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141,200 | BlueBrain/bluima | modules/bluima_jsre/src/main/java/org/itc/irst/tcc/sre/CompareExampleSet.java | CompareExampleSet.createFeatureIndex | private FeatureIndex[] createFeatureIndex(int subspaceCount) // throws
// Exception
{
logger.info("create feature index");
FeatureIndex[] index = new FeatureIndex[subspaceCount];
for (int i = 0; i < subspaceCount; i++)
index[i] = new FeatureIndex(false, 1);
return index;
} | java | private FeatureIndex[] createFeatureIndex(int subspaceCount) // throws
// Exception
{
logger.info("create feature index");
FeatureIndex[] index = new FeatureIndex[subspaceCount];
for (int i = 0; i < subspaceCount; i++)
index[i] = new FeatureIndex(false, 1);
return index;
} | [
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141,201 | BlueBrain/bluima | modules/bluima_corpora/src/main/java/ch/epfl/bbp/uima/cr/GeniaCorpusCollectionReader.java | GeniaCorpusCollectionReader.annotatateContent | private static String annotatateContent(JCas jcas, Object contentObj,
int start) {
LOG.trace("annotate: " + reflectionToString(contentObj));
int end = start;
StringBuilder internalSb = new StringBuilder();
if (contentObj instanceof String) {
String c = (String) contentObj;
internalSb.append(c);
end += c.length();
} else if (contentObj instanceof Cons) {
Cons cons = (Cons) contentObj;
for (Object o : cons.getContent()) {
String parse = annotatateContent(jcas, o, end);
end += parse.length();
internalSb.append(parse);
}
BioEntityMention entity = new BioEntityMention(jcas, start, end);
entity.setSpecificType(cons.getSem());
entity.setComponentId(GeniaCorpusCollectionReader.COMPONENT_ID);
entity.setTextualRepresentation(cons.getLex());
entity.addToIndexes();
}
return internalSb.toString();
} | java | private static String annotatateContent(JCas jcas, Object contentObj,
int start) {
LOG.trace("annotate: " + reflectionToString(contentObj));
int end = start;
StringBuilder internalSb = new StringBuilder();
if (contentObj instanceof String) {
String c = (String) contentObj;
internalSb.append(c);
end += c.length();
} else if (contentObj instanceof Cons) {
Cons cons = (Cons) contentObj;
for (Object o : cons.getContent()) {
String parse = annotatateContent(jcas, o, end);
end += parse.length();
internalSb.append(parse);
}
BioEntityMention entity = new BioEntityMention(jcas, start, end);
entity.setSpecificType(cons.getSem());
entity.setComponentId(GeniaCorpusCollectionReader.COMPONENT_ID);
entity.setTextualRepresentation(cons.getLex());
entity.addToIndexes();
}
return internalSb.toString();
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_corpora/src/main/java/ch/epfl/bbp/uima/cr/GeniaCorpusCollectionReader.java#L115-L144 |
141,202 | BlueBrain/bluima | modules/bluima_corpora/src/main/java/ch/epfl/bbp/uima/cr/GeniaCorpusCollectionReader.java | GeniaCorpusCollectionReader.getProteins | public static Collection<BioEntityMention> getProteins(
Collection<BioEntityMention> mentions) {
ArrayList<BioEntityMention> ret = new ArrayList<BioEntityMention>();
for (BioEntityMention mention : mentions) {
if (mention.getSpecificType() != null
&& mention.getSpecificType().startsWith("G#protein"))
ret.add(mention);
}
return ret;
} | java | public static Collection<BioEntityMention> getProteins(
Collection<BioEntityMention> mentions) {
ArrayList<BioEntityMention> ret = new ArrayList<BioEntityMention>();
for (BioEntityMention mention : mentions) {
if (mention.getSpecificType() != null
&& mention.getSpecificType().startsWith("G#protein"))
ret.add(mention);
}
return ret;
} | [
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141,203 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Measure.java | Measure.getNormalizedValue | public float getNormalizedValue() {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_normalizedValue == null)
jcasType.jcas.throwFeatMissing("normalizedValue", "ch.epfl.bbp.uima.types.Measure");
return jcasType.ll_cas.ll_getFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_normalizedValue);} | java | public float getNormalizedValue() {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_normalizedValue == null)
jcasType.jcas.throwFeatMissing("normalizedValue", "ch.epfl.bbp.uima.types.Measure");
return jcasType.ll_cas.ll_getFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_normalizedValue);} | [
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@return value of the feature | [
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141,204 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Measure.java | Measure.setNormalizedValue | public void setNormalizedValue(float v) {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_normalizedValue == null)
jcasType.jcas.throwFeatMissing("normalizedValue", "ch.epfl.bbp.uima.types.Measure");
jcasType.ll_cas.ll_setFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_normalizedValue, v);} | java | public void setNormalizedValue(float v) {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_normalizedValue == null)
jcasType.jcas.throwFeatMissing("normalizedValue", "ch.epfl.bbp.uima.types.Measure");
jcasType.ll_cas.ll_setFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_normalizedValue, v);} | [
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141,205 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Measure.java | Measure.getRangeStartValue | public float getRangeStartValue() {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_rangeStartValue == null)
jcasType.jcas.throwFeatMissing("rangeStartValue", "ch.epfl.bbp.uima.types.Measure");
return jcasType.ll_cas.ll_getFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_rangeStartValue);} | java | public float getRangeStartValue() {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_rangeStartValue == null)
jcasType.jcas.throwFeatMissing("rangeStartValue", "ch.epfl.bbp.uima.types.Measure");
return jcasType.ll_cas.ll_getFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_rangeStartValue);} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Measure.java#L152-L155 |
141,206 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Measure.java | Measure.setRangeStartValue | public void setRangeStartValue(float v) {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_rangeStartValue == null)
jcasType.jcas.throwFeatMissing("rangeStartValue", "ch.epfl.bbp.uima.types.Measure");
jcasType.ll_cas.ll_setFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_rangeStartValue, v);} | java | public void setRangeStartValue(float v) {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_rangeStartValue == null)
jcasType.jcas.throwFeatMissing("rangeStartValue", "ch.epfl.bbp.uima.types.Measure");
jcasType.ll_cas.ll_setFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_rangeStartValue, v);} | [
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141,207 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Measure.java | Measure.getRangeEndValue | public float getRangeEndValue() {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_rangeEndValue == null)
jcasType.jcas.throwFeatMissing("rangeEndValue", "ch.epfl.bbp.uima.types.Measure");
return jcasType.ll_cas.ll_getFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_rangeEndValue);} | java | public float getRangeEndValue() {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_rangeEndValue == null)
jcasType.jcas.throwFeatMissing("rangeEndValue", "ch.epfl.bbp.uima.types.Measure");
return jcasType.ll_cas.ll_getFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_rangeEndValue);} | [
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141,208 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Measure.java | Measure.setRangeEndValue | public void setRangeEndValue(float v) {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_rangeEndValue == null)
jcasType.jcas.throwFeatMissing("rangeEndValue", "ch.epfl.bbp.uima.types.Measure");
jcasType.ll_cas.ll_setFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_rangeEndValue, v);} | java | public void setRangeEndValue(float v) {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_rangeEndValue == null)
jcasType.jcas.throwFeatMissing("rangeEndValue", "ch.epfl.bbp.uima.types.Measure");
jcasType.ll_cas.ll_setFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_rangeEndValue, v);} | [
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141,209 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Measure.java | Measure.getMeanValue | public float getMeanValue() {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_meanValue == null)
jcasType.jcas.throwFeatMissing("meanValue", "ch.epfl.bbp.uima.types.Measure");
return jcasType.ll_cas.ll_getFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_meanValue);} | java | public float getMeanValue() {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_meanValue == null)
jcasType.jcas.throwFeatMissing("meanValue", "ch.epfl.bbp.uima.types.Measure");
return jcasType.ll_cas.ll_getFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_meanValue);} | [
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] | getter for meanValue - gets
@generated
@return value of the feature | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Measure.java#L196-L199 |
141,210 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Measure.java | Measure.setMeanValue | public void setMeanValue(float v) {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_meanValue == null)
jcasType.jcas.throwFeatMissing("meanValue", "ch.epfl.bbp.uima.types.Measure");
jcasType.ll_cas.ll_setFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_meanValue, v);} | java | public void setMeanValue(float v) {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_meanValue == null)
jcasType.jcas.throwFeatMissing("meanValue", "ch.epfl.bbp.uima.types.Measure");
jcasType.ll_cas.ll_setFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_meanValue, v);} | [
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@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/ch/epfl/bbp/uima/types/Measure.java#L205-L208 |
141,211 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Measure.java | Measure.getStandardErrorValue | public float getStandardErrorValue() {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_standardErrorValue == null)
jcasType.jcas.throwFeatMissing("standardErrorValue", "ch.epfl.bbp.uima.types.Measure");
return jcasType.ll_cas.ll_getFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_standardErrorValue);} | java | public float getStandardErrorValue() {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_standardErrorValue == null)
jcasType.jcas.throwFeatMissing("standardErrorValue", "ch.epfl.bbp.uima.types.Measure");
return jcasType.ll_cas.ll_getFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_standardErrorValue);} | [
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@return value of the feature | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Measure.java#L218-L221 |
141,212 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Measure.java | Measure.setStandardErrorValue | public void setStandardErrorValue(float v) {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_standardErrorValue == null)
jcasType.jcas.throwFeatMissing("standardErrorValue", "ch.epfl.bbp.uima.types.Measure");
jcasType.ll_cas.ll_setFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_standardErrorValue, v);} | java | public void setStandardErrorValue(float v) {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_standardErrorValue == null)
jcasType.jcas.throwFeatMissing("standardErrorValue", "ch.epfl.bbp.uima.types.Measure");
jcasType.ll_cas.ll_setFloatValue(addr, ((Measure_Type)jcasType).casFeatCode_standardErrorValue, v);} | [
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@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/ch/epfl/bbp/uima/types/Measure.java#L227-L230 |
141,213 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Measure.java | Measure.getUnit | public String getUnit() {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_unit == null)
jcasType.jcas.throwFeatMissing("unit", "ch.epfl.bbp.uima.types.Measure");
return jcasType.ll_cas.ll_getStringValue(addr, ((Measure_Type)jcasType).casFeatCode_unit);} | java | public String getUnit() {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_unit == null)
jcasType.jcas.throwFeatMissing("unit", "ch.epfl.bbp.uima.types.Measure");
return jcasType.ll_cas.ll_getStringValue(addr, ((Measure_Type)jcasType).casFeatCode_unit);} | [
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@generated
@return value of the feature | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Measure.java#L264-L267 |
141,214 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Measure.java | Measure.setUnit | public void setUnit(String v) {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_unit == null)
jcasType.jcas.throwFeatMissing("unit", "ch.epfl.bbp.uima.types.Measure");
jcasType.ll_cas.ll_setStringValue(addr, ((Measure_Type)jcasType).casFeatCode_unit, v);} | java | public void setUnit(String v) {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_unit == null)
jcasType.jcas.throwFeatMissing("unit", "ch.epfl.bbp.uima.types.Measure");
jcasType.ll_cas.ll_setStringValue(addr, ((Measure_Type)jcasType).casFeatCode_unit, 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/ch/epfl/bbp/uima/types/Measure.java#L273-L276 |
141,215 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Measure.java | Measure.getNormalizedUnit | public String getNormalizedUnit() {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_normalizedUnit == null)
jcasType.jcas.throwFeatMissing("normalizedUnit", "ch.epfl.bbp.uima.types.Measure");
return jcasType.ll_cas.ll_getStringValue(addr, ((Measure_Type)jcasType).casFeatCode_normalizedUnit);} | java | public String getNormalizedUnit() {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_normalizedUnit == null)
jcasType.jcas.throwFeatMissing("normalizedUnit", "ch.epfl.bbp.uima.types.Measure");
return jcasType.ll_cas.ll_getStringValue(addr, ((Measure_Type)jcasType).casFeatCode_normalizedUnit);} | [
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@generated
@return value of the feature | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Measure.java#L286-L289 |
141,216 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Measure.java | Measure.setNormalizedUnit | public void setNormalizedUnit(String v) {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_normalizedUnit == null)
jcasType.jcas.throwFeatMissing("normalizedUnit", "ch.epfl.bbp.uima.types.Measure");
jcasType.ll_cas.ll_setStringValue(addr, ((Measure_Type)jcasType).casFeatCode_normalizedUnit, v);} | java | public void setNormalizedUnit(String v) {
if (Measure_Type.featOkTst && ((Measure_Type)jcasType).casFeat_normalizedUnit == null)
jcasType.jcas.throwFeatMissing("normalizedUnit", "ch.epfl.bbp.uima.types.Measure");
jcasType.ll_cas.ll_setStringValue(addr, ((Measure_Type)jcasType).casFeatCode_normalizedUnit, v);} | [
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@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/ch/epfl/bbp/uima/types/Measure.java#L295-L298 |
141,217 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/TopicDistribution.java | TopicDistribution.getProbability | public double getProbability(int i) {
if (TopicDistribution_Type.featOkTst && ((TopicDistribution_Type)jcasType).casFeat_probability == null)
jcasType.jcas.throwFeatMissing("probability", "ch.epfl.bbp.uima.types.TopicDistribution");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((TopicDistribution_Type)jcasType).casFeatCode_probability), i);
return jcasType.ll_cas.ll_getDoubleArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((TopicDistribution_Type)jcasType).casFeatCode_probability), i);} | java | public double getProbability(int i) {
if (TopicDistribution_Type.featOkTst && ((TopicDistribution_Type)jcasType).casFeat_probability == null)
jcasType.jcas.throwFeatMissing("probability", "ch.epfl.bbp.uima.types.TopicDistribution");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((TopicDistribution_Type)jcasType).casFeatCode_probability), i);
return jcasType.ll_cas.ll_getDoubleArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((TopicDistribution_Type)jcasType).casFeatCode_probability), i);} | [
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@param i index in the array to get
@return value of the element at index i | [
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141,218 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/TopicDistribution.java | TopicDistribution.setProbability | public void setProbability(int i, double v) {
if (TopicDistribution_Type.featOkTst && ((TopicDistribution_Type)jcasType).casFeat_probability == null)
jcasType.jcas.throwFeatMissing("probability", "ch.epfl.bbp.uima.types.TopicDistribution");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((TopicDistribution_Type)jcasType).casFeatCode_probability), i);
jcasType.ll_cas.ll_setDoubleArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((TopicDistribution_Type)jcasType).casFeatCode_probability), i, v);} | java | public void setProbability(int i, double v) {
if (TopicDistribution_Type.featOkTst && ((TopicDistribution_Type)jcasType).casFeat_probability == null)
jcasType.jcas.throwFeatMissing("probability", "ch.epfl.bbp.uima.types.TopicDistribution");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((TopicDistribution_Type)jcasType).casFeatCode_probability), i);
jcasType.ll_cas.ll_setDoubleArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((TopicDistribution_Type)jcasType).casFeatCode_probability), i, v);} | [
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141,219 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/lookup/SoftDictionary.java | SoftDictionary.load | public void load(File file,boolean ids) throws IOException,FileNotFoundException
{
LineNumberReader in = new LineNumberReader(new FileReader(file));
String line;
while ((line = in.readLine())!=null) {
if (ids) put(Integer.toString(in.getLineNumber()), line, line);
else put(line,line);
}
in.close();
} | java | public void load(File file,boolean ids) throws IOException,FileNotFoundException
{
LineNumberReader in = new LineNumberReader(new FileReader(file));
String line;
while ((line = in.readLine())!=null) {
if (ids) put(Integer.toString(in.getLineNumber()), line, line);
else put(line,line);
}
in.close();
} | [
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] | Insert all lines in a file as items mapping to themselves. If
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<p>This is mostly for testing the id feature. | [
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141,220 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/lookup/SoftDictionary.java | SoftDictionary.loadAliases | public void loadAliases(File file) throws IOException,FileNotFoundException
{
LineNumberReader in = new LineNumberReader(new FileReader(file));
String line;
while ((line = in.readLine())!=null) {
String[] parts = line.split("\\t");
for (int j=1; j<parts.length; j++) {
put( parts[j], parts[j], parts[0] );
}
}
in.close();
} | java | public void loadAliases(File file) throws IOException,FileNotFoundException
{
LineNumberReader in = new LineNumberReader(new FileReader(file));
String line;
while ((line = in.readLine())!=null) {
String[] parts = line.split("\\t");
for (int j=1; j<parts.length; j++) {
put( parts[j], parts[j], parts[0] );
}
}
in.close();
} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_abbreviations/src/main/java/com/wcohen/ss/lookup/SoftDictionary.java#L124-L135 |
141,221 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/lookup/SoftDictionary.java | SoftDictionary.put | public void put(String id, StringWrapper toInsert,Object value)
{
MyWrapper wrapper = asMyWrapper(toInsert);
Token[] tokens = wrapper.getTokens();
for (int i=0; i<tokens.length; i++) {
ArrayList stringsWithToken = (ArrayList) index.get(tokens[i]);
if (stringsWithToken==null) index.put( tokens[i], (stringsWithToken=new ArrayList()) );
stringsWithToken.add( wrapper );
}
map.put( wrapper, value );
if (id!=null) idMap.put( wrapper, id );
distance = null; // mark distance as "out of date"
totalEntries++;
} | java | public void put(String id, StringWrapper toInsert,Object value)
{
MyWrapper wrapper = asMyWrapper(toInsert);
Token[] tokens = wrapper.getTokens();
for (int i=0; i<tokens.length; i++) {
ArrayList stringsWithToken = (ArrayList) index.get(tokens[i]);
if (stringsWithToken==null) index.put( tokens[i], (stringsWithToken=new ArrayList()) );
stringsWithToken.add( wrapper );
}
map.put( wrapper, value );
if (id!=null) idMap.put( wrapper, id );
distance = null; // mark distance as "out of date"
totalEntries++;
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<p>Id is a special tag used to handle 'leave one out'
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_abbreviations/src/main/java/com/wcohen/ss/lookup/SoftDictionary.java#L164-L177 |
141,222 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/lookup/SoftDictionary.java | SoftDictionary.doLookup | private void doLookup(String id,StringWrapper toFind)
{
// retrain if necessary
if (distance==null) {
distance = new MyTeacher().train( distanceLearner );
}
// used cached values if it's ok
if (lastLookup==toFind) return;
closeMatches = new HashSet();
closestMatch = null;
distanceToClosestMatch = -Double.MAX_VALUE;
// lookup best match to wrapper
MyWrapper wrapper = asMyWrapper(toFind);
Token[] tokens = wrapper.getTokens();
for (int i=0; i<tokens.length; i++) {
ArrayList stringsWithToken = (ArrayList) index.get(tokens[i]);
if (stringsWithToken!=null && ((double)stringsWithToken.size()/totalEntries) < maxFraction) {
for (Iterator j=stringsWithToken.iterator(); j.hasNext(); ) {
MyWrapper wj = (MyWrapper)j.next();
String wjId = (String)idMap.get(wj);
//if (DEBUG) System.out.println("id:"+id+" wjId:"+wjId);
if (!closeMatches.contains(wj) && (wjId==null || !wjId.equals(id))) {
double score = distance.score( wrapper.getDistanceWrapper(), wj.getDistanceWrapper() );
if (DEBUG) System.out.println("score for "+wj+": "+score);
//if (DEBUG) System.out.println(distance.explainScore(wrapper.getDistanceWrapper(),wj.getDistanceWrapper()));
closeMatches.add( wj );
if (score>=distanceToClosestMatch) {
//if (DEBUG) System.out.println("closest so far");
distanceToClosestMatch = score;
closestMatch = wj;
}
}
}
}
}
lastLookup = toFind;
} | java | private void doLookup(String id,StringWrapper toFind)
{
// retrain if necessary
if (distance==null) {
distance = new MyTeacher().train( distanceLearner );
}
// used cached values if it's ok
if (lastLookup==toFind) return;
closeMatches = new HashSet();
closestMatch = null;
distanceToClosestMatch = -Double.MAX_VALUE;
// lookup best match to wrapper
MyWrapper wrapper = asMyWrapper(toFind);
Token[] tokens = wrapper.getTokens();
for (int i=0; i<tokens.length; i++) {
ArrayList stringsWithToken = (ArrayList) index.get(tokens[i]);
if (stringsWithToken!=null && ((double)stringsWithToken.size()/totalEntries) < maxFraction) {
for (Iterator j=stringsWithToken.iterator(); j.hasNext(); ) {
MyWrapper wj = (MyWrapper)j.next();
String wjId = (String)idMap.get(wj);
//if (DEBUG) System.out.println("id:"+id+" wjId:"+wjId);
if (!closeMatches.contains(wj) && (wjId==null || !wjId.equals(id))) {
double score = distance.score( wrapper.getDistanceWrapper(), wj.getDistanceWrapper() );
if (DEBUG) System.out.println("score for "+wj+": "+score);
//if (DEBUG) System.out.println(distance.explainScore(wrapper.getDistanceWrapper(),wj.getDistanceWrapper()));
closeMatches.add( wj );
if (score>=distanceToClosestMatch) {
//if (DEBUG) System.out.println("closest so far");
distanceToClosestMatch = score;
closestMatch = wj;
}
}
}
}
}
lastLookup = toFind;
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] | Lookup a string in the dictionary, cache result in closeMatches.
<p>If id==null, consider any match. If id is non-null, consider
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a null id. | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_abbreviations/src/main/java/com/wcohen/ss/lookup/SoftDictionary.java#L192-L230 |
141,223 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/lookup/SoftDictionary.java | SoftDictionary.lookup | public Object lookup(String id,String toFind)
{
return lookup(id,new MyWrapper(toFind));
} | java | public Object lookup(String id,String toFind)
{
return lookup(id,new MyWrapper(toFind));
} | [
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141,224 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/lookup/SoftDictionary.java | SoftDictionary.lookup | public Object lookup(String id,StringWrapper toFind)
{
doLookup(id,toFind);
return closestMatch;
} | java | public Object lookup(String id,StringWrapper toFind)
{
doLookup(id,toFind);
return closestMatch;
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141,225 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/lookup/SoftDictionary.java | SoftDictionary.asMyWrapper | private MyWrapper asMyWrapper(StringWrapper w)
{
if (w instanceof MyWrapper) return (MyWrapper)w;
else return new MyWrapper(w.unwrap());
} | java | private MyWrapper asMyWrapper(StringWrapper w)
{
if (w instanceof MyWrapper) return (MyWrapper)w;
else return new MyWrapper(w.unwrap());
} | [
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141,226 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/lookup/SoftDictionary.java | SoftDictionary.main | static public void main(String[] argv) throws IOException,FileNotFoundException
{
SoftDictionary m = new SoftDictionary();
System.out.println("loading...");
m.loadAliases(new File(argv[0]));
System.out.println("loaded...");
for (int i=1; i<argv.length; i++) {
System.out.println("lookup: "+argv[i]);
String[] f = argv[i].split(":");
if (f.length==1) {
System.out.println(argv[i] +" => "+m.lookup(argv[i])+" at "+m.lookupDistance(argv[i]));
} else {
System.out.println(f[1] +" => "+m.lookup(f[0],f[1])+" at "+m.lookupDistance(f[0],f[1]));
}
}
} | java | static public void main(String[] argv) throws IOException,FileNotFoundException
{
SoftDictionary m = new SoftDictionary();
System.out.println("loading...");
m.loadAliases(new File(argv[0]));
System.out.println("loaded...");
for (int i=1; i<argv.length; i++) {
System.out.println("lookup: "+argv[i]);
String[] f = argv[i].split(":");
if (f.length==1) {
System.out.println(argv[i] +" => "+m.lookup(argv[i])+" at "+m.lookupDistance(argv[i]));
} else {
System.out.println(f[1] +" => "+m.lookup(f[0],f[1])+" at "+m.lookupDistance(f[0],f[1]));
}
}
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_abbreviations/src/main/java/com/wcohen/ss/lookup/SoftDictionary.java#L365-L380 |
141,227 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/muc7/Coref.java | Coref.getId | public int getId() {
if (Coref_Type.featOkTst && ((Coref_Type)jcasType).casFeat_id == null)
jcasType.jcas.throwFeatMissing("id", "de.julielab.jules.types.muc7.Coref");
return jcasType.ll_cas.ll_getIntValue(addr, ((Coref_Type)jcasType).casFeatCode_id);} | java | public int getId() {
if (Coref_Type.featOkTst && ((Coref_Type)jcasType).casFeat_id == null)
jcasType.jcas.throwFeatMissing("id", "de.julielab.jules.types.muc7.Coref");
return jcasType.ll_cas.ll_getIntValue(addr, ((Coref_Type)jcasType).casFeatCode_id);} | [
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141,228 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/muc7/Coref.java | Coref.setId | public void setId(int v) {
if (Coref_Type.featOkTst && ((Coref_Type)jcasType).casFeat_id == null)
jcasType.jcas.throwFeatMissing("id", "de.julielab.jules.types.muc7.Coref");
jcasType.ll_cas.ll_setIntValue(addr, ((Coref_Type)jcasType).casFeatCode_id, v);} | java | public void setId(int v) {
if (Coref_Type.featOkTst && ((Coref_Type)jcasType).casFeat_id == null)
jcasType.jcas.throwFeatMissing("id", "de.julielab.jules.types.muc7.Coref");
jcasType.ll_cas.ll_setIntValue(addr, ((Coref_Type)jcasType).casFeatCode_id, v);} | [
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141,229 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/muc7/Coref.java | Coref.getCorefType | public String getCorefType() {
if (Coref_Type.featOkTst && ((Coref_Type)jcasType).casFeat_corefType == null)
jcasType.jcas.throwFeatMissing("corefType", "de.julielab.jules.types.muc7.Coref");
return jcasType.ll_cas.ll_getStringValue(addr, ((Coref_Type)jcasType).casFeatCode_corefType);} | java | public String getCorefType() {
if (Coref_Type.featOkTst && ((Coref_Type)jcasType).casFeat_corefType == null)
jcasType.jcas.throwFeatMissing("corefType", "de.julielab.jules.types.muc7.Coref");
return jcasType.ll_cas.ll_getStringValue(addr, ((Coref_Type)jcasType).casFeatCode_corefType);} | [
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141,230 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/muc7/Coref.java | Coref.setCorefType | public void setCorefType(String v) {
if (Coref_Type.featOkTst && ((Coref_Type)jcasType).casFeat_corefType == null)
jcasType.jcas.throwFeatMissing("corefType", "de.julielab.jules.types.muc7.Coref");
jcasType.ll_cas.ll_setStringValue(addr, ((Coref_Type)jcasType).casFeatCode_corefType, v);} | java | public void setCorefType(String v) {
if (Coref_Type.featOkTst && ((Coref_Type)jcasType).casFeat_corefType == null)
jcasType.jcas.throwFeatMissing("corefType", "de.julielab.jules.types.muc7.Coref");
jcasType.ll_cas.ll_setStringValue(addr, ((Coref_Type)jcasType).casFeatCode_corefType, v);} | [
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141,231 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/muc7/Coref.java | Coref.getRef | public Coref getRef() {
if (Coref_Type.featOkTst && ((Coref_Type)jcasType).casFeat_ref == null)
jcasType.jcas.throwFeatMissing("ref", "de.julielab.jules.types.muc7.Coref");
return (Coref)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((Coref_Type)jcasType).casFeatCode_ref)));} | java | public Coref getRef() {
if (Coref_Type.featOkTst && ((Coref_Type)jcasType).casFeat_ref == null)
jcasType.jcas.throwFeatMissing("ref", "de.julielab.jules.types.muc7.Coref");
return (Coref)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((Coref_Type)jcasType).casFeatCode_ref)));} | [
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141,232 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/muc7/Coref.java | Coref.setRef | public void setRef(Coref v) {
if (Coref_Type.featOkTst && ((Coref_Type)jcasType).casFeat_ref == null)
jcasType.jcas.throwFeatMissing("ref", "de.julielab.jules.types.muc7.Coref");
jcasType.ll_cas.ll_setRefValue(addr, ((Coref_Type)jcasType).casFeatCode_ref, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setRef(Coref v) {
if (Coref_Type.featOkTst && ((Coref_Type)jcasType).casFeat_ref == null)
jcasType.jcas.throwFeatMissing("ref", "de.julielab.jules.types.muc7.Coref");
jcasType.ll_cas.ll_setRefValue(addr, ((Coref_Type)jcasType).casFeatCode_ref, jcasType.ll_cas.ll_getFSRef(v));} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/muc7/Coref.java#L139-L142 |
141,233 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ArgumentMention.java | ArgumentMention.getRef | public Annotation getRef() {
if (ArgumentMention_Type.featOkTst && ((ArgumentMention_Type)jcasType).casFeat_ref == null)
jcasType.jcas.throwFeatMissing("ref", "de.julielab.jules.types.ArgumentMention");
return (Annotation)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((ArgumentMention_Type)jcasType).casFeatCode_ref)));} | java | public Annotation getRef() {
if (ArgumentMention_Type.featOkTst && ((ArgumentMention_Type)jcasType).casFeat_ref == null)
jcasType.jcas.throwFeatMissing("ref", "de.julielab.jules.types.ArgumentMention");
return (Annotation)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((ArgumentMention_Type)jcasType).casFeatCode_ref)));} | [
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141,234 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ArgumentMention.java | ArgumentMention.setRef | public void setRef(Annotation v) {
if (ArgumentMention_Type.featOkTst && ((ArgumentMention_Type)jcasType).casFeat_ref == null)
jcasType.jcas.throwFeatMissing("ref", "de.julielab.jules.types.ArgumentMention");
jcasType.ll_cas.ll_setRefValue(addr, ((ArgumentMention_Type)jcasType).casFeatCode_ref, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setRef(Annotation v) {
if (ArgumentMention_Type.featOkTst && ((ArgumentMention_Type)jcasType).casFeat_ref == null)
jcasType.jcas.throwFeatMissing("ref", "de.julielab.jules.types.ArgumentMention");
jcasType.ll_cas.ll_setRefValue(addr, ((ArgumentMention_Type)jcasType).casFeatCode_ref, jcasType.ll_cas.ll_getFSRef(v));} | [
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141,235 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ArgumentMention.java | ArgumentMention.setRole | public void setRole(String v) {
if (ArgumentMention_Type.featOkTst && ((ArgumentMention_Type)jcasType).casFeat_role == null)
jcasType.jcas.throwFeatMissing("role", "de.julielab.jules.types.ArgumentMention");
jcasType.ll_cas.ll_setStringValue(addr, ((ArgumentMention_Type)jcasType).casFeatCode_role, v);} | java | public void setRole(String v) {
if (ArgumentMention_Type.featOkTst && ((ArgumentMention_Type)jcasType).casFeat_role == null)
jcasType.jcas.throwFeatMissing("role", "de.julielab.jules.types.ArgumentMention");
jcasType.ll_cas.ll_setStringValue(addr, ((ArgumentMention_Type)jcasType).casFeatCode_role, v);} | [
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141,236 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/postag/POSDictionary.java | POSDictionary.getTags | public String[] getTags(String word) {
if (caseSensitive) {
return (String[]) dictionary.get(word);
}
else {
//System.err.println(java.util.Arrays.asList((String[]) dictionary.get(word.toLowerCase())));
return (String[]) dictionary.get(word.toLowerCase());
}
} | java | public String[] getTags(String word) {
if (caseSensitive) {
return (String[]) dictionary.get(word);
}
else {
//System.err.println(java.util.Arrays.asList((String[]) dictionary.get(word.toLowerCase())));
return (String[]) dictionary.get(word.toLowerCase());
}
} | [
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141,237 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java | OntRelationMention.getDomain | public Annotation getDomain() {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_domain == null)
jcasType.jcas.throwFeatMissing("domain", "de.julielab.jules.types.OntRelationMention");
return (Annotation)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_domain)));} | java | public Annotation getDomain() {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_domain == null)
jcasType.jcas.throwFeatMissing("domain", "de.julielab.jules.types.OntRelationMention");
return (Annotation)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_domain)));} | [
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@return value of the feature | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java#L86-L89 |
141,238 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java | OntRelationMention.setDomain | public void setDomain(Annotation v) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_domain == null)
jcasType.jcas.throwFeatMissing("domain", "de.julielab.jules.types.OntRelationMention");
jcasType.ll_cas.ll_setRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_domain, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setDomain(Annotation v) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_domain == null)
jcasType.jcas.throwFeatMissing("domain", "de.julielab.jules.types.OntRelationMention");
jcasType.ll_cas.ll_setRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_domain, jcasType.ll_cas.ll_getFSRef(v));} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java#L95-L98 |
141,239 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java | OntRelationMention.getRange | public Annotation getRange() {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_range == null)
jcasType.jcas.throwFeatMissing("range", "de.julielab.jules.types.OntRelationMention");
return (Annotation)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_range)));} | java | public Annotation getRange() {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_range == null)
jcasType.jcas.throwFeatMissing("range", "de.julielab.jules.types.OntRelationMention");
return (Annotation)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_range)));} | [
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@return value of the feature | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java#L108-L111 |
141,240 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java | OntRelationMention.setRange | public void setRange(Annotation v) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_range == null)
jcasType.jcas.throwFeatMissing("range", "de.julielab.jules.types.OntRelationMention");
jcasType.ll_cas.ll_setRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_range, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setRange(Annotation v) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_range == null)
jcasType.jcas.throwFeatMissing("range", "de.julielab.jules.types.OntRelationMention");
jcasType.ll_cas.ll_setRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_range, jcasType.ll_cas.ll_getFSRef(v));} | [
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@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/OntRelationMention.java#L117-L120 |
141,241 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java | OntRelationMention.getDomainList | public FSArray getDomainList() {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_domainList == null)
jcasType.jcas.throwFeatMissing("domainList", "de.julielab.jules.types.OntRelationMention");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_domainList)));} | java | public FSArray getDomainList() {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_domainList == null)
jcasType.jcas.throwFeatMissing("domainList", "de.julielab.jules.types.OntRelationMention");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_domainList)));} | [
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] | getter for domainList - gets
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@return value of the feature | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java#L130-L133 |
141,242 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java | OntRelationMention.setDomainList | public void setDomainList(FSArray v) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_domainList == null)
jcasType.jcas.throwFeatMissing("domainList", "de.julielab.jules.types.OntRelationMention");
jcasType.ll_cas.ll_setRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_domainList, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setDomainList(FSArray v) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_domainList == null)
jcasType.jcas.throwFeatMissing("domainList", "de.julielab.jules.types.OntRelationMention");
jcasType.ll_cas.ll_setRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_domainList, jcasType.ll_cas.ll_getFSRef(v));} | [
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] | setter for domainList - sets
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@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/OntRelationMention.java#L139-L142 |
141,243 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java | OntRelationMention.getDomainList | public Annotation getDomainList(int i) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_domainList == null)
jcasType.jcas.throwFeatMissing("domainList", "de.julielab.jules.types.OntRelationMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_domainList), i);
return (Annotation)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_domainList), i)));} | java | public Annotation getDomainList(int i) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_domainList == null)
jcasType.jcas.throwFeatMissing("domainList", "de.julielab.jules.types.OntRelationMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_domainList), i);
return (Annotation)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_domainList), i)));} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java#L149-L153 |
141,244 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java | OntRelationMention.setDomainList | public void setDomainList(int i, Annotation v) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_domainList == null)
jcasType.jcas.throwFeatMissing("domainList", "de.julielab.jules.types.OntRelationMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_domainList), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_domainList), i, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setDomainList(int i, Annotation v) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_domainList == null)
jcasType.jcas.throwFeatMissing("domainList", "de.julielab.jules.types.OntRelationMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_domainList), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_domainList), i, jcasType.ll_cas.ll_getFSRef(v));} | [
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] | indexed setter for domainList - sets an indexed value -
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java#L160-L164 |
141,245 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java | OntRelationMention.getRangeList | public FSArray getRangeList() {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_rangeList == null)
jcasType.jcas.throwFeatMissing("rangeList", "de.julielab.jules.types.OntRelationMention");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_rangeList)));} | java | public FSArray getRangeList() {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_rangeList == null)
jcasType.jcas.throwFeatMissing("rangeList", "de.julielab.jules.types.OntRelationMention");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_rangeList)));} | [
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@return value of the feature | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java#L174-L177 |
141,246 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java | OntRelationMention.setRangeList | public void setRangeList(FSArray v) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_rangeList == null)
jcasType.jcas.throwFeatMissing("rangeList", "de.julielab.jules.types.OntRelationMention");
jcasType.ll_cas.ll_setRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_rangeList, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setRangeList(FSArray v) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_rangeList == null)
jcasType.jcas.throwFeatMissing("rangeList", "de.julielab.jules.types.OntRelationMention");
jcasType.ll_cas.ll_setRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_rangeList, jcasType.ll_cas.ll_getFSRef(v));} | [
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@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/OntRelationMention.java#L183-L186 |
141,247 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java | OntRelationMention.getRangeList | public Annotation getRangeList(int i) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_rangeList == null)
jcasType.jcas.throwFeatMissing("rangeList", "de.julielab.jules.types.OntRelationMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_rangeList), i);
return (Annotation)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_rangeList), i)));} | java | public Annotation getRangeList(int i) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_rangeList == null)
jcasType.jcas.throwFeatMissing("rangeList", "de.julielab.jules.types.OntRelationMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_rangeList), i);
return (Annotation)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_rangeList), i)));} | [
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] | indexed getter for rangeList - gets an indexed value -
@generated
@param i index in the array to get
@return value of the element at index i | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java#L193-L197 |
141,248 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java | OntRelationMention.setRangeList | public void setRangeList(int i, Annotation v) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_rangeList == null)
jcasType.jcas.throwFeatMissing("rangeList", "de.julielab.jules.types.OntRelationMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_rangeList), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_rangeList), i, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setRangeList(int i, Annotation v) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_rangeList == null)
jcasType.jcas.throwFeatMissing("rangeList", "de.julielab.jules.types.OntRelationMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_rangeList), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_rangeList), i, jcasType.ll_cas.ll_getFSRef(v));} | [
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] | indexed setter for rangeList - sets an indexed value -
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@param i index in the array to set
@param v value to set into the array | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java#L204-L208 |
141,249 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java | OntRelationMention.getOntRelationId | public String getOntRelationId() {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_ontRelationId == null)
jcasType.jcas.throwFeatMissing("ontRelationId", "de.julielab.jules.types.OntRelationMention");
return jcasType.ll_cas.ll_getStringValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_ontRelationId);} | java | public String getOntRelationId() {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_ontRelationId == null)
jcasType.jcas.throwFeatMissing("ontRelationId", "de.julielab.jules.types.OntRelationMention");
return jcasType.ll_cas.ll_getStringValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_ontRelationId);} | [
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] | getter for ontRelationId - gets ID of the ontology relation the relation mention refers to.
@generated
@return value of the feature | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java#L240-L243 |
141,250 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java | OntRelationMention.setOntRelationId | public void setOntRelationId(String v) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_ontRelationId == null)
jcasType.jcas.throwFeatMissing("ontRelationId", "de.julielab.jules.types.OntRelationMention");
jcasType.ll_cas.ll_setStringValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_ontRelationId, v);} | java | public void setOntRelationId(String v) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_ontRelationId == null)
jcasType.jcas.throwFeatMissing("ontRelationId", "de.julielab.jules.types.OntRelationMention");
jcasType.ll_cas.ll_setStringValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_ontRelationId, v);} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java#L249-L252 |
141,251 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java | OntRelationMention.getSourceOntology | public String getSourceOntology() {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_sourceOntology == null)
jcasType.jcas.throwFeatMissing("sourceOntology", "de.julielab.jules.types.OntRelationMention");
return jcasType.ll_cas.ll_getStringValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_sourceOntology);} | java | public String getSourceOntology() {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_sourceOntology == null)
jcasType.jcas.throwFeatMissing("sourceOntology", "de.julielab.jules.types.OntRelationMention");
return jcasType.ll_cas.ll_getStringValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_sourceOntology);} | [
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@return value of the feature | [
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141,252 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntRelationMention.java | OntRelationMention.setSourceOntology | public void setSourceOntology(String v) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_sourceOntology == null)
jcasType.jcas.throwFeatMissing("sourceOntology", "de.julielab.jules.types.OntRelationMention");
jcasType.ll_cas.ll_setStringValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_sourceOntology, v);} | java | public void setSourceOntology(String v) {
if (OntRelationMention_Type.featOkTst && ((OntRelationMention_Type)jcasType).casFeat_sourceOntology == null)
jcasType.jcas.throwFeatMissing("sourceOntology", "de.julielab.jules.types.OntRelationMention");
jcasType.ll_cas.ll_setStringValue(addr, ((OntRelationMention_Type)jcasType).casFeatCode_sourceOntology, v);} | [
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141,253 | BlueBrain/bluima | utils/blue_commons/src/main/java/ch/epfl/bbp/io/IOUtils.java | IOUtils.sniffContentType | protected static String sniffContentType(InputStream inputStream)
throws IOException {
if (inputStream == null)
return null;
byte[] bytes = new byte[8];
inputStream.read(bytes);
String[] hex = new String[8];
String hexString = "";
for (int i = 0; i < 8; i++) {
hex[i] = getHexValue(bytes[i]);
hexString += hex[i] + " ";
}
String prefix = new String(bytes);
if (prefix.startsWith("GIF87") || prefix.startsWith("GIF89"))
return "image/gif";
if (hex[0].equals("ff") && hex[1].equals("d8"))
return "image/jpeg";
if (hex[0].equals("42") && hex[1].equals("4d"))
return "image/bmp";
if (hex[0].equals("00") && hex[1].equals("00") && hex[2].equals("01")
&& hex[3].equals("00"))
return "image/vnd.microsoft.icon";
if (hexString.trim().equals("89 50 4e 47 0d 0a 1a 0a"))
return "image/png";
return null;
} | java | protected static String sniffContentType(InputStream inputStream)
throws IOException {
if (inputStream == null)
return null;
byte[] bytes = new byte[8];
inputStream.read(bytes);
String[] hex = new String[8];
String hexString = "";
for (int i = 0; i < 8; i++) {
hex[i] = getHexValue(bytes[i]);
hexString += hex[i] + " ";
}
String prefix = new String(bytes);
if (prefix.startsWith("GIF87") || prefix.startsWith("GIF89"))
return "image/gif";
if (hex[0].equals("ff") && hex[1].equals("d8"))
return "image/jpeg";
if (hex[0].equals("42") && hex[1].equals("4d"))
return "image/bmp";
if (hex[0].equals("00") && hex[1].equals("00") && hex[2].equals("01")
&& hex[3].equals("00"))
return "image/vnd.microsoft.icon";
if (hexString.trim().equals("89 50 4e 47 0d 0a 1a 0a"))
return "image/png";
return null;
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141,254 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/Front.java | Front.getDefListOrListOrNotes | public java.util.List<Object> getDefListOrListOrNotes() {
if (defListOrListOrNotes == null) {
defListOrListOrNotes = new ArrayList<Object>();
}
return this.defListOrListOrNotes;
} | java | public java.util.List<Object> getDefListOrListOrNotes() {
if (defListOrListOrNotes == null) {
defListOrListOrNotes = new ArrayList<Object>();
}
return this.defListOrListOrNotes;
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141,255 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/pubmed/EndingDate.java | EndingDate.getMonthOrDayOrSeason | public List<java.lang.Object> getMonthOrDayOrSeason() {
if (monthOrDayOrSeason == null) {
monthOrDayOrSeason = new ArrayList<java.lang.Object>();
}
return this.monthOrDayOrSeason;
} | java | public List<java.lang.Object> getMonthOrDayOrSeason() {
if (monthOrDayOrSeason == null) {
monthOrDayOrSeason = new ArrayList<java.lang.Object>();
}
return this.monthOrDayOrSeason;
} | [
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getMonthOrDayOrSeason().add(newItem);
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{@link Season } | [
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141,256 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/TextObject.java | TextObject.getObjectType | public String getObjectType() {
if (TextObject_Type.featOkTst && ((TextObject_Type)jcasType).casFeat_objectType == null)
jcasType.jcas.throwFeatMissing("objectType", "de.julielab.jules.types.TextObject");
return jcasType.ll_cas.ll_getStringValue(addr, ((TextObject_Type)jcasType).casFeatCode_objectType);} | java | public String getObjectType() {
if (TextObject_Type.featOkTst && ((TextObject_Type)jcasType).casFeat_objectType == null)
jcasType.jcas.throwFeatMissing("objectType", "de.julielab.jules.types.TextObject");
return jcasType.ll_cas.ll_getStringValue(addr, ((TextObject_Type)jcasType).casFeatCode_objectType);} | [
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141,257 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/TextObject.java | TextObject.setObjectType | public void setObjectType(String v) {
if (TextObject_Type.featOkTst && ((TextObject_Type)jcasType).casFeat_objectType == null)
jcasType.jcas.throwFeatMissing("objectType", "de.julielab.jules.types.TextObject");
jcasType.ll_cas.ll_setStringValue(addr, ((TextObject_Type)jcasType).casFeatCode_objectType, v);} | java | public void setObjectType(String v) {
if (TextObject_Type.featOkTst && ((TextObject_Type)jcasType).casFeat_objectType == null)
jcasType.jcas.throwFeatMissing("objectType", "de.julielab.jules.types.TextObject");
jcasType.ll_cas.ll_setStringValue(addr, ((TextObject_Type)jcasType).casFeatCode_objectType, v);} | [
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141,258 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/TextObject.java | TextObject.getObjectId | public String getObjectId() {
if (TextObject_Type.featOkTst && ((TextObject_Type)jcasType).casFeat_objectId == null)
jcasType.jcas.throwFeatMissing("objectId", "de.julielab.jules.types.TextObject");
return jcasType.ll_cas.ll_getStringValue(addr, ((TextObject_Type)jcasType).casFeatCode_objectId);} | java | public String getObjectId() {
if (TextObject_Type.featOkTst && ((TextObject_Type)jcasType).casFeat_objectId == null)
jcasType.jcas.throwFeatMissing("objectId", "de.julielab.jules.types.TextObject");
return jcasType.ll_cas.ll_getStringValue(addr, ((TextObject_Type)jcasType).casFeatCode_objectId);} | [
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141,259 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/TextObject.java | TextObject.setObjectId | public void setObjectId(String v) {
if (TextObject_Type.featOkTst && ((TextObject_Type)jcasType).casFeat_objectId == null)
jcasType.jcas.throwFeatMissing("objectId", "de.julielab.jules.types.TextObject");
jcasType.ll_cas.ll_setStringValue(addr, ((TextObject_Type)jcasType).casFeatCode_objectId, v);} | java | public void setObjectId(String v) {
if (TextObject_Type.featOkTst && ((TextObject_Type)jcasType).casFeat_objectId == null)
jcasType.jcas.throwFeatMissing("objectId", "de.julielab.jules.types.TextObject");
jcasType.ll_cas.ll_setStringValue(addr, ((TextObject_Type)jcasType).casFeatCode_objectId, v);} | [
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141,260 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/TextObject.java | TextObject.getObjectLabel | public String getObjectLabel() {
if (TextObject_Type.featOkTst && ((TextObject_Type)jcasType).casFeat_objectLabel == null)
jcasType.jcas.throwFeatMissing("objectLabel", "de.julielab.jules.types.TextObject");
return jcasType.ll_cas.ll_getStringValue(addr, ((TextObject_Type)jcasType).casFeatCode_objectLabel);} | java | public String getObjectLabel() {
if (TextObject_Type.featOkTst && ((TextObject_Type)jcasType).casFeat_objectLabel == null)
jcasType.jcas.throwFeatMissing("objectLabel", "de.julielab.jules.types.TextObject");
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141,261 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/TextObject.java | TextObject.setObjectLabel | public void setObjectLabel(String v) {
if (TextObject_Type.featOkTst && ((TextObject_Type)jcasType).casFeat_objectLabel == null)
jcasType.jcas.throwFeatMissing("objectLabel", "de.julielab.jules.types.TextObject");
jcasType.ll_cas.ll_setStringValue(addr, ((TextObject_Type)jcasType).casFeatCode_objectLabel, v);} | java | public void setObjectLabel(String v) {
if (TextObject_Type.featOkTst && ((TextObject_Type)jcasType).casFeat_objectLabel == null)
jcasType.jcas.throwFeatMissing("objectLabel", "de.julielab.jules.types.TextObject");
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141,262 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/TextObject.java | TextObject.getObjectCaption | public Caption getObjectCaption() {
if (TextObject_Type.featOkTst && ((TextObject_Type)jcasType).casFeat_objectCaption == null)
jcasType.jcas.throwFeatMissing("objectCaption", "de.julielab.jules.types.TextObject");
return (Caption)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((TextObject_Type)jcasType).casFeatCode_objectCaption)));} | java | public Caption getObjectCaption() {
if (TextObject_Type.featOkTst && ((TextObject_Type)jcasType).casFeat_objectCaption == null)
jcasType.jcas.throwFeatMissing("objectCaption", "de.julielab.jules.types.TextObject");
return (Caption)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((TextObject_Type)jcasType).casFeatCode_objectCaption)));} | [
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141,263 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/TextObject.java | TextObject.setObjectCaption | public void setObjectCaption(Caption v) {
if (TextObject_Type.featOkTst && ((TextObject_Type)jcasType).casFeat_objectCaption == null)
jcasType.jcas.throwFeatMissing("objectCaption", "de.julielab.jules.types.TextObject");
jcasType.ll_cas.ll_setRefValue(addr, ((TextObject_Type)jcasType).casFeatCode_objectCaption, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setObjectCaption(Caption v) {
if (TextObject_Type.featOkTst && ((TextObject_Type)jcasType).casFeat_objectCaption == null)
jcasType.jcas.throwFeatMissing("objectCaption", "de.julielab.jules.types.TextObject");
jcasType.ll_cas.ll_setRefValue(addr, ((TextObject_Type)jcasType).casFeatCode_objectCaption, jcasType.ll_cas.ll_getFSRef(v));} | [
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141,264 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/Annotation.java | Annotation.getAce_role | public String getAce_role() {
if (Annotation_Type.featOkTst && ((Annotation_Type)jcasType).casFeat_ace_role == null)
jcasType.jcas.throwFeatMissing("ace_role", "de.julielab.jules.types.ace.Annotation");
return jcasType.ll_cas.ll_getStringValue(addr, ((Annotation_Type)jcasType).casFeatCode_ace_role);} | java | public String getAce_role() {
if (Annotation_Type.featOkTst && ((Annotation_Type)jcasType).casFeat_ace_role == null)
jcasType.jcas.throwFeatMissing("ace_role", "de.julielab.jules.types.ace.Annotation");
return jcasType.ll_cas.ll_getStringValue(addr, ((Annotation_Type)jcasType).casFeatCode_ace_role);} | [
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141,265 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/Annotation.java | Annotation.setAce_role | public void setAce_role(String v) {
if (Annotation_Type.featOkTst && ((Annotation_Type)jcasType).casFeat_ace_role == null)
jcasType.jcas.throwFeatMissing("ace_role", "de.julielab.jules.types.ace.Annotation");
jcasType.ll_cas.ll_setStringValue(addr, ((Annotation_Type)jcasType).casFeatCode_ace_role, v);} | java | public void setAce_role(String v) {
if (Annotation_Type.featOkTst && ((Annotation_Type)jcasType).casFeat_ace_role == null)
jcasType.jcas.throwFeatMissing("ace_role", "de.julielab.jules.types.ace.Annotation");
jcasType.ll_cas.ll_setStringValue(addr, ((Annotation_Type)jcasType).casFeatCode_ace_role, v);} | [
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141,266 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/sentdetect/SentenceDetectorME.java | SentenceDetectorME.sentDetect | public String[] sentDetect(String s) {
int[] starts = sentPosDetect(s);
if (starts.length == 0) {
return new String[] {s};
}
boolean leftover = starts[starts.length - 1] != s.length();
String[] sents = new String[leftover? starts.length + 1 : starts.length];
sents[0] = s.substring(0,starts[0]);
for (int si = 1; si < starts.length; si++) {
sents[si] = s.substring(starts[si - 1], starts[si]);
}
if (leftover) {
sents[sents.length - 1] = s.substring(starts[starts.length - 1]);
}
return (sents);
} | java | public String[] sentDetect(String s) {
int[] starts = sentPosDetect(s);
if (starts.length == 0) {
return new String[] {s};
}
boolean leftover = starts[starts.length - 1] != s.length();
String[] sents = new String[leftover? starts.length + 1 : starts.length];
sents[0] = s.substring(0,starts[0]);
for (int si = 1; si < starts.length; si++) {
sents[si] = s.substring(starts[si - 1], starts[si]);
}
if (leftover) {
sents[sents.length - 1] = s.substring(starts[starts.length - 1]);
}
return (sents);
} | [
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@param s The string to be processed.
@return A string array containing individual sentences as elements. | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/sentdetect/SentenceDetectorME.java#L120-L138 |
141,267 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/sentdetect/SentenceDetectorME.java | SentenceDetectorME.sentPosDetect | public int[] sentPosDetect(String s) {
double sentProb = 1;
sentProbs.clear();
StringBuffer sb = new StringBuffer(s);
List enders = scanner.getPositions(s);
List positions = new ArrayList(enders.size());
for (int i = 0, end = enders.size(), index = 0; i < end; i++) {
Integer candidate = (Integer) enders.get(i);
int cint = candidate.intValue();
// skip over the leading parts of non-token final delimiters
int fws = getFirstWS(s,cint + 1);
if (((i + 1) < end) && (((Integer) enders.get(i + 1)).intValue() < fws)) {
continue;
}
Pair pair = new Pair(sb, candidate);
double[] probs = model.eval(cgen.getContext(pair));
String bestOutcome = model.getBestOutcome(probs);
sentProb *= probs[model.getIndex(bestOutcome)];
if (bestOutcome.equals("T") && isAcceptableBreak(s, index, cint)) {
if (index != cint) {
positions.add(INT_POOL.get(getFirstNonWS(s, getFirstWS(s,cint + 1))));
sentProbs.add(new Double(probs[model.getIndex(bestOutcome)]));
}
index = cint + 1;
}
}
int[] sentPositions = new int[positions.size()];
for (int i = 0; i < sentPositions.length; i++) {
sentPositions[i] = ((Integer) positions.get(i)).intValue();
}
return sentPositions;
} | java | public int[] sentPosDetect(String s) {
double sentProb = 1;
sentProbs.clear();
StringBuffer sb = new StringBuffer(s);
List enders = scanner.getPositions(s);
List positions = new ArrayList(enders.size());
for (int i = 0, end = enders.size(), index = 0; i < end; i++) {
Integer candidate = (Integer) enders.get(i);
int cint = candidate.intValue();
// skip over the leading parts of non-token final delimiters
int fws = getFirstWS(s,cint + 1);
if (((i + 1) < end) && (((Integer) enders.get(i + 1)).intValue() < fws)) {
continue;
}
Pair pair = new Pair(sb, candidate);
double[] probs = model.eval(cgen.getContext(pair));
String bestOutcome = model.getBestOutcome(probs);
sentProb *= probs[model.getIndex(bestOutcome)];
if (bestOutcome.equals("T") && isAcceptableBreak(s, index, cint)) {
if (index != cint) {
positions.add(INT_POOL.get(getFirstNonWS(s, getFirstWS(s,cint + 1))));
sentProbs.add(new Double(probs[model.getIndex(bestOutcome)]));
}
index = cint + 1;
}
}
int[] sentPositions = new int[positions.size()];
for (int i = 0; i < sentPositions.length; i++) {
sentPositions[i] = ((Integer) positions.get(i)).intValue();
}
return sentPositions;
} | [
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] | Detect the position of the first words of sentences in a String.
@param s The string to be processed.
@return A integer array containing the positions of the end index of
every sentence | [
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141,268 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/sentdetect/SentenceDetectorME.java | SentenceDetectorME.train | public static GISModel train(File inFile, int iterations, int cut, EndOfSentenceScanner scanner) throws IOException {
EventStream es;
DataStream ds;
Reader reader;
reader = new BufferedReader(new FileReader(inFile));
ds = new PlainTextByLineDataStream(reader);
es = new SDEventStream(ds, scanner);
return GIS.trainModel(es, iterations, cut);
} | java | public static GISModel train(File inFile, int iterations, int cut, EndOfSentenceScanner scanner) throws IOException {
EventStream es;
DataStream ds;
Reader reader;
reader = new BufferedReader(new FileReader(inFile));
ds = new PlainTextByLineDataStream(reader);
es = new SDEventStream(ds, scanner);
return GIS.trainModel(es, iterations, cut);
} | [
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141,269 | BlueBrain/bluima | modules/bluima_jsre/src/main/java/org/itc/irst/tcc/sre/KernelMatrix.java | KernelMatrix.calculateKernelMatrix | private void calculateKernelMatrix(ExampleSet set, ZipModel model) throws Exception
{
// save kernel matrix
File matrixFile = File.createTempFile("kernel-matrix", null);
matrixFile.deleteOnExit();
PrintWriter pw = new PrintWriter(new FileWriter(matrixFile));
DecimalFormat decFormatter = new DecimalFormat("0.0");
logger.info("calculate kernel matrix");
logger.debug("data set size " + set.size());
int size = set.size();
//double[][] matrix = new double[size][size];
pw.println(size + " " + size);
for (int i=0;i<size;i++)
{
Vector v1 = (Vector) set.x(i);
/*
for (int j=0;j<i;j++)
{
matrix[i][j] = matrix[j][i];
System.out.print(decFormatter.format(matrix[i][j]) + " ");
}
*/
//for (int j=i;j<size;j++)
for (int j=0;j<size;j++)
{
Vector v2 = (Vector) set.x(j);
double dot = v1.dotProduct(v2);
/*
matrix[i][j] = v1.dotProduct(v2);
if (matrix[i][j] < 0.3)
matrix[i][j] = 0;
*/
//pw.print(decFormatter.format(matrix[i][j]) + " ");
pw.print(dot + " ");
}
//logger.debug(i + " : " + set.y(i) + "\t" + set.id(i) + "\t" + set.x(i));
pw.print("\n");
pw.flush();
}
//pw.flush();
pw.close();
// add the kernel matrix to the model
model.add(matrixFile, "kernel-matrix");
/*
System.out.print("\n");
//for (int i=0;i<set.size();i++)
for (int i=0;i<size;i++)
{
Vector v1 = (Vector) set.x(i);
//logger.info(i + " : " + v1);
for (int j=0;j<i;j++)
System.out.print(0.0 + " ");
//for (int j=i;j<set.size();j++)
for (int j=i;j<size;j++)
{
Vector v2 = (Vector) set.x(j);
double dot = v1.dotProduct(v2);
System.out.print(decFormatter.format(dot) + " ");
}
//logger.debug(i + " : " + set.y(i) + "\t" + set.id(i) + "\t" + set.x(i));
System.out.print("\n");
}
System.out.print("\n");
System.out.println(size + " " + size);
//for (int i=0;i<set.size();i++)
for (int i=0;i<size;i++)
{
Vector v1 = (Vector) set.x(i);
//logger.info(i + " : " + v1);
//for (int j=i;j<set.size();j++)
for (int j=i;j<size;j++)
{
Vector v2 = (Vector) set.x(j);
double dot = v1.dotProduct(v2);
System.out.print(i + " " + j + " ");
System.out.println(decFormatter.format(dot) + " ");
}
//logger.debug(i + " : " + set.y(i) + "\t" + set.id(i) + "\t" + set.x(i));
System.out.print("\n");
}
*/
} | java | private void calculateKernelMatrix(ExampleSet set, ZipModel model) throws Exception
{
// save kernel matrix
File matrixFile = File.createTempFile("kernel-matrix", null);
matrixFile.deleteOnExit();
PrintWriter pw = new PrintWriter(new FileWriter(matrixFile));
DecimalFormat decFormatter = new DecimalFormat("0.0");
logger.info("calculate kernel matrix");
logger.debug("data set size " + set.size());
int size = set.size();
//double[][] matrix = new double[size][size];
pw.println(size + " " + size);
for (int i=0;i<size;i++)
{
Vector v1 = (Vector) set.x(i);
/*
for (int j=0;j<i;j++)
{
matrix[i][j] = matrix[j][i];
System.out.print(decFormatter.format(matrix[i][j]) + " ");
}
*/
//for (int j=i;j<size;j++)
for (int j=0;j<size;j++)
{
Vector v2 = (Vector) set.x(j);
double dot = v1.dotProduct(v2);
/*
matrix[i][j] = v1.dotProduct(v2);
if (matrix[i][j] < 0.3)
matrix[i][j] = 0;
*/
//pw.print(decFormatter.format(matrix[i][j]) + " ");
pw.print(dot + " ");
}
//logger.debug(i + " : " + set.y(i) + "\t" + set.id(i) + "\t" + set.x(i));
pw.print("\n");
pw.flush();
}
//pw.flush();
pw.close();
// add the kernel matrix to the model
model.add(matrixFile, "kernel-matrix");
/*
System.out.print("\n");
//for (int i=0;i<set.size();i++)
for (int i=0;i<size;i++)
{
Vector v1 = (Vector) set.x(i);
//logger.info(i + " : " + v1);
for (int j=0;j<i;j++)
System.out.print(0.0 + " ");
//for (int j=i;j<set.size();j++)
for (int j=i;j<size;j++)
{
Vector v2 = (Vector) set.x(j);
double dot = v1.dotProduct(v2);
System.out.print(decFormatter.format(dot) + " ");
}
//logger.debug(i + " : " + set.y(i) + "\t" + set.id(i) + "\t" + set.x(i));
System.out.print("\n");
}
System.out.print("\n");
System.out.println(size + " " + size);
//for (int i=0;i<set.size();i++)
for (int i=0;i<size;i++)
{
Vector v1 = (Vector) set.x(i);
//logger.info(i + " : " + v1);
//for (int j=i;j<set.size();j++)
for (int j=i;j<size;j++)
{
Vector v2 = (Vector) set.x(j);
double dot = v1.dotProduct(v2);
System.out.print(i + " " + j + " ");
System.out.println(decFormatter.format(dot) + " ");
}
//logger.debug(i + " : " + set.y(i) + "\t" + set.id(i) + "\t" + set.x(i));
System.out.print("\n");
}
*/
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"}"
] | calculate kernel matrix | [
"calculate",
"kernel",
"matrix"
] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_jsre/src/main/java/org/itc/irst/tcc/sre/KernelMatrix.java#L216-L312 |
141,270 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/pubmed/Article.java | Article.getPaginationOrELocationID | public List<java.lang.Object> getPaginationOrELocationID() {
if (paginationOrELocationID == null) {
paginationOrELocationID = new ArrayList<java.lang.Object>();
}
return this.paginationOrELocationID;
} | java | public List<java.lang.Object> getPaginationOrELocationID() {
if (paginationOrELocationID == null) {
paginationOrELocationID = new ArrayList<java.lang.Object>();
}
return this.paginationOrELocationID;
} | [
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This is why there is not a <CODE>set</CODE> method for the paginationOrELocationID property.
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</pre>
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Objects of the following type(s) are allowed in the list
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141,271 | BlueBrain/bluima | modules/bluima_text2pmid/src/main/java/ch/epfl/bbp/uima/txt2pmid/LuceneHelper.java | LuceneHelper.subsumes | public static float subsumes(String haystack, final String needle) {
if (needle == null || needle.length() < 0 || haystack == null
|| haystack.length() < 0)
return 0f;
try {
// index the cleaned text
RAMDirectory idx = new RAMDirectory();
IndexWriterConfig iwc = new IndexWriterConfig(LUCENE_41, anal);
IndexWriter writer = new IndexWriter(idx, iwc);
// index
Document doc = new Document();
doc.add(new TextField(CONTENT_FIELD, haystack, Store.YES));
writer.addDocument(doc);
writer.close();
// search
IndexReader reader = open(idx);
Query query = parser.parse(getNGram(needle, 3));
TopDocs results = new IndexSearcher(reader).search(query, 1);
float score = 0;
for (ScoreDoc hit : results.scoreDocs) {
score += hit.score;
}
reader.close();
idx.close();
return score;
} catch (Exception e) {
LOG.warn("could not computeSimilarity for " + needle, e);
}
return 0f;
} | java | public static float subsumes(String haystack, final String needle) {
if (needle == null || needle.length() < 0 || haystack == null
|| haystack.length() < 0)
return 0f;
try {
// index the cleaned text
RAMDirectory idx = new RAMDirectory();
IndexWriterConfig iwc = new IndexWriterConfig(LUCENE_41, anal);
IndexWriter writer = new IndexWriter(idx, iwc);
// index
Document doc = new Document();
doc.add(new TextField(CONTENT_FIELD, haystack, Store.YES));
writer.addDocument(doc);
writer.close();
// search
IndexReader reader = open(idx);
Query query = parser.parse(getNGram(needle, 3));
TopDocs results = new IndexSearcher(reader).search(query, 1);
float score = 0;
for (ScoreDoc hit : results.scoreDocs) {
score += hit.score;
}
reader.close();
idx.close();
return score;
} catch (Exception e) {
LOG.warn("could not computeSimilarity for " + needle, e);
}
return 0f;
} | [
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@return a score that reflects if needle subsumes haystack | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_text2pmid/src/main/java/ch/epfl/bbp/uima/txt2pmid/LuceneHelper.java#L148-L182 |
141,272 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/bootstrep/RegulationOfGeneExpression.java | RegulationOfGeneExpression.getPhysicalContact | public String getPhysicalContact() {
if (RegulationOfGeneExpression_Type.featOkTst && ((RegulationOfGeneExpression_Type)jcasType).casFeat_physicalContact == null)
jcasType.jcas.throwFeatMissing("physicalContact", "de.julielab.jules.types.bootstrep.RegulationOfGeneExpression");
return jcasType.ll_cas.ll_getStringValue(addr, ((RegulationOfGeneExpression_Type)jcasType).casFeatCode_physicalContact);} | java | public String getPhysicalContact() {
if (RegulationOfGeneExpression_Type.featOkTst && ((RegulationOfGeneExpression_Type)jcasType).casFeat_physicalContact == null)
jcasType.jcas.throwFeatMissing("physicalContact", "de.julielab.jules.types.bootstrep.RegulationOfGeneExpression");
return jcasType.ll_cas.ll_getStringValue(addr, ((RegulationOfGeneExpression_Type)jcasType).casFeatCode_physicalContact);} | [
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141,273 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/bootstrep/RegulationOfGeneExpression.java | RegulationOfGeneExpression.setPhysicalContact | public void setPhysicalContact(String v) {
if (RegulationOfGeneExpression_Type.featOkTst && ((RegulationOfGeneExpression_Type)jcasType).casFeat_physicalContact == null)
jcasType.jcas.throwFeatMissing("physicalContact", "de.julielab.jules.types.bootstrep.RegulationOfGeneExpression");
jcasType.ll_cas.ll_setStringValue(addr, ((RegulationOfGeneExpression_Type)jcasType).casFeatCode_physicalContact, v);} | java | public void setPhysicalContact(String v) {
if (RegulationOfGeneExpression_Type.featOkTst && ((RegulationOfGeneExpression_Type)jcasType).casFeat_physicalContact == null)
jcasType.jcas.throwFeatMissing("physicalContact", "de.julielab.jules.types.bootstrep.RegulationOfGeneExpression");
jcasType.ll_cas.ll_setStringValue(addr, ((RegulationOfGeneExpression_Type)jcasType).casFeatCode_physicalContact, v);} | [
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141,274 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/TableWrap.java | TableWrap.getDispQuoteOrSpeechOrStatement | public java.util.List<Object> getDispQuoteOrSpeechOrStatement() {
if (dispQuoteOrSpeechOrStatement == null) {
dispQuoteOrSpeechOrStatement = new ArrayList<Object>();
}
return this.dispQuoteOrSpeechOrStatement;
} | java | public java.util.List<Object> getDispQuoteOrSpeechOrStatement() {
if (dispQuoteOrSpeechOrStatement == null) {
dispQuoteOrSpeechOrStatement = new ArrayList<Object>();
}
return this.dispQuoteOrSpeechOrStatement;
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141,275 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/TableWrap.java | TableWrap.getTableWrapFootOrAttribOrPermissions | public java.util.List<Object> getTableWrapFootOrAttribOrPermissions() {
if (tableWrapFootOrAttribOrPermissions == null) {
tableWrapFootOrAttribOrPermissions = new ArrayList<Object>();
}
return this.tableWrapFootOrAttribOrPermissions;
} | java | public java.util.List<Object> getTableWrapFootOrAttribOrPermissions() {
if (tableWrapFootOrAttribOrPermissions == null) {
tableWrapFootOrAttribOrPermissions = new ArrayList<Object>();
}
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141,276 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/GOMention.java | GOMention.getCategories | public StringArray getCategories() {
if (GOMention_Type.featOkTst && ((GOMention_Type)jcasType).casFeat_categories == null)
jcasType.jcas.throwFeatMissing("categories", "de.julielab.jules.types.GOMention");
return (StringArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((GOMention_Type)jcasType).casFeatCode_categories)));} | java | public StringArray getCategories() {
if (GOMention_Type.featOkTst && ((GOMention_Type)jcasType).casFeat_categories == null)
jcasType.jcas.throwFeatMissing("categories", "de.julielab.jules.types.GOMention");
return (StringArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((GOMention_Type)jcasType).casFeatCode_categories)));} | [
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141,277 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/GOMention.java | GOMention.setCategories | public void setCategories(StringArray v) {
if (GOMention_Type.featOkTst && ((GOMention_Type)jcasType).casFeat_categories == null)
jcasType.jcas.throwFeatMissing("categories", "de.julielab.jules.types.GOMention");
jcasType.ll_cas.ll_setRefValue(addr, ((GOMention_Type)jcasType).casFeatCode_categories, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setCategories(StringArray v) {
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jcasType.jcas.throwFeatMissing("categories", "de.julielab.jules.types.GOMention");
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141,278 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/GOMention.java | GOMention.getCategories | public String getCategories(int i) {
if (GOMention_Type.featOkTst && ((GOMention_Type)jcasType).casFeat_categories == null)
jcasType.jcas.throwFeatMissing("categories", "de.julielab.jules.types.GOMention");
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return jcasType.ll_cas.ll_getStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((GOMention_Type)jcasType).casFeatCode_categories), i);} | java | public String getCategories(int i) {
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jcasType.jcas.throwFeatMissing("categories", "de.julielab.jules.types.GOMention");
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141,279 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/GOMention.java | GOMention.setCategories | public void setCategories(int i, String v) {
if (GOMention_Type.featOkTst && ((GOMention_Type)jcasType).casFeat_categories == null)
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jcasType.ll_cas.ll_setStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((GOMention_Type)jcasType).casFeatCode_categories), i, v);} | java | public void setCategories(int i, String v) {
if (GOMention_Type.featOkTst && ((GOMention_Type)jcasType).casFeat_categories == null)
jcasType.jcas.throwFeatMissing("categories", "de.julielab.jules.types.GOMention");
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141,280 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/GOMention.java | GOMention.getGoID | public String getGoID() {
if (GOMention_Type.featOkTst && ((GOMention_Type)jcasType).casFeat_goID == null)
jcasType.jcas.throwFeatMissing("goID", "de.julielab.jules.types.GOMention");
return jcasType.ll_cas.ll_getStringValue(addr, ((GOMention_Type)jcasType).casFeatCode_goID);} | java | public String getGoID() {
if (GOMention_Type.featOkTst && ((GOMention_Type)jcasType).casFeat_goID == null)
jcasType.jcas.throwFeatMissing("goID", "de.julielab.jules.types.GOMention");
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141,281 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/GOMention.java | GOMention.setGoID | public void setGoID(String v) {
if (GOMention_Type.featOkTst && ((GOMention_Type)jcasType).casFeat_goID == null)
jcasType.jcas.throwFeatMissing("goID", "de.julielab.jules.types.GOMention");
jcasType.ll_cas.ll_setStringValue(addr, ((GOMention_Type)jcasType).casFeatCode_goID, v);} | java | public void setGoID(String v) {
if (GOMention_Type.featOkTst && ((GOMention_Type)jcasType).casFeat_goID == null)
jcasType.jcas.throwFeatMissing("goID", "de.julielab.jules.types.GOMention");
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141,282 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/ListItem.java | ListItem.getPOrDefListOrList | public java.util.List<Object> getPOrDefListOrList() {
if (pOrDefListOrList == null) {
pOrDefListOrList = new ArrayList<Object>();
}
return this.pOrDefListOrList;
} | java | public java.util.List<Object> getPOrDefListOrList() {
if (pOrDefListOrList == null) {
pOrDefListOrList = new ArrayList<Object>();
}
return this.pOrDefListOrList;
} | [
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141,283 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/parser/ParserME.java | ParserME.parse | public Parse parse(Parse tokens) {
Parse p = parse(tokens,1)[0];
setParents(p);
return p;
} | java | public Parse parse(Parse tokens) {
Parse p = parse(tokens,1)[0];
setParents(p);
return p;
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141,284 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/parser/ParserME.java | ParserME.mapParseIndex | private int mapParseIndex(int index, Parse[] nonPunctParses, Parse[] parses) {
int parseIndex = index;
while (parses[parseIndex] != nonPunctParses[index]) {
parseIndex++;
}
return parseIndex;
} | java | private int mapParseIndex(int index, Parse[] nonPunctParses, Parse[] parses) {
int parseIndex = index;
while (parses[parseIndex] != nonPunctParses[index]) {
parseIndex++;
}
return parseIndex;
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141,285 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/parser/ParserME.java | ParserME.collapsePunctuation | public static Parse[] collapsePunctuation(Parse[] chunks, Set punctSet) {
List collapsedParses = new ArrayList(chunks.length);
int lastNonPunct = -1;
int nextNonPunct = -1;
for (int ci=0,cn=chunks.length;ci<cn;ci++) {
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chunks[lastNonPunct].addNextPunctuation(chunks[ci]);
}
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if (!punctSet.contains(chunks[nextNonPunct].getType())) {
break;
}
}
if (nextNonPunct < cn) {
chunks[nextNonPunct].addPreviousPunctuation(chunks[ci]);
}
}
else {
collapsedParses.add(chunks[ci]);
lastNonPunct = ci;
}
}
if (collapsedParses.size() == chunks.length) {
return chunks;
}
//System.err.println("collapsedPunctuation: collapsedParses"+collapsedParses);
return (Parse[]) collapsedParses.toArray(new Parse[collapsedParses.size()]);
} | java | public static Parse[] collapsePunctuation(Parse[] chunks, Set punctSet) {
List collapsedParses = new ArrayList(chunks.length);
int lastNonPunct = -1;
int nextNonPunct = -1;
for (int ci=0,cn=chunks.length;ci<cn;ci++) {
if (punctSet.contains(chunks[ci].getType())) {
if (lastNonPunct >= 0) {
chunks[lastNonPunct].addNextPunctuation(chunks[ci]);
}
for (nextNonPunct=ci+1;nextNonPunct<cn;nextNonPunct++) {
if (!punctSet.contains(chunks[nextNonPunct].getType())) {
break;
}
}
if (nextNonPunct < cn) {
chunks[nextNonPunct].addPreviousPunctuation(chunks[ci]);
}
}
else {
collapsedParses.add(chunks[ci]);
lastNonPunct = ci;
}
}
if (collapsedParses.size() == chunks.length) {
return chunks;
}
//System.err.println("collapsedPunctuation: collapsedParses"+collapsedParses);
return (Parse[]) collapsedParses.toArray(new Parse[collapsedParses.size()]);
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141,286 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java | DataTable.getTableId | public int getTableId() {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_tableId == null)
jcasType.jcas.throwFeatMissing("tableId", "ch.epfl.bbp.uima.types.DataTable");
return jcasType.ll_cas.ll_getIntValue(addr, ((DataTable_Type)jcasType).casFeatCode_tableId);} | java | public int getTableId() {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_tableId == null)
jcasType.jcas.throwFeatMissing("tableId", "ch.epfl.bbp.uima.types.DataTable");
return jcasType.ll_cas.ll_getIntValue(addr, ((DataTable_Type)jcasType).casFeatCode_tableId);} | [
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141,287 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java | DataTable.setTableId | public void setTableId(int v) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_tableId == null)
jcasType.jcas.throwFeatMissing("tableId", "ch.epfl.bbp.uima.types.DataTable");
jcasType.ll_cas.ll_setIntValue(addr, ((DataTable_Type)jcasType).casFeatCode_tableId, v);} | java | public void setTableId(int v) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_tableId == null)
jcasType.jcas.throwFeatMissing("tableId", "ch.epfl.bbp.uima.types.DataTable");
jcasType.ll_cas.ll_setIntValue(addr, ((DataTable_Type)jcasType).casFeatCode_tableId, v);} | [
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141,288 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java | DataTable.getRowCount | public int getRowCount() {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_rowCount == null)
jcasType.jcas.throwFeatMissing("rowCount", "ch.epfl.bbp.uima.types.DataTable");
return jcasType.ll_cas.ll_getIntValue(addr, ((DataTable_Type)jcasType).casFeatCode_rowCount);} | java | public int getRowCount() {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_rowCount == null)
jcasType.jcas.throwFeatMissing("rowCount", "ch.epfl.bbp.uima.types.DataTable");
return jcasType.ll_cas.ll_getIntValue(addr, ((DataTable_Type)jcasType).casFeatCode_rowCount);} | [
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141,289 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java | DataTable.setRowCount | public void setRowCount(int v) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_rowCount == null)
jcasType.jcas.throwFeatMissing("rowCount", "ch.epfl.bbp.uima.types.DataTable");
jcasType.ll_cas.ll_setIntValue(addr, ((DataTable_Type)jcasType).casFeatCode_rowCount, v);} | java | public void setRowCount(int v) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_rowCount == null)
jcasType.jcas.throwFeatMissing("rowCount", "ch.epfl.bbp.uima.types.DataTable");
jcasType.ll_cas.ll_setIntValue(addr, ((DataTable_Type)jcasType).casFeatCode_rowCount, v);} | [
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141,290 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java | DataTable.getColumnCount | public int getColumnCount() {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_columnCount == null)
jcasType.jcas.throwFeatMissing("columnCount", "ch.epfl.bbp.uima.types.DataTable");
return jcasType.ll_cas.ll_getIntValue(addr, ((DataTable_Type)jcasType).casFeatCode_columnCount);} | java | public int getColumnCount() {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_columnCount == null)
jcasType.jcas.throwFeatMissing("columnCount", "ch.epfl.bbp.uima.types.DataTable");
return jcasType.ll_cas.ll_getIntValue(addr, ((DataTable_Type)jcasType).casFeatCode_columnCount);} | [
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141,291 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java | DataTable.setColumnCount | public void setColumnCount(int v) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_columnCount == null)
jcasType.jcas.throwFeatMissing("columnCount", "ch.epfl.bbp.uima.types.DataTable");
jcasType.ll_cas.ll_setIntValue(addr, ((DataTable_Type)jcasType).casFeatCode_columnCount, v);} | java | public void setColumnCount(int v) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_columnCount == null)
jcasType.jcas.throwFeatMissing("columnCount", "ch.epfl.bbp.uima.types.DataTable");
jcasType.ll_cas.ll_setIntValue(addr, ((DataTable_Type)jcasType).casFeatCode_columnCount, v);} | [
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@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/ch/epfl/bbp/uima/types/DataTable.java#L140-L143 |
141,292 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java | DataTable.getCaption | public String getCaption() {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_caption == null)
jcasType.jcas.throwFeatMissing("caption", "ch.epfl.bbp.uima.types.DataTable");
return jcasType.ll_cas.ll_getStringValue(addr, ((DataTable_Type)jcasType).casFeatCode_caption);} | java | public String getCaption() {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_caption == null)
jcasType.jcas.throwFeatMissing("caption", "ch.epfl.bbp.uima.types.DataTable");
return jcasType.ll_cas.ll_getStringValue(addr, ((DataTable_Type)jcasType).casFeatCode_caption);} | [
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@generated
@return value of the feature | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java#L153-L156 |
141,293 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java | DataTable.setCaption | public void setCaption(String v) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_caption == null)
jcasType.jcas.throwFeatMissing("caption", "ch.epfl.bbp.uima.types.DataTable");
jcasType.ll_cas.ll_setStringValue(addr, ((DataTable_Type)jcasType).casFeatCode_caption, v);} | java | public void setCaption(String v) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_caption == null)
jcasType.jcas.throwFeatMissing("caption", "ch.epfl.bbp.uima.types.DataTable");
jcasType.ll_cas.ll_setStringValue(addr, ((DataTable_Type)jcasType).casFeatCode_caption, v);} | [
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] | setter for caption - sets
@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/ch/epfl/bbp/uima/types/DataTable.java#L162-L165 |
141,294 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java | DataTable.getHeadings | public StringArray getHeadings() {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_headings == null)
jcasType.jcas.throwFeatMissing("headings", "ch.epfl.bbp.uima.types.DataTable");
return (StringArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((DataTable_Type)jcasType).casFeatCode_headings)));} | java | public StringArray getHeadings() {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_headings == null)
jcasType.jcas.throwFeatMissing("headings", "ch.epfl.bbp.uima.types.DataTable");
return (StringArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((DataTable_Type)jcasType).casFeatCode_headings)));} | [
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] | getter for headings - gets
@generated
@return value of the feature | [
"getter",
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java#L175-L178 |
141,295 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java | DataTable.setHeadings | public void setHeadings(StringArray v) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_headings == null)
jcasType.jcas.throwFeatMissing("headings", "ch.epfl.bbp.uima.types.DataTable");
jcasType.ll_cas.ll_setRefValue(addr, ((DataTable_Type)jcasType).casFeatCode_headings, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setHeadings(StringArray v) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_headings == null)
jcasType.jcas.throwFeatMissing("headings", "ch.epfl.bbp.uima.types.DataTable");
jcasType.ll_cas.ll_setRefValue(addr, ((DataTable_Type)jcasType).casFeatCode_headings, jcasType.ll_cas.ll_getFSRef(v));} | [
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] | setter for headings - sets
@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/ch/epfl/bbp/uima/types/DataTable.java#L184-L187 |
141,296 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java | DataTable.getHeadings | public String getHeadings(int i) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_headings == null)
jcasType.jcas.throwFeatMissing("headings", "ch.epfl.bbp.uima.types.DataTable");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((DataTable_Type)jcasType).casFeatCode_headings), i);
return jcasType.ll_cas.ll_getStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((DataTable_Type)jcasType).casFeatCode_headings), i);} | java | public String getHeadings(int i) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_headings == null)
jcasType.jcas.throwFeatMissing("headings", "ch.epfl.bbp.uima.types.DataTable");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((DataTable_Type)jcasType).casFeatCode_headings), i);
return jcasType.ll_cas.ll_getStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((DataTable_Type)jcasType).casFeatCode_headings), i);} | [
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] | indexed getter for headings - gets an indexed value -
@generated
@param i index in the array to get
@return value of the element at index i | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java#L194-L198 |
141,297 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java | DataTable.setHeadings | public void setHeadings(int i, String v) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_headings == null)
jcasType.jcas.throwFeatMissing("headings", "ch.epfl.bbp.uima.types.DataTable");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((DataTable_Type)jcasType).casFeatCode_headings), i);
jcasType.ll_cas.ll_setStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((DataTable_Type)jcasType).casFeatCode_headings), i, v);} | java | public void setHeadings(int i, String v) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_headings == null)
jcasType.jcas.throwFeatMissing("headings", "ch.epfl.bbp.uima.types.DataTable");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((DataTable_Type)jcasType).casFeatCode_headings), i);
jcasType.ll_cas.ll_setStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((DataTable_Type)jcasType).casFeatCode_headings), i, v);} | [
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] | indexed setter for headings - sets an indexed value -
@generated
@param i index in the array to set
@param v value to set into the array | [
"indexed",
"setter",
"for",
"headings",
"-",
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"an",
"indexed",
"value",
"-"
] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java#L205-L209 |
141,298 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java | DataTable.getBody | public StringArray getBody() {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_body == null)
jcasType.jcas.throwFeatMissing("body", "ch.epfl.bbp.uima.types.DataTable");
return (StringArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((DataTable_Type)jcasType).casFeatCode_body)));} | java | public StringArray getBody() {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_body == null)
jcasType.jcas.throwFeatMissing("body", "ch.epfl.bbp.uima.types.DataTable");
return (StringArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((DataTable_Type)jcasType).casFeatCode_body)));} | [
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] | getter for body - gets the body of the table that contains data
@generated
@return value of the feature | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java#L219-L222 |
141,299 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/DataTable.java | DataTable.setBody | public void setBody(StringArray v) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_body == null)
jcasType.jcas.throwFeatMissing("body", "ch.epfl.bbp.uima.types.DataTable");
jcasType.ll_cas.ll_setRefValue(addr, ((DataTable_Type)jcasType).casFeatCode_body, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setBody(StringArray v) {
if (DataTable_Type.featOkTst && ((DataTable_Type)jcasType).casFeat_body == null)
jcasType.jcas.throwFeatMissing("body", "ch.epfl.bbp.uima.types.DataTable");
jcasType.ll_cas.ll_setRefValue(addr, ((DataTable_Type)jcasType).casFeatCode_body, jcasType.ll_cas.ll_getFSRef(v));} | [
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] | setter for body - sets the body of the table that contains data
@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/ch/epfl/bbp/uima/types/DataTable.java#L228-L231 |
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