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BlueBrain/bluima | modules/bluima_lexica/src/main/java/ch/epfl/bbp/uima/obo/OBOOntology.java | OBOOntology.getIdsForIdWithAncestors | public Set<String> getIdsForIdWithAncestors(String termId) {
if (!terms.containsKey(termId))
return new HashSet<String>();
Stack<String> idsToConsider = new Stack<String>();
idsToConsider.add(termId);
Set<String> resultIds = new HashSet<String>();
while (!idsToConsider.isEmpty()) {
String id = idsToConsider.pop();
if (!resultIds.contains(id)) {
resultIds.add(id);
idsToConsider.addAll(terms.get(id).getIsA());
}
}
return resultIds;
} | java | public Set<String> getIdsForIdWithAncestors(String termId) {
if (!terms.containsKey(termId))
return new HashSet<String>();
Stack<String> idsToConsider = new Stack<String>();
idsToConsider.add(termId);
Set<String> resultIds = new HashSet<String>();
while (!idsToConsider.isEmpty()) {
String id = idsToConsider.pop();
if (!resultIds.contains(id)) {
resultIds.add(id);
idsToConsider.addAll(terms.get(id).getIsA());
}
}
return resultIds;
} | [
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BlueBrain/bluima | modules/bluima_lexica/src/main/java/ch/epfl/bbp/uima/obo/OBOOntology.java | OBOOntology.getIdsForTermWithAncestors | public Set<String> getIdsForTermWithAncestors(String s) {
if (!indexByName.containsKey(s))
return new HashSet<String>();
Stack<String> idsToConsider = new Stack<String>();
idsToConsider.addAll(getIdsForTerm(s));
Set<String> resultIds = new HashSet<String>();
while (!idsToConsider.isEmpty()) {
String id = idsToConsider.pop();
if (!resultIds.contains(id)) {
resultIds.add(id);
idsToConsider.addAll(terms.get(id).getIsA());
}
}
return resultIds;
} | java | public Set<String> getIdsForTermWithAncestors(String s) {
if (!indexByName.containsKey(s))
return new HashSet<String>();
Stack<String> idsToConsider = new Stack<String>();
idsToConsider.addAll(getIdsForTerm(s));
Set<String> resultIds = new HashSet<String>();
while (!idsToConsider.isEmpty()) {
String id = idsToConsider.pop();
if (!resultIds.contains(id)) {
resultIds.add(id);
idsToConsider.addAll(terms.get(id).getIsA());
}
}
return resultIds;
} | [
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BlueBrain/bluima | modules/bluima_lexica/src/main/java/ch/epfl/bbp/uima/obo/OBOOntology.java | OBOOntology.getIdsForIdWithDescendants | public Set<String> getIdsForIdWithDescendants(String s) {
buildIsTypeOf();
Stack<String> idsToConsider = new Stack<String>();
idsToConsider.add(s);
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).getIsTypeOf());
}
}
return resultIds;
} | java | public Set<String> getIdsForIdWithDescendants(String s) {
buildIsTypeOf();
Stack<String> idsToConsider = new Stack<String>();
idsToConsider.add(s);
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).getIsTypeOf());
}
}
return resultIds;
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BlueBrain/bluima | modules/bluima_lexica/src/main/java/ch/epfl/bbp/uima/obo/OBOOntology.java | OBOOntology.getNameForID | public String getNameForID(String id) {
if (!terms.containsKey(id))
return null;
return terms.get(id).getName();
} | java | public String getNameForID(String id) {
if (!terms.containsKey(id))
return null;
return terms.get(id).getName();
} | [
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BlueBrain/bluima | modules/bluima_lexica/src/main/java/ch/epfl/bbp/uima/obo/OBOOntology.java | OBOOntology.getDefinitionForID | public String getDefinitionForID(String id) {
if (!terms.containsKey(id))
return null;
return terms.get(id).getDef();
} | java | public String getDefinitionForID(String id) {
if (!terms.containsKey(id))
return null;
return terms.get(id).getDef();
} | [
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BlueBrain/bluima | modules/bluima_regions/src/main/java/w/ch/epfl/bbp/nlp/br/normalize/Normalize.java | Normalize.processMentionString | public Set<String> processMentionString(String mention) {
Set<String> result = new HashSet<String>();
result.add(mention);
for (MentionEditor editor : editors) {
Set<String> newResult = new HashSet<String>();
for (String mentionEdit : result) {
newResult.addAll(editor.editMention(mentionEdit));
}
result.addAll(newResult);
}
return result;
} | java | public Set<String> processMentionString(String mention) {
Set<String> result = new HashSet<String>();
result.add(mention);
for (MentionEditor editor : editors) {
Set<String> newResult = new HashSet<String>();
for (String mentionEdit : result) {
newResult.addAll(editor.editMention(mentionEdit));
}
result.addAll(newResult);
}
return result;
} | [
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BlueBrain/bluima | utils/blue_commons/src/main/java/ch/epfl/bbp/Histogram.java | Histogram.add | public void add(T value) {
if (value == null)
return;
if (map.containsKey(value)) {
map.put(value, map.get(value) + 1);
} else {
map.put(value, 1l);
}
} | java | public void add(T value) {
if (value == null)
return;
if (map.containsKey(value)) {
map.put(value, map.get(value) + 1);
} else {
map.put(value, 1l);
}
} | [
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BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/PubmedXmlParser.java | PubmedXmlParser.parseAsArticles | public List<MedlineCitation> parseAsArticles(InputStream is) {
try {
MedlineCitationSet parse = (MedlineCitationSet) unmarshaller
.unmarshal(is);
return parse.getMedlineCitation();
} catch (Exception e) {
LOG.warn("could not parse article ", e);
return null;
} finally {
IOUtils.closeQuietly(is);
}
} | java | public List<MedlineCitation> parseAsArticles(InputStream is) {
try {
MedlineCitationSet parse = (MedlineCitationSet) unmarshaller
.unmarshal(is);
return parse.getMedlineCitation();
} catch (Exception e) {
LOG.warn("could not parse article ", e);
return null;
} finally {
IOUtils.closeQuietly(is);
}
} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/FullTextLink.java | FullTextLink.getUrl | public String getUrl() {
if (FullTextLink_Type.featOkTst && ((FullTextLink_Type)jcasType).casFeat_url == null)
jcasType.jcas.throwFeatMissing("url", "de.julielab.jules.types.FullTextLink");
return jcasType.ll_cas.ll_getStringValue(addr, ((FullTextLink_Type)jcasType).casFeatCode_url);} | java | public String getUrl() {
if (FullTextLink_Type.featOkTst && ((FullTextLink_Type)jcasType).casFeat_url == null)
jcasType.jcas.throwFeatMissing("url", "de.julielab.jules.types.FullTextLink");
return jcasType.ll_cas.ll_getStringValue(addr, ((FullTextLink_Type)jcasType).casFeatCode_url);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/FullTextLink.java | FullTextLink.setUrl | public void setUrl(String v) {
if (FullTextLink_Type.featOkTst && ((FullTextLink_Type)jcasType).casFeat_url == null)
jcasType.jcas.throwFeatMissing("url", "de.julielab.jules.types.FullTextLink");
jcasType.ll_cas.ll_setStringValue(addr, ((FullTextLink_Type)jcasType).casFeatCode_url, v);} | java | public void setUrl(String v) {
if (FullTextLink_Type.featOkTst && ((FullTextLink_Type)jcasType).casFeat_url == null)
jcasType.jcas.throwFeatMissing("url", "de.julielab.jules.types.FullTextLink");
jcasType.ll_cas.ll_setStringValue(addr, ((FullTextLink_Type)jcasType).casFeatCode_url, v);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/FullTextLink.java | FullTextLink.getIconUrl | public String getIconUrl() {
if (FullTextLink_Type.featOkTst && ((FullTextLink_Type)jcasType).casFeat_iconUrl == null)
jcasType.jcas.throwFeatMissing("iconUrl", "de.julielab.jules.types.FullTextLink");
return jcasType.ll_cas.ll_getStringValue(addr, ((FullTextLink_Type)jcasType).casFeatCode_iconUrl);} | java | public String getIconUrl() {
if (FullTextLink_Type.featOkTst && ((FullTextLink_Type)jcasType).casFeat_iconUrl == null)
jcasType.jcas.throwFeatMissing("iconUrl", "de.julielab.jules.types.FullTextLink");
return jcasType.ll_cas.ll_getStringValue(addr, ((FullTextLink_Type)jcasType).casFeatCode_iconUrl);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/FullTextLink.java | FullTextLink.setIconUrl | public void setIconUrl(String v) {
if (FullTextLink_Type.featOkTst && ((FullTextLink_Type)jcasType).casFeat_iconUrl == null)
jcasType.jcas.throwFeatMissing("iconUrl", "de.julielab.jules.types.FullTextLink");
jcasType.ll_cas.ll_setStringValue(addr, ((FullTextLink_Type)jcasType).casFeatCode_iconUrl, v);} | java | public void setIconUrl(String v) {
if (FullTextLink_Type.featOkTst && ((FullTextLink_Type)jcasType).casFeat_iconUrl == null)
jcasType.jcas.throwFeatMissing("iconUrl", "de.julielab.jules.types.FullTextLink");
jcasType.ll_cas.ll_setStringValue(addr, ((FullTextLink_Type)jcasType).casFeatCode_iconUrl, v);} | [
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BlueBrain/bluima | modules/bluima_regions/src/main/java/ubic/whitetext/BrainRegionPipes.java | BrainRegionPipes.addFullTextPipes | private static void addFullTextPipes(List<String> usedPipeNames,
List<Pipe> pipes) {
// blabla 24 24
pipes.add(new LongRegexSpaced("digit_then_other_then_digit", Pattern
.compile("\\d+[^\\d]+\\d+"), 2, 4));
// 30 mM K SO , 5 mM MgCl 6H O, 10 mM 24 24 22 HEPES
pipes.add(new LongRegexSpaced(
"digit_then_other_then_digit_then_other_then_digit", Pattern
.compile(".*\\d+[^\\d\\n]+\\d+[^\\d\\n]+\\d+.*"), 4, 9));
// n 19
// n 5
pipes.add(new LongRegexSpaced("n_space_digit", Pattern
.compile("n \\d+"), 2, 2));
pipes.add(new LongRegexSpaced("parenthesis_n_space_digit_parenthesis",
Pattern.compile("\\( n \\d+ \\)"), 3, 4));
pipes.add(new LongRegexSpaced("n_space_digit_parenthesis", Pattern
.compile("n \\d+ \\)"), 3, 4));
pipes.add(new LongRegexSpaced("parenthesis_n_space_digit", Pattern
.compile("\\( n \\d+"), 3, 4));
// Fig is never found in any lexicon
pipes.add(new RegexMatches("Figure", Pattern.compile(".*Fig.*")));
} | java | private static void addFullTextPipes(List<String> usedPipeNames,
List<Pipe> pipes) {
// blabla 24 24
pipes.add(new LongRegexSpaced("digit_then_other_then_digit", Pattern
.compile("\\d+[^\\d]+\\d+"), 2, 4));
// 30 mM K SO , 5 mM MgCl 6H O, 10 mM 24 24 22 HEPES
pipes.add(new LongRegexSpaced(
"digit_then_other_then_digit_then_other_then_digit", Pattern
.compile(".*\\d+[^\\d\\n]+\\d+[^\\d\\n]+\\d+.*"), 4, 9));
// n 19
// n 5
pipes.add(new LongRegexSpaced("n_space_digit", Pattern
.compile("n \\d+"), 2, 2));
pipes.add(new LongRegexSpaced("parenthesis_n_space_digit_parenthesis",
Pattern.compile("\\( n \\d+ \\)"), 3, 4));
pipes.add(new LongRegexSpaced("n_space_digit_parenthesis", Pattern
.compile("n \\d+ \\)"), 3, 4));
pipes.add(new LongRegexSpaced("parenthesis_n_space_digit", Pattern
.compile("\\( n \\d+"), 3, 4));
// Fig is never found in any lexicon
pipes.add(new RegexMatches("Figure", Pattern.compile(".*Fig.*")));
} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAttribute.java | MMAXAttribute.getValue | public String getValue() {
if (MMAXAttribute_Type.featOkTst && ((MMAXAttribute_Type)jcasType).casFeat_value == null)
jcasType.jcas.throwFeatMissing("value", "de.julielab.jules.types.mmax.MMAXAttribute");
return jcasType.ll_cas.ll_getStringValue(addr, ((MMAXAttribute_Type)jcasType).casFeatCode_value);} | java | public String getValue() {
if (MMAXAttribute_Type.featOkTst && ((MMAXAttribute_Type)jcasType).casFeat_value == null)
jcasType.jcas.throwFeatMissing("value", "de.julielab.jules.types.mmax.MMAXAttribute");
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BlueBrain/bluima | modules/bluima_banner/src/main/java/banner/tagging/CRFTagger.java | CRFTagger.write | public void write(File f)
{
try
{
ObjectOutputStream oos = new ObjectOutputStream(new GZIPOutputStream(new FileOutputStream(f)));
oos.writeObject(textDirection);
if (textDirection.doForward())
oos.writeObject(forwardCRF);
if (textDirection.doReverse())
oos.writeObject(reverseCRF);
oos.writeObject(basePipe);
oos.writeInt(order);
oos.writeBoolean(useFeatureInduction);
oos.writeObject(format);
oos.close();
}
catch (IOException e)
{
System.err.println("Exception writing file " + f + ": " + e);
}
} | java | public void write(File f)
{
try
{
ObjectOutputStream oos = new ObjectOutputStream(new GZIPOutputStream(new FileOutputStream(f)));
oos.writeObject(textDirection);
if (textDirection.doForward())
oos.writeObject(forwardCRF);
if (textDirection.doReverse())
oos.writeObject(reverseCRF);
oos.writeObject(basePipe);
oos.writeInt(order);
oos.writeBoolean(useFeatureInduction);
oos.writeObject(format);
oos.close();
}
catch (IOException e)
{
System.err.println("Exception writing file " + f + ": " + e);
}
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DictTerm.java | DictTerm.getEntityId | public String getEntityId() {
if (DictTerm_Type.featOkTst && ((DictTerm_Type)jcasType).casFeat_entityId == null)
jcasType.jcas.throwFeatMissing("entityId", "ch.epfl.bbp.uima.types.DictTerm");
return jcasType.ll_cas.ll_getStringValue(addr, ((DictTerm_Type)jcasType).casFeatCode_entityId);} | java | public String getEntityId() {
if (DictTerm_Type.featOkTst && ((DictTerm_Type)jcasType).casFeat_entityId == null)
jcasType.jcas.throwFeatMissing("entityId", "ch.epfl.bbp.uima.types.DictTerm");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DictTerm.java | DictTerm.setEntityId | public void setEntityId(String v) {
if (DictTerm_Type.featOkTst && ((DictTerm_Type)jcasType).casFeat_entityId == null)
jcasType.jcas.throwFeatMissing("entityId", "ch.epfl.bbp.uima.types.DictTerm");
jcasType.ll_cas.ll_setStringValue(addr, ((DictTerm_Type)jcasType).casFeatCode_entityId, v);} | java | public void setEntityId(String v) {
if (DictTerm_Type.featOkTst && ((DictTerm_Type)jcasType).casFeat_entityId == null)
jcasType.jcas.throwFeatMissing("entityId", "ch.epfl.bbp.uima.types.DictTerm");
jcasType.ll_cas.ll_setStringValue(addr, ((DictTerm_Type)jcasType).casFeatCode_entityId, v);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DictTerm.java | DictTerm.getAnnotType | public String getAnnotType() {
if (DictTerm_Type.featOkTst && ((DictTerm_Type)jcasType).casFeat_annotType == null)
jcasType.jcas.throwFeatMissing("annotType", "ch.epfl.bbp.uima.types.DictTerm");
return jcasType.ll_cas.ll_getStringValue(addr, ((DictTerm_Type)jcasType).casFeatCode_annotType);} | java | public String getAnnotType() {
if (DictTerm_Type.featOkTst && ((DictTerm_Type)jcasType).casFeat_annotType == null)
jcasType.jcas.throwFeatMissing("annotType", "ch.epfl.bbp.uima.types.DictTerm");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DictTerm.java | DictTerm.setAnnotType | public void setAnnotType(String v) {
if (DictTerm_Type.featOkTst && ((DictTerm_Type)jcasType).casFeat_annotType == null)
jcasType.jcas.throwFeatMissing("annotType", "ch.epfl.bbp.uima.types.DictTerm");
jcasType.ll_cas.ll_setStringValue(addr, ((DictTerm_Type)jcasType).casFeatCode_annotType, v);} | java | public void setAnnotType(String v) {
if (DictTerm_Type.featOkTst && ((DictTerm_Type)jcasType).casFeat_annotType == null)
jcasType.jcas.throwFeatMissing("annotType", "ch.epfl.bbp.uima.types.DictTerm");
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BlueBrain/bluima | modules/bluima_utils/src/main/java/ch/epfl/bbp/uima/annotationviewer/BlueAnnotationViewGenerator.java | BlueAnnotationViewGenerator.getTemplates | private Templates getTemplates(String filename) {
// InputStream is =
// AnnotationViewGenerator.class.getResourceAsStream(filename);
Templates templates;
InputStream is = null;
try {
is = ResourceHelper.getInputStream("viewer/" + filename);
templates = mTFactory.newTemplates(new StreamSource(is));
} catch (Exception e) {
throw new UIMARuntimeException(e);
} finally {
IOUtils.closeQuietly(is);
}
return templates;
} | java | private Templates getTemplates(String filename) {
// InputStream is =
// AnnotationViewGenerator.class.getResourceAsStream(filename);
Templates templates;
InputStream is = null;
try {
is = ResourceHelper.getInputStream("viewer/" + filename);
templates = mTFactory.newTemplates(new StreamSource(is));
} catch (Exception e) {
throw new UIMARuntimeException(e);
} finally {
IOUtils.closeQuietly(is);
}
return templates;
} | [
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BlueBrain/bluima | modules/bluima_utils/src/main/java/ch/epfl/bbp/uima/annotationviewer/BlueAnnotationViewGenerator.java | BlueAnnotationViewGenerator.writeToFile | private void writeToFile(String filename, File outputDir) {
File outFile = new File(outputDir, filename);
OutputStream os;
try {
os = new FileOutputStream(outFile);
} catch (FileNotFoundException e) {
throw new UIMARuntimeException(e);
}
InputStream is = null;
try {
is = ResourceHelper.getInputStream("viewer/" + filename);
byte[] buf = new byte[1024];
int numRead;
while ((numRead = is.read(buf)) > 0) {
os.write(buf, 0, numRead);
}
} catch (IOException e) {
throw new UIMARuntimeException(e);
} finally {
try {
is.close();
} catch (IOException e) {
// ignore close errors
}
try {
os.close();
} catch (IOException e) {
// ignore close errors
}
}
} | java | private void writeToFile(String filename, File outputDir) {
File outFile = new File(outputDir, filename);
OutputStream os;
try {
os = new FileOutputStream(outFile);
} catch (FileNotFoundException e) {
throw new UIMARuntimeException(e);
}
InputStream is = null;
try {
is = ResourceHelper.getInputStream("viewer/" + filename);
byte[] buf = new byte[1024];
int numRead;
while ((numRead = is.read(buf)) > 0) {
os.write(buf, 0, numRead);
}
} catch (IOException e) {
throw new UIMARuntimeException(e);
} finally {
try {
is.close();
} catch (IOException e) {
// ignore close errors
}
try {
os.close();
} catch (IOException e) {
// ignore close errors
}
}
} | [
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BlueBrain/bluima | modules/bluima_utils/src/main/java/ch/epfl/bbp/uima/annotationviewer/BlueAnnotationViewGenerator.java | BlueAnnotationViewGenerator.autoGenerateStyleMap | public static String autoGenerateStyleMap(
AnalysisEngineMetaData aTaeMetaData) {
// styles used in automatically generated style maps
final String[] STYLES = { "color:black; background:lightblue;",
"color:black; background:lightgreen;",
"color:black; background:orange;",
"color:black; background:yellow;",
"color:black; background:pink;",
"color:black; background:salmon;",
"color:black; background:cyan;",
"color:black; background:violet;",
"color:black; background:tan;",
"color:white; background:brown;",
"color:white; background:blue;",
"color:white; background:green;",
"color:white; background:red;",
"color:white; background:mediumpurple;" };
// get list of output types from TAE
ArrayList outputTypes = new ArrayList();
Capability[] capabilities = aTaeMetaData.getCapabilities();
for (int i = 0; i < capabilities.length; i++) {
TypeOrFeature[] outputs = capabilities[i].getOutputs();
for (int j = 0; j < outputs.length; j++) {
if (outputs[j].isType()
&& !outputTypes.contains(outputs[j].getName())) {
outputTypes.add(outputs[j].getName());
}
}
}
// generate style map by mapping each type to a background color
StringBuffer buf = new StringBuffer();
buf.append("<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>\n");
buf.append("<styleMap>\n");
int i = 0;
Iterator it = outputTypes.iterator();
while (it.hasNext()) {
String outputType = (String) it.next();
String label = outputType;
int lastDot = outputType.lastIndexOf('.');
if (lastDot > -1) {
label = outputType.substring(lastDot + 1);
}
buf.append("<rule>\n");
buf.append("<pattern>");
buf.append(outputType);
buf.append("</pattern>\n");
buf.append("<label>");
buf.append(label);
buf.append("</label>\n");
buf.append("<style>");
buf.append(STYLES[i % STYLES.length]);
buf.append("</style>\n");
buf.append("</rule>\n");
i++;
}
buf.append("</styleMap>\n");
return buf.toString();
} | java | public static String autoGenerateStyleMap(
AnalysisEngineMetaData aTaeMetaData) {
// styles used in automatically generated style maps
final String[] STYLES = { "color:black; background:lightblue;",
"color:black; background:lightgreen;",
"color:black; background:orange;",
"color:black; background:yellow;",
"color:black; background:pink;",
"color:black; background:salmon;",
"color:black; background:cyan;",
"color:black; background:violet;",
"color:black; background:tan;",
"color:white; background:brown;",
"color:white; background:blue;",
"color:white; background:green;",
"color:white; background:red;",
"color:white; background:mediumpurple;" };
// get list of output types from TAE
ArrayList outputTypes = new ArrayList();
Capability[] capabilities = aTaeMetaData.getCapabilities();
for (int i = 0; i < capabilities.length; i++) {
TypeOrFeature[] outputs = capabilities[i].getOutputs();
for (int j = 0; j < outputs.length; j++) {
if (outputs[j].isType()
&& !outputTypes.contains(outputs[j].getName())) {
outputTypes.add(outputs[j].getName());
}
}
}
// generate style map by mapping each type to a background color
StringBuffer buf = new StringBuffer();
buf.append("<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>\n");
buf.append("<styleMap>\n");
int i = 0;
Iterator it = outputTypes.iterator();
while (it.hasNext()) {
String outputType = (String) it.next();
String label = outputType;
int lastDot = outputType.lastIndexOf('.');
if (lastDot > -1) {
label = outputType.substring(lastDot + 1);
}
buf.append("<rule>\n");
buf.append("<pattern>");
buf.append(outputType);
buf.append("</pattern>\n");
buf.append("<label>");
buf.append(label);
buf.append("</label>\n");
buf.append("<style>");
buf.append(STYLES[i % STYLES.length]);
buf.append("</style>\n");
buf.append("</rule>\n");
i++;
}
buf.append("</styleMap>\n");
return buf.toString();
} | [
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BlueBrain/bluima | modules/bluima_utils/src/main/java/ch/epfl/bbp/uima/annotationviewer/BlueAnnotationViewGenerator.java | BlueAnnotationViewGenerator.autoGenerateStyleMap | public static String autoGenerateStyleMap(TypeSystemDescription aTypeSystem) {
// styles used in automatically generated style maps
final String[] STYLES = { "color:black; background:lightblue;",
"color:black; background:lightgreen;",
"color:black; background:orange;",
"color:black; background:yellow;",
"color:black; background:pink;",
"color:black; background:salmon;",
"color:black; background:cyan;",
"color:black; background:violet;",
"color:black; background:tan;",
"color:white; background:brown;",
"color:white; background:blue;",
"color:white; background:green;",
"color:white; background:red;",
"color:white; background:mediumpurple;" };
TypeDescription[] types = aTypeSystem.getTypes();
// generate style map by mapping each type to a background color
StringBuffer buf = new StringBuffer();
buf.append("<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>\n");
buf.append("<styleMap>\n");
for (int i = 0; i < types.length; i++) {
String outputType = types[i].getName();
String label = outputType;
int lastDot = outputType.lastIndexOf('.');
if (lastDot > -1) {
label = outputType.substring(lastDot + 1);
}
buf.append("<rule>\n");
buf.append("<pattern>");
buf.append(outputType);
buf.append("</pattern>\n");
buf.append("<label>");
buf.append(label);
buf.append("</label>\n");
buf.append("<style>");
buf.append(STYLES[i % STYLES.length]);
buf.append("</style>\n");
buf.append("</rule>\n");
}
buf.append("</styleMap>\n");
return buf.toString();
} | java | public static String autoGenerateStyleMap(TypeSystemDescription aTypeSystem) {
// styles used in automatically generated style maps
final String[] STYLES = { "color:black; background:lightblue;",
"color:black; background:lightgreen;",
"color:black; background:orange;",
"color:black; background:yellow;",
"color:black; background:pink;",
"color:black; background:salmon;",
"color:black; background:cyan;",
"color:black; background:violet;",
"color:black; background:tan;",
"color:white; background:brown;",
"color:white; background:blue;",
"color:white; background:green;",
"color:white; background:red;",
"color:white; background:mediumpurple;" };
TypeDescription[] types = aTypeSystem.getTypes();
// generate style map by mapping each type to a background color
StringBuffer buf = new StringBuffer();
buf.append("<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>\n");
buf.append("<styleMap>\n");
for (int i = 0; i < types.length; i++) {
String outputType = types[i].getName();
String label = outputType;
int lastDot = outputType.lastIndexOf('.');
if (lastDot > -1) {
label = outputType.substring(lastDot + 1);
}
buf.append("<rule>\n");
buf.append("<pattern>");
buf.append(outputType);
buf.append("</pattern>\n");
buf.append("<label>");
buf.append(label);
buf.append("</label>\n");
buf.append("<style>");
buf.append(STYLES[i % STYLES.length]);
buf.append("</style>\n");
buf.append("</rule>\n");
}
buf.append("</styleMap>\n");
return buf.toString();
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BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/maxent/FileEventStream.java | FileEventStream.toLine | public static String toLine(Event event) {
StringBuffer sb = new StringBuffer();
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}
sb.append(System.getProperty("line.separator"));
return sb.toString();
} | java | public static String toLine(Event event) {
StringBuffer sb = new StringBuffer();
sb.append(event.getOutcome());
String[] context = event.getContext();
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BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/maxent/FileEventStream.java | FileEventStream.main | public static void main(String[] args) throws IOException {
if (args.length == 0) {
System.err.println("Usage: FileEventStream eventfile [iterations cutoff]");
System.exit(1);
}
int ai=0;
String eventFile = args[ai++];
EventStream es = new FileEventStream(eventFile);
int iterations = 100;
int cutoff = 5;
if (ai < args.length) {
iterations = Integer.parseInt(args[ai++]);
cutoff = Integer.parseInt(args[ai++]);
}
GISModel model = GIS.trainModel(es,iterations,cutoff);
new SuffixSensitiveGISModelWriter(model, new File(eventFile+".bin.gz")).persist();
} | java | public static void main(String[] args) throws IOException {
if (args.length == 0) {
System.err.println("Usage: FileEventStream eventfile [iterations cutoff]");
System.exit(1);
}
int ai=0;
String eventFile = args[ai++];
EventStream es = new FileEventStream(eventFile);
int iterations = 100;
int cutoff = 5;
if (ai < args.length) {
iterations = Integer.parseInt(args[ai++]);
cutoff = Integer.parseInt(args[ai++]);
}
GISModel model = GIS.trainModel(es,iterations,cutoff);
new SuffixSensitiveGISModelWriter(model, new File(eventFile+".bin.gz")).persist();
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BlueBrain/bluima | modules/bluima_scripting/src/main/java/ch/epfl/bbp/uima/laucher/Pipeline.java | Pipeline.addCapabilities | private void addCapabilities(CollectionReaderDescription crd) {
for (Capability capability : crd.getCollectionReaderMetaData()
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for (TypeOrFeature output : capability.getOutputs()) {
// LOG.info("add @TypeCapability: " + output.getName());
outputTypes.add(output.getName());
}
}
} | java | private void addCapabilities(CollectionReaderDescription crd) {
for (Capability capability : crd.getCollectionReaderMetaData()
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for (TypeOrFeature output : capability.getOutputs()) {
// LOG.info("add @TypeCapability: " + output.getName());
outputTypes.add(output.getName());
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}
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BlueBrain/bluima | modules/bluima_scripting/src/main/java/ch/epfl/bbp/uima/laucher/Pipeline.java | Pipeline.checkAndAddCapabilities | private void checkAndAddCapabilities(AnalysisEngineDescription aed) {
for (Capability capability : aed.getAnalysisEngineMetaData()
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for (TypeOrFeature input : capability.getInputs())
if (!outputTypes.contains(input.getName()))
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}
for (Capability capability : aed.getAnalysisEngineMetaData()
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for (TypeOrFeature output : capability.getOutputs()) {
// LOG.info("add @TypeCapability: " + output.getName());
outputTypes.add(output.getName());
}
}
} | java | private void checkAndAddCapabilities(AnalysisEngineDescription aed) {
for (Capability capability : aed.getAnalysisEngineMetaData()
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for (TypeOrFeature input : capability.getInputs())
if (!outputTypes.contains(input.getName()))
LOG.error("AnalysisEngine "
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}
for (Capability capability : aed.getAnalysisEngineMetaData()
.getCapabilities()) {
for (TypeOrFeature output : capability.getOutputs()) {
// LOG.info("add @TypeCapability: " + output.getName());
outputTypes.add(output.getName());
}
}
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/LinnaeusSpecies.java | LinnaeusSpecies.getMostProbableSpeciesId | public String getMostProbableSpeciesId() {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/LinnaeusSpecies.java | LinnaeusSpecies.setMostProbableSpeciesId | public void setMostProbableSpeciesId(String v) {
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if (LinnaeusSpecies_Type.featOkTst && ((LinnaeusSpecies_Type)jcasType).casFeat_mostProbableSpeciesId == null)
jcasType.jcas.throwFeatMissing("mostProbableSpeciesId", "ch.epfl.bbp.uima.types.LinnaeusSpecies");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/LinnaeusSpecies.java | LinnaeusSpecies.getAllIdsString | public String getAllIdsString() {
if (LinnaeusSpecies_Type.featOkTst && ((LinnaeusSpecies_Type)jcasType).casFeat_allIdsString == null)
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if (LinnaeusSpecies_Type.featOkTst && ((LinnaeusSpecies_Type)jcasType).casFeat_allIdsString == null)
jcasType.jcas.throwFeatMissing("allIdsString", "ch.epfl.bbp.uima.types.LinnaeusSpecies");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/LinnaeusSpecies.java | LinnaeusSpecies.setAllIdsString | public void setAllIdsString(String v) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/LinnaeusSpecies.java | LinnaeusSpecies.getAmbigous | public boolean getAmbigous() {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/LinnaeusSpecies.java | LinnaeusSpecies.setAmbigous | public void setAmbigous(boolean v) {
if (LinnaeusSpecies_Type.featOkTst && ((LinnaeusSpecies_Type)jcasType).casFeat_ambigous == null)
jcasType.jcas.throwFeatMissing("ambigous", "ch.epfl.bbp.uima.types.LinnaeusSpecies");
jcasType.ll_cas.ll_setBooleanValue(addr, ((LinnaeusSpecies_Type)jcasType).casFeatCode_ambigous, v);} | java | public void setAmbigous(boolean v) {
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/TagLink.java | TagLink.getMinStringSize | private double getMinStringSize(String[] tTokens, String[] uTokens) {
double tSize = 0, uSize = 0;
for (int i = 0; i < tTokens.length; i++) {
tSize += tTokens[i].length();
}
for (int i = 0; i < uTokens.length; i++) {
uSize += uTokens[i].length();
}
return Math.min(tSize, uSize);
} | java | private double getMinStringSize(String[] tTokens, String[] uTokens) {
double tSize = 0, uSize = 0;
for (int i = 0; i < tTokens.length; i++) {
tSize += tTokens[i].length();
}
for (int i = 0; i < uTokens.length; i++) {
uSize += uTokens[i].length();
}
return Math.min(tSize, uSize);
} | [
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/TagLink.java | TagLink.score | public double score(StringWrapper s, StringWrapper t) {
checkTrainingHasHappened(s,t);
UnitVector sBag = asUnitVector(s);
UnitVector tBag = asUnitVector(t);
if (s.unwrap().equals(t.unwrap())) {
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String[] sTokens = getTokenArray(sBag),
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double[] sIdfArray = getIDFArray(sBag),
tIdfArray = getIDFArray(tBag);
return algorithm1(sTokens, tTokens, sIdfArray, tIdfArray);
}
} | java | public double score(StringWrapper s, StringWrapper t) {
checkTrainingHasHappened(s,t);
UnitVector sBag = asUnitVector(s);
UnitVector tBag = asUnitVector(t);
if (s.unwrap().equals(t.unwrap())) {
return 1.0;
}
else {
String[] sTokens = getTokenArray(sBag),
tTokens = getTokenArray(tBag);
double[] sIdfArray = getIDFArray(sBag),
tIdfArray = getIDFArray(tBag);
return algorithm1(sTokens, tTokens, sIdfArray, tIdfArray);
}
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/TagLink.java | TagLink.getIDFArray | private double[] getIDFArray(BagOfTokens bag) {
double[] idfArray = new double[bag.size()];
Iterator it = bag.tokenIterator();
int i = 0;
while (it.hasNext()) {
Token tok = (Token) it.next();
idfArray[i] = bag.getWeight(tok);
i++;
}
return idfArray;
} | java | private double[] getIDFArray(BagOfTokens bag) {
double[] idfArray = new double[bag.size()];
Iterator it = bag.tokenIterator();
int i = 0;
while (it.hasNext()) {
Token tok = (Token) it.next();
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/TagLink.java | TagLink.algorithm1 | private double algorithm1(String[] tTokens, String[] uTokens,
double[] tIdfArray, double[] uIdfArray) {
ArrayList candidateList = obtainCandidateList(tTokens, uTokens, tIdfArray,
uIdfArray);
sortCandidateList(candidateList);
double scoreValue = 0.0;
HashMap tMap = new HashMap(),
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Iterator it = candidateList.iterator();
while (it.hasNext()) {
Candidates actualCandidates = (Candidates) it.next();
Integer tPos = new Integer(actualCandidates.getTPos());
Integer uPos = new Integer(actualCandidates.getUPos());
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double actualScore = actualCandidates.getScore();
scoreValue += actualScore;
tMap.put(tPos, null);
uMap.put(uPos, null);
}
}
return scoreValue;
} | java | private double algorithm1(String[] tTokens, String[] uTokens,
double[] tIdfArray, double[] uIdfArray) {
ArrayList candidateList = obtainCandidateList(tTokens, uTokens, tIdfArray,
uIdfArray);
sortCandidateList(candidateList);
double scoreValue = 0.0;
HashMap tMap = new HashMap(),
uMap = new HashMap();
Iterator it = candidateList.iterator();
while (it.hasNext()) {
Candidates actualCandidates = (Candidates) it.next();
Integer tPos = new Integer(actualCandidates.getTPos());
Integer uPos = new Integer(actualCandidates.getUPos());
if ( (!tMap.containsKey(tPos)) &&
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double actualScore = actualCandidates.getScore();
scoreValue += actualScore;
tMap.put(tPos, null);
uMap.put(uPos, null);
}
}
return scoreValue;
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/TagLink.java | TagLink.obtainCandidateList | private ArrayList obtainCandidateList(String[] tTokens, String[] uTokens,
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ArrayList candidateList = new ArrayList();
double minStringSize = getMinStringSize(tTokens, uTokens);
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double weightMatched = matched / minStringSize,
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if (innerScore == 1) {
lastTr = tr;
}
candidateList.add(new Candidates(t, u, innerScore * weight));
}
}
}
}
return candidateList;
} | java | private ArrayList obtainCandidateList(String[] tTokens, String[] uTokens,
double[] tIdfArray, double[] uIdfArray) {
ArrayList candidateList = new ArrayList();
double minStringSize = getMinStringSize(tTokens, uTokens);
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int lastTr = -1;
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int tr = Math.abs(t - u);
if (lastTr >= 0 && lastTr < tr) {
flag = 1;
}
else {
String tTok = tTokens[t], uTok = uTokens[u];
double innerScore = tokenDistance.score(tTok,
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if (innerScore >= 0.0) {
double matched = 0.0;
if (innerScore == 1.0) {
matched = tTokens[t].length();
}
else {
matched = ( (TagLinkToken) tokenDistance).getMatched();
}
double weightMatched = matched / minStringSize,
weightTFIDF = tIdfArray[t] * uIdfArray[u],
weight = (weightTFIDF + weightMatched) / 2.0;
if (innerScore == 1) {
lastTr = tr;
}
candidateList.add(new Candidates(t, u, innerScore * weight));
}
}
}
}
return candidateList;
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/TagLink.java | TagLink.sortCandidateList | private void sortCandidateList(ArrayList list) {
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if (scoreU < scoreT) {
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return 0;
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}
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} | java | private void sortCandidateList(ArrayList list) {
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/TagLink.java | TagLink.round | private double round(double number) {
int round = (int) (number * 1000.00);
double rest = (number * 1000.00) - round;
if (rest >= 0.5) {
round++;
}
return (round / 1000.00);
} | java | private double round(double number) {
int round = (int) (number * 1000.00);
double rest = (number * 1000.00) - round;
if (rest >= 0.5) {
round++;
}
return (round / 1000.00);
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/BagOfSourcedTokens.java | BagOfSourcedTokens.getEquivalentToken | SourcedToken getEquivalentToken(Token tok) {
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} else {
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} | java | SourcedToken getEquivalentToken(Token tok) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/Relation.java | Relation.getArguments | public FSArray getArguments() {
if (Relation_Type.featOkTst && ((Relation_Type)jcasType).casFeat_arguments == null)
jcasType.jcas.throwFeatMissing("arguments", "de.julielab.jules.types.ace.Relation");
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if (Relation_Type.featOkTst && ((Relation_Type)jcasType).casFeat_arguments == null)
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ResourceEntry.java | ResourceEntry.getEntryId | public String getEntryId() {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ResourceEntry.java | ResourceEntry.setEntryId | public void setEntryId(String v) {
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jcasType.ll_cas.ll_setStringValue(addr, ((ResourceEntry_Type)jcasType).casFeatCode_entryId, v);} | java | public void setEntryId(String v) {
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ResourceEntry.java#L116-L119 | train |
BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ResourceEntry.java | ResourceEntry.getVersion | public String getVersion() {
if (ResourceEntry_Type.featOkTst && ((ResourceEntry_Type)jcasType).casFeat_version == null)
jcasType.jcas.throwFeatMissing("version", "de.julielab.jules.types.ResourceEntry");
return jcasType.ll_cas.ll_getStringValue(addr, ((ResourceEntry_Type)jcasType).casFeatCode_version);} | java | public String getVersion() {
if (ResourceEntry_Type.featOkTst && ((ResourceEntry_Type)jcasType).casFeat_version == null)
jcasType.jcas.throwFeatMissing("version", "de.julielab.jules.types.ResourceEntry");
return jcasType.ll_cas.ll_getStringValue(addr, ((ResourceEntry_Type)jcasType).casFeatCode_version);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ResourceEntry.java | ResourceEntry.setVersion | public void setVersion(String v) {
if (ResourceEntry_Type.featOkTst && ((ResourceEntry_Type)jcasType).casFeat_version == null)
jcasType.jcas.throwFeatMissing("version", "de.julielab.jules.types.ResourceEntry");
jcasType.ll_cas.ll_setStringValue(addr, ((ResourceEntry_Type)jcasType).casFeatCode_version, v);} | java | public void setVersion(String v) {
if (ResourceEntry_Type.featOkTst && ((ResourceEntry_Type)jcasType).casFeat_version == null)
jcasType.jcas.throwFeatMissing("version", "de.julielab.jules.types.ResourceEntry");
jcasType.ll_cas.ll_setStringValue(addr, ((ResourceEntry_Type)jcasType).casFeatCode_version, v);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ListItem.java | ListItem.getLevel | public int getLevel() {
if (ListItem_Type.featOkTst && ((ListItem_Type)jcasType).casFeat_level == null)
jcasType.jcas.throwFeatMissing("level", "de.julielab.jules.types.ListItem");
return jcasType.ll_cas.ll_getIntValue(addr, ((ListItem_Type)jcasType).casFeatCode_level);} | java | public int getLevel() {
if (ListItem_Type.featOkTst && ((ListItem_Type)jcasType).casFeat_level == null)
jcasType.jcas.throwFeatMissing("level", "de.julielab.jules.types.ListItem");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ListItem.java | ListItem.setLevel | public void setLevel(int v) {
if (ListItem_Type.featOkTst && ((ListItem_Type)jcasType).casFeat_level == null)
jcasType.jcas.throwFeatMissing("level", "de.julielab.jules.types.ListItem");
jcasType.ll_cas.ll_setIntValue(addr, ((ListItem_Type)jcasType).casFeatCode_level, v);} | java | public void setLevel(int v) {
if (ListItem_Type.featOkTst && ((ListItem_Type)jcasType).casFeat_level == null)
jcasType.jcas.throwFeatMissing("level", "de.julielab.jules.types.ListItem");
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BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/List.java | List.getListItemOrX | public java.util.List<Object> getListItemOrX() {
if (listItemOrX == null) {
listItemOrX = new ArrayList<Object>();
}
return this.listItemOrX;
} | java | public java.util.List<Object> getListItemOrX() {
if (listItemOrX == null) {
listItemOrX = new ArrayList<Object>();
}
return this.listItemOrX;
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/Event.java | Event.setPolarity | public void setPolarity(String v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_polarity == null)
jcasType.jcas.throwFeatMissing("polarity", "de.julielab.jules.types.ace.Event");
jcasType.ll_cas.ll_setStringValue(addr, ((Event_Type)jcasType).casFeatCode_polarity, v);} | java | public void setPolarity(String v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_polarity == null)
jcasType.jcas.throwFeatMissing("polarity", "de.julielab.jules.types.ace.Event");
jcasType.ll_cas.ll_setStringValue(addr, ((Event_Type)jcasType).casFeatCode_polarity, v);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/Event.java | Event.getGenericity | public String getGenericity() {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_genericity == null)
jcasType.jcas.throwFeatMissing("genericity", "de.julielab.jules.types.ace.Event");
return jcasType.ll_cas.ll_getStringValue(addr, ((Event_Type)jcasType).casFeatCode_genericity);} | java | public String getGenericity() {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_genericity == null)
jcasType.jcas.throwFeatMissing("genericity", "de.julielab.jules.types.ace.Event");
return jcasType.ll_cas.ll_getStringValue(addr, ((Event_Type)jcasType).casFeatCode_genericity);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/Event.java | Event.setGenericity | public void setGenericity(String v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_genericity == null)
jcasType.jcas.throwFeatMissing("genericity", "de.julielab.jules.types.ace.Event");
jcasType.ll_cas.ll_setStringValue(addr, ((Event_Type)jcasType).casFeatCode_genericity, v);} | java | public void setGenericity(String v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_genericity == null)
jcasType.jcas.throwFeatMissing("genericity", "de.julielab.jules.types.ace.Event");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/Event.java | Event.setMentions | public void setMentions(int i, EventMention v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_mentions == null)
jcasType.jcas.throwFeatMissing("mentions", "de.julielab.jules.types.ace.Event");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_mentions), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_mentions), i, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setMentions(int i, EventMention v) {
if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_mentions == null)
jcasType.jcas.throwFeatMissing("mentions", "de.julielab.jules.types.ace.Event");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_mentions), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_mentions), i, jcasType.ll_cas.ll_getFSRef(v));} | [
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BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/Debug.java | Debug.printTableMeta | public static void printTableMeta(String outputDirPath, File pdfFile, String meta) {
try {
File middleDir = new File(outputDirPath, "metadata");
if (!middleDir.exists()) {
middleDir.mkdirs();
}
File tableMetaFile = new File(middleDir, pdfFile.getName() + ".metadata");
BufferedWriter bw0 = new BufferedWriter(new FileWriter(tableMetaFile));
//System.out.println(meta);
bw0.write(meta);
bw0.close();
}
catch (IOException e){
System.out.printf("[Debug Error] IOException\n");
}
} | java | public static void printTableMeta(String outputDirPath, File pdfFile, String meta) {
try {
File middleDir = new File(outputDirPath, "metadata");
if (!middleDir.exists()) {
middleDir.mkdirs();
}
File tableMetaFile = new File(middleDir, pdfFile.getName() + ".metadata");
BufferedWriter bw0 = new BufferedWriter(new FileWriter(tableMetaFile));
//System.out.println(meta);
bw0.write(meta);
bw0.close();
}
catch (IOException e){
System.out.printf("[Debug Error] IOException\n");
}
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BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/Debug.java | Debug.printStatInfo | public static void printStatInfo(String outputDirPath, File pdfFile, int pageNum, int tableNum) {
try {
File classificationData = new File(outputDirPath, "statInfo");
if (!classificationData.exists()) {
classificationData.mkdirs();
}
File fileName = new File(classificationData, "tableNumStatInfo.txt");
BufferedWriter bw0 = new BufferedWriter(new FileWriter(fileName, true));
bw0.append(outputDirPath+pdfFile.getName() + "\t\t" + pageNum + " PAGES\t\t" + tableNum + " TABLES\n");
bw0.close();
}
catch (IOException e){
System.out.printf("[Debug Error] IOException\n");
}
} | java | public static void printStatInfo(String outputDirPath, File pdfFile, int pageNum, int tableNum) {
try {
File classificationData = new File(outputDirPath, "statInfo");
if (!classificationData.exists()) {
classificationData.mkdirs();
}
File fileName = new File(classificationData, "tableNumStatInfo.txt");
BufferedWriter bw0 = new BufferedWriter(new FileWriter(fileName, true));
bw0.append(outputDirPath+pdfFile.getName() + "\t\t" + pageNum + " PAGES\t\t" + tableNum + " TABLES\n");
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catch (IOException e){
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/RelatedArticle.java | RelatedArticle.getRelatedArticle | public String getRelatedArticle() {
if (RelatedArticle_Type.featOkTst && ((RelatedArticle_Type)jcasType).casFeat_relatedArticle == null)
jcasType.jcas.throwFeatMissing("relatedArticle", "de.julielab.jules.types.RelatedArticle");
return jcasType.ll_cas.ll_getStringValue(addr, ((RelatedArticle_Type)jcasType).casFeatCode_relatedArticle);} | java | public String getRelatedArticle() {
if (RelatedArticle_Type.featOkTst && ((RelatedArticle_Type)jcasType).casFeat_relatedArticle == null)
jcasType.jcas.throwFeatMissing("relatedArticle", "de.julielab.jules.types.RelatedArticle");
return jcasType.ll_cas.ll_getStringValue(addr, ((RelatedArticle_Type)jcasType).casFeatCode_relatedArticle);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/RelatedArticle.java | RelatedArticle.setRelatedArticle | public void setRelatedArticle(String v) {
if (RelatedArticle_Type.featOkTst && ((RelatedArticle_Type)jcasType).casFeat_relatedArticle == null)
jcasType.jcas.throwFeatMissing("relatedArticle", "de.julielab.jules.types.RelatedArticle");
jcasType.ll_cas.ll_setStringValue(addr, ((RelatedArticle_Type)jcasType).casFeatCode_relatedArticle, v);} | java | public void setRelatedArticle(String v) {
if (RelatedArticle_Type.featOkTst && ((RelatedArticle_Type)jcasType).casFeat_relatedArticle == null)
jcasType.jcas.throwFeatMissing("relatedArticle", "de.julielab.jules.types.RelatedArticle");
jcasType.ll_cas.ll_setStringValue(addr, ((RelatedArticle_Type)jcasType).casFeatCode_relatedArticle, v);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.getMeSHList | public FSArray getMeSHList() {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_meSHList == null)
jcasType.jcas.throwFeatMissing("meSHList", "de.julielab.jules.types.pubmed.ManualDescriptor");
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jcasType.jcas.throwFeatMissing("meSHList", "de.julielab.jules.types.pubmed.ManualDescriptor");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.setMeSHList | public void setMeSHList(FSArray v) {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_meSHList == null)
jcasType.jcas.throwFeatMissing("meSHList", "de.julielab.jules.types.pubmed.ManualDescriptor");
jcasType.ll_cas.ll_setRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_meSHList, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setMeSHList(FSArray v) {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_meSHList == null)
jcasType.jcas.throwFeatMissing("meSHList", "de.julielab.jules.types.pubmed.ManualDescriptor");
jcasType.ll_cas.ll_setRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_meSHList, jcasType.ll_cas.ll_getFSRef(v));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.getMeSHList | public MeshHeading getMeSHList(int i) {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_meSHList == null)
jcasType.jcas.throwFeatMissing("meSHList", "de.julielab.jules.types.pubmed.ManualDescriptor");
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if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_meSHList == null)
jcasType.jcas.throwFeatMissing("meSHList", "de.julielab.jules.types.pubmed.ManualDescriptor");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.setMeSHList | public void setMeSHList(int i, MeshHeading v) {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_meSHList == null)
jcasType.jcas.throwFeatMissing("meSHList", "de.julielab.jules.types.pubmed.ManualDescriptor");
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jcasType.jcas.throwFeatMissing("meSHList", "de.julielab.jules.types.pubmed.ManualDescriptor");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.getChemicalList | public FSArray getChemicalList() {
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jcasType.jcas.throwFeatMissing("chemicalList", "de.julielab.jules.types.pubmed.ManualDescriptor");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_chemicalList)));} | java | public FSArray getChemicalList() {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_chemicalList == null)
jcasType.jcas.throwFeatMissing("chemicalList", "de.julielab.jules.types.pubmed.ManualDescriptor");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.setChemicalList | public void setChemicalList(FSArray v) {
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jcasType.jcas.throwFeatMissing("chemicalList", "de.julielab.jules.types.pubmed.ManualDescriptor");
jcasType.ll_cas.ll_setRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_chemicalList, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setChemicalList(FSArray v) {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_chemicalList == null)
jcasType.jcas.throwFeatMissing("chemicalList", "de.julielab.jules.types.pubmed.ManualDescriptor");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.getChemicalList | public Chemical getChemicalList(int i) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.setChemicalList | public void setChemicalList(int i, Chemical v) {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_chemicalList == null)
jcasType.jcas.throwFeatMissing("chemicalList", "de.julielab.jules.types.pubmed.ManualDescriptor");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.getDBInfoList | public FSArray getDBInfoList() {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.setDBInfoList | public void setDBInfoList(FSArray v) {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_dBInfoList == null)
jcasType.jcas.throwFeatMissing("dBInfoList", "de.julielab.jules.types.pubmed.ManualDescriptor");
jcasType.ll_cas.ll_setRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_dBInfoList, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setDBInfoList(FSArray v) {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_dBInfoList == null)
jcasType.jcas.throwFeatMissing("dBInfoList", "de.julielab.jules.types.pubmed.ManualDescriptor");
jcasType.ll_cas.ll_setRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_dBInfoList, jcasType.ll_cas.ll_getFSRef(v));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.getDBInfoList | public DBInfo getDBInfoList(int i) {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_dBInfoList == null)
jcasType.jcas.throwFeatMissing("dBInfoList", "de.julielab.jules.types.pubmed.ManualDescriptor");
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if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_dBInfoList == null)
jcasType.jcas.throwFeatMissing("dBInfoList", "de.julielab.jules.types.pubmed.ManualDescriptor");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.setDBInfoList | public void setDBInfoList(int i, DBInfo v) {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_dBInfoList == null)
jcasType.jcas.throwFeatMissing("dBInfoList", "de.julielab.jules.types.pubmed.ManualDescriptor");
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if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_dBInfoList == null)
jcasType.jcas.throwFeatMissing("dBInfoList", "de.julielab.jules.types.pubmed.ManualDescriptor");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_dBInfoList), i);
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.getKeywordList | public FSArray getKeywordList() {
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jcasType.jcas.throwFeatMissing("keywordList", "de.julielab.jules.types.pubmed.ManualDescriptor");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_keywordList)));} | java | public FSArray getKeywordList() {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_keywordList == null)
jcasType.jcas.throwFeatMissing("keywordList", "de.julielab.jules.types.pubmed.ManualDescriptor");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.setKeywordList | public void setKeywordList(FSArray v) {
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jcasType.jcas.throwFeatMissing("keywordList", "de.julielab.jules.types.pubmed.ManualDescriptor");
jcasType.ll_cas.ll_setRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_keywordList, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setKeywordList(FSArray v) {
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jcasType.jcas.throwFeatMissing("keywordList", "de.julielab.jules.types.pubmed.ManualDescriptor");
jcasType.ll_cas.ll_setRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_keywordList, jcasType.ll_cas.ll_getFSRef(v));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.getKeywordList | public Keyword getKeywordList(int i) {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_keywordList == null)
jcasType.jcas.throwFeatMissing("keywordList", "de.julielab.jules.types.pubmed.ManualDescriptor");
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jcasType.jcas.throwFeatMissing("keywordList", "de.julielab.jules.types.pubmed.ManualDescriptor");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.setKeywordList | public void setKeywordList(int i, Keyword v) {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_keywordList == null)
jcasType.jcas.throwFeatMissing("keywordList", "de.julielab.jules.types.pubmed.ManualDescriptor");
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jcasType.jcas.throwFeatMissing("keywordList", "de.julielab.jules.types.pubmed.ManualDescriptor");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.getGeneSymbolList | public StringArray getGeneSymbolList() {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_geneSymbolList == null)
jcasType.jcas.throwFeatMissing("geneSymbolList", "de.julielab.jules.types.pubmed.ManualDescriptor");
return (StringArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_geneSymbolList)));} | java | public StringArray getGeneSymbolList() {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.setGeneSymbolList | public void setGeneSymbolList(StringArray v) {
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jcasType.ll_cas.ll_setRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_geneSymbolList, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setGeneSymbolList(StringArray v) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.getGeneSymbolList | public String getGeneSymbolList(int i) {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_geneSymbolList == null)
jcasType.jcas.throwFeatMissing("geneSymbolList", "de.julielab.jules.types.pubmed.ManualDescriptor");
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return jcasType.ll_cas.ll_getStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_geneSymbolList), i);} | java | public String getGeneSymbolList(int i) {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_geneSymbolList == null)
jcasType.jcas.throwFeatMissing("geneSymbolList", "de.julielab.jules.types.pubmed.ManualDescriptor");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/ManualDescriptor.java | ManualDescriptor.setGeneSymbolList | public void setGeneSymbolList(int i, String v) {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_geneSymbolList == null)
jcasType.jcas.throwFeatMissing("geneSymbolList", "de.julielab.jules.types.pubmed.ManualDescriptor");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_geneSymbolList), i);
jcasType.ll_cas.ll_setStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_geneSymbolList), i, v);} | java | public void setGeneSymbolList(int i, String v) {
if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_geneSymbolList == null)
jcasType.jcas.throwFeatMissing("geneSymbolList", "de.julielab.jules.types.pubmed.ManualDescriptor");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_geneSymbolList), i);
jcasType.ll_cas.ll_setStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_geneSymbolList), i, v);} | [
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BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/maxent/BasicEventStream.java | BasicEventStream.nextEvent | public Event nextEvent () {
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BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/maxent/BasicEventStream.java | BasicEventStream.hasNext | public boolean hasNext () {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/BodyCitation.java | BodyCitation.getTextValue | public String getTextValue() {
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return jcasType.ll_cas.ll_getStringValue(addr, ((BodyCitation_Type)jcasType).casFeatCode_textValue);} | java | public String getTextValue() {
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jcasType.jcas.throwFeatMissing("textValue", "ch.epfl.bbp.uima.types.BodyCitation");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/BodyCitation.java | BodyCitation.setTextValue | public void setTextValue(String v) {
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jcasType.ll_cas.ll_setStringValue(addr, ((BodyCitation_Type)jcasType).casFeatCode_textValue, v);} | java | public void setTextValue(String v) {
if (BodyCitation_Type.featOkTst && ((BodyCitation_Type)jcasType).casFeat_textValue == null)
jcasType.jcas.throwFeatMissing("textValue", "ch.epfl.bbp.uima.types.BodyCitation");
jcasType.ll_cas.ll_setStringValue(addr, ((BodyCitation_Type)jcasType).casFeatCode_textValue, v);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/Header.java | Header.getCitationStatus | public String getCitationStatus() {
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return jcasType.ll_cas.ll_getStringValue(addr, ((Header_Type)jcasType).casFeatCode_citationStatus);} | java | public String getCitationStatus() {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/pubmed/Header.java | Header.setCitationStatus | public void setCitationStatus(String v) {
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jcasType.ll_cas.ll_setStringValue(addr, ((Header_Type)jcasType).casFeatCode_citationStatus, v);} | java | public void setCitationStatus(String v) {
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jcasType.jcas.throwFeatMissing("citationStatus", "de.julielab.jules.types.pubmed.Header");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EventMention.java | EventMention.getAnchor | public Anchor getAnchor() {
if (EventMention_Type.featOkTst && ((EventMention_Type)jcasType).casFeat_anchor == null)
jcasType.jcas.throwFeatMissing("anchor", "de.julielab.jules.types.ace.EventMention");
return (Anchor)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((EventMention_Type)jcasType).casFeatCode_anchor)));} | java | public Anchor getAnchor() {
if (EventMention_Type.featOkTst && ((EventMention_Type)jcasType).casFeat_anchor == null)
jcasType.jcas.throwFeatMissing("anchor", "de.julielab.jules.types.ace.EventMention");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EventMention.java | EventMention.setAnchor | public void setAnchor(Anchor v) {
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if (EventMention_Type.featOkTst && ((EventMention_Type)jcasType).casFeat_anchor == null)
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EventMention.java | EventMention.getLevel | public String getLevel() {
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return jcasType.ll_cas.ll_getStringValue(addr, ((EventMention_Type)jcasType).casFeatCode_level);} | java | public String getLevel() {
if (EventMention_Type.featOkTst && ((EventMention_Type)jcasType).casFeat_level == null)
jcasType.jcas.throwFeatMissing("level", "de.julielab.jules.types.ace.EventMention");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EventMention.java | EventMention.setLevel | public void setLevel(String v) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EventMention.java | EventMention.getLdc_scope | public LDC_Scope getLdc_scope() {
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if (EventMention_Type.featOkTst && ((EventMention_Type)jcasType).casFeat_ldc_scope == null)
jcasType.jcas.throwFeatMissing("ldc_scope", "de.julielab.jules.types.ace.EventMention");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EventMention.java | EventMention.setLdc_scope | public void setLdc_scope(LDC_Scope v) {
if (EventMention_Type.featOkTst && ((EventMention_Type)jcasType).casFeat_ldc_scope == null)
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")",
"jcasType",
".",
"jcas",
".",
"throwF... | setter for ldc_scope - sets
@generated
@param v value to set into the feature | [
"setter",
"for",
"ldc_scope",
"-",
"sets"
] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EventMention.java#L183-L186 | train |
BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EventMention.java | EventMention.getEvent_ref | public Event getEvent_ref() {
if (EventMention_Type.featOkTst && ((EventMention_Type)jcasType).casFeat_event_ref == null)
jcasType.jcas.throwFeatMissing("event_ref", "de.julielab.jules.types.ace.EventMention");
return (Event)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((EventMention_Type)jcasType).casFeatCode_event_ref)));} | java | public Event getEvent_ref() {
if (EventMention_Type.featOkTst && ((EventMention_Type)jcasType).casFeat_event_ref == null)
jcasType.jcas.throwFeatMissing("event_ref", "de.julielab.jules.types.ace.EventMention");
return (Event)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((EventMention_Type)jcasType).casFeatCode_event_ref)));} | [
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... | getter for event_ref - gets
@generated
@return value of 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/ace/EventMention.java#L196-L199 | train |
BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EventMention.java | EventMention.setEvent_ref | public void setEvent_ref(Event v) {
if (EventMention_Type.featOkTst && ((EventMention_Type)jcasType).casFeat_event_ref == null)
jcasType.jcas.throwFeatMissing("event_ref", "de.julielab.jules.types.ace.EventMention");
jcasType.ll_cas.ll_setRefValue(addr, ((EventMention_Type)jcasType).casFeatCode_event_ref, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setEvent_ref(Event v) {
if (EventMention_Type.featOkTst && ((EventMention_Type)jcasType).casFeat_event_ref == null)
jcasType.jcas.throwFeatMissing("event_ref", "de.julielab.jules.types.ace.EventMention");
jcasType.ll_cas.ll_setRefValue(addr, ((EventMention_Type)jcasType).casFeatCode_event_ref, jcasType.ll_cas.ll_getFSRef(v));} | [
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@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/ace/EventMention.java#L205-L208 | train |
BlueBrain/bluima | modules/bluima_utils/src/main/java/ch/epfl/bbp/uima/BlueCasUtil.java | BlueCasUtil.fixNoSentences | public static void fixNoSentences(JCas jCas) {
Collection<Sentence> sentences = select(jCas, Sentence.class);
if (sentences.size() == 0) {
String text = jCas.getDocumentText();
Sentence sentence = new Sentence(jCas, 0, text.length());
sentence.addToIndexes();
}
} | java | public static void fixNoSentences(JCas jCas) {
Collection<Sentence> sentences = select(jCas, Sentence.class);
if (sentences.size() == 0) {
String text = jCas.getDocumentText();
Sentence sentence = new Sentence(jCas, 0, text.length());
sentence.addToIndexes();
}
} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/GENIAConstituent.java | GENIAConstituent.getSyn | public String getSyn() {
if (GENIAConstituent_Type.featOkTst && ((GENIAConstituent_Type)jcasType).casFeat_syn == null)
jcasType.jcas.throwFeatMissing("syn", "de.julielab.jules.types.GENIAConstituent");
return jcasType.ll_cas.ll_getStringValue(addr, ((GENIAConstituent_Type)jcasType).casFeatCode_syn);} | java | public String getSyn() {
if (GENIAConstituent_Type.featOkTst && ((GENIAConstituent_Type)jcasType).casFeat_syn == null)
jcasType.jcas.throwFeatMissing("syn", "de.julielab.jules.types.GENIAConstituent");
return jcasType.ll_cas.ll_getStringValue(addr, ((GENIAConstituent_Type)jcasType).casFeatCode_syn);} | [
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@generated
@return value of the feature | [
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"O"
] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/GENIAConstituent.java#L85-L88 | train |
BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/GENIAConstituent.java | GENIAConstituent.setSyn | public void setSyn(String v) {
if (GENIAConstituent_Type.featOkTst && ((GENIAConstituent_Type)jcasType).casFeat_syn == null)
jcasType.jcas.throwFeatMissing("syn", "de.julielab.jules.types.GENIAConstituent");
jcasType.ll_cas.ll_setStringValue(addr, ((GENIAConstituent_Type)jcasType).casFeatCode_syn, v);} | java | public void setSyn(String v) {
if (GENIAConstituent_Type.featOkTst && ((GENIAConstituent_Type)jcasType).casFeat_syn == null)
jcasType.jcas.throwFeatMissing("syn", "de.julielab.jules.types.GENIAConstituent");
jcasType.ll_cas.ll_setStringValue(addr, ((GENIAConstituent_Type)jcasType).casFeatCode_syn, v);} | [
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@generated
@param v value to set into the feature | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/GENIAConstituent.java#L94-L97 | train |
BlueBrain/bluima | modules/bluima_topic_models/src/main/scala/cc/mallet/topics/MyTopicInferencer.java | MyTopicInferencer.writeInferredDistributions | public void writeInferredDistributions(InstanceList instances,
File distributionsFile,
int numIterations, int thinning, int burnIn,
double threshold, int max) throws IOException {
PrintWriter out = new PrintWriter(distributionsFile);
out.print ("#doc source topic proportion ...\n");
IDSorter[] sortedTopics = new IDSorter[ numTopics ];
for (int topic = 0; topic < numTopics; topic++) {
// Initialize the sorters with dummy values
sortedTopics[topic] = new IDSorter(topic, topic);
}
if (max < 0 || max > numTopics) {
max = numTopics;
}
int doc = 0;
for (Instance instance: instances) {
double[] topicDistribution =
getSampledDistribution(instance, numIterations,
thinning, burnIn);
out.print (doc); out.print (' ');
// Print the Source field of the instance
if (instance.getSource() != null) {
out.print (instance.getSource());
}
else {
out.print ("null-source");
}
out.print (' ');
for (int topic = 0; topic < numTopics; topic++) {
sortedTopics[topic].set(topic, topicDistribution[topic]);
}
Arrays.sort(sortedTopics);
for (int i = 0; i < max; i++) {
if (sortedTopics[i].getWeight() < threshold) { break; }
out.print (sortedTopics[i].getID() + " " +
sortedTopics[i].getWeight() + " ");
}
out.print (" \n");
doc++;
}
out.close();
} | java | public void writeInferredDistributions(InstanceList instances,
File distributionsFile,
int numIterations, int thinning, int burnIn,
double threshold, int max) throws IOException {
PrintWriter out = new PrintWriter(distributionsFile);
out.print ("#doc source topic proportion ...\n");
IDSorter[] sortedTopics = new IDSorter[ numTopics ];
for (int topic = 0; topic < numTopics; topic++) {
// Initialize the sorters with dummy values
sortedTopics[topic] = new IDSorter(topic, topic);
}
if (max < 0 || max > numTopics) {
max = numTopics;
}
int doc = 0;
for (Instance instance: instances) {
double[] topicDistribution =
getSampledDistribution(instance, numIterations,
thinning, burnIn);
out.print (doc); out.print (' ');
// Print the Source field of the instance
if (instance.getSource() != null) {
out.print (instance.getSource());
}
else {
out.print ("null-source");
}
out.print (' ');
for (int topic = 0; topic < numTopics; topic++) {
sortedTopics[topic].set(topic, topicDistribution[topic]);
}
Arrays.sort(sortedTopics);
for (int i = 0; i < max; i++) {
if (sortedTopics[i].getWeight() < threshold) { break; }
out.print (sortedTopics[i].getID() + " " +
sortedTopics[i].getWeight() + " ");
}
out.print (" \n");
doc++;
}
out.close();
} | [
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write distributions to the provided file.
@param instances
@param distributionsFile
@param numIterations The total number of iterations of sampling per document
@param thinning The number of iterations between saved samples
@param burnIn The number of iterations before the first saved sample
@param threshold The minimum proportion of a given topic that will be written
@param max The total number of topics to report per document] | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_topic_models/src/main/scala/cc/mallet/topics/MyTopicInferencer.java#L419-L472 | train |
BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/SourceFile.java | SourceFile.getAuthor | public String getAuthor() {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_author == null)
jcasType.jcas.throwFeatMissing("author", "de.julielab.jules.types.ace.SourceFile");
return jcasType.ll_cas.ll_getStringValue(addr, ((SourceFile_Type)jcasType).casFeatCode_author);} | java | public String getAuthor() {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_author == null)
jcasType.jcas.throwFeatMissing("author", "de.julielab.jules.types.ace.SourceFile");
return jcasType.ll_cas.ll_getStringValue(addr, ((SourceFile_Type)jcasType).casFeatCode_author);} | [
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"(",
"\"autho... | getter for author - gets
@generated
@return value of the feature | [
"getter",
"for",
"author",
"-",
"gets"
] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/SourceFile.java#L86-L89 | train |
BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/SourceFile.java | SourceFile.setAuthor | public void setAuthor(String v) {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_author == null)
jcasType.jcas.throwFeatMissing("author", "de.julielab.jules.types.ace.SourceFile");
jcasType.ll_cas.ll_setStringValue(addr, ((SourceFile_Type)jcasType).casFeatCode_author, v);} | java | public void setAuthor(String v) {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_author == null)
jcasType.jcas.throwFeatMissing("author", "de.julielab.jules.types.ace.SourceFile");
jcasType.ll_cas.ll_setStringValue(addr, ((SourceFile_Type)jcasType).casFeatCode_author, v);} | [
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... | setter for author - sets
@generated
@param v value to set into the feature | [
"setter",
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"author",
"-",
"sets"
] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/SourceFile.java#L95-L98 | train |
BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/SourceFile.java | SourceFile.setUri | public void setUri(String v) {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_uri == null)
jcasType.jcas.throwFeatMissing("uri", "de.julielab.jules.types.ace.SourceFile");
jcasType.ll_cas.ll_setStringValue(addr, ((SourceFile_Type)jcasType).casFeatCode_uri, v);} | java | public void setUri(String v) {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_uri == null)
jcasType.jcas.throwFeatMissing("uri", "de.julielab.jules.types.ace.SourceFile");
jcasType.ll_cas.ll_setStringValue(addr, ((SourceFile_Type)jcasType).casFeatCode_uri, v);} | [
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"throwFeatMissing",
"(",... | setter for uri - sets
@generated
@param v value to set into the feature | [
"setter",
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"uri",
"-",
"sets"
] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/SourceFile.java#L117-L120 | train |
BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/SourceFile.java | SourceFile.getEncoding | public String getEncoding() {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_encoding == null)
jcasType.jcas.throwFeatMissing("encoding", "de.julielab.jules.types.ace.SourceFile");
return jcasType.ll_cas.ll_getStringValue(addr, ((SourceFile_Type)jcasType).casFeatCode_encoding);} | java | public String getEncoding() {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_encoding == null)
jcasType.jcas.throwFeatMissing("encoding", "de.julielab.jules.types.ace.SourceFile");
return jcasType.ll_cas.ll_getStringValue(addr, ((SourceFile_Type)jcasType).casFeatCode_encoding);} | [
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"(",
"\"e... | getter for encoding - gets
@generated
@return value of the feature | [
"getter",
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"-",
"gets"
] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/SourceFile.java#L130-L133 | train |
BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/SourceFile.java | SourceFile.setEncoding | public void setEncoding(String v) {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_encoding == null)
jcasType.jcas.throwFeatMissing("encoding", "de.julielab.jules.types.ace.SourceFile");
jcasType.ll_cas.ll_setStringValue(addr, ((SourceFile_Type)jcasType).casFeatCode_encoding, v);} | java | public void setEncoding(String v) {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_encoding == null)
jcasType.jcas.throwFeatMissing("encoding", "de.julielab.jules.types.ace.SourceFile");
jcasType.ll_cas.ll_setStringValue(addr, ((SourceFile_Type)jcasType).casFeatCode_encoding, v);} | [
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"throwFeatMissin... | setter for encoding - sets
@generated
@param v value to set into the feature | [
"setter",
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"encoding",
"-",
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/SourceFile.java#L139-L142 | train |
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