id int32 0 165k | repo stringlengths 7 58 | path stringlengths 12 218 | func_name stringlengths 3 140 | original_string stringlengths 73 34.1k | language stringclasses 1 value | code stringlengths 73 34.1k | code_tokens list | docstring stringlengths 3 16k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 105 339 |
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140,900 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/SourceFile.java | SourceFile.getEncoding | public String getEncoding() {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_encoding == null)
jcasType.jcas.throwFeatMissing("encoding", "de.julielab.jules.types.ace.SourceFile");
return jcasType.ll_cas.ll_getStringValue(addr, ((SourceFile_Type)jcasType).casFeatCode_encoding);} | java | public String getEncoding() {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_encoding == null)
jcasType.jcas.throwFeatMissing("encoding", "de.julielab.jules.types.ace.SourceFile");
return jcasType.ll_cas.ll_getStringValue(addr, ((SourceFile_Type)jcasType).casFeatCode_encoding);} | [
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140,901 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/SourceFile.java | SourceFile.setEncoding | public void setEncoding(String v) {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_encoding == null)
jcasType.jcas.throwFeatMissing("encoding", "de.julielab.jules.types.ace.SourceFile");
jcasType.ll_cas.ll_setStringValue(addr, ((SourceFile_Type)jcasType).casFeatCode_encoding, v);} | java | public void setEncoding(String v) {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_encoding == null)
jcasType.jcas.throwFeatMissing("encoding", "de.julielab.jules.types.ace.SourceFile");
jcasType.ll_cas.ll_setStringValue(addr, ((SourceFile_Type)jcasType).casFeatCode_encoding, v);} | [
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140,902 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/SourceFile.java | SourceFile.getDocuments | public FSArray getDocuments() {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_documents == null)
jcasType.jcas.throwFeatMissing("documents", "de.julielab.jules.types.ace.SourceFile");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((SourceFile_Type)jcasType).casFeatCode_documents)));} | java | public FSArray getDocuments() {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_documents == null)
jcasType.jcas.throwFeatMissing("documents", "de.julielab.jules.types.ace.SourceFile");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((SourceFile_Type)jcasType).casFeatCode_documents)));} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/SourceFile.java#L196-L199 |
140,903 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/SourceFile.java | SourceFile.setDocuments | public void setDocuments(FSArray v) {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_documents == null)
jcasType.jcas.throwFeatMissing("documents", "de.julielab.jules.types.ace.SourceFile");
jcasType.ll_cas.ll_setRefValue(addr, ((SourceFile_Type)jcasType).casFeatCode_documents, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setDocuments(FSArray v) {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_documents == null)
jcasType.jcas.throwFeatMissing("documents", "de.julielab.jules.types.ace.SourceFile");
jcasType.ll_cas.ll_setRefValue(addr, ((SourceFile_Type)jcasType).casFeatCode_documents, jcasType.ll_cas.ll_getFSRef(v));} | [
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140,904 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/SourceFile.java | SourceFile.getDocuments | public Document getDocuments(int i) {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_documents == null)
jcasType.jcas.throwFeatMissing("documents", "de.julielab.jules.types.ace.SourceFile");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((SourceFile_Type)jcasType).casFeatCode_documents), i);
return (Document)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((SourceFile_Type)jcasType).casFeatCode_documents), i)));} | java | public Document getDocuments(int i) {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_documents == null)
jcasType.jcas.throwFeatMissing("documents", "de.julielab.jules.types.ace.SourceFile");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((SourceFile_Type)jcasType).casFeatCode_documents), i);
return (Document)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((SourceFile_Type)jcasType).casFeatCode_documents), i)));} | [
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140,905 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/SourceFile.java | SourceFile.setDocuments | public void setDocuments(int i, Document v) {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_documents == null)
jcasType.jcas.throwFeatMissing("documents", "de.julielab.jules.types.ace.SourceFile");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((SourceFile_Type)jcasType).casFeatCode_documents), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((SourceFile_Type)jcasType).casFeatCode_documents), i, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setDocuments(int i, Document v) {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_documents == null)
jcasType.jcas.throwFeatMissing("documents", "de.julielab.jules.types.ace.SourceFile");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((SourceFile_Type)jcasType).casFeatCode_documents), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((SourceFile_Type)jcasType).casFeatCode_documents), i, jcasType.ll_cas.ll_getFSRef(v));} | [
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140,906 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/SourceFile.java | SourceFile.getAce_type | public String getAce_type() {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_ace_type == null)
jcasType.jcas.throwFeatMissing("ace_type", "de.julielab.jules.types.ace.SourceFile");
return jcasType.ll_cas.ll_getStringValue(addr, ((SourceFile_Type)jcasType).casFeatCode_ace_type);} | java | public String getAce_type() {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_ace_type == null)
jcasType.jcas.throwFeatMissing("ace_type", "de.julielab.jules.types.ace.SourceFile");
return jcasType.ll_cas.ll_getStringValue(addr, ((SourceFile_Type)jcasType).casFeatCode_ace_type);} | [
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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/ace/SourceFile.java#L240-L243 |
140,907 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/SourceFile.java | SourceFile.setAce_type | public void setAce_type(String v) {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_ace_type == null)
jcasType.jcas.throwFeatMissing("ace_type", "de.julielab.jules.types.ace.SourceFile");
jcasType.ll_cas.ll_setStringValue(addr, ((SourceFile_Type)jcasType).casFeatCode_ace_type, v);} | java | public void setAce_type(String v) {
if (SourceFile_Type.featOkTst && ((SourceFile_Type)jcasType).casFeat_ace_type == null)
jcasType.jcas.throwFeatMissing("ace_type", "de.julielab.jules.types.ace.SourceFile");
jcasType.ll_cas.ll_setStringValue(addr, ((SourceFile_Type)jcasType).casFeatCode_ace_type, v);} | [
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140,908 | BlueBrain/bluima | modules/bluima_jsre/src/main/java/org/itc/irst/tcc/sre/data/ExampleSet.java | ExampleSet.addAll | public void addAll(ExampleSet data)
{
for (int i=0;i<data.size();i++)
add(data.x(i), data.y(i), data.id(i));
} | java | public void addAll(ExampleSet data)
{
for (int i=0;i<data.size();i++)
add(data.x(i), data.y(i), data.id(i));
} | [
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140,909 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java | MMAXAnnotation.getAnnotationLevel | public String getAnnotationLevel() {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_annotationLevel == null)
jcasType.jcas.throwFeatMissing("annotationLevel", "de.julielab.jules.types.mmax.MMAXAnnotation");
return jcasType.ll_cas.ll_getStringValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_annotationLevel);} | java | public String getAnnotationLevel() {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_annotationLevel == null)
jcasType.jcas.throwFeatMissing("annotationLevel", "de.julielab.jules.types.mmax.MMAXAnnotation");
return jcasType.ll_cas.ll_getStringValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_annotationLevel);} | [
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] | getter for annotationLevel - gets The MMAX annotation level.
@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/mmax/MMAXAnnotation.java#L87-L90 |
140,910 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java | MMAXAnnotation.setAnnotationLevel | public void setAnnotationLevel(String v) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_annotationLevel == null)
jcasType.jcas.throwFeatMissing("annotationLevel", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.ll_cas.ll_setStringValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_annotationLevel, v);} | java | public void setAnnotationLevel(String v) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_annotationLevel == null)
jcasType.jcas.throwFeatMissing("annotationLevel", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.ll_cas.ll_setStringValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_annotationLevel, v);} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java#L96-L99 |
140,911 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java | MMAXAnnotation.getSegmentList | public FSArray getSegmentList() {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_segmentList == null)
jcasType.jcas.throwFeatMissing("segmentList", "de.julielab.jules.types.mmax.MMAXAnnotation");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_segmentList)));} | java | public FSArray getSegmentList() {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_segmentList == null)
jcasType.jcas.throwFeatMissing("segmentList", "de.julielab.jules.types.mmax.MMAXAnnotation");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_segmentList)));} | [
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] | getter for segmentList - gets List of MMAX annotation segements that make up the MMAX annotation.
@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/mmax/MMAXAnnotation.java#L133-L136 |
140,912 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java | MMAXAnnotation.setSegmentList | public void setSegmentList(FSArray v) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_segmentList == null)
jcasType.jcas.throwFeatMissing("segmentList", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.ll_cas.ll_setRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_segmentList, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setSegmentList(FSArray v) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_segmentList == null)
jcasType.jcas.throwFeatMissing("segmentList", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.ll_cas.ll_setRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_segmentList, 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/mmax/MMAXAnnotation.java#L142-L145 |
140,913 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java | MMAXAnnotation.getSegmentList | public AnnotationSegment getSegmentList(int i) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_segmentList == null)
jcasType.jcas.throwFeatMissing("segmentList", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_segmentList), i);
return (AnnotationSegment)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_segmentList), i)));} | java | public AnnotationSegment getSegmentList(int i) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_segmentList == null)
jcasType.jcas.throwFeatMissing("segmentList", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_segmentList), i);
return (AnnotationSegment)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_segmentList), i)));} | [
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] | indexed getter for segmentList - gets an indexed value - List of MMAX annotation segements that make up the MMAX annotation.
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@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/mmax/MMAXAnnotation.java#L152-L156 |
140,914 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java | MMAXAnnotation.setSegmentList | public void setSegmentList(int i, AnnotationSegment v) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_segmentList == null)
jcasType.jcas.throwFeatMissing("segmentList", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_segmentList), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_segmentList), i, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setSegmentList(int i, AnnotationSegment v) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_segmentList == null)
jcasType.jcas.throwFeatMissing("segmentList", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_segmentList), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_segmentList), i, jcasType.ll_cas.ll_getFSRef(v));} | [
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] | indexed setter for segmentList - sets an indexed value - List of MMAX annotation segements that make up the MMAX annotation.
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@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/mmax/MMAXAnnotation.java#L163-L167 |
140,915 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java | MMAXAnnotation.getAttributeList | public FSArray getAttributeList() {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_attributeList == null)
jcasType.jcas.throwFeatMissing("attributeList", "de.julielab.jules.types.mmax.MMAXAnnotation");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_attributeList)));} | java | public FSArray getAttributeList() {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_attributeList == null)
jcasType.jcas.throwFeatMissing("attributeList", "de.julielab.jules.types.mmax.MMAXAnnotation");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_attributeList)));} | [
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] | getter for attributeList - gets List of attributes of the MMAX annotation.
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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/mmax/MMAXAnnotation.java#L177-L180 |
140,916 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java | MMAXAnnotation.setAttributeList | public void setAttributeList(FSArray v) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_attributeList == null)
jcasType.jcas.throwFeatMissing("attributeList", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.ll_cas.ll_setRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_attributeList, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setAttributeList(FSArray v) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_attributeList == null)
jcasType.jcas.throwFeatMissing("attributeList", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.ll_cas.ll_setRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_attributeList, jcasType.ll_cas.ll_getFSRef(v));} | [
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140,917 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java | MMAXAnnotation.getAttributeList | public MMAXAttribute getAttributeList(int i) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_attributeList == null)
jcasType.jcas.throwFeatMissing("attributeList", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_attributeList), i);
return (MMAXAttribute)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_attributeList), i)));} | java | public MMAXAttribute getAttributeList(int i) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_attributeList == null)
jcasType.jcas.throwFeatMissing("attributeList", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_attributeList), i);
return (MMAXAttribute)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_attributeList), i)));} | [
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140,918 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java | MMAXAnnotation.setAttributeList | public void setAttributeList(int i, MMAXAttribute v) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_attributeList == null)
jcasType.jcas.throwFeatMissing("attributeList", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_attributeList), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_attributeList), i, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setAttributeList(int i, MMAXAttribute v) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_attributeList == null)
jcasType.jcas.throwFeatMissing("attributeList", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_attributeList), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_attributeList), i, jcasType.ll_cas.ll_getFSRef(v));} | [
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140,919 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java | MMAXAnnotation.getPointerList | public FSArray getPointerList() {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_pointerList == null)
jcasType.jcas.throwFeatMissing("pointerList", "de.julielab.jules.types.mmax.MMAXAnnotation");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_pointerList)));} | java | public FSArray getPointerList() {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_pointerList == null)
jcasType.jcas.throwFeatMissing("pointerList", "de.julielab.jules.types.mmax.MMAXAnnotation");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_pointerList)));} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java#L221-L224 |
140,920 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java | MMAXAnnotation.setPointerList | public void setPointerList(FSArray v) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_pointerList == null)
jcasType.jcas.throwFeatMissing("pointerList", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.ll_cas.ll_setRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_pointerList, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setPointerList(FSArray v) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_pointerList == null)
jcasType.jcas.throwFeatMissing("pointerList", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.ll_cas.ll_setRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_pointerList, jcasType.ll_cas.ll_getFSRef(v));} | [
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140,921 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java | MMAXAnnotation.getPointerList | public MMAXPointer getPointerList(int i) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_pointerList == null)
jcasType.jcas.throwFeatMissing("pointerList", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_pointerList), i);
return (MMAXPointer)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_pointerList), i)));} | java | public MMAXPointer getPointerList(int i) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_pointerList == null)
jcasType.jcas.throwFeatMissing("pointerList", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_pointerList), i);
return (MMAXPointer)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_pointerList), i)));} | [
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] | indexed getter for pointerList - gets an indexed value - The list of MMAX pointers of the MMAX annotation.
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java#L240-L244 |
140,922 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java | MMAXAnnotation.setPointerList | public void setPointerList(int i, MMAXPointer v) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_pointerList == null)
jcasType.jcas.throwFeatMissing("pointerList", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_pointerList), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_pointerList), i, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setPointerList(int i, MMAXPointer v) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_pointerList == null)
jcasType.jcas.throwFeatMissing("pointerList", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_pointerList), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_pointerList), i, jcasType.ll_cas.ll_getFSRef(v));} | [
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140,923 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java | MMAXAnnotation.getAdaptedCoveredText | public String getAdaptedCoveredText() {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_adaptedCoveredText == null)
jcasType.jcas.throwFeatMissing("adaptedCoveredText", "de.julielab.jules.types.mmax.MMAXAnnotation");
return jcasType.ll_cas.ll_getStringValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_adaptedCoveredText);} | java | public String getAdaptedCoveredText() {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_adaptedCoveredText == null)
jcasType.jcas.throwFeatMissing("adaptedCoveredText", "de.julielab.jules.types.mmax.MMAXAnnotation");
return jcasType.ll_cas.ll_getStringValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_adaptedCoveredText);} | [
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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/mmax/MMAXAnnotation.java#L265-L268 |
140,924 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java | MMAXAnnotation.setAdaptedCoveredText | public void setAdaptedCoveredText(String v) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_adaptedCoveredText == null)
jcasType.jcas.throwFeatMissing("adaptedCoveredText", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.ll_cas.ll_setStringValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_adaptedCoveredText, v);} | java | public void setAdaptedCoveredText(String v) {
if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_adaptedCoveredText == null)
jcasType.jcas.throwFeatMissing("adaptedCoveredText", "de.julielab.jules.types.mmax.MMAXAnnotation");
jcasType.ll_cas.ll_setStringValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_adaptedCoveredText, v);} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/mmax/MMAXAnnotation.java#L274-L277 |
140,925 | BlueBrain/bluima | modules/bluima_utils/src/main/java/ch/epfl/bbp/uima/uimafit/StatusCallbackListenerImpl.java | StatusCallbackListenerImpl.initializationComplete | public void initializationComplete() {
if (UIMAFramework.getLogger().isLoggable(Level.CONFIG)) {
UIMAFramework.getLogger(this.getClass()).logrb(Level.CONFIG, this.getClass().getName(),
"process", CPMUtils.CPM_LOG_RESOURCE_BUNDLE, "UIMA_CPM_cpm_init_complete__CONFIG",
new Object[] { Thread.currentThread().getName() });
}
} | java | public void initializationComplete() {
if (UIMAFramework.getLogger().isLoggable(Level.CONFIG)) {
UIMAFramework.getLogger(this.getClass()).logrb(Level.CONFIG, this.getClass().getName(),
"process", CPMUtils.CPM_LOG_RESOURCE_BUNDLE, "UIMA_CPM_cpm_init_complete__CONFIG",
new Object[] { Thread.currentThread().getName() });
}
} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_utils/src/main/java/ch/epfl/bbp/uima/uimafit/StatusCallbackListenerImpl.java#L48-L54 |
140,926 | BlueBrain/bluima | modules/bluima_utils/src/main/java/ch/epfl/bbp/uima/uimafit/StatusCallbackListenerImpl.java | StatusCallbackListenerImpl.batchProcessComplete | public synchronized void batchProcessComplete() {
if (UIMAFramework.getLogger().isLoggable(Level.FINEST)) {
UIMAFramework.getLogger(this.getClass()).logrb(Level.FINEST, this.getClass().getName(),
"process", CPMUtils.CPM_LOG_RESOURCE_BUNDLE, "UIMA_CPM_method_ping__FINEST",
new Object[] { Thread.currentThread().getName() });
}
} | java | public synchronized void batchProcessComplete() {
if (UIMAFramework.getLogger().isLoggable(Level.FINEST)) {
UIMAFramework.getLogger(this.getClass()).logrb(Level.FINEST, this.getClass().getName(),
"process", CPMUtils.CPM_LOG_RESOURCE_BUNDLE, "UIMA_CPM_method_ping__FINEST",
new Object[] { Thread.currentThread().getName() });
}
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_utils/src/main/java/ch/epfl/bbp/uima/uimafit/StatusCallbackListenerImpl.java#L62-L68 |
140,927 | sonatype/sisu | examples/guice-rcp/guice-rcp-plugin/src/org/sonatype/examples/guice/rcp/NavigationView.java | NavigationView.createDummyModel | private TreeObject createDummyModel() {
TreeObject to1 = new TreeObject("Inbox");
TreeObject to2 = new TreeObject("Drafts");
TreeObject to3 = new TreeObject("Sent");
TreeParent p1 = new TreeParent("me@this.com");
p1.addChild(to1);
p1.addChild(to2);
p1.addChild(to3);
TreeObject to4 = new TreeObject("Inbox");
TreeParent p2 = new TreeParent("other@aol.com");
p2.addChild(to4);
TreeParent root = new TreeParent("");
root.addChild(p1);
root.addChild(p2);
return root;
} | java | private TreeObject createDummyModel() {
TreeObject to1 = new TreeObject("Inbox");
TreeObject to2 = new TreeObject("Drafts");
TreeObject to3 = new TreeObject("Sent");
TreeParent p1 = new TreeParent("me@this.com");
p1.addChild(to1);
p1.addChild(to2);
p1.addChild(to3);
TreeObject to4 = new TreeObject("Inbox");
TreeParent p2 = new TreeParent("other@aol.com");
p2.addChild(to4);
TreeParent root = new TreeParent("");
root.addChild(p1);
root.addChild(p2);
return root;
} | [
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code, you will connect to a real model and expose its hierarchy. | [
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] | a3dd122e19a5c3bc3266b9196fe47a3ea664a289 | https://github.com/sonatype/sisu/blob/a3dd122e19a5c3bc3266b9196fe47a3ea664a289/examples/guice-rcp/guice-rcp-plugin/src/org/sonatype/examples/guice/rcp/NavigationView.java#L125-L142 |
140,928 | BlueBrain/bluima | modules/bluima_scripting/src/main/java/ch/epfl/bbp/uima/laucher/Launcher.java | Launcher.runPipeline | public static void runPipeline(File scriptFile, List<String> cliArgs)
throws IOException, UIMAException, ParseException {
if (!scriptFile.exists()) {
throw new IOException("Script file does not exist ("
+ scriptFile.getAbsolutePath() + ")");
}
LOG.info("Parsing pipeline script at '{}'",
scriptFile.getAbsolutePath() + " \n with CLI parameters: "
+ join(cliArgs, ", "));
Pipeline pipeline = null;
try {
pipeline = PipelineScriptParser.parse(scriptFile, cliArgs);
} catch (ParseException e) {
throw new ParseException("\nERROR parsing '" + scriptFile.getName()
+ "'\n" + e.getMessage()
+ "\n(see the README.txt for the pipeline script format)",
e.getErrorOffset());
}
LOG.info("Successfully parsed pipeline script, now starting pipeline...");
LOG.info("*************************************************************");
pipeline.run();
// will be printed if no exception.
// used in pipeline tests, do not change
System.out.println(OK_MESSAGE);
} | java | public static void runPipeline(File scriptFile, List<String> cliArgs)
throws IOException, UIMAException, ParseException {
if (!scriptFile.exists()) {
throw new IOException("Script file does not exist ("
+ scriptFile.getAbsolutePath() + ")");
}
LOG.info("Parsing pipeline script at '{}'",
scriptFile.getAbsolutePath() + " \n with CLI parameters: "
+ join(cliArgs, ", "));
Pipeline pipeline = null;
try {
pipeline = PipelineScriptParser.parse(scriptFile, cliArgs);
} catch (ParseException e) {
throw new ParseException("\nERROR parsing '" + scriptFile.getName()
+ "'\n" + e.getMessage()
+ "\n(see the README.txt for the pipeline script format)",
e.getErrorOffset());
}
LOG.info("Successfully parsed pipeline script, now starting pipeline...");
LOG.info("*************************************************************");
pipeline.run();
// will be printed if no exception.
// used in pipeline tests, do not change
System.out.println(OK_MESSAGE);
} | [
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] | Parse this pipeline and run it
@return true if no error during processing
@throws ParseException | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_scripting/src/main/java/ch/epfl/bbp/uima/laucher/Launcher.java#L174-L200 |
140,929 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/maxent/DomainToModelMap.java | DomainToModelMap.getModel | public MaxentModel getModel (ModelDomain domain) {
if (map.containsKey(domain)) {
return (MaxentModel)map.get(domain);
} else {
throw new NoSuchElementException("No model has been created for "+
"domain: " + domain);
}
} | java | public MaxentModel getModel (ModelDomain domain) {
if (map.containsKey(domain)) {
return (MaxentModel)map.get(domain);
} else {
throw new NoSuchElementException("No model has been created for "+
"domain: " + domain);
}
} | [
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] | Get the model mapped to by the given ModelDomain key.
@param domain The ModelDomain object which keys to the desired model.
@return The MaxentModel corresponding to the given domain. | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/maxent/DomainToModelMap.java#L54-L61 |
140,930 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/org/apache/uima/examples/RoomNumber.java | RoomNumber.getBuilding | public String getBuilding() {
if (RoomNumber_Type.featOkTst && ((RoomNumber_Type)jcasType).casFeat_building == null)
jcasType.jcas.throwFeatMissing("building", "org.apache.uima.examples.RoomNumber");
return jcasType.ll_cas.ll_getStringValue(addr, ((RoomNumber_Type)jcasType).casFeatCode_building);} | java | public String getBuilding() {
if (RoomNumber_Type.featOkTst && ((RoomNumber_Type)jcasType).casFeat_building == null)
jcasType.jcas.throwFeatMissing("building", "org.apache.uima.examples.RoomNumber");
return jcasType.ll_cas.ll_getStringValue(addr, ((RoomNumber_Type)jcasType).casFeatCode_building);} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/org/apache/uima/examples/RoomNumber.java#L86-L89 |
140,931 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/org/apache/uima/examples/RoomNumber.java | RoomNumber.setBuilding | public void setBuilding(String v) {
if (RoomNumber_Type.featOkTst && ((RoomNumber_Type)jcasType).casFeat_building == null)
jcasType.jcas.throwFeatMissing("building", "org.apache.uima.examples.RoomNumber");
jcasType.ll_cas.ll_setStringValue(addr, ((RoomNumber_Type)jcasType).casFeatCode_building, v);} | java | public void setBuilding(String v) {
if (RoomNumber_Type.featOkTst && ((RoomNumber_Type)jcasType).casFeat_building == null)
jcasType.jcas.throwFeatMissing("building", "org.apache.uima.examples.RoomNumber");
jcasType.ll_cas.ll_setStringValue(addr, ((RoomNumber_Type)jcasType).casFeatCode_building, 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/org/apache/uima/examples/RoomNumber.java#L95-L98 |
140,932 | BlueBrain/bluima | modules/bluima_regions/src/main/java/ch/epfl/bbp/uima/BrainRegionsHelper.java | BrainRegionsHelper.getBrainregionRules | @Deprecated(/* Use script directly with appropriate paths */)
public static AnalysisEngineDescription getBrainregionRules()
throws ResourceInitializationException {
return createEngineDescription(RutaEngine.class,//
PARAM_MAIN_SCRIPT, "Main",//
PARAM_SCRIPT_PATHS, BRAIN_REGIONS_HOME + RESOURCES_PATH
+ "ruta",//
PARAM_RESOURCE_PATHS, LEXICON_HOME);
} | java | @Deprecated(/* Use script directly with appropriate paths */)
public static AnalysisEngineDescription getBrainregionRules()
throws ResourceInitializationException {
return createEngineDescription(RutaEngine.class,//
PARAM_MAIN_SCRIPT, "Main",//
PARAM_SCRIPT_PATHS, BRAIN_REGIONS_HOME + RESOURCES_PATH
+ "ruta",//
PARAM_RESOURCE_PATHS, LEXICON_HOME);
} | [
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140,933 | BlueBrain/bluima | modules/bluima_utils/src/main/java/ch/epfl/bbp/uima/filter/SectionAnnotator.java | SectionAnnotator.cleanBlockText | public static String cleanBlockText(String text) {
// only keep text longer that 5
if (text == null || text.length() < 6)
return null;
// only keep text longer that 5
if (text.length() < 6) {
return null;
}
// keep only 1st line
int firstReturn = text.indexOf("\n");
if (firstReturn > -1) {
text = text.substring(0, firstReturn);
}
// remove double spaces
text = text.replaceAll(" +", " ").trim();
// remove numbers at beg, tabs
text = text.replaceAll("^\\d*", "").replaceAll("\t", " ").trim();
// then, remove dot at beg
if (text.length() > 0 && text.charAt(0) == '.') {
text = text.substring(1).trim();
}
// check that at least 50% of chars are letters
double letters = 0;
for (int i = 0; i < text.length(); i++) {
if (Character.isLetter(text.charAt(i)))
letters++;
}
if ((letters / (text.length() + 0d)) < 0.5d) {
return null;
}
// stemming
String stemmed = "";
for (String token : text.trim().split(" ")) {
stemmed += stemmer.stem(token) + " ";
}
// trim at 30 chars
String snippet = StringUtils.snippetize(stemmed.trim(), 30);
return snippet.trim();
} | java | public static String cleanBlockText(String text) {
// only keep text longer that 5
if (text == null || text.length() < 6)
return null;
// only keep text longer that 5
if (text.length() < 6) {
return null;
}
// keep only 1st line
int firstReturn = text.indexOf("\n");
if (firstReturn > -1) {
text = text.substring(0, firstReturn);
}
// remove double spaces
text = text.replaceAll(" +", " ").trim();
// remove numbers at beg, tabs
text = text.replaceAll("^\\d*", "").replaceAll("\t", " ").trim();
// then, remove dot at beg
if (text.length() > 0 && text.charAt(0) == '.') {
text = text.substring(1).trim();
}
// check that at least 50% of chars are letters
double letters = 0;
for (int i = 0; i < text.length(); i++) {
if (Character.isLetter(text.charAt(i)))
letters++;
}
if ((letters / (text.length() + 0d)) < 0.5d) {
return null;
}
// stemming
String stemmed = "";
for (String token : text.trim().split(" ")) {
stemmed += stemmer.stem(token) + " ";
}
// trim at 30 chars
String snippet = StringUtils.snippetize(stemmed.trim(), 30);
return snippet.trim();
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@param the
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@return the cleaned up 1st line of that block, if "valid". NOT
lowercased. | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_utils/src/main/java/ch/epfl/bbp/uima/filter/SectionAnnotator.java#L180-L223 |
140,934 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/BoxedText.java | BoxedText.getSec | public java.util.List<Sec> getSec() {
if (sec == null) {
sec = new ArrayList<Sec>();
}
return this.sec;
} | java | public java.util.List<Sec> getSec() {
if (sec == null) {
sec = new ArrayList<Sec>();
}
return this.sec;
} | [
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140,935 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/BoxedText.java | BoxedText.getNotesOrFnGroupOrGlossary | public java.util.List<Object> getNotesOrFnGroupOrGlossary() {
if (notesOrFnGroupOrGlossary == null) {
notesOrFnGroupOrGlossary = new ArrayList<Object>();
}
return this.notesOrFnGroupOrGlossary;
} | java | public java.util.List<Object> getNotesOrFnGroupOrGlossary() {
if (notesOrFnGroupOrGlossary == null) {
notesOrFnGroupOrGlossary = new ArrayList<Object>();
}
return this.notesOrFnGroupOrGlossary;
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Objects of the following type(s) are allowed in the list
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{@link FnGroup }
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140,936 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/SourcedMatchData.java | SourcedMatchData.addInstance | public void addInstance(String src,String id,String text)
{
Instance inst = new Instance(src,id,text);
ArrayList list = (ArrayList)sourceLists.get(src);
if (list==null) {
list = new ArrayList();
sourceLists.put(src,list);
sourceNames.add(src);
}
list.add(inst);
} | java | public void addInstance(String src,String id,String text)
{
Instance inst = new Instance(src,id,text);
ArrayList list = (ArrayList)sourceLists.get(src);
if (list==null) {
list = new ArrayList();
sourceLists.put(src,list);
sourceNames.add(src);
}
list.add(inst);
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140,937 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/SourcedMatchData.java | SourcedMatchData.getInstance | public Instance getInstance(String src, int j) {
return (Instance)((ArrayList)sourceLists.get(src)).get(j);
} | java | public Instance getInstance(String src, int j) {
return (Instance)((ArrayList)sourceLists.get(src)).get(j);
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140,938 | BlueBrain/bluima | utils/blue_commons/src/main/java/ch/epfl/bbp/StringUtils.java | StringUtils.maxTruncStr | public static String maxTruncStr(String source, int maxNrChars) {
if (source != null && source.length() > maxNrChars) {
return source.substring(0, maxNrChars);
} else {
return source;
}
} | java | public static String maxTruncStr(String source, int maxNrChars) {
if (source != null && source.length() > maxNrChars) {
return source.substring(0, maxNrChars);
} else {
return source;
}
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140,939 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/tokens/TagLinkToken.java | TagLinkToken.score | public double score(StringWrapper s, StringWrapper t) {
String S = s.unwrap(),
T =t.unwrap();
totalScore = 0.0;
if (S.equals(T)) {
matched = S.length();
return 1.0;
}
else {
sSize = S.length();
tSize = T.length();
// let S be the largest token
if (sSize < tSize) {
String tmp1 = S;
S = T;
T = tmp1;
double tmp2 = sSize;
sSize = tSize;
tSize = tmp2;
tokenT = T;
}
tokenT = S;
ArrayList candidateList = algorithm1(S, T);
sortList(candidateList);
totalScore = getScore(candidateList);
totalScore = (totalScore / ( (double) sSize) + totalScore / ( (double) tSize)) / 2.0;
return winkler(totalScore, S, T);
}
} | java | public double score(StringWrapper s, StringWrapper t) {
String S = s.unwrap(),
T =t.unwrap();
totalScore = 0.0;
if (S.equals(T)) {
matched = S.length();
return 1.0;
}
else {
sSize = S.length();
tSize = T.length();
// let S be the largest token
if (sSize < tSize) {
String tmp1 = S;
S = T;
T = tmp1;
double tmp2 = sSize;
sSize = tSize;
tSize = tmp2;
tokenT = T;
}
tokenT = S;
ArrayList candidateList = algorithm1(S, T);
sortList(candidateList);
totalScore = getScore(candidateList);
totalScore = (totalScore / ( (double) sSize) + totalScore / ( (double) tSize)) / 2.0;
return winkler(totalScore, S, T);
}
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@param T StringWrapper
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140,940 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/tokens/TagLinkToken.java | TagLinkToken.explainScore | public String explainScore(StringWrapper s, StringWrapper t) {
String S = s.unwrap(),
T = t.unwrap();
StringBuffer buff = new StringBuffer();
buff.append("\n****TagLinkToken****\n");
buff.append("Si=" + S + ", Tj=" + T + "\n");
double totalScore = 0.0;
if (S.equals(T)) {
matched = S.length();
buff.append("Sij=1.0");
}
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sSize = S.length();
tSize = T.length();
// let S be the biggest token
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String tmp1 = S;
S = T;
T = tmp1;
double tmp2 = sSize;
sSize = tSize;
tSize = tmp2;
}
ArrayList candidateList = algorithm1(S, T);
sortList(candidateList);
buff.append("Common characteres:\n");
buff.append("Si\tTj\tScore_ij(Si,Tj)\n");
matched = 0;
HashMap tMap = new HashMap(),
uMap = new HashMap();
java.util.Iterator it = candidateList.iterator();
while (it.hasNext()) {
TagLink.Candidates actualCandidates = (TagLink.Candidates) it.next();
Integer sPos = new Integer(actualCandidates.getTPos()),
tPos = new Integer(actualCandidates.getUPos());
if ( (!tMap.containsKey(sPos)) &&
(!uMap.containsKey(tPos))) {
double actualScore = actualCandidates.getScore();
totalScore += actualScore;
tMap.put(sPos, null);
uMap.put(tPos, null);
buff.append(S.charAt(sPos.intValue()) + "\t" + T.charAt(tPos.intValue()) +
"\t" + round(actualScore) + "\n");
matched++;
}
}
totalScore = (totalScore / ( (double) sSize) + totalScore / ( (double) tSize)) / 2.0;
System.out.println("score " + totalScore);
buff.append("Score_ij(S,T)=" + round(winkler(totalScore, S, T)));
buff.append("\nMatched characters=" + matched);
}
return buff.toString();
} | java | public String explainScore(StringWrapper s, StringWrapper t) {
String S = s.unwrap(),
T = t.unwrap();
StringBuffer buff = new StringBuffer();
buff.append("\n****TagLinkToken****\n");
buff.append("Si=" + S + ", Tj=" + T + "\n");
double totalScore = 0.0;
if (S.equals(T)) {
matched = S.length();
buff.append("Sij=1.0");
}
else {
sSize = S.length();
tSize = T.length();
// let S be the biggest token
if (sSize < tSize) {
String tmp1 = S;
S = T;
T = tmp1;
double tmp2 = sSize;
sSize = tSize;
tSize = tmp2;
}
ArrayList candidateList = algorithm1(S, T);
sortList(candidateList);
buff.append("Common characteres:\n");
buff.append("Si\tTj\tScore_ij(Si,Tj)\n");
matched = 0;
HashMap tMap = new HashMap(),
uMap = new HashMap();
java.util.Iterator it = candidateList.iterator();
while (it.hasNext()) {
TagLink.Candidates actualCandidates = (TagLink.Candidates) it.next();
Integer sPos = new Integer(actualCandidates.getTPos()),
tPos = new Integer(actualCandidates.getUPos());
if ( (!tMap.containsKey(sPos)) &&
(!uMap.containsKey(tPos))) {
double actualScore = actualCandidates.getScore();
totalScore += actualScore;
tMap.put(sPos, null);
uMap.put(tPos, null);
buff.append(S.charAt(sPos.intValue()) + "\t" + T.charAt(tPos.intValue()) +
"\t" + round(actualScore) + "\n");
matched++;
}
}
totalScore = (totalScore / ( (double) sSize) + totalScore / ( (double) tSize)) / 2.0;
System.out.println("score " + totalScore);
buff.append("Score_ij(S,T)=" + round(winkler(totalScore, S, T)));
buff.append("\nMatched characters=" + matched);
}
return buff.toString();
} | [
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computed.
@param S StringWrapper
@param T StringWrapper
@return String | [
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140,941 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/tokens/TagLinkToken.java | TagLinkToken.getScore | private double getScore(ArrayList candidateList) {
matched = 0;
largestIndex = -1;
double scoreValue = 0;
HashMap tMap = new HashMap(),
uMap = new HashMap();
java.util.Iterator it = candidateList.iterator();
while (it.hasNext()) {
TagLink.Candidates actualCandidates = (TagLink.Candidates) it.next();
Integer actualTPos = new Integer(actualCandidates.getTPos()),
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if ( (!tMap.containsKey(actualTPos)) &&
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double actualScore = actualCandidates.getScore();
scoreValue += actualScore;
tMap.put(actualTPos, null);
uMap.put(actualUPos, null);
if (largestIndex < actualTPos.intValue()) {
largestIndex = actualTPos.intValue();
}
matched++;
}
}
return scoreValue;
} | java | private double getScore(ArrayList candidateList) {
matched = 0;
largestIndex = -1;
double scoreValue = 0;
HashMap tMap = new HashMap(),
uMap = new HashMap();
java.util.Iterator it = candidateList.iterator();
while (it.hasNext()) {
TagLink.Candidates actualCandidates = (TagLink.Candidates) it.next();
Integer actualTPos = new Integer(actualCandidates.getTPos()),
actualUPos = new Integer(actualCandidates.getUPos());
if ( (!tMap.containsKey(actualTPos)) &&
(!uMap.containsKey(actualUPos))) {
double actualScore = actualCandidates.getScore();
scoreValue += actualScore;
tMap.put(actualTPos, null);
uMap.put(actualUPos, null);
if (largestIndex < actualTPos.intValue()) {
largestIndex = actualTPos.intValue();
}
matched++;
}
}
return scoreValue;
} | [
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@param candidateList ArrayList
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_abbreviations/src/main/java/com/wcohen/ss/tokens/TagLinkToken.java#L163-L187 |
140,942 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/tokens/TagLinkToken.java | TagLinkToken.algorithm1 | private ArrayList algorithm1(String S, String T) {
ArrayList candidateList = new ArrayList();
int bound = (int) (1.0 / tr);
for (int t = 0; t < S.length(); t++) {
char chT = S.charAt(t);
double lastTr = -1;
for (int u = Math.max(0, t - bound), flag = 0;
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double tr2 = ( (double) Math.abs(t - u));
if ( (lastTr >= 0.0) && (lastTr < tr2)) {
flag = 1;
}
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char chU = T.charAt(u);
double charScore = 0.0;
if(chT==chU){
charScore = 1.0;
}
if (charScore > 0.0) {
if (charScore == 1.0) {
lastTr = tr2;
}
charScore = charScore - (tr * tr2);
if (charScore == 1.0) {
flag = 1;
}
candidateList.add(new TagLink.Candidates(t, u, charScore));
}
}
}
}
return candidateList;
} | java | private ArrayList algorithm1(String S, String T) {
ArrayList candidateList = new ArrayList();
int bound = (int) (1.0 / tr);
for (int t = 0; t < S.length(); t++) {
char chT = S.charAt(t);
double lastTr = -1;
for (int u = Math.max(0, t - bound), flag = 0;
u < Math.min(t + bound + 1, T.length()) && flag == 0; u++) {
double tr2 = ( (double) Math.abs(t - u));
if ( (lastTr >= 0.0) && (lastTr < tr2)) {
flag = 1;
}
else {
char chU = T.charAt(u);
double charScore = 0.0;
if(chT==chU){
charScore = 1.0;
}
if (charScore > 0.0) {
if (charScore == 1.0) {
lastTr = tr2;
}
charScore = charScore - (tr * tr2);
if (charScore == 1.0) {
flag = 1;
}
candidateList.add(new TagLink.Candidates(t, u, charScore));
}
}
}
}
return candidateList;
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] | algorithm1 select the considered most appropiate character pairs are return
a list of candidates.
@param S String
@param T String
@return ArrayList | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_abbreviations/src/main/java/com/wcohen/ss/tokens/TagLinkToken.java#L197-L229 |
140,943 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/tokens/TagLinkToken.java | TagLinkToken.sortList | private void sortList(ArrayList candidateList) {
java.util.Collections.sort(candidateList, new java.util.Comparator() {
public int compare(Object o1, Object o2) {
double scoreT = ( (TagLink.Candidates) o1).getScore();
double scoreU = ( (TagLink.Candidates) o2).getScore();
if(scoreU > scoreT){
return 1;
}
if(scoreU > scoreT){
return -1;
}
return 0;
}
}
);
} | java | private void sortList(ArrayList candidateList) {
java.util.Collections.sort(candidateList, new java.util.Comparator() {
public int compare(Object o1, Object o2) {
double scoreT = ( (TagLink.Candidates) o1).getScore();
double scoreU = ( (TagLink.Candidates) o2).getScore();
if(scoreU > scoreT){
return 1;
}
if(scoreU > scoreT){
return -1;
}
return 0;
}
}
);
} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_abbreviations/src/main/java/com/wcohen/ss/tokens/TagLinkToken.java#L236-L251 |
140,944 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/tokens/TagLinkToken.java | TagLinkToken.winkler | private double winkler(double totalScore, String S, String T) {
totalScore = totalScore + (getPrefix(S, T) * 0.1 * (1.0 - totalScore));
return totalScore;
} | java | private double winkler(double totalScore, String S, String T) {
totalScore = totalScore + (getPrefix(S, T) * 0.1 * (1.0 - totalScore));
return totalScore;
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@param T String
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140,945 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Style.java | Style.getStyleName | public String getStyleName() {
if (Style_Type.featOkTst && ((Style_Type)jcasType).casFeat_styleName == null)
jcasType.jcas.throwFeatMissing("styleName", "de.julielab.jules.types.Style");
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return jcasType.ll_cas.ll_getStringValue(addr, ((Style_Type)jcasType).casFeatCode_styleName);} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Style.java#L85-L88 |
140,946 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Style.java | Style.setStyleName | public void setStyleName(String v) {
if (Style_Type.featOkTst && ((Style_Type)jcasType).casFeat_styleName == null)
jcasType.jcas.throwFeatMissing("styleName", "de.julielab.jules.types.Style");
jcasType.ll_cas.ll_setStringValue(addr, ((Style_Type)jcasType).casFeatCode_styleName, v);} | java | public void setStyleName(String v) {
if (Style_Type.featOkTst && ((Style_Type)jcasType).casFeat_styleName == null)
jcasType.jcas.throwFeatMissing("styleName", "de.julielab.jules.types.Style");
jcasType.ll_cas.ll_setStringValue(addr, ((Style_Type)jcasType).casFeatCode_styleName, v);} | [
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140,947 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/BLine.java | BLine.compareTo | @Override
public int compareTo(BLine other) {
int pageCompare = new Integer(pageId).compareTo(other.pageId);
if (pageCompare != 0) {
return pageCompare;
}
int xCompare = new Float(region.x).compareTo(other.region.x);
if (xCompare != 0) {
return xCompare;
}
int yCompare = new Float(region.y).compareTo(other.region.y);
return yCompare;
} | java | @Override
public int compareTo(BLine other) {
int pageCompare = new Integer(pageId).compareTo(other.pageId);
if (pageCompare != 0) {
return pageCompare;
}
int xCompare = new Float(region.x).compareTo(other.region.x);
if (xCompare != 0) {
return xCompare;
}
int yCompare = new Float(region.y).compareTo(other.region.y);
return yCompare;
} | [
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140,948 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/maxent/GISModel.java | GISModel.eval | public final double[] eval(String[] context, double[] outsums) {
int[] activeOutcomes;
double[] activeParameters;
for (int oid=0; oid<numOutcomes; oid++) {
outsums[oid] = iprob;
numfeats[oid] = 0;
}
for (int i=0; i<context.length; i++) {
int contextIndex = pmap.get(context[i]);
if (contextIndex >= 0) {
Context predParams = params[contextIndex];
activeOutcomes = predParams.getOutcomes();
activeParameters = predParams.getParameters();
for (int j=0; j<activeOutcomes.length; j++) {
int oid = activeOutcomes[j];
numfeats[oid]++;
outsums[oid] += activeParameters[j];
}
}
}
double normal = 0.0;
for (int oid=0; oid<numOutcomes; oid++) {
outsums[oid] = Math.exp((outsums[oid]*fval)
+ ((1.0 -(numfeats[oid]/correctionConstant))
* correctionParam));
normal += outsums[oid];
}
for (int oid=0; oid<numOutcomes; oid++)
outsums[oid] /= normal;
return outsums;
} | java | public final double[] eval(String[] context, double[] outsums) {
int[] activeOutcomes;
double[] activeParameters;
for (int oid=0; oid<numOutcomes; oid++) {
outsums[oid] = iprob;
numfeats[oid] = 0;
}
for (int i=0; i<context.length; i++) {
int contextIndex = pmap.get(context[i]);
if (contextIndex >= 0) {
Context predParams = params[contextIndex];
activeOutcomes = predParams.getOutcomes();
activeParameters = predParams.getParameters();
for (int j=0; j<activeOutcomes.length; j++) {
int oid = activeOutcomes[j];
numfeats[oid]++;
outsums[oid] += activeParameters[j];
}
}
}
double normal = 0.0;
for (int oid=0; oid<numOutcomes; oid++) {
outsums[oid] = Math.exp((outsums[oid]*fval)
+ ((1.0 -(numfeats[oid]/correctionConstant))
* correctionParam));
normal += outsums[oid];
}
for (int oid=0; oid<numOutcomes; oid++)
outsums[oid] /= normal;
return outsums;
} | [
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likelihood of each outcome given that context.
@param context The names of the predicates which have been observed at
the present decision point.
@param outsums This is where the distribution is stored.
@return The normalized probabilities for the outcomes given the
context. The indexes of the double[] are the outcome
ids, and the actual string representation of the
outcomes can be obtained from the method
getOutcome(int i). | [
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140,949 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/maxent/GISModel.java | GISModel.getBestOutcome | public final String getBestOutcome(double[] ocs) {
int best = 0;
for (int i = 1; i<ocs.length; i++)
if (ocs[i] > ocs[best]) best = i;
return ocNames[best];
} | java | public final String getBestOutcome(double[] ocs) {
int best = 0;
for (int i = 1; i<ocs.length; i++)
if (ocs[i] > ocs[best]) best = i;
return ocNames[best];
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140,950 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/maxent/GISModel.java | GISModel.getIndex | public int getIndex (String outcome) {
for (int i=0; i<ocNames.length; i++) {
if (ocNames[i].equals(outcome))
return i;
}
return -1;
} | java | public int getIndex (String outcome) {
for (int i=0; i<ocNames.length; i++) {
if (ocNames[i].equals(outcome))
return i;
}
return -1;
} | [
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@param outcome the String name of the outcome for which the
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@return the index if the given outcome label exists for this
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140,951 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/PmcNxmlHelper.java | PmcNxmlHelper.extractText | public static String extractText(Article article) {
StringBuilder sb = new StringBuilder();
// extract abstract
List<Abstract> abstracts = article.getFront().getArticleMeta()
.getAbstract();
for (Abstract abstrct : abstracts) {
for (Sec sec : abstrct.getSec()) {
processTextContent(sec.getAddressOrAlternativesOrArray(), sb,
true);
}
}
sb.append('\n');
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Body body = article.getBody();
if (body != null) {
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Title title = sec.getTitle();
if (title != null && title.getContent() != null) {
processTextContent(title.getContent(), sb, true);
sb.append('\n');
}
processTextContent(sec.getAddressOrAlternativesOrArray(), sb,
false);
}
}
return removeNoise(sb.toString());
} | java | public static String extractText(Article article) {
StringBuilder sb = new StringBuilder();
// extract abstract
List<Abstract> abstracts = article.getFront().getArticleMeta()
.getAbstract();
for (Abstract abstrct : abstracts) {
for (Sec sec : abstrct.getSec()) {
processTextContent(sec.getAddressOrAlternativesOrArray(), sb,
true);
}
}
sb.append('\n');
// extract text
Body body = article.getBody();
if (body != null) {
for (Sec sec : body.getSec()) {
Title title = sec.getTitle();
if (title != null && title.getContent() != null) {
processTextContent(title.getContent(), sb, true);
sb.append('\n');
}
processTextContent(sec.getAddressOrAlternativesOrArray(), sb,
false);
}
}
return removeNoise(sb.toString());
} | [
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@param article
@return the extracted text from this article | [
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140,952 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/PmcNxmlHelper.java | PmcNxmlHelper.removeNoise | private static String removeNoise(String s) {
return s.replace(" ", " ").replace(" ", " ")//
// caused by omitting xref tags
.replace(" , ", " ").replace(" ( )", "")//
.replace(" ", " ").replace(" ", " ")// nbsp
.replace("[ – ]", " ").replace("[ ]", "");//
} | java | private static String removeNoise(String s) {
return s.replace(" ", " ").replace(" ", " ")//
// caused by omitting xref tags
.replace(" , ", " ").replace(" ( )", "")//
.replace(" ", " ").replace(" ", " ")// nbsp
.replace("[ – ]", " ").replace("[ ]", "");//
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140,953 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/LicenseP.java | LicenseP.getContent | public java.util.List<Object> getContent() {
if (content == null) {
content = new ArrayList<Object>();
}
return this.content;
} | java | public java.util.List<Object> getContent() {
if (content == null) {
content = new ArrayList<Object>();
}
return this.content;
} | [
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] | Gets the value of the content property.
<p>
This accessor method returns a reference to the live list,
not a snapshot. Therefore any modification you make to the
returned list will be present inside the JAXB object.
This is why there is not a <CODE>set</CODE> method for the content property.
<p>
For example, to add a new item, do as follows:
<pre>
getContent().add(newItem);
</pre>
<p>
Objects of the following type(s) are allowed in the list
{@link SansSerif }
{@link Graphic }
{@link ExtLink }
{@link Roman }
{@link BoxedText }
{@link Address }
{@link UnderlineEnd }
{@link Bold }
{@link TableWrapGroup }
{@link PrivateChar }
{@link Alternatives }
{@link InlineFormula }
{@link OverlineStart }
{@link UnderlineStart }
{@link MilestoneEnd }
{@link InlineGraphic }
{@link Hr }
{@link ChemStruct }
{@link TableWrap }
{@link OverlineEnd }
{@link Abbrev }
{@link Email }
{@link JAXBElement }{@code <}{@link MathType }{@code >}
{@link DispFormula }
{@link Ack }
{@link Statement }
{@link Underline }
{@link AwardId }
{@link Monospace }
{@link FigGroup }
{@link Array }
{@link Media }
{@link MilestoneStart }
{@link X }
{@link Xref }
{@link Fig }
{@link MixedCitation }
{@link Sup }
{@link Italic }
{@link SupplementaryMaterial }
{@link Sc }
{@link NlmCitation }
{@link RelatedObject }
{@link DispFormulaGroup }
{@link Target }
{@link ChemStructWrap }
{@link ch.epfl.bbp.uima.xml.archivearticle3.List }
{@link DispQuote }
{@link RelatedArticle }
{@link StyledContent }
{@link Fn }
{@link Strike }
{@link OpenAccess }
{@link Sub }
{@link Overline }
{@link FundingSource }
{@link Speech }
{@link Preformat }
{@link ElementCitation }
{@link NamedContent }
{@link VerseGroup }
{@link TexMath }
{@link Price }
{@link String }
{@link InlineSupplementaryMaterial }
{@link DefList }
{@link Uri } | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/LicenseP.java#L272-L277 |
140,954 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/SurfaceForm.java | SurfaceForm.getSemtype | public String getSemtype() {
if (SurfaceForm_Type.featOkTst && ((SurfaceForm_Type)jcasType).casFeat_semtype == null)
jcasType.jcas.throwFeatMissing("semtype", "ch.epfl.bbp.uima.types.SurfaceForm");
return jcasType.ll_cas.ll_getStringValue(addr, ((SurfaceForm_Type)jcasType).casFeatCode_semtype);} | java | public String getSemtype() {
if (SurfaceForm_Type.featOkTst && ((SurfaceForm_Type)jcasType).casFeat_semtype == null)
jcasType.jcas.throwFeatMissing("semtype", "ch.epfl.bbp.uima.types.SurfaceForm");
return jcasType.ll_cas.ll_getStringValue(addr, ((SurfaceForm_Type)jcasType).casFeatCode_semtype);} | [
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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/SurfaceForm.java#L130-L133 |
140,955 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/SurfaceForm.java | SurfaceForm.setSemtype | public void setSemtype(String v) {
if (SurfaceForm_Type.featOkTst && ((SurfaceForm_Type)jcasType).casFeat_semtype == null)
jcasType.jcas.throwFeatMissing("semtype", "ch.epfl.bbp.uima.types.SurfaceForm");
jcasType.ll_cas.ll_setStringValue(addr, ((SurfaceForm_Type)jcasType).casFeatCode_semtype, v);} | java | public void setSemtype(String v) {
if (SurfaceForm_Type.featOkTst && ((SurfaceForm_Type)jcasType).casFeat_semtype == null)
jcasType.jcas.throwFeatMissing("semtype", "ch.epfl.bbp.uima.types.SurfaceForm");
jcasType.ll_cas.ll_setStringValue(addr, ((SurfaceForm_Type)jcasType).casFeatCode_semtype, 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/SurfaceForm.java#L139-L142 |
140,956 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/maxent/BasicContextGenerator.java | BasicContextGenerator.getContext | public String[] getContext(Object o) {
String s = (String)o;
int prevIndex = -1;
int index = s.indexOf(' ');
List cuts = new ArrayList();
while (index != -1) {
cuts.add(s.substring(prevIndex+1, index));
prevIndex = index;
index = s.indexOf(' ', ++index);
}
cuts.add(s.substring(prevIndex+1, s.length()));
return (String[])cuts.toArray(new String[cuts.size()]);
} | java | public String[] getContext(Object o) {
String s = (String)o;
int prevIndex = -1;
int index = s.indexOf(' ');
List cuts = new ArrayList();
while (index != -1) {
cuts.add(s.substring(prevIndex+1, index));
prevIndex = index;
index = s.indexOf(' ', ++index);
}
cuts.add(s.substring(prevIndex+1, s.length()));
return (String[])cuts.toArray(new String[cuts.size()]);
} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/maxent/BasicContextGenerator.java#L39-L51 |
140,957 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/bootstrep/GeneRegulationTemplate.java | GeneRegulationTemplate.getRelation | public RegulationOfGeneExpression getRelation() {
if (GeneRegulationTemplate_Type.featOkTst && ((GeneRegulationTemplate_Type)jcasType).casFeat_relation == null)
jcasType.jcas.throwFeatMissing("relation", "de.julielab.jules.types.bootstrep.GeneRegulationTemplate");
return (RegulationOfGeneExpression)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((GeneRegulationTemplate_Type)jcasType).casFeatCode_relation)));} | java | public RegulationOfGeneExpression getRelation() {
if (GeneRegulationTemplate_Type.featOkTst && ((GeneRegulationTemplate_Type)jcasType).casFeat_relation == null)
jcasType.jcas.throwFeatMissing("relation", "de.julielab.jules.types.bootstrep.GeneRegulationTemplate");
return (RegulationOfGeneExpression)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((GeneRegulationTemplate_Type)jcasType).casFeatCode_relation)));} | [
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] | getter for relation - gets mention of gene regulation relation
@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/de/julielab/jules/types/bootstrep/GeneRegulationTemplate.java#L87-L90 |
140,958 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/bootstrep/GeneRegulationTemplate.java | GeneRegulationTemplate.setRelation | public void setRelation(RegulationOfGeneExpression v) {
if (GeneRegulationTemplate_Type.featOkTst && ((GeneRegulationTemplate_Type)jcasType).casFeat_relation == null)
jcasType.jcas.throwFeatMissing("relation", "de.julielab.jules.types.bootstrep.GeneRegulationTemplate");
jcasType.ll_cas.ll_setRefValue(addr, ((GeneRegulationTemplate_Type)jcasType).casFeatCode_relation, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setRelation(RegulationOfGeneExpression v) {
if (GeneRegulationTemplate_Type.featOkTst && ((GeneRegulationTemplate_Type)jcasType).casFeat_relation == null)
jcasType.jcas.throwFeatMissing("relation", "de.julielab.jules.types.bootstrep.GeneRegulationTemplate");
jcasType.ll_cas.ll_setRefValue(addr, ((GeneRegulationTemplate_Type)jcasType).casFeatCode_relation, 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/bootstrep/GeneRegulationTemplate.java#L96-L99 |
140,959 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/bootstrep/GeneRegulationTemplate.java | GeneRegulationTemplate.getLigand | public Chemicals getLigand() {
if (GeneRegulationTemplate_Type.featOkTst && ((GeneRegulationTemplate_Type)jcasType).casFeat_ligand == null)
jcasType.jcas.throwFeatMissing("ligand", "de.julielab.jules.types.bootstrep.GeneRegulationTemplate");
return (Chemicals)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((GeneRegulationTemplate_Type)jcasType).casFeatCode_ligand)));} | java | public Chemicals getLigand() {
if (GeneRegulationTemplate_Type.featOkTst && ((GeneRegulationTemplate_Type)jcasType).casFeat_ligand == null)
jcasType.jcas.throwFeatMissing("ligand", "de.julielab.jules.types.bootstrep.GeneRegulationTemplate");
return (Chemicals)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((GeneRegulationTemplate_Type)jcasType).casFeatCode_ligand)));} | [
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] | getter for ligand - gets chemical particpating in the gene regulation process
@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/bootstrep/GeneRegulationTemplate.java#L109-L112 |
140,960 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/bootstrep/GeneRegulationTemplate.java | GeneRegulationTemplate.setLigand | public void setLigand(Chemicals v) {
if (GeneRegulationTemplate_Type.featOkTst && ((GeneRegulationTemplate_Type)jcasType).casFeat_ligand == null)
jcasType.jcas.throwFeatMissing("ligand", "de.julielab.jules.types.bootstrep.GeneRegulationTemplate");
jcasType.ll_cas.ll_setRefValue(addr, ((GeneRegulationTemplate_Type)jcasType).casFeatCode_ligand, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setLigand(Chemicals v) {
if (GeneRegulationTemplate_Type.featOkTst && ((GeneRegulationTemplate_Type)jcasType).casFeat_ligand == null)
jcasType.jcas.throwFeatMissing("ligand", "de.julielab.jules.types.bootstrep.GeneRegulationTemplate");
jcasType.ll_cas.ll_setRefValue(addr, ((GeneRegulationTemplate_Type)jcasType).casFeatCode_ligand, jcasType.ll_cas.ll_getFSRef(v));} | [
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140,961 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/bootstrep/GeneRegulationTemplate.java | GeneRegulationTemplate.getCellGrowthCondition | public CellGrowthCondition getCellGrowthCondition() {
if (GeneRegulationTemplate_Type.featOkTst && ((GeneRegulationTemplate_Type)jcasType).casFeat_cellGrowthCondition == null)
jcasType.jcas.throwFeatMissing("cellGrowthCondition", "de.julielab.jules.types.bootstrep.GeneRegulationTemplate");
return (CellGrowthCondition)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((GeneRegulationTemplate_Type)jcasType).casFeatCode_cellGrowthCondition)));} | java | public CellGrowthCondition getCellGrowthCondition() {
if (GeneRegulationTemplate_Type.featOkTst && ((GeneRegulationTemplate_Type)jcasType).casFeat_cellGrowthCondition == null)
jcasType.jcas.throwFeatMissing("cellGrowthCondition", "de.julielab.jules.types.bootstrep.GeneRegulationTemplate");
return (CellGrowthCondition)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((GeneRegulationTemplate_Type)jcasType).casFeatCode_cellGrowthCondition)));} | [
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] | getter for cellGrowthCondition - gets cell growth condition
@generated
@return value of the feature | [
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"condition"
] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/bootstrep/GeneRegulationTemplate.java#L131-L134 |
140,962 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/bootstrep/GeneRegulationTemplate.java | GeneRegulationTemplate.setCellGrowthCondition | public void setCellGrowthCondition(CellGrowthCondition v) {
if (GeneRegulationTemplate_Type.featOkTst && ((GeneRegulationTemplate_Type)jcasType).casFeat_cellGrowthCondition == null)
jcasType.jcas.throwFeatMissing("cellGrowthCondition", "de.julielab.jules.types.bootstrep.GeneRegulationTemplate");
jcasType.ll_cas.ll_setRefValue(addr, ((GeneRegulationTemplate_Type)jcasType).casFeatCode_cellGrowthCondition, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setCellGrowthCondition(CellGrowthCondition v) {
if (GeneRegulationTemplate_Type.featOkTst && ((GeneRegulationTemplate_Type)jcasType).casFeat_cellGrowthCondition == null)
jcasType.jcas.throwFeatMissing("cellGrowthCondition", "de.julielab.jules.types.bootstrep.GeneRegulationTemplate");
jcasType.ll_cas.ll_setRefValue(addr, ((GeneRegulationTemplate_Type)jcasType).casFeatCode_cellGrowthCondition, jcasType.ll_cas.ll_getFSRef(v));} | [
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] | setter for cellGrowthCondition - sets cell growth condition
@generated
@param v value to set into the feature | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/bootstrep/GeneRegulationTemplate.java#L140-L143 |
140,963 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/bootstrep/GeneRegulationTemplate.java | GeneRegulationTemplate.getInvestigationTechnique | public InvestigationTechnique getInvestigationTechnique() {
if (GeneRegulationTemplate_Type.featOkTst && ((GeneRegulationTemplate_Type)jcasType).casFeat_investigationTechnique == null)
jcasType.jcas.throwFeatMissing("investigationTechnique", "de.julielab.jules.types.bootstrep.GeneRegulationTemplate");
return (InvestigationTechnique)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((GeneRegulationTemplate_Type)jcasType).casFeatCode_investigationTechnique)));} | java | public InvestigationTechnique getInvestigationTechnique() {
if (GeneRegulationTemplate_Type.featOkTst && ((GeneRegulationTemplate_Type)jcasType).casFeat_investigationTechnique == null)
jcasType.jcas.throwFeatMissing("investigationTechnique", "de.julielab.jules.types.bootstrep.GeneRegulationTemplate");
return (InvestigationTechnique)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((GeneRegulationTemplate_Type)jcasType).casFeatCode_investigationTechnique)));} | [
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] | getter for investigationTechnique - gets investigation technique for the detection of the gene regulation relation
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@return value of the feature | [
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140,964 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/bootstrep/GeneRegulationTemplate.java | GeneRegulationTemplate.setInvestigationTechnique | public void setInvestigationTechnique(InvestigationTechnique v) {
if (GeneRegulationTemplate_Type.featOkTst && ((GeneRegulationTemplate_Type)jcasType).casFeat_investigationTechnique == null)
jcasType.jcas.throwFeatMissing("investigationTechnique", "de.julielab.jules.types.bootstrep.GeneRegulationTemplate");
jcasType.ll_cas.ll_setRefValue(addr, ((GeneRegulationTemplate_Type)jcasType).casFeatCode_investigationTechnique, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setInvestigationTechnique(InvestigationTechnique v) {
if (GeneRegulationTemplate_Type.featOkTst && ((GeneRegulationTemplate_Type)jcasType).casFeat_investigationTechnique == null)
jcasType.jcas.throwFeatMissing("investigationTechnique", "de.julielab.jules.types.bootstrep.GeneRegulationTemplate");
jcasType.ll_cas.ll_setRefValue(addr, ((GeneRegulationTemplate_Type)jcasType).casFeatCode_investigationTechnique, jcasType.ll_cas.ll_getFSRef(v));} | [
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] | setter for investigationTechnique - sets investigation technique for the detection of the gene regulation relation
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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/bootstrep/GeneRegulationTemplate.java#L162-L165 |
140,965 | BlueBrain/bluima | modules/bluima_jsre/src/main/java/org/itc/irst/tcc/sre/data/context/AgentContext.java | AgentContext.filter | public Sentence filter(Sentence sent)
{
//logger.debug("\"" + Array.toString(sent) + "\"");
int start = 0, end = sent.length() - 1;
boolean b = false;
for (int i=0;i<sent.length();i++)
{
if (sent.wordAt(i).getRole().equals(Word.AGENT_LABEL))
{
start = i - getSize();
b = true;
break;
}
} // end for i
if (!b)
return null;
end = start + 2 * getSize() + 1;
if (start < 0)
start = 0;
if (end > sent.length())
end = sent.length();
return sent.fragment(start, end);
} | java | public Sentence filter(Sentence sent)
{
//logger.debug("\"" + Array.toString(sent) + "\"");
int start = 0, end = sent.length() - 1;
boolean b = false;
for (int i=0;i<sent.length();i++)
{
if (sent.wordAt(i).getRole().equals(Word.AGENT_LABEL))
{
start = i - getSize();
b = true;
break;
}
} // end for i
if (!b)
return null;
end = start + 2 * getSize() + 1;
if (start < 0)
start = 0;
if (end > sent.length())
end = sent.length();
return sent.fragment(start, end);
} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_jsre/src/main/java/org/itc/irst/tcc/sre/data/context/AgentContext.java#L71-L100 |
140,966 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/AuthorInfo.java | AuthorInfo.getForeName | public String getForeName() {
if (AuthorInfo_Type.featOkTst && ((AuthorInfo_Type)jcasType).casFeat_foreName == null)
jcasType.jcas.throwFeatMissing("foreName", "de.julielab.jules.types.AuthorInfo");
return jcasType.ll_cas.ll_getStringValue(addr, ((AuthorInfo_Type)jcasType).casFeatCode_foreName);} | java | public String getForeName() {
if (AuthorInfo_Type.featOkTst && ((AuthorInfo_Type)jcasType).casFeat_foreName == null)
jcasType.jcas.throwFeatMissing("foreName", "de.julielab.jules.types.AuthorInfo");
return jcasType.ll_cas.ll_getStringValue(addr, ((AuthorInfo_Type)jcasType).casFeatCode_foreName);} | [
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] | getter for foreName - gets An authors forename
@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/AuthorInfo.java#L85-L88 |
140,967 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/AuthorInfo.java | AuthorInfo.setForeName | public void setForeName(String v) {
if (AuthorInfo_Type.featOkTst && ((AuthorInfo_Type)jcasType).casFeat_foreName == null)
jcasType.jcas.throwFeatMissing("foreName", "de.julielab.jules.types.AuthorInfo");
jcasType.ll_cas.ll_setStringValue(addr, ((AuthorInfo_Type)jcasType).casFeatCode_foreName, v);} | java | public void setForeName(String v) {
if (AuthorInfo_Type.featOkTst && ((AuthorInfo_Type)jcasType).casFeat_foreName == null)
jcasType.jcas.throwFeatMissing("foreName", "de.julielab.jules.types.AuthorInfo");
jcasType.ll_cas.ll_setStringValue(addr, ((AuthorInfo_Type)jcasType).casFeatCode_foreName, v);} | [
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@generated
@param v value to set into the feature | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/AuthorInfo.java#L94-L97 |
140,968 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/AuthorInfo.java | AuthorInfo.getAffiliation | public String getAffiliation() {
if (AuthorInfo_Type.featOkTst && ((AuthorInfo_Type)jcasType).casFeat_affiliation == null)
jcasType.jcas.throwFeatMissing("affiliation", "de.julielab.jules.types.AuthorInfo");
return jcasType.ll_cas.ll_getStringValue(addr, ((AuthorInfo_Type)jcasType).casFeatCode_affiliation);} | java | public String getAffiliation() {
if (AuthorInfo_Type.featOkTst && ((AuthorInfo_Type)jcasType).casFeat_affiliation == null)
jcasType.jcas.throwFeatMissing("affiliation", "de.julielab.jules.types.AuthorInfo");
return jcasType.ll_cas.ll_getStringValue(addr, ((AuthorInfo_Type)jcasType).casFeatCode_affiliation);} | [
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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/AuthorInfo.java#L107-L110 |
140,969 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/AuthorInfo.java | AuthorInfo.setAffiliation | public void setAffiliation(String v) {
if (AuthorInfo_Type.featOkTst && ((AuthorInfo_Type)jcasType).casFeat_affiliation == null)
jcasType.jcas.throwFeatMissing("affiliation", "de.julielab.jules.types.AuthorInfo");
jcasType.ll_cas.ll_setStringValue(addr, ((AuthorInfo_Type)jcasType).casFeatCode_affiliation, v);} | java | public void setAffiliation(String v) {
if (AuthorInfo_Type.featOkTst && ((AuthorInfo_Type)jcasType).casFeat_affiliation == null)
jcasType.jcas.throwFeatMissing("affiliation", "de.julielab.jules.types.AuthorInfo");
jcasType.ll_cas.ll_setStringValue(addr, ((AuthorInfo_Type)jcasType).casFeatCode_affiliation, v);} | [
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@generated
@param v value to set into the feature | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/AuthorInfo.java#L116-L119 |
140,970 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/AuthorInfo.java | AuthorInfo.getLastName | public String getLastName() {
if (AuthorInfo_Type.featOkTst && ((AuthorInfo_Type)jcasType).casFeat_lastName == null)
jcasType.jcas.throwFeatMissing("lastName", "de.julielab.jules.types.AuthorInfo");
return jcasType.ll_cas.ll_getStringValue(addr, ((AuthorInfo_Type)jcasType).casFeatCode_lastName);} | java | public String getLastName() {
if (AuthorInfo_Type.featOkTst && ((AuthorInfo_Type)jcasType).casFeat_lastName == null)
jcasType.jcas.throwFeatMissing("lastName", "de.julielab.jules.types.AuthorInfo");
return jcasType.ll_cas.ll_getStringValue(addr, ((AuthorInfo_Type)jcasType).casFeatCode_lastName);} | [
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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/de/julielab/jules/types/AuthorInfo.java#L151-L154 |
140,971 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/AuthorInfo.java | AuthorInfo.setLastName | public void setLastName(String v) {
if (AuthorInfo_Type.featOkTst && ((AuthorInfo_Type)jcasType).casFeat_lastName == null)
jcasType.jcas.throwFeatMissing("lastName", "de.julielab.jules.types.AuthorInfo");
jcasType.ll_cas.ll_setStringValue(addr, ((AuthorInfo_Type)jcasType).casFeatCode_lastName, v);} | java | public void setLastName(String v) {
if (AuthorInfo_Type.featOkTst && ((AuthorInfo_Type)jcasType).casFeat_lastName == null)
jcasType.jcas.throwFeatMissing("lastName", "de.julielab.jules.types.AuthorInfo");
jcasType.ll_cas.ll_setStringValue(addr, ((AuthorInfo_Type)jcasType).casFeatCode_lastName, v);} | [
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140,972 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/AuthorInfo.java | AuthorInfo.getInitials | public String getInitials() {
if (AuthorInfo_Type.featOkTst && ((AuthorInfo_Type)jcasType).casFeat_initials == null)
jcasType.jcas.throwFeatMissing("initials", "de.julielab.jules.types.AuthorInfo");
return jcasType.ll_cas.ll_getStringValue(addr, ((AuthorInfo_Type)jcasType).casFeatCode_initials);} | java | public String getInitials() {
if (AuthorInfo_Type.featOkTst && ((AuthorInfo_Type)jcasType).casFeat_initials == null)
jcasType.jcas.throwFeatMissing("initials", "de.julielab.jules.types.AuthorInfo");
return jcasType.ll_cas.ll_getStringValue(addr, ((AuthorInfo_Type)jcasType).casFeatCode_initials);} | [
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140,973 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/AuthorInfo.java | AuthorInfo.setInitials | public void setInitials(String v) {
if (AuthorInfo_Type.featOkTst && ((AuthorInfo_Type)jcasType).casFeat_initials == null)
jcasType.jcas.throwFeatMissing("initials", "de.julielab.jules.types.AuthorInfo");
jcasType.ll_cas.ll_setStringValue(addr, ((AuthorInfo_Type)jcasType).casFeatCode_initials, v);} | java | public void setInitials(String v) {
if (AuthorInfo_Type.featOkTst && ((AuthorInfo_Type)jcasType).casFeat_initials == null)
jcasType.jcas.throwFeatMissing("initials", "de.julielab.jules.types.AuthorInfo");
jcasType.ll_cas.ll_setStringValue(addr, ((AuthorInfo_Type)jcasType).casFeatCode_initials, v);} | [
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140,974 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/util/Sequence.java | Sequence.add | public void add(String outcome, double p) {
outcomes.add(outcome);
probs.add(new Double(p));
score += Math.log(p);
} | java | public void add(String outcome, double p) {
outcomes.add(outcome);
probs.add(new Double(p));
score += Math.log(p);
} | [
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140,975 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/util/Sequence.java | Sequence.getProbs | public void getProbs(double[] ps) {
for (int pi=0,pl=probs.size();pi<pl;pi++) {
ps[pi] = ((Double) probs.get(pi)).doubleValue();
}
} | java | public void getProbs(double[] ps) {
for (int pi=0,pl=probs.size();pi<pl;pi++) {
ps[pi] = ((Double) probs.get(pi)).doubleValue();
}
} | [
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140,976 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/grobid/diff_match_patch.java | diff_match_patch.diff_main | public LinkedList<Diff> diff_main(String text1, String text2,
boolean checklines) {
// Set a deadline by which time the diff must be complete.
long deadline;
if (Diff_Timeout <= 0) {
deadline = Long.MAX_VALUE;
} else {
deadline = System.currentTimeMillis()
+ (long) (Diff_Timeout * 1000);
}
return diff_main(text1, text2, checklines, deadline);
} | java | public LinkedList<Diff> diff_main(String text1, String text2,
boolean checklines) {
// Set a deadline by which time the diff must be complete.
long deadline;
if (Diff_Timeout <= 0) {
deadline = Long.MAX_VALUE;
} else {
deadline = System.currentTimeMillis()
+ (long) (Diff_Timeout * 1000);
}
return diff_main(text1, text2, checklines, deadline);
} | [
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140,977 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/grobid/diff_match_patch.java | diff_match_patch.diff_main | private LinkedList<Diff> diff_main(String text1, String text2,
boolean checklines, long deadline) {
// Check for null inputs.
if (text1 == null || text2 == null) {
throw new IllegalArgumentException("Null inputs. (diff_main)");
}
// Check for equality (speedup).
LinkedList<Diff> diffs;
if (text1.equals(text2)) {
diffs = new LinkedList<Diff>();
if (text1.length() != 0) {
diffs.add(new Diff(Operation.EQUAL, text1));
}
return diffs;
}
// Trim off common prefix (speedup).
int commonlength = diff_commonPrefix(text1, text2);
String commonprefix = text1.substring(0, commonlength);
text1 = text1.substring(commonlength);
text2 = text2.substring(commonlength);
// Trim off common suffix (speedup).
commonlength = diff_commonSuffix(text1, text2);
String commonsuffix = text1.substring(text1.length() - commonlength);
text1 = text1.substring(0, text1.length() - commonlength);
text2 = text2.substring(0, text2.length() - commonlength);
// Compute the diff on the middle block.
diffs = diff_compute(text1, text2, checklines, deadline);
// Restore the prefix and suffix.
if (commonprefix.length() != 0) {
diffs.addFirst(new Diff(Operation.EQUAL, commonprefix));
}
if (commonsuffix.length() != 0) {
diffs.addLast(new Diff(Operation.EQUAL, commonsuffix));
}
diff_cleanupMerge(diffs);
return diffs;
} | java | private LinkedList<Diff> diff_main(String text1, String text2,
boolean checklines, long deadline) {
// Check for null inputs.
if (text1 == null || text2 == null) {
throw new IllegalArgumentException("Null inputs. (diff_main)");
}
// Check for equality (speedup).
LinkedList<Diff> diffs;
if (text1.equals(text2)) {
diffs = new LinkedList<Diff>();
if (text1.length() != 0) {
diffs.add(new Diff(Operation.EQUAL, text1));
}
return diffs;
}
// Trim off common prefix (speedup).
int commonlength = diff_commonPrefix(text1, text2);
String commonprefix = text1.substring(0, commonlength);
text1 = text1.substring(commonlength);
text2 = text2.substring(commonlength);
// Trim off common suffix (speedup).
commonlength = diff_commonSuffix(text1, text2);
String commonsuffix = text1.substring(text1.length() - commonlength);
text1 = text1.substring(0, text1.length() - commonlength);
text2 = text2.substring(0, text2.length() - commonlength);
// Compute the diff on the middle block.
diffs = diff_compute(text1, text2, checklines, deadline);
// Restore the prefix and suffix.
if (commonprefix.length() != 0) {
diffs.addFirst(new Diff(Operation.EQUAL, commonprefix));
}
if (commonsuffix.length() != 0) {
diffs.addLast(new Diff(Operation.EQUAL, commonsuffix));
}
diff_cleanupMerge(diffs);
return diffs;
} | [
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Time when the diff should be complete by. Used internally for
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140,978 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/grobid/diff_match_patch.java | diff_match_patch.diff_prettyHtml | public String diff_prettyHtml(LinkedList<Diff> diffs) {
StringBuilder html = new StringBuilder();
for (Diff aDiff : diffs) {
String text = aDiff.text.replace("&", "&").replace("<", "<")
.replace(">", ">").replace("\n", "¶<br>");
switch (aDiff.operation) {
case INSERT:
html.append("<ins style=\"background:#e6ffe6;\">").append(text)
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break;
case DELETE:
html.append("<del style=\"background:#ffe6e6;\">").append(text)
.append("</del>");
break;
case EQUAL:
html.append("<span>").append(text).append("</span>");
break;
}
}
return html.toString();
} | java | public String diff_prettyHtml(LinkedList<Diff> diffs) {
StringBuilder html = new StringBuilder();
for (Diff aDiff : diffs) {
String text = aDiff.text.replace("&", "&").replace("<", "<")
.replace(">", ">").replace("\n", "¶<br>");
switch (aDiff.operation) {
case INSERT:
html.append("<ins style=\"background:#e6ffe6;\">").append(text)
.append("</ins>");
break;
case DELETE:
html.append("<del style=\"background:#ffe6e6;\">").append(text)
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break;
case EQUAL:
html.append("<span>").append(text).append("</span>");
break;
}
}
return html.toString();
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/grobid/diff_match_patch.java#L1453-L1473 |
140,979 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/grobid/diff_match_patch.java | diff_match_patch.diff_toDelta | public String diff_toDelta(LinkedList<Diff> diffs) {
StringBuilder text = new StringBuilder();
for (Diff aDiff : diffs) {
switch (aDiff.operation) {
case INSERT:
try {
text.append("+")
.append(URLEncoder.encode(aDiff.text, "UTF-8")
.replace('+', ' ')).append("\t");
} catch (UnsupportedEncodingException e) {
// Not likely on modern system.
throw new Error("This system does not support UTF-8.", e);
}
break;
case DELETE:
text.append("-").append(aDiff.text.length()).append("\t");
break;
case EQUAL:
text.append("=").append(aDiff.text.length()).append("\t");
break;
}
}
String delta = text.toString();
if (delta.length() != 0) {
// Strip off trailing tab character.
delta = delta.substring(0, delta.length() - 1);
delta = unescapeForEncodeUriCompatability(delta);
}
return delta;
} | java | public String diff_toDelta(LinkedList<Diff> diffs) {
StringBuilder text = new StringBuilder();
for (Diff aDiff : diffs) {
switch (aDiff.operation) {
case INSERT:
try {
text.append("+")
.append(URLEncoder.encode(aDiff.text, "UTF-8")
.replace('+', ' ')).append("\t");
} catch (UnsupportedEncodingException e) {
// Not likely on modern system.
throw new Error("This system does not support UTF-8.", e);
}
break;
case DELETE:
text.append("-").append(aDiff.text.length()).append("\t");
break;
case EQUAL:
text.append("=").append(aDiff.text.length()).append("\t");
break;
}
}
String delta = text.toString();
if (delta.length() != 0) {
// Strip off trailing tab character.
delta = delta.substring(0, delta.length() - 1);
delta = unescapeForEncodeUriCompatability(delta);
}
return delta;
} | [
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required to transform text1 into text2. E.g. =3\t-2\t+ing -> Keep 3
chars, delete 2 chars, insert 'ing'. Operations are tab-separated.
Inserted text is escaped using %xx notation.
@param diffs
Array of Diff objects.
@return Delta text. | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/grobid/diff_match_patch.java#L1551-L1580 |
140,980 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/grobid/diff_match_patch.java | diff_match_patch.match_main | public static int match_main(String text, String pattern, int loc) {
// Check for null inputs.
if (text == null || pattern == null) {
throw new IllegalArgumentException("Null inputs. (match_main)");
}
loc = Math.max(0, Math.min(loc, text.length()));
if (text.equals(pattern)) {
// Shortcut (potentially not guaranteed by the algorithm)
return 0;
} else if (text.length() == 0) {
// Nothing to match.
return -1;
} else if (loc + pattern.length() <= text.length()
&& text.substring(loc, loc + pattern.length()).equals(pattern)) {
// Perfect match at the perfect spot! (Includes case of null
// pattern)
return loc;
} else {
// Do a fuzzy compare.
return match_bitap(text, pattern, loc);
}
} | java | public static int match_main(String text, String pattern, int loc) {
// Check for null inputs.
if (text == null || pattern == null) {
throw new IllegalArgumentException("Null inputs. (match_main)");
}
loc = Math.max(0, Math.min(loc, text.length()));
if (text.equals(pattern)) {
// Shortcut (potentially not guaranteed by the algorithm)
return 0;
} else if (text.length() == 0) {
// Nothing to match.
return -1;
} else if (loc + pattern.length() <= text.length()
&& text.substring(loc, loc + pattern.length()).equals(pattern)) {
// Perfect match at the perfect spot! (Includes case of null
// pattern)
return loc;
} else {
// Do a fuzzy compare.
return match_bitap(text, pattern, loc);
}
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@param text
The text to search.
@param pattern
The pattern to search for.
@param loc
The location to search around.
@return Best match index or -1. | [
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140,981 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/grobid/diff_match_patch.java | diff_match_patch.match_bitapScore | @SuppressWarnings("unused")
private static double match_bitapScore(int e, int x, int loc, String pattern) {
float accuracy = (float) e / pattern.length();
int proximity = Math.abs(loc - x);
if (Match_Distance == 0) {
// Dodge divide by zero error.
return proximity == 0 ? accuracy : 1.0;
}
return accuracy + (proximity / (float) Match_Distance);
} | java | @SuppressWarnings("unused")
private static double match_bitapScore(int e, int x, int loc, String pattern) {
float accuracy = (float) e / pattern.length();
int proximity = Math.abs(loc - x);
if (Match_Distance == 0) {
// Dodge divide by zero error.
return proximity == 0 ? accuracy : 1.0;
}
return accuracy + (proximity / (float) Match_Distance);
} | [
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Expected location of match.
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140,982 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/grobid/diff_match_patch.java | diff_match_patch.match_alphabet | protected static Map<Character, Integer> match_alphabet(String pattern) {
Map<Character, Integer> s = new HashMap<Character, Integer>();
char[] char_pattern = pattern.toCharArray();
for (char c : char_pattern) {
s.put(c, 0);
}
int i = 0;
for (char c : char_pattern) {
s.put(c, s.get(c) | (1 << (pattern.length() - i - 1)));
i++;
}
return s;
} | java | protected static Map<Character, Integer> match_alphabet(String pattern) {
Map<Character, Integer> s = new HashMap<Character, Integer>();
char[] char_pattern = pattern.toCharArray();
for (char c : char_pattern) {
s.put(c, 0);
}
int i = 0;
for (char c : char_pattern) {
s.put(c, s.get(c) | (1 << (pattern.length() - i - 1)));
i++;
}
return s;
} | [
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140,983 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/grobid/diff_match_patch.java | diff_match_patch.patch_addContext | protected void patch_addContext(Patch patch, String text) {
if (text.length() == 0) {
return;
}
String pattern = text.substring(patch.start2, patch.start2
+ patch.length1);
int padding = 0;
// Look for the first and last matches of pattern in text. If two
// different
// matches are found, increase the pattern length.
while (text.indexOf(pattern) != text.lastIndexOf(pattern)
&& pattern.length() < Match_MaxBits - Patch_Margin
- Patch_Margin) {
padding += Patch_Margin;
pattern = text.substring(
Math.max(0, patch.start2 - padding),
Math.min(text.length(), patch.start2 + patch.length1
+ padding));
}
// Add one chunk for good luck.
padding += Patch_Margin;
// Add the prefix.
String prefix = text.substring(Math.max(0, patch.start2 - padding),
patch.start2);
if (prefix.length() != 0) {
patch.diffs.addFirst(new Diff(Operation.EQUAL, prefix));
}
// Add the suffix.
String suffix = text
.substring(
patch.start2 + patch.length1,
Math.min(text.length(), patch.start2 + patch.length1
+ padding));
if (suffix.length() != 0) {
patch.diffs.addLast(new Diff(Operation.EQUAL, suffix));
}
// Roll back the start points.
patch.start1 -= prefix.length();
patch.start2 -= prefix.length();
// Extend the lengths.
patch.length1 += prefix.length() + suffix.length();
patch.length2 += prefix.length() + suffix.length();
} | java | protected void patch_addContext(Patch patch, String text) {
if (text.length() == 0) {
return;
}
String pattern = text.substring(patch.start2, patch.start2
+ patch.length1);
int padding = 0;
// Look for the first and last matches of pattern in text. If two
// different
// matches are found, increase the pattern length.
while (text.indexOf(pattern) != text.lastIndexOf(pattern)
&& pattern.length() < Match_MaxBits - Patch_Margin
- Patch_Margin) {
padding += Patch_Margin;
pattern = text.substring(
Math.max(0, patch.start2 - padding),
Math.min(text.length(), patch.start2 + patch.length1
+ padding));
}
// Add one chunk for good luck.
padding += Patch_Margin;
// Add the prefix.
String prefix = text.substring(Math.max(0, patch.start2 - padding),
patch.start2);
if (prefix.length() != 0) {
patch.diffs.addFirst(new Diff(Operation.EQUAL, prefix));
}
// Add the suffix.
String suffix = text
.substring(
patch.start2 + patch.length1,
Math.min(text.length(), patch.start2 + patch.length1
+ padding));
if (suffix.length() != 0) {
patch.diffs.addLast(new Diff(Operation.EQUAL, suffix));
}
// Roll back the start points.
patch.start1 -= prefix.length();
patch.start2 -= prefix.length();
// Extend the lengths.
patch.length1 += prefix.length() + suffix.length();
patch.length2 += prefix.length() + suffix.length();
} | [
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] | Increase the context until it is unique, but don't let the pattern expand
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@param patch
The patch to grow.
@param text
Source text. | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/grobid/diff_match_patch.java#L1875-L1920 |
140,984 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/grobid/diff_match_patch.java | diff_match_patch.patch_make | public LinkedList<Patch> patch_make(String text1, String text2) {
if (text1 == null || text2 == null) {
throw new IllegalArgumentException("Null inputs. (patch_make)");
}
// No diffs provided, compute our own.
LinkedList<Diff> diffs = diff_main(text1, text2, true);
if (diffs.size() > 2) {
diff_cleanupSemantic(diffs);
diff_cleanupEfficiency(diffs);
}
return patch_make(text1, diffs);
} | java | public LinkedList<Patch> patch_make(String text1, String text2) {
if (text1 == null || text2 == null) {
throw new IllegalArgumentException("Null inputs. (patch_make)");
}
// No diffs provided, compute our own.
LinkedList<Diff> diffs = diff_main(text1, text2, true);
if (diffs.size() > 2) {
diff_cleanupSemantic(diffs);
diff_cleanupEfficiency(diffs);
}
return patch_make(text1, diffs);
} | [
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140,985 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/grobid/diff_match_patch.java | diff_match_patch.patch_make | public LinkedList<Patch> patch_make(LinkedList<Diff> diffs) {
if (diffs == null) {
throw new IllegalArgumentException("Null inputs. (patch_make)");
}
// No origin string provided, compute our own.
String text1 = diff_text1(diffs);
return patch_make(text1, diffs);
} | java | public LinkedList<Patch> patch_make(LinkedList<Diff> diffs) {
if (diffs == null) {
throw new IllegalArgumentException("Null inputs. (patch_make)");
}
// No origin string provided, compute our own.
String text1 = diff_text1(diffs);
return patch_make(text1, diffs);
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140,986 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/grobid/diff_match_patch.java | diff_match_patch.patch_make | public LinkedList<Patch> patch_make(String text1, String text2,
LinkedList<Diff> diffs) {
return patch_make(text1, diffs);
} | java | public LinkedList<Patch> patch_make(String text1, String text2,
LinkedList<Diff> diffs) {
return patch_make(text1, diffs);
} | [
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140,987 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/grobid/diff_match_patch.java | diff_match_patch.patch_deepCopy | public LinkedList<Patch> patch_deepCopy(LinkedList<Patch> patches) {
LinkedList<Patch> patchesCopy = new LinkedList<Patch>();
for (Patch aPatch : patches) {
Patch patchCopy = new Patch();
for (Diff aDiff : aPatch.diffs) {
Diff diffCopy = new Diff(aDiff.operation, aDiff.text);
patchCopy.diffs.add(diffCopy);
}
patchCopy.start1 = aPatch.start1;
patchCopy.start2 = aPatch.start2;
patchCopy.length1 = aPatch.length1;
patchCopy.length2 = aPatch.length2;
patchesCopy.add(patchCopy);
}
return patchesCopy;
} | java | public LinkedList<Patch> patch_deepCopy(LinkedList<Patch> patches) {
LinkedList<Patch> patchesCopy = new LinkedList<Patch>();
for (Patch aPatch : patches) {
Patch patchCopy = new Patch();
for (Diff aDiff : aPatch.diffs) {
Diff diffCopy = new Diff(aDiff.operation, aDiff.text);
patchCopy.diffs.add(diffCopy);
}
patchCopy.start1 = aPatch.start1;
patchCopy.start2 = aPatch.start2;
patchCopy.length1 = aPatch.length1;
patchCopy.length2 = aPatch.length2;
patchesCopy.add(patchCopy);
}
return patchesCopy;
} | [
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140,988 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/grobid/diff_match_patch.java | diff_match_patch.patch_addPadding | public String patch_addPadding(LinkedList<Patch> patches) {
short paddingLength = Patch_Margin;
String nullPadding = "";
for (short x = 1; x <= paddingLength; x++) {
nullPadding += String.valueOf((char) x);
}
// Bump all the patches forward.
for (Patch aPatch : patches) {
aPatch.start1 += paddingLength;
aPatch.start2 += paddingLength;
}
// Add some padding on start of first diff.
Patch patch = patches.getFirst();
LinkedList<Diff> diffs = patch.diffs;
if (diffs.isEmpty() || diffs.getFirst().operation != Operation.EQUAL) {
// Add nullPadding equality.
diffs.addFirst(new Diff(Operation.EQUAL, nullPadding));
patch.start1 -= paddingLength; // Should be 0.
patch.start2 -= paddingLength; // Should be 0.
patch.length1 += paddingLength;
patch.length2 += paddingLength;
} else if (paddingLength > diffs.getFirst().text.length()) {
// Grow first equality.
Diff firstDiff = diffs.getFirst();
int extraLength = paddingLength - firstDiff.text.length();
firstDiff.text = nullPadding.substring(firstDiff.text.length())
+ firstDiff.text;
patch.start1 -= extraLength;
patch.start2 -= extraLength;
patch.length1 += extraLength;
patch.length2 += extraLength;
}
// Add some padding on end of last diff.
patch = patches.getLast();
diffs = patch.diffs;
if (diffs.isEmpty() || diffs.getLast().operation != Operation.EQUAL) {
// Add nullPadding equality.
diffs.addLast(new Diff(Operation.EQUAL, nullPadding));
patch.length1 += paddingLength;
patch.length2 += paddingLength;
} else if (paddingLength > diffs.getLast().text.length()) {
// Grow last equality.
Diff lastDiff = diffs.getLast();
int extraLength = paddingLength - lastDiff.text.length();
lastDiff.text += nullPadding.substring(0, extraLength);
patch.length1 += extraLength;
patch.length2 += extraLength;
}
return nullPadding;
} | java | public String patch_addPadding(LinkedList<Patch> patches) {
short paddingLength = Patch_Margin;
String nullPadding = "";
for (short x = 1; x <= paddingLength; x++) {
nullPadding += String.valueOf((char) x);
}
// Bump all the patches forward.
for (Patch aPatch : patches) {
aPatch.start1 += paddingLength;
aPatch.start2 += paddingLength;
}
// Add some padding on start of first diff.
Patch patch = patches.getFirst();
LinkedList<Diff> diffs = patch.diffs;
if (diffs.isEmpty() || diffs.getFirst().operation != Operation.EQUAL) {
// Add nullPadding equality.
diffs.addFirst(new Diff(Operation.EQUAL, nullPadding));
patch.start1 -= paddingLength; // Should be 0.
patch.start2 -= paddingLength; // Should be 0.
patch.length1 += paddingLength;
patch.length2 += paddingLength;
} else if (paddingLength > diffs.getFirst().text.length()) {
// Grow first equality.
Diff firstDiff = diffs.getFirst();
int extraLength = paddingLength - firstDiff.text.length();
firstDiff.text = nullPadding.substring(firstDiff.text.length())
+ firstDiff.text;
patch.start1 -= extraLength;
patch.start2 -= extraLength;
patch.length1 += extraLength;
patch.length2 += extraLength;
}
// Add some padding on end of last diff.
patch = patches.getLast();
diffs = patch.diffs;
if (diffs.isEmpty() || diffs.getLast().operation != Operation.EQUAL) {
// Add nullPadding equality.
diffs.addLast(new Diff(Operation.EQUAL, nullPadding));
patch.length1 += paddingLength;
patch.length2 += paddingLength;
} else if (paddingLength > diffs.getLast().text.length()) {
// Grow last equality.
Diff lastDiff = diffs.getLast();
int extraLength = paddingLength - lastDiff.text.length();
lastDiff.text += nullPadding.substring(0, extraLength);
patch.length1 += extraLength;
patch.length2 += extraLength;
}
return nullPadding;
} | [
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] | Add some padding on text start and end so that edges can match something.
Intended to be called only from within patch_apply.
@param patches
Array of Patch objects.
@return The padding string added to each side. | [
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140,989 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/grobid/diff_match_patch.java | diff_match_patch.patch_toText | public String patch_toText(List<Patch> patches) {
StringBuilder text = new StringBuilder();
for (Patch aPatch : patches) {
text.append(aPatch);
}
return text.toString();
} | java | public String patch_toText(List<Patch> patches) {
StringBuilder text = new StringBuilder();
for (Patch aPatch : patches) {
text.append(aPatch);
}
return text.toString();
} | [
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] | Take a list of patches and return a textual representation.
@param patches
List of Patch objects.
@return Text representation of patches. | [
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140,990 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/grobid/diff_match_patch.java | diff_match_patch.unescapeForEncodeUriCompatability | private static String unescapeForEncodeUriCompatability(String str) {
return str.replace("%21", "!").replace("%7E", "~").replace("%27", "'")
.replace("%28", "(").replace("%29", ")").replace("%3B", ";")
.replace("%2F", "/").replace("%3F", "?").replace("%3A", ":")
.replace("%40", "@").replace("%26", "&").replace("%3D", "=")
.replace("%2B", "+").replace("%24", "$").replace("%2C", ",")
.replace("%23", "#");
} | java | private static String unescapeForEncodeUriCompatability(String str) {
return str.replace("%21", "!").replace("%7E", "~").replace("%27", "'")
.replace("%28", "(").replace("%29", ")").replace("%3B", ";")
.replace("%2F", "/").replace("%3F", "?").replace("%3A", ":")
.replace("%40", "@").replace("%26", "&").replace("%3D", "=")
.replace("%2B", "+").replace("%24", "$").replace("%2C", ",")
.replace("%23", "#");
} | [
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140,991 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/pubmed/PubmedArticleSet.java | PubmedArticleSet.getPubmedArticleOrPubmedBookArticle | public List<java.lang.Object> getPubmedArticleOrPubmedBookArticle() {
if (pubmedArticleOrPubmedBookArticle == null) {
pubmedArticleOrPubmedBookArticle = new ArrayList<java.lang.Object>();
}
return this.pubmedArticleOrPubmedBookArticle;
} | java | public List<java.lang.Object> getPubmedArticleOrPubmedBookArticle() {
if (pubmedArticleOrPubmedBookArticle == null) {
pubmedArticleOrPubmedBookArticle = new ArrayList<java.lang.Object>();
}
return this.pubmedArticleOrPubmedBookArticle;
} | [
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140,992 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Journal.java | Journal.getISSN | public String getISSN() {
if (Journal_Type.featOkTst && ((Journal_Type)jcasType).casFeat_ISSN == null)
jcasType.jcas.throwFeatMissing("ISSN", "de.julielab.jules.types.Journal");
return jcasType.ll_cas.ll_getStringValue(addr, ((Journal_Type)jcasType).casFeatCode_ISSN);} | java | public String getISSN() {
if (Journal_Type.featOkTst && ((Journal_Type)jcasType).casFeat_ISSN == null)
jcasType.jcas.throwFeatMissing("ISSN", "de.julielab.jules.types.Journal");
return jcasType.ll_cas.ll_getStringValue(addr, ((Journal_Type)jcasType).casFeatCode_ISSN);} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Journal.java#L85-L88 |
140,993 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Journal.java | Journal.setISSN | public void setISSN(String v) {
if (Journal_Type.featOkTst && ((Journal_Type)jcasType).casFeat_ISSN == null)
jcasType.jcas.throwFeatMissing("ISSN", "de.julielab.jules.types.Journal");
jcasType.ll_cas.ll_setStringValue(addr, ((Journal_Type)jcasType).casFeatCode_ISSN, v);} | java | public void setISSN(String v) {
if (Journal_Type.featOkTst && ((Journal_Type)jcasType).casFeat_ISSN == null)
jcasType.jcas.throwFeatMissing("ISSN", "de.julielab.jules.types.Journal");
jcasType.ll_cas.ll_setStringValue(addr, ((Journal_Type)jcasType).casFeatCode_ISSN, v);} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Journal.java#L94-L97 |
140,994 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Journal.java | Journal.getVolume | public String getVolume() {
if (Journal_Type.featOkTst && ((Journal_Type)jcasType).casFeat_volume == null)
jcasType.jcas.throwFeatMissing("volume", "de.julielab.jules.types.Journal");
return jcasType.ll_cas.ll_getStringValue(addr, ((Journal_Type)jcasType).casFeatCode_volume);} | java | public String getVolume() {
if (Journal_Type.featOkTst && ((Journal_Type)jcasType).casFeat_volume == null)
jcasType.jcas.throwFeatMissing("volume", "de.julielab.jules.types.Journal");
return jcasType.ll_cas.ll_getStringValue(addr, ((Journal_Type)jcasType).casFeatCode_volume);} | [
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140,995 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Journal.java | Journal.setVolume | public void setVolume(String v) {
if (Journal_Type.featOkTst && ((Journal_Type)jcasType).casFeat_volume == null)
jcasType.jcas.throwFeatMissing("volume", "de.julielab.jules.types.Journal");
jcasType.ll_cas.ll_setStringValue(addr, ((Journal_Type)jcasType).casFeatCode_volume, v);} | java | public void setVolume(String v) {
if (Journal_Type.featOkTst && ((Journal_Type)jcasType).casFeat_volume == null)
jcasType.jcas.throwFeatMissing("volume", "de.julielab.jules.types.Journal");
jcasType.ll_cas.ll_setStringValue(addr, ((Journal_Type)jcasType).casFeatCode_volume, v);} | [
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140,996 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Journal.java | Journal.getTitle | public String getTitle() {
if (Journal_Type.featOkTst && ((Journal_Type)jcasType).casFeat_title == null)
jcasType.jcas.throwFeatMissing("title", "de.julielab.jules.types.Journal");
return jcasType.ll_cas.ll_getStringValue(addr, ((Journal_Type)jcasType).casFeatCode_title);} | java | public String getTitle() {
if (Journal_Type.featOkTst && ((Journal_Type)jcasType).casFeat_title == null)
jcasType.jcas.throwFeatMissing("title", "de.julielab.jules.types.Journal");
return jcasType.ll_cas.ll_getStringValue(addr, ((Journal_Type)jcasType).casFeatCode_title);} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Journal.java#L129-L132 |
140,997 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Journal.java | Journal.setTitle | public void setTitle(String v) {
if (Journal_Type.featOkTst && ((Journal_Type)jcasType).casFeat_title == null)
jcasType.jcas.throwFeatMissing("title", "de.julielab.jules.types.Journal");
jcasType.ll_cas.ll_setStringValue(addr, ((Journal_Type)jcasType).casFeatCode_title, v);} | java | public void setTitle(String v) {
if (Journal_Type.featOkTst && ((Journal_Type)jcasType).casFeat_title == null)
jcasType.jcas.throwFeatMissing("title", "de.julielab.jules.types.Journal");
jcasType.ll_cas.ll_setStringValue(addr, ((Journal_Type)jcasType).casFeatCode_title, v);} | [
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140,998 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Journal.java | Journal.getImpactFactor | public String getImpactFactor() {
if (Journal_Type.featOkTst && ((Journal_Type)jcasType).casFeat_impactFactor == null)
jcasType.jcas.throwFeatMissing("impactFactor", "de.julielab.jules.types.Journal");
return jcasType.ll_cas.ll_getStringValue(addr, ((Journal_Type)jcasType).casFeatCode_impactFactor);} | java | public String getImpactFactor() {
if (Journal_Type.featOkTst && ((Journal_Type)jcasType).casFeat_impactFactor == null)
jcasType.jcas.throwFeatMissing("impactFactor", "de.julielab.jules.types.Journal");
return jcasType.ll_cas.ll_getStringValue(addr, ((Journal_Type)jcasType).casFeatCode_impactFactor);} | [
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140,999 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Journal.java | Journal.setImpactFactor | public void setImpactFactor(String v) {
if (Journal_Type.featOkTst && ((Journal_Type)jcasType).casFeat_impactFactor == null)
jcasType.jcas.throwFeatMissing("impactFactor", "de.julielab.jules.types.Journal");
jcasType.ll_cas.ll_setStringValue(addr, ((Journal_Type)jcasType).casFeatCode_impactFactor, v);} | java | public void setImpactFactor(String v) {
if (Journal_Type.featOkTst && ((Journal_Type)jcasType).casFeat_impactFactor == null)
jcasType.jcas.throwFeatMissing("impactFactor", "de.julielab.jules.types.Journal");
jcasType.ll_cas.ll_setStringValue(addr, ((Journal_Type)jcasType).casFeatCode_impactFactor, v);} | [
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] | setter for impactFactor - sets The impact factor of the journal at the time of publication, O
@generated
@param v value to set into the feature | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Journal.java#L160-L163 |
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