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
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java | DataTable.getReferenceText | public String getReferenceText() {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_referenceText == null)
jcasType.jcas.throwFeatMissing("referenceText", "ch.epfl.bbp.uima.types.DataTable");
return jcasType.ll_cas.ll_getStringValue(addr, ((DataTable_Type)jcasType).casFeatCode_referenceT... | java | public String getReferenceText() {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_referenceText == null)
jcasType.jcas.throwFeatMissing("referenceText", "ch.epfl.bbp.uima.types.DataTable");
return jcasType.ll_cas.ll_getStringValue(addr, ((DataTable_Type)jcasType).casFeatCode_referenceT... | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java | DataTable.setReferenceText | public void setReferenceText(String v) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_referenceText == null)
jcasType.jcas.throwFeatMissing("referenceText", "ch.epfl.bbp.uima.types.DataTable");
jcasType.ll_cas.ll_setStringValue(addr, ((DataTable_Type)jcasType).casFeatCode_referenceTe... | java | public void setReferenceText(String v) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_referenceText == null)
jcasType.jcas.throwFeatMissing("referenceText", "ch.epfl.bbp.uima.types.DataTable");
jcasType.ll_cas.ll_setStringValue(addr, ((DataTable_Type)jcasType).casFeatCode_referenceTe... | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java | DataTable.getPageNumber | public int getPageNumber() {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_pageNumber == null)
jcasType.jcas.throwFeatMissing("pageNumber", "ch.epfl.bbp.uima.types.DataTable");
return jcasType.ll_cas.ll_getIntValue(addr, ((DataTable_Type)jcasType).casFeatCode_pageNumber);} | java | public int getPageNumber() {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_pageNumber == null)
jcasType.jcas.throwFeatMissing("pageNumber", "ch.epfl.bbp.uima.types.DataTable");
return jcasType.ll_cas.ll_getIntValue(addr, ((DataTable_Type)jcasType).casFeatCode_pageNumber);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java | DataTable.setPageNumber | public void setPageNumber(int v) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_pageNumber == null)
jcasType.jcas.throwFeatMissing("pageNumber", "ch.epfl.bbp.uima.types.DataTable");
jcasType.ll_cas.ll_setIntValue(addr, ((DataTable_Type)jcasType).casFeatCode_pageNumber, v);} | java | public void setPageNumber(int v) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_pageNumber == null)
jcasType.jcas.throwFeatMissing("pageNumber", "ch.epfl.bbp.uima.types.DataTable");
jcasType.ll_cas.ll_setIntValue(addr, ((DataTable_Type)jcasType).casFeatCode_pageNumber, v);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/Token.java | Token.getWordForms | public FSArray getWordForms() {
if (Token_Type.featOkTst && ((Token_Type)jcasType).casFeat_wordForms == null)
jcasType.jcas.throwFeatMissing("wordForms", "com.digitalpebble.rasp.Token");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((Token_Type)jcasType).casFeatCode... | java | public FSArray getWordForms() {
if (Token_Type.featOkTst && ((Token_Type)jcasType).casFeat_wordForms == null)
jcasType.jcas.throwFeatMissing("wordForms", "com.digitalpebble.rasp.Token");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((Token_Type)jcasType).casFeatCode... | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/Token.java | Token.setWordForms | public void setWordForms(FSArray v) {
if (Token_Type.featOkTst && ((Token_Type)jcasType).casFeat_wordForms == null)
jcasType.jcas.throwFeatMissing("wordForms", "com.digitalpebble.rasp.Token");
jcasType.ll_cas.ll_setRefValue(addr, ((Token_Type)jcasType).casFeatCode_wordForms, jcasType.ll_cas.ll_getFSRef(v)... | java | public void setWordForms(FSArray v) {
if (Token_Type.featOkTst && ((Token_Type)jcasType).casFeat_wordForms == null)
jcasType.jcas.throwFeatMissing("wordForms", "com.digitalpebble.rasp.Token");
jcasType.ll_cas.ll_setRefValue(addr, ((Token_Type)jcasType).casFeatCode_wordForms, jcasType.ll_cas.ll_getFSRef(v)... | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/Token.java | Token.getWordForms | public WordForm getWordForms(int i) {
if (Token_Type.featOkTst && ((Token_Type)jcasType).casFeat_wordForms == null)
jcasType.jcas.throwFeatMissing("wordForms", "com.digitalpebble.rasp.Token");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Token_Type)jcasType).casFeatCode_wordForms)... | java | public WordForm getWordForms(int i) {
if (Token_Type.featOkTst && ((Token_Type)jcasType).casFeat_wordForms == null)
jcasType.jcas.throwFeatMissing("wordForms", "com.digitalpebble.rasp.Token");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Token_Type)jcasType).casFeatCode_wordForms)... | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/Token.java | Token.setWordForms | public void setWordForms(int i, WordForm v) {
if (Token_Type.featOkTst && ((Token_Type)jcasType).casFeat_wordForms == null)
jcasType.jcas.throwFeatMissing("wordForms", "com.digitalpebble.rasp.Token");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Token_Type)jcasType).casFeatCode_w... | java | public void setWordForms(int i, WordForm v) {
if (Token_Type.featOkTst && ((Token_Type)jcasType).casFeat_wordForms == null)
jcasType.jcas.throwFeatMissing("wordForms", "com.digitalpebble.rasp.Token");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Token_Type)jcasType).casFeatCode_w... | [
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/abbvGapsHmm/AlignmentPredictionModel.java | AlignmentPredictionModel.trainOnAll | public boolean trainOnAll() {
List<Map<String, String>> trueLabels = loadLabels(_trueLabelsFile);
List<String> corpus = loadTrainingCorpus(_trainingCorpusFile);
List<List<Acronym>> trainingExtractedCandidates = new ArrayList<List<Acronym>>();
List<Map<String, String>> trueLabelsForTraining = new ArrayList<Map... | java | public boolean trainOnAll() {
List<Map<String, String>> trueLabels = loadLabels(_trueLabelsFile);
List<String> corpus = loadTrainingCorpus(_trainingCorpusFile);
List<List<Acronym>> trainingExtractedCandidates = new ArrayList<List<Acronym>>();
List<Map<String, String>> trueLabelsForTraining = new ArrayList<Map... | [
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/abbvGapsHmm/AlignmentPredictionModel.java | AlignmentPredictionModel.trainOnCandidates | public boolean trainOnCandidates() {
List<String> corpus = loadTrainingCorpus(_trainingCorpusFile);
List<List<Acronym>> trainingExtractedCandidates = new ArrayList<List<Acronym>>();
for (Integer docID = 0; docID < corpus.size(); ++docID) {
// Adds to training examples, all the extracted pairs from the
//... | java | public boolean trainOnCandidates() {
List<String> corpus = loadTrainingCorpus(_trainingCorpusFile);
List<List<Acronym>> trainingExtractedCandidates = new ArrayList<List<Acronym>>();
for (Integer docID = 0; docID < corpus.size(); ++docID) {
// Adds to training examples, all the extracted pairs from the
//... | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/POSVerb.java | POSVerb.getBiolexicon_id | public String getBiolexicon_id() {
if (POSVerb_Type.featOkTst && ((POSVerb_Type)jcasType).casFeat_biolexicon_id == null)
jcasType.jcas.throwFeatMissing("biolexicon_id", "ch.epfl.bbp.uima.types.POSVerb");
return jcasType.ll_cas.ll_getStringValue(addr, ((POSVerb_Type)jcasType).casFeatCode_biolexicon_id);} | java | public String getBiolexicon_id() {
if (POSVerb_Type.featOkTst && ((POSVerb_Type)jcasType).casFeat_biolexicon_id == null)
jcasType.jcas.throwFeatMissing("biolexicon_id", "ch.epfl.bbp.uima.types.POSVerb");
return jcasType.ll_cas.ll_getStringValue(addr, ((POSVerb_Type)jcasType).casFeatCode_biolexicon_id);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/POSVerb.java | POSVerb.setBiolexicon_id | public void setBiolexicon_id(String v) {
if (POSVerb_Type.featOkTst && ((POSVerb_Type)jcasType).casFeat_biolexicon_id == null)
jcasType.jcas.throwFeatMissing("biolexicon_id", "ch.epfl.bbp.uima.types.POSVerb");
jcasType.ll_cas.ll_setStringValue(addr, ((POSVerb_Type)jcasType).casFeatCode_biolexicon_id, v);} | java | public void setBiolexicon_id(String v) {
if (POSVerb_Type.featOkTst && ((POSVerb_Type)jcasType).casFeat_biolexicon_id == null)
jcasType.jcas.throwFeatMissing("biolexicon_id", "ch.epfl.bbp.uima.types.POSVerb");
jcasType.ll_cas.ll_setStringValue(addr, ((POSVerb_Type)jcasType).casFeatCode_biolexicon_id, v);} | [
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BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/model/Table.java | Table.setBody | public void setBody(String body)
{
String xbody = body;
String [] row = xbody.split("\n");
for(int i=0; i<row.length; i++){
this.m_xbody.add(row[i]);
}
} | java | public void setBody(String body)
{
String xbody = body;
String [] row = xbody.split("\n");
for(int i=0; i<row.length; i++){
this.m_xbody.add(row[i]);
}
} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/model/Table.java#L231-L238 | train |
BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/model/Table.java | Table.setHeading | public void setHeading(String heading)
{
String m_heading = heading;
String [] preCol = m_heading.split("\n");
String [][] cells = new String[preCol.length][this.m_columnNumber];
for(int i=0; i<preCol.length; i++)
cells[i] = preCol[i].split(";", this.m_col... | java | public void setHeading(String heading)
{
String m_heading = heading;
String [] preCol = m_heading.split("\n");
String [][] cells = new String[preCol.length][this.m_columnNumber];
for(int i=0; i<preCol.length; i++)
cells[i] = preCol[i].split(";", this.m_col... | [
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BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/model/Table.java | Table.setValidTable | public void setValidTable(TableCandidate tc)
{
/**
* TODO [improve]: Table/TableCandidate not match
* */
this.setHeight(tc.getHeight());
this.setWidth(tc.getWidth());
this.setCaption(tc.getCaption());
this.setRowNumber(tc.getRows().size());
this.setColumnNumber(tc.... | java | public void setValidTable(TableCandidate tc)
{
/**
* TODO [improve]: Table/TableCandidate not match
* */
this.setHeight(tc.getHeight());
this.setWidth(tc.getWidth());
this.setCaption(tc.getCaption());
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/RelationMention.java | RelationMention.getLexical_condition | public String getLexical_condition() {
if (RelationMention_Type.featOkTst && ((RelationMention_Type)jcasType).casFeat_lexical_condition == null)
jcasType.jcas.throwFeatMissing("lexical_condition", "de.julielab.jules.types.ace.RelationMention");
return jcasType.ll_cas.ll_getStringValue(addr, ((RelationMent... | java | public String getLexical_condition() {
if (RelationMention_Type.featOkTst && ((RelationMention_Type)jcasType).casFeat_lexical_condition == null)
jcasType.jcas.throwFeatMissing("lexical_condition", "de.julielab.jules.types.ace.RelationMention");
return jcasType.ll_cas.ll_getStringValue(addr, ((RelationMent... | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/RelationMention.java | RelationMention.setLexical_condition | public void setLexical_condition(String v) {
if (RelationMention_Type.featOkTst && ((RelationMention_Type)jcasType).casFeat_lexical_condition == null)
jcasType.jcas.throwFeatMissing("lexical_condition", "de.julielab.jules.types.ace.RelationMention");
jcasType.ll_cas.ll_setStringValue(addr, ((RelationMenti... | java | public void setLexical_condition(String v) {
if (RelationMention_Type.featOkTst && ((RelationMention_Type)jcasType).casFeat_lexical_condition == null)
jcasType.jcas.throwFeatMissing("lexical_condition", "de.julielab.jules.types.ace.RelationMention");
jcasType.ll_cas.ll_setStringValue(addr, ((RelationMenti... | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/RelationMention.java | RelationMention.getRelation_ref | public Relation getRelation_ref() {
if (RelationMention_Type.featOkTst && ((RelationMention_Type)jcasType).casFeat_relation_ref == null)
jcasType.jcas.throwFeatMissing("relation_ref", "de.julielab.jules.types.ace.RelationMention");
return (Relation)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRef... | java | public Relation getRelation_ref() {
if (RelationMention_Type.featOkTst && ((RelationMention_Type)jcasType).casFeat_relation_ref == null)
jcasType.jcas.throwFeatMissing("relation_ref", "de.julielab.jules.types.ace.RelationMention");
return (Relation)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRef... | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/RelationMention.java | RelationMention.setRelation_ref | public void setRelation_ref(Relation v) {
if (RelationMention_Type.featOkTst && ((RelationMention_Type)jcasType).casFeat_relation_ref == null)
jcasType.jcas.throwFeatMissing("relation_ref", "de.julielab.jules.types.ace.RelationMention");
jcasType.ll_cas.ll_setRefValue(addr, ((RelationMention_Type)jcasType... | java | public void setRelation_ref(Relation v) {
if (RelationMention_Type.featOkTst && ((RelationMention_Type)jcasType).casFeat_relation_ref == null)
jcasType.jcas.throwFeatMissing("relation_ref", "de.julielab.jules.types.ace.RelationMention");
jcasType.ll_cas.ll_setRefValue(addr, ((RelationMention_Type)jcasType... | [
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BlueBrain/bluima | modules/bluima_opennlp/src/main/java/de/julielab/jules/ae/opennlp/ParseAnnotator.java | ParseAnnotator.loadMappings | private void loadMappings() {
for (int i = 0; i < mappings.length; i++) {
String[] pair = mappings[i].split(";");
if (pair.length < 2) {
try {
throw new AnnotatorConfigurationException();
} catch (AnnotatorConfigurationException e) {
LOGGER.error("[OpenNLP Parser: ]" + e.getMessage());
... | java | private void loadMappings() {
for (int i = 0; i < mappings.length; i++) {
String[] pair = mappings[i].split(";");
if (pair.length < 2) {
try {
throw new AnnotatorConfigurationException();
} catch (AnnotatorConfigurationException e) {
LOGGER.error("[OpenNLP Parser: ]" + e.getMessage());
... | [
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BlueBrain/bluima | modules/bluima_opennlp/src/main/java/de/julielab/jules/ae/opennlp/ParseAnnotator.java | ParseAnnotator.annotate | private void annotate(Parse parse, JCas cas, Constituent parent)
throws SecurityException, IllegalArgumentException,
ClassNotFoundException, NoSuchMethodException,
InstantiationException, IllegalAccessException,
InvocationTargetException {
Constituent cons = null;
Span span = parse.getSpan();
String l... | java | private void annotate(Parse parse, JCas cas, Constituent parent)
throws SecurityException, IllegalArgumentException,
ClassNotFoundException, NoSuchMethodException,
InstantiationException, IllegalAccessException,
InvocationTargetException {
Constituent cons = null;
Span span = parse.getSpan();
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BlueBrain/bluima | modules/bluima_opennlp/src/main/java/de/julielab/jules/ae/opennlp/ParseAnnotator.java | ParseAnnotator.makeFunAnnotations | private void makeFunAnnotations(Constituent cons, String[] funCatLabels) {
if (funCatLabels != null && funCatLabels.length > 1) {
String labeltype;
for (int i = 1; i < funCatLabels.length; i++) {
labeltype = funTable.get(funCatLabels[i]);
if (labeltype != null) {
Class c = cons.getClass();
if... | java | private void makeFunAnnotations(Constituent cons, String[] funCatLabels) {
if (funCatLabels != null && funCatLabels.length > 1) {
String labeltype;
for (int i = 1; i < funCatLabels.length; i++) {
labeltype = funTable.get(funCatLabels[i]);
if (labeltype != null) {
Class c = cons.getClass();
if... | [
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BlueBrain/bluima | modules/bluima_opennlp/src/main/java/de/julielab/jules/ae/opennlp/ParseAnnotator.java | ParseAnnotator.initBracketMap | private void initBracketMap() {
escMap.put("(", "-LRB-");
escMap.put(")", "-RRB-");
escMap.put("{", "-LCB-");
escMap.put("}", "-RCB-");
escMap.put("[", "-LSB-");
escMap.put("]", "-RSB-");
} | java | private void initBracketMap() {
escMap.put("(", "-LRB-");
escMap.put(")", "-RRB-");
escMap.put("{", "-LCB-");
escMap.put("}", "-RCB-");
escMap.put("[", "-LSB-");
escMap.put("]", "-RSB-");
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BlueBrain/bluima | modules/bluima_opennlp/src/main/java/de/julielab/jules/ae/opennlp/ParseAnnotator.java | ParseAnnotator.initFunMap | private void initFunMap() {
funTable.put("ADV", "formFuncDisc");
funTable.put("NOM", "formFuncDisc");
funTable.put("DTV", "gramRole");
funTable.put("LGS", "gramRole");
funTable.put("PRD", "gramRole");
funTable.put("PUT", "gramRole");
funTable.put("SBJ", "gramRole");
funTable.put("VOC", "gramRole");
... | java | private void initFunMap() {
funTable.put("ADV", "formFuncDisc");
funTable.put("NOM", "formFuncDisc");
funTable.put("DTV", "gramRole");
funTable.put("LGS", "gramRole");
funTable.put("PRD", "gramRole");
funTable.put("PUT", "gramRole");
funTable.put("SBJ", "gramRole");
funTable.put("VOC", "gramRole");
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BlueBrain/bluima | modules/bluima_bbp/src/main/java/ch/epfl/bbp/uima/ae/ExtractBrainregionsCoocurrences2.java | ExtractBrainregionsCoocurrences2.getLoadline | private String[] getLoadline(Pair<BrainRegion, BrainRegion> pair, int pmId) {
BrainRegion br1 = pair.getKey();
BrainRegion br2 = pair.getValue();
return new String[] {
pmId + "",//
br1.getCoveredText().replaceAll("(\\r|\\n|\\t)", ""),
br1.getBegi... | java | private String[] getLoadline(Pair<BrainRegion, BrainRegion> pair, int pmId) {
BrainRegion br1 = pair.getKey();
BrainRegion br2 = pair.getValue();
return new String[] {
pmId + "",//
br1.getCoveredText().replaceAll("(\\r|\\n|\\t)", ""),
br1.getBegi... | [
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BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/maxent/GISTrainer.java | GISTrainer.eval | public void eval(int[] context, double[] outsums) {
for (int oid = 0; oid < numOutcomes; oid++) {
outsums[oid] = iprob;
numfeats[oid] = 0;
}
int[] activeOutcomes;
double[] activeParameters;
for (int i = 0; i < context.length; i++) {
Context predParams = params[context[i]];
a... | java | public void eval(int[] context, double[] outsums) {
for (int oid = 0; oid < numOutcomes; oid++) {
outsums[oid] = iprob;
numfeats[oid] = 0;
}
int[] activeOutcomes;
double[] activeParameters;
for (int i = 0; i < context.length; i++) {
Context predParams = params[context[i]];
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DocumentBlock.java | DocumentBlock.getHasBold | public boolean getHasBold() {
if (DocumentBlock_Type.featOkTst && ((DocumentBlock_Type)jcasType).casFeat_hasBold == null)
jcasType.jcas.throwFeatMissing("hasBold", "ch.epfl.bbp.uima.types.DocumentBlock");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DocumentBlock.java | DocumentBlock.setHasBold | public void setHasBold(boolean v) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DocumentBlock.java | DocumentBlock.getHasManyFontsizes | public boolean getHasManyFontsizes() {
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if (DocumentBlock_Type.featOkTst && ((DocumentBlock_Type)jcasType).casFeat_hasManyFontsizes == null)
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DocumentBlock.java | DocumentBlock.setHasManyFontsizes | public void setHasManyFontsizes(boolean v) {
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BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/AppGroup.java | AppGroup.getAppOrRefList | public java.util.List<Object> getAppOrRefList() {
if (appOrRefList == null) {
appOrRefList = new ArrayList<Object>();
}
return this.appOrRefList;
} | java | public java.util.List<Object> getAppOrRefList() {
if (appOrRefList == null) {
appOrRefList = new ArrayList<Object>();
}
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BlueBrain/bluima | modules/bluima_jsre/src/main/java/org/itc/irst/tcc/sre/data/SentenceSet2VectorSet.java | SentenceSet2VectorSet.getHelp | private static String getHelp()
{
StringBuffer sb = new StringBuffer();
// SRE
sb.append("\njSRE: Simple Relation Extraction V1.10\t 30.08.06\n");
sb.append("developed by Claudio Giuliano (giuliano@itc.it)\n\n");
// License
sb.append("Copyright 2005 FBK-irst (http://www.fbk.eu)\n");
sb.append("\n");
... | java | private static String getHelp()
{
StringBuffer sb = new StringBuffer();
// SRE
sb.append("\njSRE: Simple Relation Extraction V1.10\t 30.08.06\n");
sb.append("developed by Claudio Giuliano (giuliano@itc.it)\n\n");
// License
sb.append("Copyright 2005 FBK-irst (http://www.fbk.eu)\n");
sb.append("\n");
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/MatchExptScript.java | MatchExptScript.clear | public void clear(String what)
{
if (what.equals("blockers")) blockers.clear();
else if (what.equals("datasets")) datasets.clear();
else if (what.equals("learners")) learners.clear();
else if (what.equals("all")) {
clear("blockers"); clear("datasets"); clear("learners");
} else {
System.out.println... | java | public void clear(String what)
{
if (what.equals("blockers")) blockers.clear();
else if (what.equals("datasets")) datasets.clear();
else if (what.equals("learners")) learners.clear();
else if (what.equals("all")) {
clear("blockers"); clear("datasets"); clear("learners");
} else {
System.out.println... | [
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/MatchExptScript.java | MatchExptScript.show | public void show(String what)
{
if (what.equals("blockers")) showList("blockers",blockerNames);
else if (what.equals("datasets")) showList("datasets", datasetNames);
else if (what.equals("learners")) showList("learners", learnerNames);
else if (what.equals("all")) {
show("blockers"); show("datasets"); ... | java | public void show(String what)
{
if (what.equals("blockers")) showList("blockers",blockerNames);
else if (what.equals("datasets")) showList("datasets", datasetNames);
else if (what.equals("learners")) showList("learners", learnerNames);
else if (what.equals("all")) {
show("blockers"); show("datasets"); ... | [
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/MatchExptScript.java | MatchExptScript.dataset | public void dataset(String dataFile) throws MatchData.InputFormatException
{
datasets.add( new MatchData(dataFile) );
datasetNames.add( dataFile );
expt = null;
} | java | public void dataset(String dataFile) throws MatchData.InputFormatException
{
datasets.add( new MatchData(dataFile) );
datasetNames.add( dataFile );
expt = null;
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/MatchExptScript.java | MatchExptScript.learner | public void learner(String learnerClass)
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learners.add( DistanceLearnerFactory.build( learnerClass ));
learnerNames.add( learnerClass );
expt = null;
} | java | public void learner(String learnerClass)
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learners.add( DistanceLearnerFactory.build( learnerClass ));
learnerNames.add( learnerClass );
expt = null;
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/MatchExptScript.java | MatchExptScript.blocker | public void blocker(String blockerClass)
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{
blockers.add( Class.forName(BLOCKER_PACKAGE+blockerClass).newInstance() );
blockerNames.add( blockerClass );
expt = null;
} | java | public void blocker(String blockerClass)
throws ClassNotFoundException,InstantiationException,IllegalAccessException
{
blockers.add( Class.forName(BLOCKER_PACKAGE+blockerClass).newInstance() );
blockerNames.add( blockerClass );
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/MatchExptScript.java | MatchExptScript.blocker | public void blocker(String blockerClass, String param, String value)
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{
Blocker blocker = (Blocker)Class.forName(BLOCKER_PACKAGE+blockerClass).newInstance();
// upperCase the first l... | java | public void blocker(String blockerClass, String param, String value)
throws ClassNotFoundException,InstantiationException,IllegalAccessException,
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Blocker blocker = (Blocker)Class.forName(BLOCKER_PACKAGE+blockerClass).newInstance();
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/MatchExptScript.java | MatchExptScript.compute | public void compute()
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if (!computable) {
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expt = new MatchExpt[blockers.size()][learners.size()][datasets.size()];
for (int i=0; i<blockers.size(); i++) {
Blocker blocker = (Blocker)blockers.get(i);
for (int j=0... | java | public void compute()
{
if (!computable) {
throw new RuntimeException("can't re-'compute' experiment results after a 'restore'");
}
expt = new MatchExpt[blockers.size()][learners.size()][datasets.size()];
for (int i=0; i<blockers.size(); i++) {
Blocker blocker = (Blocker)blockers.get(i);
for (int j=0... | [
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/MatchExptScript.java | MatchExptScript.table | public void table(String what) throws NoSuchMethodException,IllegalAccessException,InvocationTargetException
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PrintfFormat dfmt = new PrintfFormat("Dataset %2d:");
PrintfFormat fmt = new PrintfFormat(" %9.5f ");
PrintfFormat nfmt = new PrintfFormat(" %11s");
if (expt==null) compute();
for (int i=0; i<block... | java | public void table(String what) throws NoSuchMethodException,IllegalAccessException,InvocationTargetException
{
PrintfFormat dfmt = new PrintfFormat("Dataset %2d:");
PrintfFormat fmt = new PrintfFormat(" %9.5f ");
PrintfFormat nfmt = new PrintfFormat(" %11s");
if (expt==null) compute();
for (int i=0; i<block... | [
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/MatchExptScript.java | MatchExptScript.save | public void save(String file) throws IOException,FileNotFoundException
{
ObjectOutputStream oos = new ObjectOutputStream(new FileOutputStream(file));
oos.writeObject(blockerNames);
oos.writeObject(datasetNames);
oos.writeObject(learnerNames);
oos.writeObject(expt);
oos.close();
} | java | public void save(String file) throws IOException,FileNotFoundException
{
ObjectOutputStream oos = new ObjectOutputStream(new FileOutputStream(file));
oos.writeObject(blockerNames);
oos.writeObject(datasetNames);
oos.writeObject(learnerNames);
oos.writeObject(expt);
oos.close();
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/MatchExptScript.java | MatchExptScript.restore | public void restore(String file) throws IOException,FileNotFoundException,ClassNotFoundException
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ObjectInputStream ois = new ObjectInputStream(new FileInputStream(file));
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datasetNames = (List)ois.readObject();
learnerNames = (List)ois.readObject();
expt = (MatchExpt[]... | java | public void restore(String file) throws IOException,FileNotFoundException,ClassNotFoundException
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/MatchExptScript.java | MatchExptScript.runScript | public void runScript(String configFileName)
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/MatchExptScript.java | MatchExptScript.execCommand | private void execCommand(String command,List args)
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/TokenFelligiSunter.java | TokenFelligiSunter.prepare | public StringWrapper prepare(String s) {
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Integer dfInteger = (Inte... | java | public StringWrapper prepare(String s) {
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BlueBrain/bluima | utils/blue_commons/src/main/java/ch/epfl/bbp/MissingUtils.java | MissingUtils.format | public static String format(String msg, Object... args) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/wikipedia/Descriptor.java | Descriptor.getCategories | public FSArray getCategories() {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/wikipedia/Descriptor.java | Descriptor.setCategories | public void setCategories(FSArray v) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/wikipedia/Descriptor.java | Descriptor.getCategories | public Title getCategories(int i) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/wikipedia/Descriptor.java | Descriptor.setCategories | public void setCategories(int i, Title v) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/wikipedia/Descriptor.java | Descriptor.getOutgoingLinks | public FSArray getOutgoingLinks() {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/wikipedia/Descriptor.java | Descriptor.setOutgoingLinks | public void setOutgoingLinks(FSArray v) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/wikipedia/Descriptor.java | Descriptor.getOutgoingLinks | public Title getOutgoingLinks(int i) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/wikipedia/Descriptor.java | Descriptor.getRedirects | public String getRedirects(int i) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/wikipedia/Descriptor.java | Descriptor.setRedirects | public void setRedirects(int i, String v) {
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BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/Bio.java | Bio.getRid | public java.util.List<Object> getRid() {
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BlueBrain/bluima | modules/bluima_scripting/src/main/java/ch/epfl/bbp/uima/laucher/PipelineScriptParser.java | PipelineScriptParser.parse | public static Pipeline parse(File scriptFile, List<String> replacementVars)
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BlueBrain/bluima | modules/bluima_scripting/src/main/java/ch/epfl/bbp/uima/laucher/PipelineScriptParser.java | PipelineScriptParser.parse | public static Pipeline parse(List<String> scriptLines,
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BlueBrain/bluima | modules/bluima_scripting/src/main/java/ch/epfl/bbp/uima/laucher/PipelineScriptParser.java | PipelineScriptParser.parsePython | private static void parsePython(IteratorWithPrevious<String> it,
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BlueBrain/bluima | modules/bluima_scripting/src/main/java/ch/epfl/bbp/uima/laucher/PipelineScriptParser.java | PipelineScriptParser.parseJava | private static void parseJava(IteratorWithPrevious<String> it,
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BlueBrain/bluima | modules/bluima_scripting/src/main/java/ch/epfl/bbp/uima/laucher/PipelineScriptParser.java | PipelineScriptParser.parseInclude | private static void parseInclude(String line, Pipeline pipeline,
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BlueBrain/bluima | modules/bluima_scripting/src/main/java/ch/epfl/bbp/uima/laucher/PipelineScriptParser.java | PipelineScriptParser.validateParams | private static void validateParams(List<Object> params, Class<?> classz) {
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duracloud/duracloud | security/src/main/java/org/duracloud/security/vote/VoterUtil.java | VoterUtil.debugText | protected static String debugText(String heading,
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duracloud/duracloud | common/src/main/java/org/duracloud/common/util/IOUtil.java | IOUtil.addFileToZipOutputStream | public static void addFileToZipOutputStream(File file, ZipOutputStream zipOs) throws IOException {
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zipEntry.setSize(file.length());
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duracloud/duracloud | glacierstorageprovider/src/main/java/org/duracloud/glacierstorage/GlacierStorageProvider.java | GlacierStorageProvider.checkStorageState | private void checkStorageState(StorageException e) {
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duracloud/duracloud | durastore/src/main/java/org/duracloud/durastore/rest/ManifestRest.java | ManifestRest.generateAsynchronously | private URI generateAsynchronously(String account,
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duracloud/duracloud | durastore/src/main/java/org/duracloud/durastore/util/StorageProviderFactoryImpl.java | StorageProviderFactoryImpl.getStorageAccounts | @Override
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List<StorageAccount> accts = new ArrayList<>();
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duracloud/duracloud | durastore/src/main/java/org/duracloud/durastore/util/StorageProviderFactoryImpl.java | StorageProviderFactoryImpl.getStorageProvider | @Override
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duracloud/duracloud | durastore/src/main/java/org/duracloud/durastore/util/StorageProviderFactoryImpl.java | StorageProviderFactoryImpl.expireStorageProvider | @Override
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storageAccountId = checkStorageAccountId(storageAccountId);
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duracloud/duracloud | durastore/src/main/java/org/duracloud/durastore/util/ProviderFactoryBase.java | ProviderFactoryBase.initialize | public void initialize(DuraStoreInitConfig initConfig,
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duracloud/duracloud | common-queue/src/main/java/org/duracloud/common/queue/task/Task.java | Task.getAttempts | public int getAttempts() {
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duracloud/duracloud | s3storageprovider/src/main/java/org/duracloud/s3task/streaminghls/GetHlsSignedCookiesUrlTaskRunner.java | GetHlsSignedCookiesUrlTaskRunner.performTask | public String performTask(String taskParameters) {
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duracloud/duracloud | retrievaltool/src/main/java/org/duracloud/retrieval/mgmt/RetrievalManager.java | RetrievalManager.run | public void run() {
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duracloud/duracloud | retrievaltool/src/main/java/org/duracloud/retrieval/mgmt/RetrievalManager.java | RetrievalManager.shutdown | public void shutdown() {
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duracloud/duracloud | common-xml/src/main/java/org/duracloud/common/xml/XmlSerializer.java | XmlSerializer.serialize | public String serialize(T obj) {
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duracloud/duracloud | common-xml/src/main/java/org/duracloud/common/xml/XmlSerializer.java | XmlSerializer.deserialize | public T deserialize(String xml) {
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duracloud/duracloud | common-xml/src/main/java/org/duracloud/common/xml/XmlSerializer.java | XmlSerializer.deserialize | public T deserialize(InputStream stream) {
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duracloud/duracloud | storageprovider/src/main/java/org/duracloud/storage/provider/StorageProviderBase.java | StorageProviderBase.getSpaceProperties | public Map<String, String> getSpaceProperties(String spaceId) {
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duracloud/duracloud | storageprovider/src/main/java/org/duracloud/storage/provider/StorageProviderBase.java | StorageProviderBase.setNewSpaceProperties | public void setNewSpaceProperties(String spaceId,
Map<String, String> spaceProperties) {
setNewSpaceProperties(spaceId, spaceProperties, getSpaceACLs(spaceId));
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setNewSpaceProperties(spaceId, spaceProperties, getSpaceACLs(spaceId));
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duracloud/duracloud | storageprovider/src/main/java/org/duracloud/storage/provider/StorageProviderBase.java | StorageProviderBase.setNewSpaceProperties | public void setNewSpaceProperties(String spaceId,
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duracloud/duracloud | storageprovider/src/main/java/org/duracloud/storage/provider/StorageProviderBase.java | StorageProviderBase.deleteSpaceSync | public void deleteSpaceSync(String spaceId) {
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doSetSpaceProperties(spaceId, allProps);
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allProps.put("is-delete", "true");
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duracloud/duracloud | durastore/src/main/java/org/duracloud/durastore/rest/TaskRest.java | TaskRest.getSupportedTasks | @GET
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duracloud/duracloud | durastore/src/main/java/org/duracloud/durastore/rest/TaskRest.java | TaskRest.performTask | @Path("/{taskName}")
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public Response performTask(@PathParam("taskName") String taskName,
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task... | java | @Path("/{taskName}")
@POST
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duracloud/duracloud | durastore/src/main/java/org/duracloud/durastore/rest/ContentResourceImpl.java | ContentResourceImpl.getContent | @Override
public RetrievedContent getContent(String spaceID,
String contentID,
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duracloud/duracloud | durastore/src/main/java/org/duracloud/durastore/rest/ContentResourceImpl.java | ContentResourceImpl.getContentProperties | @Override
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duracloud/duracloud | durastore/src/main/java/org/duracloud/durastore/rest/ContentResourceImpl.java | ContentResourceImpl.updateContentProperties | @Override
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duracloud/duracloud | durastore/src/main/java/org/duracloud/durastore/rest/ContentResourceImpl.java | ContentResourceImpl.addContent | @Override
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duracloud/duracloud | common-notification/src/main/java/org/duracloud/common/notification/NotificationManager.java | NotificationManager.initializeNotifiers | public void initializeNotifiers(Collection<NotificationConfig> notificationConfigs) {
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duracloud/duracloud | common-notification/src/main/java/org/duracloud/common/notification/NotificationManager.java | NotificationManager.sendNotification | public void sendNotification(NotificationType type,
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String message,
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String message,
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duracloud/duracloud | common-notification/src/main/java/org/duracloud/common/notification/NotificationManager.java | NotificationManager.sendAdminNotification | public void sendAdminNotification(NotificationType type,
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String message) {
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String subject,
String message) {
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duracloud/duracloud | s3storageprovider/src/main/java/org/duracloud/s3storage/StringDataStore.java | StringDataStore.storeData | public String storeData(String cookieData) {
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try {
String token = generateToken();
ensureSpaceExists();
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duracloud/duracloud | s3storageprovider/src/main/java/org/duracloud/s3storage/StringDataStore.java | StringDataStore.retrieveData | public String retrieveData(String token) {
try {
RetrievedContent data = this.s3StorageProvider.getContent(this.hiddenSpaceName, token);
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} catch (NotFoundException ex) {
return null;
} catch (E... | java | public String retrieveData(String token) {
try {
RetrievedContent data = this.s3StorageProvider.getContent(this.hiddenSpaceName, token);
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} catch (NotFoundException ex) {
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duracloud/duracloud | retrievaltool/src/main/java/org/duracloud/retrieval/mgmt/RetrievalWorker.java | RetrievalWorker.retrieveToFile | protected Map<String, String> retrieveToFile(File localFile, RetrievalListener listener) throws IOException {
try {
contentStream = new Retrier(5, 4000, 3).execute(() -> {
return source.getSourceContent(contentItem, listener);
});
} catch (Exception ex) {
... | java | protected Map<String, String> retrieveToFile(File localFile, RetrievalListener listener) throws IOException {
try {
contentStream = new Retrier(5, 4000, 3).execute(() -> {
return source.getSourceContent(contentItem, listener);
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... | Transfers the remote file stream to the local file
@param localFile
@param listener
@return
@throws IOException
@returns the checksum of the File upon successful retrieval. Successful
retrieval means the checksum of the local file and remote file match,
otherwise an IOException is thrown. | [
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] | dc4f3a1716d43543cc3b2e1880605f9389849b66 | https://github.com/duracloud/duracloud/blob/dc4f3a1716d43543cc3b2e1880605f9389849b66/retrievaltool/src/main/java/org/duracloud/retrieval/mgmt/RetrievalWorker.java#L233-L269 | train |
duracloud/duracloud | common-xml/src/main/java/org/duracloud/common/xml/SchemaGenerator.java | SchemaGenerator.generateSchema | public void generateSchema(Class... classes)
throws JAXBException, IOException {
if (!baseDir.exists()) {
baseDir.mkdirs();
}
JAXBContext context = JAXBContext.newInstance(classes);
context.generateSchema(this);
} | java | public void generateSchema(Class... classes)
throws JAXBException, IOException {
if (!baseDir.exists()) {
baseDir.mkdirs();
}
JAXBContext context = JAXBContext.newInstance(classes);
context.generateSchema(this);
} | [
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duracloud/duracloud | common-xml/src/main/java/org/duracloud/common/xml/SchemaGenerator.java | SchemaGenerator.createOutput | @Override
public Result createOutput(String namespaceUri, String defaultFileName)
throws IOException {
if (null == fileName) {
fileName = defaultFileName;
}
return new StreamResult(new File(baseDir, fileName));
} | java | @Override
public Result createOutput(String namespaceUri, String defaultFileName)
throws IOException {
if (null == fileName) {
fileName = defaultFileName;
}
return new StreamResult(new File(baseDir, fileName));
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