch/epfl/bbp/uima/obo/OBOOntology.java#L136-L162 | train |
BlueBrain/bluima | modules/bluima_lexica/src/main/java/ch/epfl/bbp/uima/obo/OBOOntology.java | OBOOntology.getIdsForIdsWithAncestors | public Set<String> getIdsForIdsWithAncestors(Collection<String> termIds) {
Stack<String> idsToConsider = new Stack<String>();
idsToConsider.addAll(termIds);
Set<String> resultIds = new HashSet<String>();
while (!idsToConsider.isEmpty()) {
String id = idsToConsider.pop();
if (!resultIds.contains(id)) {
resultIds.add(id);
if (terms.containsKey(id))
idsToConsider.addAll(terms.get(id).getIsA());
}
}
return resultIds;
} | java | public Set<String> getIdsForIdsWithAncestors(Collection<String> termIds) {
Stack<String> idsToConsider = new Stack<String>();
idsToConsider.addAll(termIds);
Set<String> resultIds = new HashSet<String>();
while (!idsToConsider.isEmpty()) {
String id = idsToConsider.pop();
if (!resultIds.contains(id)) {
resultIds.add(id);
if (terms.containsKey(id))
idsToConsider.addAll(terms.get(id).getIsA());
}
}
return resultIds;
} | [
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parents of those IDs, the grandparents, etc.
@param termIds
The initial "seed" IDs.
@return The full set of IDs. | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_lexica/src/main/java/ch/epfl/bbp/uima/obo/OBOOntology.java#L183-L196 | train |
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