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140,600 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/RefList.java | RefList.getAddressOrAlternativesOrArray | public java.util.List<Object> getAddressOrAlternativesOrArray() {
if (addressOrAlternativesOrArray == null) {
addressOrAlternativesOrArray = new ArrayList<Object>();
}
return this.addressOrAlternativesOrArray;
} | java | public java.util.List<Object> getAddressOrAlternativesOrArray() {
if (addressOrAlternativesOrArray == null) {
addressOrAlternativesOrArray = new ArrayList<Object>();
}
return this.addressOrAlternativesOrArray;
} | [
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{@link Ref } | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/RefList.java#L236-L241 |
140,601 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/RefList.java | RefList.getRefList | public java.util.List<RefList> getRefList() {
if (refList == null) {
refList = new ArrayList<RefList>();
}
return this.refList;
} | java | public java.util.List<RefList> getRefList() {
if (refList == null) {
refList = new ArrayList<RefList>();
}
return this.refList;
} | [
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This is why there is not a <CODE>set</CODE> method for the refList property.
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140,602 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntClassMention.java | OntClassMention.getOntClassId | public String getOntClassId() {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_ontClassId == null)
jcasType.jcas.throwFeatMissing("ontClassId", "de.julielab.jules.types.OntClassMention");
return jcasType.ll_cas.ll_getStringValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_ontClassId);} | java | public String getOntClassId() {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_ontClassId == null)
jcasType.jcas.throwFeatMissing("ontClassId", "de.julielab.jules.types.OntClassMention");
return jcasType.ll_cas.ll_getStringValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_ontClassId);} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntClassMention.java#L87-L90 |
140,603 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntClassMention.java | OntClassMention.setOntClassId | public void setOntClassId(String v) {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_ontClassId == null)
jcasType.jcas.throwFeatMissing("ontClassId", "de.julielab.jules.types.OntClassMention");
jcasType.ll_cas.ll_setStringValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_ontClassId, v);} | java | public void setOntClassId(String v) {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_ontClassId == null)
jcasType.jcas.throwFeatMissing("ontClassId", "de.julielab.jules.types.OntClassMention");
jcasType.ll_cas.ll_setStringValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_ontClassId, v);} | [
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140,604 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntClassMention.java | OntClassMention.getSemanticTypes | public StringArray getSemanticTypes() {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_semanticTypes == null)
jcasType.jcas.throwFeatMissing("semanticTypes", "de.julielab.jules.types.OntClassMention");
return (StringArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_semanticTypes)));} | java | public StringArray getSemanticTypes() {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_semanticTypes == null)
jcasType.jcas.throwFeatMissing("semanticTypes", "de.julielab.jules.types.OntClassMention");
return (StringArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_semanticTypes)));} | [
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140,605 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntClassMention.java | OntClassMention.setSemanticTypes | public void setSemanticTypes(StringArray v) {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_semanticTypes == null)
jcasType.jcas.throwFeatMissing("semanticTypes", "de.julielab.jules.types.OntClassMention");
jcasType.ll_cas.ll_setRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_semanticTypes, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setSemanticTypes(StringArray v) {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_semanticTypes == null)
jcasType.jcas.throwFeatMissing("semanticTypes", "de.julielab.jules.types.OntClassMention");
jcasType.ll_cas.ll_setRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_semanticTypes, jcasType.ll_cas.ll_getFSRef(v));} | [
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140,606 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntClassMention.java | OntClassMention.getSemanticTypes | public String getSemanticTypes(int i) {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_semanticTypes == null)
jcasType.jcas.throwFeatMissing("semanticTypes", "de.julielab.jules.types.OntClassMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_semanticTypes), i);
return jcasType.ll_cas.ll_getStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_semanticTypes), i);} | java | public String getSemanticTypes(int i) {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_semanticTypes == null)
jcasType.jcas.throwFeatMissing("semanticTypes", "de.julielab.jules.types.OntClassMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_semanticTypes), i);
return jcasType.ll_cas.ll_getStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_semanticTypes), i);} | [
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140,607 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntClassMention.java | OntClassMention.setSemanticTypes | public void setSemanticTypes(int i, String v) {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_semanticTypes == null)
jcasType.jcas.throwFeatMissing("semanticTypes", "de.julielab.jules.types.OntClassMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_semanticTypes), i);
jcasType.ll_cas.ll_setStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_semanticTypes), i, v);} | java | public void setSemanticTypes(int i, String v) {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_semanticTypes == null)
jcasType.jcas.throwFeatMissing("semanticTypes", "de.julielab.jules.types.OntClassMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_semanticTypes), i);
jcasType.ll_cas.ll_setStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_semanticTypes), i, v);} | [
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140,608 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntClassMention.java | OntClassMention.getPreferredTerm | public String getPreferredTerm() {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_preferredTerm == null)
jcasType.jcas.throwFeatMissing("preferredTerm", "de.julielab.jules.types.OntClassMention");
return jcasType.ll_cas.ll_getStringValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_preferredTerm);} | java | public String getPreferredTerm() {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_preferredTerm == null)
jcasType.jcas.throwFeatMissing("preferredTerm", "de.julielab.jules.types.OntClassMention");
return jcasType.ll_cas.ll_getStringValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_preferredTerm);} | [
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@return value of the feature | [
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140,609 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntClassMention.java | OntClassMention.setPreferredTerm | public void setPreferredTerm(String v) {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_preferredTerm == null)
jcasType.jcas.throwFeatMissing("preferredTerm", "de.julielab.jules.types.OntClassMention");
jcasType.ll_cas.ll_setStringValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_preferredTerm, v);} | java | public void setPreferredTerm(String v) {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_preferredTerm == null)
jcasType.jcas.throwFeatMissing("preferredTerm", "de.julielab.jules.types.OntClassMention");
jcasType.ll_cas.ll_setStringValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_preferredTerm, v);} | [
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140,610 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntClassMention.java | OntClassMention.getMatchedTokens | public Token getMatchedTokens(int i) {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_matchedTokens == null)
jcasType.jcas.throwFeatMissing("matchedTokens", "de.julielab.jules.types.OntClassMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_matchedTokens), i);
return (Token)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_matchedTokens), i)));} | java | public Token getMatchedTokens(int i) {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_matchedTokens == null)
jcasType.jcas.throwFeatMissing("matchedTokens", "de.julielab.jules.types.OntClassMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_matchedTokens), i);
return (Token)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_matchedTokens), i)));} | [
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140,611 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/OntClassMention.java | OntClassMention.setMatchedTokens | public void setMatchedTokens(int i, Token v) {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_matchedTokens == null)
jcasType.jcas.throwFeatMissing("matchedTokens", "de.julielab.jules.types.OntClassMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_matchedTokens), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_matchedTokens), i, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setMatchedTokens(int i, Token v) {
if (OntClassMention_Type.featOkTst && ((OntClassMention_Type)jcasType).casFeat_matchedTokens == null)
jcasType.jcas.throwFeatMissing("matchedTokens", "de.julielab.jules.types.OntClassMention");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_matchedTokens), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((OntClassMention_Type)jcasType).casFeatCode_matchedTokens), i, jcasType.ll_cas.ll_getFSRef(v));} | [
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140,612 | BlueBrain/bluima | modules/bluima_db/src/main/java/ch/epfl/bbp/uima/db/utils/Database.java | Database.generateDrop | public String generateDrop(String table) {
StringBuffer result = new StringBuffer();
result.append("DROP TABLE ");
result.append(table);
result.append(";\n");
return result.toString();
} | java | public String generateDrop(String table) {
StringBuffer result = new StringBuffer();
result.append("DROP TABLE ");
result.append(table);
result.append(";\n");
return result.toString();
} | [
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@return The SQL to drop a table. | [
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140,613 | BlueBrain/bluima | modules/bluima_db/src/main/java/ch/epfl/bbp/uima/db/utils/Database.java | Database.listTables | public Collection<String> listTables() throws SQLException {
Collection<String> result = new ArrayList<String>();
DatabaseMetaData dbm = connection.getMetaData();
String types[] = { "TABLE" };
ResultSet rs = dbm.getTables(null, null, "", types);
while (rs.next()) {
String str = rs.getString("TABLE_NAME");
result.add(str);
}
return result;
} | java | public Collection<String> listTables() throws SQLException {
Collection<String> result = new ArrayList<String>();
DatabaseMetaData dbm = connection.getMetaData();
String types[] = { "TABLE" };
ResultSet rs = dbm.getTables(null, null, "", types);
while (rs.next()) {
String str = rs.getString("TABLE_NAME");
result.add(str);
}
return result;
} | [
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@return A list of all tables in the database.
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_db/src/main/java/ch/epfl/bbp/uima/db/utils/Database.java#L143-L154 |
140,614 | BlueBrain/bluima | modules/bluima_db/src/main/java/ch/epfl/bbp/uima/db/utils/Database.java | Database.listColumns | public Collection<String> listColumns(String table) throws SQLException {
Collection<String> result = new ArrayList<String>();
DatabaseMetaData dbm = connection.getMetaData();
ResultSet rs = dbm.getColumns(null, null, table, null);
while (rs.next()) {
result.add(rs.getString("COLUMN_NAME"));
}
return result;
} | java | public Collection<String> listColumns(String table) throws SQLException {
Collection<String> result = new ArrayList<String>();
DatabaseMetaData dbm = connection.getMetaData();
ResultSet rs = dbm.getColumns(null, null, table, null);
while (rs.next()) {
result.add(rs.getString("COLUMN_NAME"));
}
return result;
} | [
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140,615 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/maxent/ModelReplacementManager.java | ModelReplacementManager.startUsingModel | public void startUsingModel () {
if (replacementThread != null) {
try { replacementThread.join(); }
catch (InterruptedException e) {}
}
replacementCanProceed = false;
users++;
} | java | public void startUsingModel () {
if (replacementThread != null) {
try { replacementThread.join(); }
catch (InterruptedException e) {}
}
replacementCanProceed = false;
users++;
} | [
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140,616 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/maxent/ModelReplacementManager.java | ModelReplacementManager.replaceModel | public synchronized void replaceModel (MaxentModel model) {
replacementThread = Thread.currentThread();
while (!replacementCanProceed) Thread.yield();
setter.setModel(model);
replacementThread = null;
} | java | public synchronized void replaceModel (MaxentModel model) {
replacementThread = Thread.currentThread();
while (!replacementCanProceed) Thread.yield();
setter.setModel(model);
replacementThread = null;
} | [
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140,617 | BlueBrain/bluima | utils/blue_commons/src/main/java/ch/epfl/bbp/triechar/TrieData.java | TrieData.toIdFile | public void toIdFile(OutputStream os) throws IOException {
BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(os));
for (TrieNodeData<T> child : root.children.values()) {
child.writeIds(writer, new char[0]);// recursive
}
writer.close();
} | java | public void toIdFile(OutputStream os) throws IOException {
BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(os));
for (TrieNodeData<T> child : root.children.values()) {
child.writeIds(writer, new char[0]);// recursive
}
writer.close();
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140,618 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/Glossary.java | Glossary.getGlossary | public java.util.List<Glossary> getGlossary() {
if (glossary == null) {
glossary = new ArrayList<Glossary>();
}
return this.glossary;
} | java | public java.util.List<Glossary> getGlossary() {
if (glossary == null) {
glossary = new ArrayList<Glossary>();
}
return this.glossary;
} | [
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140,619 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/MeshHeading.java | MeshHeading.getDescriptorName | public String getDescriptorName() {
if (MeshHeading_Type.featOkTst && ((MeshHeading_Type)jcasType).casFeat_descriptorName == null)
jcasType.jcas.throwFeatMissing("descriptorName", "de.julielab.jules.types.MeshHeading");
return jcasType.ll_cas.ll_getStringValue(addr, ((MeshHeading_Type)jcasType).casFeatCode_descriptorName);} | java | public String getDescriptorName() {
if (MeshHeading_Type.featOkTst && ((MeshHeading_Type)jcasType).casFeat_descriptorName == null)
jcasType.jcas.throwFeatMissing("descriptorName", "de.julielab.jules.types.MeshHeading");
return jcasType.ll_cas.ll_getStringValue(addr, ((MeshHeading_Type)jcasType).casFeatCode_descriptorName);} | [
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140,620 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/MeshHeading.java | MeshHeading.setDescriptorName | public void setDescriptorName(String v) {
if (MeshHeading_Type.featOkTst && ((MeshHeading_Type)jcasType).casFeat_descriptorName == null)
jcasType.jcas.throwFeatMissing("descriptorName", "de.julielab.jules.types.MeshHeading");
jcasType.ll_cas.ll_setStringValue(addr, ((MeshHeading_Type)jcasType).casFeatCode_descriptorName, v);} | java | public void setDescriptorName(String v) {
if (MeshHeading_Type.featOkTst && ((MeshHeading_Type)jcasType).casFeat_descriptorName == null)
jcasType.jcas.throwFeatMissing("descriptorName", "de.julielab.jules.types.MeshHeading");
jcasType.ll_cas.ll_setStringValue(addr, ((MeshHeading_Type)jcasType).casFeatCode_descriptorName, v);} | [
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140,621 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/MeshHeading.java | MeshHeading.getQualifierName | public String getQualifierName() {
if (MeshHeading_Type.featOkTst && ((MeshHeading_Type)jcasType).casFeat_qualifierName == null)
jcasType.jcas.throwFeatMissing("qualifierName", "de.julielab.jules.types.MeshHeading");
return jcasType.ll_cas.ll_getStringValue(addr, ((MeshHeading_Type)jcasType).casFeatCode_qualifierName);} | java | public String getQualifierName() {
if (MeshHeading_Type.featOkTst && ((MeshHeading_Type)jcasType).casFeat_qualifierName == null)
jcasType.jcas.throwFeatMissing("qualifierName", "de.julielab.jules.types.MeshHeading");
return jcasType.ll_cas.ll_getStringValue(addr, ((MeshHeading_Type)jcasType).casFeatCode_qualifierName);} | [
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140,622 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/MeshHeading.java | MeshHeading.setQualifierName | public void setQualifierName(String v) {
if (MeshHeading_Type.featOkTst && ((MeshHeading_Type)jcasType).casFeat_qualifierName == null)
jcasType.jcas.throwFeatMissing("qualifierName", "de.julielab.jules.types.MeshHeading");
jcasType.ll_cas.ll_setStringValue(addr, ((MeshHeading_Type)jcasType).casFeatCode_qualifierName, v);} | java | public void setQualifierName(String v) {
if (MeshHeading_Type.featOkTst && ((MeshHeading_Type)jcasType).casFeat_qualifierName == null)
jcasType.jcas.throwFeatMissing("qualifierName", "de.julielab.jules.types.MeshHeading");
jcasType.ll_cas.ll_setStringValue(addr, ((MeshHeading_Type)jcasType).casFeatCode_qualifierName, v);} | [
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140,623 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/MeshHeading.java | MeshHeading.getDescriptorNameMajorTopic | public boolean getDescriptorNameMajorTopic() {
if (MeshHeading_Type.featOkTst && ((MeshHeading_Type)jcasType).casFeat_descriptorNameMajorTopic == null)
jcasType.jcas.throwFeatMissing("descriptorNameMajorTopic", "de.julielab.jules.types.MeshHeading");
return jcasType.ll_cas.ll_getBooleanValue(addr, ((MeshHeading_Type)jcasType).casFeatCode_descriptorNameMajorTopic);} | java | public boolean getDescriptorNameMajorTopic() {
if (MeshHeading_Type.featOkTst && ((MeshHeading_Type)jcasType).casFeat_descriptorNameMajorTopic == null)
jcasType.jcas.throwFeatMissing("descriptorNameMajorTopic", "de.julielab.jules.types.MeshHeading");
return jcasType.ll_cas.ll_getBooleanValue(addr, ((MeshHeading_Type)jcasType).casFeatCode_descriptorNameMajorTopic);} | [
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140,624 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/MeshHeading.java | MeshHeading.setDescriptorNameMajorTopic | public void setDescriptorNameMajorTopic(boolean v) {
if (MeshHeading_Type.featOkTst && ((MeshHeading_Type)jcasType).casFeat_descriptorNameMajorTopic == null)
jcasType.jcas.throwFeatMissing("descriptorNameMajorTopic", "de.julielab.jules.types.MeshHeading");
jcasType.ll_cas.ll_setBooleanValue(addr, ((MeshHeading_Type)jcasType).casFeatCode_descriptorNameMajorTopic, v);} | java | public void setDescriptorNameMajorTopic(boolean v) {
if (MeshHeading_Type.featOkTst && ((MeshHeading_Type)jcasType).casFeat_descriptorNameMajorTopic == null)
jcasType.jcas.throwFeatMissing("descriptorNameMajorTopic", "de.julielab.jules.types.MeshHeading");
jcasType.ll_cas.ll_setBooleanValue(addr, ((MeshHeading_Type)jcasType).casFeatCode_descriptorNameMajorTopic, v);} | [
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140,625 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/MeshHeading.java | MeshHeading.getQualifierNameMajorTopic | public boolean getQualifierNameMajorTopic() {
if (MeshHeading_Type.featOkTst && ((MeshHeading_Type)jcasType).casFeat_qualifierNameMajorTopic == null)
jcasType.jcas.throwFeatMissing("qualifierNameMajorTopic", "de.julielab.jules.types.MeshHeading");
return jcasType.ll_cas.ll_getBooleanValue(addr, ((MeshHeading_Type)jcasType).casFeatCode_qualifierNameMajorTopic);} | java | public boolean getQualifierNameMajorTopic() {
if (MeshHeading_Type.featOkTst && ((MeshHeading_Type)jcasType).casFeat_qualifierNameMajorTopic == null)
jcasType.jcas.throwFeatMissing("qualifierNameMajorTopic", "de.julielab.jules.types.MeshHeading");
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140,626 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/MeshHeading.java | MeshHeading.setQualifierNameMajorTopic | public void setQualifierNameMajorTopic(boolean v) {
if (MeshHeading_Type.featOkTst && ((MeshHeading_Type)jcasType).casFeat_qualifierNameMajorTopic == null)
jcasType.jcas.throwFeatMissing("qualifierNameMajorTopic", "de.julielab.jules.types.MeshHeading");
jcasType.ll_cas.ll_setBooleanValue(addr, ((MeshHeading_Type)jcasType).casFeatCode_qualifierNameMajorTopic, v);} | java | public void setQualifierNameMajorTopic(boolean v) {
if (MeshHeading_Type.featOkTst && ((MeshHeading_Type)jcasType).casFeat_qualifierNameMajorTopic == null)
jcasType.jcas.throwFeatMissing("qualifierNameMajorTopic", "de.julielab.jules.types.MeshHeading");
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140,627 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/BioVerb.java | BioVerb.getRef_id | public String getRef_id() {
if (BioVerb_Type.featOkTst && ((BioVerb_Type)jcasType).casFeat_ref_id == null)
jcasType.jcas.throwFeatMissing("ref_id", "ch.epfl.bbp.uima.types.BioVerb");
return jcasType.ll_cas.ll_getStringValue(addr, ((BioVerb_Type)jcasType).casFeatCode_ref_id);} | java | public String getRef_id() {
if (BioVerb_Type.featOkTst && ((BioVerb_Type)jcasType).casFeat_ref_id == null)
jcasType.jcas.throwFeatMissing("ref_id", "ch.epfl.bbp.uima.types.BioVerb");
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140,628 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/BioVerb.java | BioVerb.setRef_id | public void setRef_id(String v) {
if (BioVerb_Type.featOkTst && ((BioVerb_Type)jcasType).casFeat_ref_id == null)
jcasType.jcas.throwFeatMissing("ref_id", "ch.epfl.bbp.uima.types.BioVerb");
jcasType.ll_cas.ll_setStringValue(addr, ((BioVerb_Type)jcasType).casFeatCode_ref_id, v);} | java | public void setRef_id(String v) {
if (BioVerb_Type.featOkTst && ((BioVerb_Type)jcasType).casFeat_ref_id == null)
jcasType.jcas.throwFeatMissing("ref_id", "ch.epfl.bbp.uima.types.BioVerb");
jcasType.ll_cas.ll_setStringValue(addr, ((BioVerb_Type)jcasType).casFeatCode_ref_id, v);} | [
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140,629 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/BioVerb.java | BioVerb.getCanonical | public String getCanonical() {
if (BioVerb_Type.featOkTst && ((BioVerb_Type)jcasType).casFeat_canonical == null)
jcasType.jcas.throwFeatMissing("canonical", "ch.epfl.bbp.uima.types.BioVerb");
return jcasType.ll_cas.ll_getStringValue(addr, ((BioVerb_Type)jcasType).casFeatCode_canonical);} | java | public String getCanonical() {
if (BioVerb_Type.featOkTst && ((BioVerb_Type)jcasType).casFeat_canonical == null)
jcasType.jcas.throwFeatMissing("canonical", "ch.epfl.bbp.uima.types.BioVerb");
return jcasType.ll_cas.ll_getStringValue(addr, ((BioVerb_Type)jcasType).casFeatCode_canonical);} | [
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140,630 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/BioVerb.java | BioVerb.setCanonical | public void setCanonical(String v) {
if (BioVerb_Type.featOkTst && ((BioVerb_Type)jcasType).casFeat_canonical == null)
jcasType.jcas.throwFeatMissing("canonical", "ch.epfl.bbp.uima.types.BioVerb");
jcasType.ll_cas.ll_setStringValue(addr, ((BioVerb_Type)jcasType).casFeatCode_canonical, v);} | java | public void setCanonical(String v) {
if (BioVerb_Type.featOkTst && ((BioVerb_Type)jcasType).casFeat_canonical == null)
jcasType.jcas.throwFeatMissing("canonical", "ch.epfl.bbp.uima.types.BioVerb");
jcasType.ll_cas.ll_setStringValue(addr, ((BioVerb_Type)jcasType).casFeatCode_canonical, v);} | [
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140,631 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/BioVerb.java | BioVerb.getMatchedText | public String getMatchedText() {
if (BioVerb_Type.featOkTst && ((BioVerb_Type)jcasType).casFeat_matchedText == null)
jcasType.jcas.throwFeatMissing("matchedText", "ch.epfl.bbp.uima.types.BioVerb");
return jcasType.ll_cas.ll_getStringValue(addr, ((BioVerb_Type)jcasType).casFeatCode_matchedText);} | java | public String getMatchedText() {
if (BioVerb_Type.featOkTst && ((BioVerb_Type)jcasType).casFeat_matchedText == null)
jcasType.jcas.throwFeatMissing("matchedText", "ch.epfl.bbp.uima.types.BioVerb");
return jcasType.ll_cas.ll_getStringValue(addr, ((BioVerb_Type)jcasType).casFeatCode_matchedText);} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/BioVerb.java#L156-L159 |
140,632 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/BioVerb.java | BioVerb.setMatchedText | public void setMatchedText(String v) {
if (BioVerb_Type.featOkTst && ((BioVerb_Type)jcasType).casFeat_matchedText == null)
jcasType.jcas.throwFeatMissing("matchedText", "ch.epfl.bbp.uima.types.BioVerb");
jcasType.ll_cas.ll_setStringValue(addr, ((BioVerb_Type)jcasType).casFeatCode_matchedText, v);} | java | public void setMatchedText(String v) {
if (BioVerb_Type.featOkTst && ((BioVerb_Type)jcasType).casFeat_matchedText == null)
jcasType.jcas.throwFeatMissing("matchedText", "ch.epfl.bbp.uima.types.BioVerb");
jcasType.ll_cas.ll_setStringValue(addr, ((BioVerb_Type)jcasType).casFeatCode_matchedText, 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/BioVerb.java#L165-L168 |
140,633 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/BioVerb.java | BioVerb.getMatchedTokens | public FSArray getMatchedTokens() {
if (BioVerb_Type.featOkTst && ((BioVerb_Type)jcasType).casFeat_matchedTokens == null)
jcasType.jcas.throwFeatMissing("matchedTokens", "ch.epfl.bbp.uima.types.BioVerb");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((BioVerb_Type)jcasType).casFeatCode_matchedTokens)));} | java | public FSArray getMatchedTokens() {
if (BioVerb_Type.featOkTst && ((BioVerb_Type)jcasType).casFeat_matchedTokens == null)
jcasType.jcas.throwFeatMissing("matchedTokens", "ch.epfl.bbp.uima.types.BioVerb");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((BioVerb_Type)jcasType).casFeatCode_matchedTokens)));} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/BioVerb.java#L178-L181 |
140,634 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/AdjectiveFeats.java | AdjectiveFeats.getDegree | public String getDegree() {
if (AdjectiveFeats_Type.featOkTst && ((AdjectiveFeats_Type)jcasType).casFeat_degree == null)
jcasType.jcas.throwFeatMissing("degree", "de.julielab.jules.types.AdjectiveFeats");
return jcasType.ll_cas.ll_getStringValue(addr, ((AdjectiveFeats_Type)jcasType).casFeatCode_degree);} | java | public String getDegree() {
if (AdjectiveFeats_Type.featOkTst && ((AdjectiveFeats_Type)jcasType).casFeat_degree == null)
jcasType.jcas.throwFeatMissing("degree", "de.julielab.jules.types.AdjectiveFeats");
return jcasType.ll_cas.ll_getStringValue(addr, ((AdjectiveFeats_Type)jcasType).casFeatCode_degree);} | [
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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/AdjectiveFeats.java#L85-L88 |
140,635 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/AdjectiveFeats.java | AdjectiveFeats.setDegree | public void setDegree(String v) {
if (AdjectiveFeats_Type.featOkTst && ((AdjectiveFeats_Type)jcasType).casFeat_degree == null)
jcasType.jcas.throwFeatMissing("degree", "de.julielab.jules.types.AdjectiveFeats");
jcasType.ll_cas.ll_setStringValue(addr, ((AdjectiveFeats_Type)jcasType).casFeatCode_degree, v);} | java | public void setDegree(String v) {
if (AdjectiveFeats_Type.featOkTst && ((AdjectiveFeats_Type)jcasType).casFeat_degree == null)
jcasType.jcas.throwFeatMissing("degree", "de.julielab.jules.types.AdjectiveFeats");
jcasType.ll_cas.ll_setStringValue(addr, ((AdjectiveFeats_Type)jcasType).casFeatCode_degree, v);} | [
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@generated
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/AdjectiveFeats.java#L94-L97 |
140,636 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/tokens/SimpleSourcedTokenizer.java | SimpleSourcedTokenizer.sourcedTokenize | public SourcedToken[] sourcedTokenize(String input,String source)
{
Token[] tokens = tokenize(input);
SourcedToken[] sourcedTokens = new SourcedToken[tokens.length];
for (int i=0; i<tokens.length; i++) {
String key = tokens[i].getValue()+"@"+source;
if (tokMap.get(key)==null) {
tokMap.put(key,new Integer(++nextId));
}
int id = ((Integer)tokMap.get(key)).intValue();
sourcedTokens[i] = new BasicSourcedToken(id, tokens[i].getValue(), source);
}
return sourcedTokens;
} | java | public SourcedToken[] sourcedTokenize(String input,String source)
{
Token[] tokens = tokenize(input);
SourcedToken[] sourcedTokens = new SourcedToken[tokens.length];
for (int i=0; i<tokens.length; i++) {
String key = tokens[i].getValue()+"@"+source;
if (tokMap.get(key)==null) {
tokMap.put(key,new Integer(++nextId));
}
int id = ((Integer)tokMap.get(key)).intValue();
sourcedTokens[i] = new BasicSourcedToken(id, tokens[i].getValue(), source);
}
return sourcedTokens;
} | [
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140,637 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/BagOfTokens.java | BagOfTokens.setWeight | void setWeight(Token tok, double d) {
Double oldWeight = (Double)weightMap.get(tok);
totalWeight += oldWeight==null ? d : (d - oldWeight.doubleValue());
weightMap.put(tok,new Double(d));
} | java | void setWeight(Token tok, double d) {
Double oldWeight = (Double)weightMap.get(tok);
totalWeight += oldWeight==null ? d : (d - oldWeight.doubleValue());
weightMap.put(tok,new Double(d));
} | [
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140,638 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/DBInfo.java | DBInfo.getAcList | public StringArray getAcList() {
if (DBInfo_Type.featOkTst && ((DBInfo_Type)jcasType).casFeat_acList == null)
jcasType.jcas.throwFeatMissing("acList", "de.julielab.jules.types.DBInfo");
return (StringArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((DBInfo_Type)jcasType).casFeatCode_acList)));} | java | public StringArray getAcList() {
if (DBInfo_Type.featOkTst && ((DBInfo_Type)jcasType).casFeat_acList == null)
jcasType.jcas.throwFeatMissing("acList", "de.julielab.jules.types.DBInfo");
return (StringArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((DBInfo_Type)jcasType).casFeatCode_acList)));} | [
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140,639 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/DBInfo.java | DBInfo.setAcList | public void setAcList(StringArray v) {
if (DBInfo_Type.featOkTst && ((DBInfo_Type)jcasType).casFeat_acList == null)
jcasType.jcas.throwFeatMissing("acList", "de.julielab.jules.types.DBInfo");
jcasType.ll_cas.ll_setRefValue(addr, ((DBInfo_Type)jcasType).casFeatCode_acList, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setAcList(StringArray v) {
if (DBInfo_Type.featOkTst && ((DBInfo_Type)jcasType).casFeat_acList == null)
jcasType.jcas.throwFeatMissing("acList", "de.julielab.jules.types.DBInfo");
jcasType.ll_cas.ll_setRefValue(addr, ((DBInfo_Type)jcasType).casFeatCode_acList, jcasType.ll_cas.ll_getFSRef(v));} | [
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140,640 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/DBInfo.java | DBInfo.getAcList | public String getAcList(int i) {
if (DBInfo_Type.featOkTst && ((DBInfo_Type)jcasType).casFeat_acList == null)
jcasType.jcas.throwFeatMissing("acList", "de.julielab.jules.types.DBInfo");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((DBInfo_Type)jcasType).casFeatCode_acList), i);
return jcasType.ll_cas.ll_getStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((DBInfo_Type)jcasType).casFeatCode_acList), i);} | java | public String getAcList(int i) {
if (DBInfo_Type.featOkTst && ((DBInfo_Type)jcasType).casFeat_acList == null)
jcasType.jcas.throwFeatMissing("acList", "de.julielab.jules.types.DBInfo");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((DBInfo_Type)jcasType).casFeatCode_acList), i);
return jcasType.ll_cas.ll_getStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((DBInfo_Type)jcasType).casFeatCode_acList), i);} | [
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@generated
@param i index in the array to get
@return value of the element at index i | [
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140,641 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/DBInfo.java | DBInfo.setAcList | public void setAcList(int i, String v) {
if (DBInfo_Type.featOkTst && ((DBInfo_Type)jcasType).casFeat_acList == null)
jcasType.jcas.throwFeatMissing("acList", "de.julielab.jules.types.DBInfo");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((DBInfo_Type)jcasType).casFeatCode_acList), i);
jcasType.ll_cas.ll_setStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((DBInfo_Type)jcasType).casFeatCode_acList), i, v);} | java | public void setAcList(int i, String v) {
if (DBInfo_Type.featOkTst && ((DBInfo_Type)jcasType).casFeat_acList == null)
jcasType.jcas.throwFeatMissing("acList", "de.julielab.jules.types.DBInfo");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((DBInfo_Type)jcasType).casFeatCode_acList), i);
jcasType.ll_cas.ll_setStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((DBInfo_Type)jcasType).casFeatCode_acList), i, v);} | [
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] | indexed setter for acList - sets an indexed value - A list of accession numbers for this DB, C
@generated
@param i index in the array to set
@param v value to set into the array | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/de/julielab/jules/types/DBInfo.java#L138-L142 |
140,642 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Date.java | Date.getDay | public int getDay() {
if (Date_Type.featOkTst && ((Date_Type)jcasType).casFeat_day == null)
jcasType.jcas.throwFeatMissing("day", "de.julielab.jules.types.Date");
return jcasType.ll_cas.ll_getIntValue(addr, ((Date_Type)jcasType).casFeatCode_day);} | java | public int getDay() {
if (Date_Type.featOkTst && ((Date_Type)jcasType).casFeat_day == null)
jcasType.jcas.throwFeatMissing("day", "de.julielab.jules.types.Date");
return jcasType.ll_cas.ll_getIntValue(addr, ((Date_Type)jcasType).casFeatCode_day);} | [
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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/Date.java#L85-L88 |
140,643 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Date.java | Date.setDay | public void setDay(int v) {
if (Date_Type.featOkTst && ((Date_Type)jcasType).casFeat_day == null)
jcasType.jcas.throwFeatMissing("day", "de.julielab.jules.types.Date");
jcasType.ll_cas.ll_setIntValue(addr, ((Date_Type)jcasType).casFeatCode_day, v);} | java | public void setDay(int v) {
if (Date_Type.featOkTst && ((Date_Type)jcasType).casFeat_day == null)
jcasType.jcas.throwFeatMissing("day", "de.julielab.jules.types.Date");
jcasType.ll_cas.ll_setIntValue(addr, ((Date_Type)jcasType).casFeatCode_day, 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/Date.java#L94-L97 |
140,644 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Date.java | Date.getMonth | public int getMonth() {
if (Date_Type.featOkTst && ((Date_Type)jcasType).casFeat_month == null)
jcasType.jcas.throwFeatMissing("month", "de.julielab.jules.types.Date");
return jcasType.ll_cas.ll_getIntValue(addr, ((Date_Type)jcasType).casFeatCode_month);} | java | public int getMonth() {
if (Date_Type.featOkTst && ((Date_Type)jcasType).casFeat_month == null)
jcasType.jcas.throwFeatMissing("month", "de.julielab.jules.types.Date");
return jcasType.ll_cas.ll_getIntValue(addr, ((Date_Type)jcasType).casFeatCode_month);} | [
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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/Date.java#L107-L110 |
140,645 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Date.java | Date.setMonth | public void setMonth(int v) {
if (Date_Type.featOkTst && ((Date_Type)jcasType).casFeat_month == null)
jcasType.jcas.throwFeatMissing("month", "de.julielab.jules.types.Date");
jcasType.ll_cas.ll_setIntValue(addr, ((Date_Type)jcasType).casFeatCode_month, v);} | java | public void setMonth(int v) {
if (Date_Type.featOkTst && ((Date_Type)jcasType).casFeat_month == null)
jcasType.jcas.throwFeatMissing("month", "de.julielab.jules.types.Date");
jcasType.ll_cas.ll_setIntValue(addr, ((Date_Type)jcasType).casFeatCode_month, 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/Date.java#L116-L119 |
140,646 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/SpecialMatchExpt.java | SpecialMatchExpt.averagePrecision | public Double averagePrecision()
{
double n = 0;
double sumPrecision = 0;
for (int i=0; i<pairs.length; i++) {
if (correctPair(i)) {
n++;
double precisionAtRankI = n/(i+1.0);
sumPrecision += precisionAtRankI;
}
}
return new Double(sumPrecision / numCorrectPairs);
} | java | public Double averagePrecision()
{
double n = 0;
double sumPrecision = 0;
for (int i=0; i<pairs.length; i++) {
if (correctPair(i)) {
n++;
double precisionAtRankI = n/(i+1.0);
sumPrecision += precisionAtRankI;
}
}
return new Double(sumPrecision / numCorrectPairs);
} | [
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140,647 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/SpecialMatchExpt.java | SpecialMatchExpt.maxF1 | public Double maxF1()
{
double maxF1 = -Double.MAX_VALUE;
double n = 0;
for (int i=0; i<pairs.length; i++) {
if (correctPair(i)) {
n++;
double precisionAtRankI = n/(i+1.0);
double recallAtRankI = n/numCorrectPairs;
if (precisionAtRankI>0 && recallAtRankI>0) {
double f1 = 2*(precisionAtRankI*recallAtRankI) / (precisionAtRankI + recallAtRankI);
maxF1 = Math.max( f1, maxF1 );
}
}
}
return new Double(maxF1);
} | java | public Double maxF1()
{
double maxF1 = -Double.MAX_VALUE;
double n = 0;
for (int i=0; i<pairs.length; i++) {
if (correctPair(i)) {
n++;
double precisionAtRankI = n/(i+1.0);
double recallAtRankI = n/numCorrectPairs;
if (precisionAtRankI>0 && recallAtRankI>0) {
double f1 = 2*(precisionAtRankI*recallAtRankI) / (precisionAtRankI + recallAtRankI);
maxF1 = Math.max( f1, maxF1 );
}
}
}
return new Double(maxF1);
} | [
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140,648 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/SpecialMatchExpt.java | SpecialMatchExpt.blockerRecall | public Double blockerRecall()
{
double n = 0;
for (int i=0; i<pairs.length; i++) {
if (correctPair(i)) {
n++;
}
}
return new Double(n/numCorrectPairs);
} | java | public Double blockerRecall()
{
double n = 0;
for (int i=0; i<pairs.length; i++) {
if (correctPair(i)) {
n++;
}
}
return new Double(n/numCorrectPairs);
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140,649 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/SpecialMatchExpt.java | SpecialMatchExpt.interpolated11PointPrecision | public double[] interpolated11PointPrecision()
{
double[] interpolatedPrecision = new double[11];
int numCorrectAtRankI = 0;
for (int i=0; i<pairs.length; i++) {
if (correctPair(i)) ++numCorrectAtRankI;
double recall = numCorrectAtRankI/((double)numCorrectPairs);
double precision = numCorrectAtRankI/(i+1.0);
for (int j=0; j<elevenPoints.length; j++) {
if (recall>=elevenPoints[j]) {
interpolatedPrecision[j] = Math.max(interpolatedPrecision[j], precision);
}
}
}
return interpolatedPrecision;
} | java | public double[] interpolated11PointPrecision()
{
double[] interpolatedPrecision = new double[11];
int numCorrectAtRankI = 0;
for (int i=0; i<pairs.length; i++) {
if (correctPair(i)) ++numCorrectAtRankI;
double recall = numCorrectAtRankI/((double)numCorrectPairs);
double precision = numCorrectAtRankI/(i+1.0);
for (int j=0; j<elevenPoints.length; j++) {
if (recall>=elevenPoints[j]) {
interpolatedPrecision[j] = Math.max(interpolatedPrecision[j], precision);
}
}
}
return interpolatedPrecision;
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140,650 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/SpecialMatchExpt.java | SpecialMatchExpt.graphPrecisionRecall | public void graphPrecisionRecall(PrintStream out) throws IOException
{
/** find interpolated precision - max precision at any rank point after i */
double[] interpolatedPrecision = new double[pairs.length];
double n = numCorrectPairs;
double maxPrecision = n/pairs.length;
for (int i=pairs.length-1; i>=0; i--) {
if (correctPair(i)) {
interpolatedPrecision[i] = maxPrecision;
n--;
maxPrecision = Math.max(maxPrecision, n/(i+1));
}
}
/** plot points on the graph */
n = 0;
for (int i=0; i<pairs.length; i++) {
if (correctPair(i)) {
n++;
double recallAtRankI = n/numCorrectPairs;
out.println(recallAtRankI+"\t"+interpolatedPrecision[i]);
}
}
} | java | public void graphPrecisionRecall(PrintStream out) throws IOException
{
/** find interpolated precision - max precision at any rank point after i */
double[] interpolatedPrecision = new double[pairs.length];
double n = numCorrectPairs;
double maxPrecision = n/pairs.length;
for (int i=pairs.length-1; i>=0; i--) {
if (correctPair(i)) {
interpolatedPrecision[i] = maxPrecision;
n--;
maxPrecision = Math.max(maxPrecision, n/(i+1));
}
}
/** plot points on the graph */
n = 0;
for (int i=0; i<pairs.length; i++) {
if (correctPair(i)) {
n++;
double recallAtRankI = n/numCorrectPairs;
out.println(recallAtRankI+"\t"+interpolatedPrecision[i]);
}
}
} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/SpecialMatchExpt.java#L249-L271 |
140,651 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/SpecialMatchExpt.java | SpecialMatchExpt.displayResults | public void displayResults(boolean showMismatches,PrintStream out) throws IOException
{
PrintfFormat fmt = new PrintfFormat("%s %3d %7.2f | %30s | %30s\n");
for (int i=0; i<pairs.length; i++) {
if (pairs[i]!=null) {
String label = pairs[i].isCorrect() ? "+" : "-";
String aText = (pairs[i].getA()==null) ? "***" : pairs[i].getA().unwrap();
String bText = (pairs[i].getB()==null) ? "***" : pairs[i].getB().unwrap();
if (showMismatches || "+".equals(label)) {
out.print( fmt.sprintf( new Object[] {
label,
new Integer(i+1),
new Double(pairs[i].getDistance()),
aText,
bText
}));
}
}
}
} | java | public void displayResults(boolean showMismatches,PrintStream out) throws IOException
{
PrintfFormat fmt = new PrintfFormat("%s %3d %7.2f | %30s | %30s\n");
for (int i=0; i<pairs.length; i++) {
if (pairs[i]!=null) {
String label = pairs[i].isCorrect() ? "+" : "-";
String aText = (pairs[i].getA()==null) ? "***" : pairs[i].getA().unwrap();
String bText = (pairs[i].getB()==null) ? "***" : pairs[i].getB().unwrap();
if (showMismatches || "+".equals(label)) {
out.print( fmt.sprintf( new Object[] {
label,
new Integer(i+1),
new Double(pairs[i].getDistance()),
aText,
bText
}));
}
}
}
} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/SpecialMatchExpt.java#L276-L295 |
140,652 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/SpecialMatchExpt.java | SpecialMatchExpt.dumpResults | public void dumpResults(PrintStream out) throws IOException
{
PrintfFormat fmt = new PrintfFormat("%7.2f\t%s\t%s\n");
for (int i=0; i<pairs.length; i++) {
if (pairs[i]!=null) {
String aText = (pairs[i].getA()==null) ? "***" : pairs[i].getA().unwrap();
String bText = (pairs[i].getB()==null) ? "***" : pairs[i].getB().unwrap();
out.print( fmt.sprintf( new Object[] {
new Double(pairs[i].getDistance()),
aText,
bText
}));
}
}
} | java | public void dumpResults(PrintStream out) throws IOException
{
PrintfFormat fmt = new PrintfFormat("%7.2f\t%s\t%s\n");
for (int i=0; i<pairs.length; i++) {
if (pairs[i]!=null) {
String aText = (pairs[i].getA()==null) ? "***" : pairs[i].getA().unwrap();
String bText = (pairs[i].getB()==null) ? "***" : pairs[i].getB().unwrap();
out.print( fmt.sprintf( new Object[] {
new Double(pairs[i].getDistance()),
aText,
bText
}));
}
}
} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_abbreviations/src/main/java/com/wcohen/ss/expt/SpecialMatchExpt.java#L299-L313 |
140,653 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/maxent/io/SuffixSensitiveGISModelReader.java | SuffixSensitiveGISModelReader.main | public static void main(String[] args) throws IOException {
ch.epfl.bbp.shaded.opennlp.maxent.GISModel m =
new SuffixSensitiveGISModelReader(new File(args[0])).getModel();
new SuffixSensitiveGISModelWriter(m, new File(args[1])).persist();
} | java | public static void main(String[] args) throws IOException {
ch.epfl.bbp.shaded.opennlp.maxent.GISModel m =
new SuffixSensitiveGISModelReader(new File(args[0])).getModel();
new SuffixSensitiveGISModelWriter(m, new File(args[1])).persist();
} | [
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<p>This particular example would of course be useful when you generally
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be able to inspect a few of them as plain text files. | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/maxent/io/SuffixSensitiveGISModelReader.java#L111-L115 |
140,654 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/BoxTableExtractor.java | BoxTableExtractor.unknownByPDFExtractor | private boolean unknownByPDFExtractor(ArrayList<ArrayList<TextPiece>> wordsByPage) {
ArrayList<TextPiece> wordsOfPageOne = wordsByPage.get(0);
boolean isUnknownCode = false;
int i = 0;
float codeSize = 0.0f;
while (i<wordsOfPageOne.size()) {
codeSize = codeSize + Math.max(wordsOfPageOne.get(i).getXScale(), wordsOfPageOne.get(i).getFontSize());
i++;
}
codeSize = codeSize/(float)wordsOfPageOne.size();
if (codeSize<=1.2)
isUnknownCode = true;
return(isUnknownCode);
} | java | private boolean unknownByPDFExtractor(ArrayList<ArrayList<TextPiece>> wordsByPage) {
ArrayList<TextPiece> wordsOfPageOne = wordsByPage.get(0);
boolean isUnknownCode = false;
int i = 0;
float codeSize = 0.0f;
while (i<wordsOfPageOne.size()) {
codeSize = codeSize + Math.max(wordsOfPageOne.get(i).getXScale(), wordsOfPageOne.get(i).getFontSize());
i++;
}
codeSize = codeSize/(float)wordsOfPageOne.size();
if (codeSize<=1.2)
isUnknownCode = true;
return(isUnknownCode);
} | [
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All the constant values are set based on extensive observation and experiment.
Of course, these values still need improvement for better results.
Machine learning methods can be used to tune these values.
@param wordsByPage
the extracted texts in the word level in a document
@return A boolean value: true/false | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/BoxTableExtractor.java#L237-L250 |
140,655 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/BoxTableExtractor.java | BoxTableExtractor.getDistinctSortedY | private Vector getDistinctSortedY(Vector distinctY, Vector piecesEachY, ArrayList<TextPiece> wordsOfAPage,
TableCandidate tc) {
int pieceNumThisPage = wordsOfAPage.size();
float x_columnToGetYs = m_docInfo.getMinX();
float endX_columnToGetYs = m_docInfo.getMiddleX();
if ( (tc.isWideTable()==false) && (tc.getCaptionX()>=m_docInfo.getMiddleX())){
x_columnToGetYs = m_docInfo.getMiddleX();
endX_columnToGetYs = m_docInfo.getMaxX();
}
float[] sortY = new float[pieceNumThisPage];
for (int bb=0; bb<pieceNumThisPage; bb++) {
if ( (wordsOfAPage.get(bb).getX()>=x_columnToGetYs) && (wordsOfAPage.get(bb).getEndX()<=endX_columnToGetYs) ) {
sortY[bb]=wordsOfAPage.get(bb).getY();
}
}
Arrays.sort(sortY);
int bb=0; float lastY = 0.0f;
while (bb<pieceNumThisPage) {
if (distinctY.size()>0) lastY =((Float)distinctY.lastElement()).floatValue();
if ( (sortY[bb]-lastY)>=m_docInfo.getAverageLineGap()/2.0)
distinctY.addElement(new Float(sortY[bb]));
bb++;
}
return distinctY;
} | java | private Vector getDistinctSortedY(Vector distinctY, Vector piecesEachY, ArrayList<TextPiece> wordsOfAPage,
TableCandidate tc) {
int pieceNumThisPage = wordsOfAPage.size();
float x_columnToGetYs = m_docInfo.getMinX();
float endX_columnToGetYs = m_docInfo.getMiddleX();
if ( (tc.isWideTable()==false) && (tc.getCaptionX()>=m_docInfo.getMiddleX())){
x_columnToGetYs = m_docInfo.getMiddleX();
endX_columnToGetYs = m_docInfo.getMaxX();
}
float[] sortY = new float[pieceNumThisPage];
for (int bb=0; bb<pieceNumThisPage; bb++) {
if ( (wordsOfAPage.get(bb).getX()>=x_columnToGetYs) && (wordsOfAPage.get(bb).getEndX()<=endX_columnToGetYs) ) {
sortY[bb]=wordsOfAPage.get(bb).getY();
}
}
Arrays.sort(sortY);
int bb=0; float lastY = 0.0f;
while (bb<pieceNumThisPage) {
if (distinctY.size()>0) lastY =((Float)distinctY.lastElement()).floatValue();
if ( (sortY[bb]-lastY)>=m_docInfo.getAverageLineGap()/2.0)
distinctY.addElement(new Float(sortY[bb]));
bb++;
}
return distinctY;
} | [
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] | We do not sort the text pieces according to Y values in the WHOLE page,
because if a document contains more than one column and the table is within one document column,
this action will bring the text pieces in other document columns as noise texts.
By default, we sort Y coordinate values based on the text pieces in the left part of the page
If we find a table is not a wide table and located in the right part, we only process the right half of the page
@param distinctY
the vector to store the non-duplicated Y coordinates
@param wordsOfAPage
the list of words of this document page
@param tc
the object of the table candidates
@return
the updated vector to store the non-duplicated Y coordinates | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/BoxTableExtractor.java#L988-L1013 |
140,656 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/BoxTableExtractor.java | BoxTableExtractor.getMatchedTabledKeyword | private String getMatchedTabledKeyword(String line) {
for (String keyword : Config.TABLE_KEYWORDS) {
if (line.startsWith(keyword)) {
return keyword;
}
}
return null;
} | java | private String getMatchedTabledKeyword(String line) {
for (String keyword : Config.TABLE_KEYWORDS) {
if (line.startsWith(keyword)) {
return keyword;
}
}
return null;
} | [
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@return matched keyword if found / null if not found | [
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140,657 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/BoxTableExtractor.java | BoxTableExtractor.getMatchedFigureKeyword | private String getMatchedFigureKeyword(String line) {
for (String keyword : Config.FIGURE_KEYWORDS) {
if (line.startsWith(keyword)) {
return keyword;
}
}
return null;
} | java | private String getMatchedFigureKeyword(String line) {
for (String keyword : Config.FIGURE_KEYWORDS) {
if (line.startsWith(keyword)) {
return keyword;
}
}
return null;
} | [
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140,658 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/BoxTableExtractor.java | BoxTableExtractor.findFootnoteBeginRow | private void findFootnoteBeginRow(TableCandidate tc) {
for (int i = 0; i < tc.getRows().size(); i++) {
TableRow row = tc.getRows().get(i);
TextPiece firstCell = row.getCells().get(0);
String text = firstCell.getText();
if (text.startsWith("*")
|| text.startsWith("t ")
|| text.startsWith("$")
|| text.startsWith("?")
|| text.startsWith("''")
|| text.startsWith("Note:")
|| (text.startsWith("a") && i >= tc.getRows().size() - 2 && row.isSuperScriptRow())) {
tc.setFootnoteBeginRow(i);
break;
}
}
if (tc.getFootnoteBeginRow()==-1)
tc.setFootnoteBeginRow(tc.getRows().size());
} | java | private void findFootnoteBeginRow(TableCandidate tc) {
for (int i = 0; i < tc.getRows().size(); i++) {
TableRow row = tc.getRows().get(i);
TextPiece firstCell = row.getCells().get(0);
String text = firstCell.getText();
if (text.startsWith("*")
|| text.startsWith("t ")
|| text.startsWith("$")
|| text.startsWith("?")
|| text.startsWith("''")
|| text.startsWith("Note:")
|| (text.startsWith("a") && i >= tc.getRows().size() - 2 && row.isSuperScriptRow())) {
tc.setFootnoteBeginRow(i);
break;
}
}
if (tc.getFootnoteBeginRow()==-1)
tc.setFootnoteBeginRow(tc.getRows().size());
} | [
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@param tc
the object of the table candidate | [
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140,659 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/BoxTableExtractor.java | BoxTableExtractor.determineFootnoteHeading | private void determineFootnoteHeading(TableCandidate tc) {
/*
* Gets the maximal column number based on all table rows before footnote
*/
int maxColumnNum = 0;
for (int i = 0; i < tc.getFootnoteBeginRow(); i++) {
TableRow row = tc.getRows().get(i);
if (row.getCells().size() > maxColumnNum) {
maxColumnNum = row.getCells().size();
}
}
tc.setMaxColumnNumber(maxColumnNum);
/*
* Counts the number of table column heading lines
* TODO: this heading finding algorithm should be improved
*/
int headingLineNumber = 0;
for (int i = 0; i < tc.getFootnoteBeginRow(); i++) {
TableRow row = tc.getRows().get(i);
if (row.getCells().size() < maxColumnNum) {
headingLineNumber++;
}
else break;
}
/*
* Based on observation, usually we have missing cells, especially happen in the first column
*/
if (headingLineNumber>0) headingLineNumber--;
tc.setHeadingLineNumber(Math.max(0, headingLineNumber));
} | java | private void determineFootnoteHeading(TableCandidate tc) {
/*
* Gets the maximal column number based on all table rows before footnote
*/
int maxColumnNum = 0;
for (int i = 0; i < tc.getFootnoteBeginRow(); i++) {
TableRow row = tc.getRows().get(i);
if (row.getCells().size() > maxColumnNum) {
maxColumnNum = row.getCells().size();
}
}
tc.setMaxColumnNumber(maxColumnNum);
/*
* Counts the number of table column heading lines
* TODO: this heading finding algorithm should be improved
*/
int headingLineNumber = 0;
for (int i = 0; i < tc.getFootnoteBeginRow(); i++) {
TableRow row = tc.getRows().get(i);
if (row.getCells().size() < maxColumnNum) {
headingLineNumber++;
}
else break;
}
/*
* Based on observation, usually we have missing cells, especially happen in the first column
*/
if (headingLineNumber>0) headingLineNumber--;
tc.setHeadingLineNumber(Math.max(0, headingLineNumber));
} | [
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@param tc
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/BoxTableExtractor.java#L1422-L1452 |
140,660 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/BoxTableExtractor.java | BoxTableExtractor.getTableStructure | public void getTableStructure (int cc, TableCandidate tc, ArrayList<TextPiece> wordsOfAPage) {
float minGapBtwColumns = 1000.0f;
float[] leftX_tableColumns = tc.getLeftX_tableColumns();
float[] rightX_tableColumns = tc.getRightX_tableColumns();
int YNum = tc.getRows().size();
for (int zz=1; zz<cc; zz++) {
float thisColumnGap = leftX_tableColumns[zz]-rightX_tableColumns[zz-1];
if (thisColumnGap<minGapBtwColumns)
minGapBtwColumns = thisColumnGap;
}
double columnGapThreshold = 0.0;
//if (withoutKwd==true) columnGapThreshold = parameters.ave_X_Gap_inLine*1.6;
if (minGapBtwColumns>columnGapThreshold) {
getEachCellContent(YNum, cc, tc);
getRealHeadingBasedOnCells(YNum, cc, tc);
getColumnHeading(tc);
getRowHeadingBasedOnCells(tc);
tc.setMetadataStructureLevel(YNum, cc, wordsOfAPage, m_docInfo);
//tc.setMetaStructureLevelx(YNum, cc, wordsOfAPage, m_docInfo);
if ( (tc.getFootnoteBeginRow()>1) & (tc.getMaxColumnNumber()>1) ) {}
else tc.setValid(false);
}
else {
m_docInfo.setErrorMsg("Although we detected some tabular structures in page " + (tc.getPageId_thisTable()+1) + ", we do not treat them as tables because the space gaps between columns are not large enough.");
}
} | java | public void getTableStructure (int cc, TableCandidate tc, ArrayList<TextPiece> wordsOfAPage) {
float minGapBtwColumns = 1000.0f;
float[] leftX_tableColumns = tc.getLeftX_tableColumns();
float[] rightX_tableColumns = tc.getRightX_tableColumns();
int YNum = tc.getRows().size();
for (int zz=1; zz<cc; zz++) {
float thisColumnGap = leftX_tableColumns[zz]-rightX_tableColumns[zz-1];
if (thisColumnGap<minGapBtwColumns)
minGapBtwColumns = thisColumnGap;
}
double columnGapThreshold = 0.0;
//if (withoutKwd==true) columnGapThreshold = parameters.ave_X_Gap_inLine*1.6;
if (minGapBtwColumns>columnGapThreshold) {
getEachCellContent(YNum, cc, tc);
getRealHeadingBasedOnCells(YNum, cc, tc);
getColumnHeading(tc);
getRowHeadingBasedOnCells(tc);
tc.setMetadataStructureLevel(YNum, cc, wordsOfAPage, m_docInfo);
//tc.setMetaStructureLevelx(YNum, cc, wordsOfAPage, m_docInfo);
if ( (tc.getFootnoteBeginRow()>1) & (tc.getMaxColumnNumber()>1) ) {}
else tc.setValid(false);
}
else {
m_docInfo.setErrorMsg("Although we detected some tabular structures in page " + (tc.getPageId_thisTable()+1) + ", we do not treat them as tables because the space gaps between columns are not large enough.");
}
} | [
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] | Implements the table structure decomposition step
@param cc
the number of the table columns
@param tc
the object of the table candidate
@param wordsOfAPage
the list of all the words in a document page | [
"Implements",
"the",
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/BoxTableExtractor.java#L1662-L1689 |
140,661 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/BoxTableExtractor.java | BoxTableExtractor.getRealHeadingBasedOnCells | public void getRealHeadingBasedOnCells(int YNum, int cc, TableCandidate tc) {
int footnoteLineIndex = tc.getFootnoteBeginRow();
String[][] cells = tc.getCells();
int i=0;
while (i<footnoteLineIndex) {
int j=0, nonNullCellNum = 0;
while (j<cc) {
if (cells[i][j]=="") {
break;
}
nonNullCellNum ++;
j++;
}
if (nonNullCellNum==cc) break;
else i++;
}
/*
* if the next row contain unit symbols, this row has a very large possibility to be a table column heading row
*/
if ((i+1)<footnoteLineIndex ) {
boolean hasUnitSymbols = false;
int j=0;
while (j<cc) {
if ( (cells[i+1][j].indexOf("/yg rnI--")>0) || (cells[i+1][j].indexOf("(%)")>0) || (cells[i+1][j].indexOf("w-'")>0) ||
(cells[i+1][j].indexOf("CLg g-'")>0) || (cells[i+1][j].indexOf("pg ml-1")>=0) ) {
i++;
break;
}
j++;
}
}
/*
* Based on observation, the column heading rows always contain missing cells.
* But the first data row always does not contain missing cell
*/
if (i==YNum) i=0;
if (i>0) i--;
tc.setHeadingLineNumber(i);
} | java | public void getRealHeadingBasedOnCells(int YNum, int cc, TableCandidate tc) {
int footnoteLineIndex = tc.getFootnoteBeginRow();
String[][] cells = tc.getCells();
int i=0;
while (i<footnoteLineIndex) {
int j=0, nonNullCellNum = 0;
while (j<cc) {
if (cells[i][j]=="") {
break;
}
nonNullCellNum ++;
j++;
}
if (nonNullCellNum==cc) break;
else i++;
}
/*
* if the next row contain unit symbols, this row has a very large possibility to be a table column heading row
*/
if ((i+1)<footnoteLineIndex ) {
boolean hasUnitSymbols = false;
int j=0;
while (j<cc) {
if ( (cells[i+1][j].indexOf("/yg rnI--")>0) || (cells[i+1][j].indexOf("(%)")>0) || (cells[i+1][j].indexOf("w-'")>0) ||
(cells[i+1][j].indexOf("CLg g-'")>0) || (cells[i+1][j].indexOf("pg ml-1")>=0) ) {
i++;
break;
}
j++;
}
}
/*
* Based on observation, the column heading rows always contain missing cells.
* But the first data row always does not contain missing cell
*/
if (i==YNum) i=0;
if (i>0) i--;
tc.setHeadingLineNumber(i);
} | [
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@param cc
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@param tc
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/BoxTableExtractor.java#L1777-L1815 |
140,662 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/BoxTableExtractor.java | BoxTableExtractor.getColumnHeading | public void getColumnHeading(TableCandidate tc) {
int headings = tc.getHeadingLineNumber();
String[][] cells = tc.getCells();
String columnHeadings = "";
for (int i=0; i<=headings; i++) {
int j = cells[i].length;
for (int k=0; k<j; k++) {
cells[i][k] = tc.replaceAllSpecialChracters(cells[i][k]);
columnHeadings = columnHeadings + cells[i][k] + "; ";
}
columnHeadings = columnHeadings + "\n";
}
tc.setColumnHeadings(columnHeadings);
} | java | public void getColumnHeading(TableCandidate tc) {
int headings = tc.getHeadingLineNumber();
String[][] cells = tc.getCells();
String columnHeadings = "";
for (int i=0; i<=headings; i++) {
int j = cells[i].length;
for (int k=0; k<j; k++) {
cells[i][k] = tc.replaceAllSpecialChracters(cells[i][k]);
columnHeadings = columnHeadings + cells[i][k] + "; ";
}
columnHeadings = columnHeadings + "\n";
}
tc.setColumnHeadings(columnHeadings);
} | [
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140,663 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/namefind/NameFinderEventStream.java | NameFinderEventStream.addEvents | private void addEvents(String sentence) {
String[] parts = sentence.split(" ");
String outcome = NameFinderME.OTHER;
List toks = new ArrayList();
List outcomes = new ArrayList();
for (int pi = 0, pl = parts.length; pi < pl; pi++) {
if (parts[pi].equals("<START>")) {
outcome = NameFinderME.START;
}
else if (parts[pi].equals("<END>")) {
outcome = NameFinderME.OTHER;
}
else { //regular token
toks.add(parts[pi]);
outcomes.add(outcome);
if (outcome.equals(NameFinderME.START)) {
outcome = NameFinderME.CONTINUE;
}
}
}
events = new Event[toks.size()];
for (int ti = 0, tl = toks.size(); ti < tl; ti++) {
events[ti] = new Event((String) outcomes.get(ti), cg.getContext(ti, toks, outcomes, prevTags));
}
for (int ti=0,tl=toks.size();ti<tl;ti++) {
prevTags.put(toks.get(ti),outcomes.get(ti));
}
} | java | private void addEvents(String sentence) {
String[] parts = sentence.split(" ");
String outcome = NameFinderME.OTHER;
List toks = new ArrayList();
List outcomes = new ArrayList();
for (int pi = 0, pl = parts.length; pi < pl; pi++) {
if (parts[pi].equals("<START>")) {
outcome = NameFinderME.START;
}
else if (parts[pi].equals("<END>")) {
outcome = NameFinderME.OTHER;
}
else { //regular token
toks.add(parts[pi]);
outcomes.add(outcome);
if (outcome.equals(NameFinderME.START)) {
outcome = NameFinderME.CONTINUE;
}
}
}
events = new Event[toks.size()];
for (int ti = 0, tl = toks.size(); ti < tl; ti++) {
events[ti] = new Event((String) outcomes.get(ti), cg.getContext(ti, toks, outcomes, prevTags));
}
for (int ti=0,tl=toks.size();ti<tl;ti++) {
prevTags.put(toks.get(ti),outcomes.get(ti));
}
} | [
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140,664 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/SupplementaryMaterial.java | SupplementaryMaterial.getObjectId | public java.util.List<ObjectId> getObjectId() {
if (objectId == null) {
objectId = new ArrayList<ObjectId>();
}
return this.objectId;
} | java | public java.util.List<ObjectId> getObjectId() {
if (objectId == null) {
objectId = new ArrayList<ObjectId>();
}
return this.objectId;
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140,665 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/SupplementaryMaterial.java | SupplementaryMaterial.getCaption | public java.util.List<Caption> getCaption() {
if (caption == null) {
caption = new ArrayList<Caption>();
}
return this.caption;
} | java | public java.util.List<Caption> getCaption() {
if (caption == null) {
caption = new ArrayList<Caption>();
}
return this.caption;
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140,666 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/SupplementaryMaterial.java | SupplementaryMaterial.getAltTextOrLongDescOrEmail | public java.util.List<Object> getAltTextOrLongDescOrEmail() {
if (altTextOrLongDescOrEmail == null) {
altTextOrLongDescOrEmail = new ArrayList<Object>();
}
return this.altTextOrLongDescOrEmail;
} | java | public java.util.List<Object> getAltTextOrLongDescOrEmail() {
if (altTextOrLongDescOrEmail == null) {
altTextOrLongDescOrEmail = new ArrayList<Object>();
}
return this.altTextOrLongDescOrEmail;
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Objects of the following type(s) are allowed in the list
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140,667 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/SupplementaryMaterial.java | SupplementaryMaterial.getDispFormulaOrDispFormulaGroupOrChemStructWrap | public java.util.List<Object> getDispFormulaOrDispFormulaGroupOrChemStructWrap() {
if (dispFormulaOrDispFormulaGroupOrChemStructWrap == null) {
dispFormulaOrDispFormulaGroupOrChemStructWrap = new ArrayList<Object>();
}
return this.dispFormulaOrDispFormulaGroupOrChemStructWrap;
} | java | public java.util.List<Object> getDispFormulaOrDispFormulaGroupOrChemStructWrap() {
if (dispFormulaOrDispFormulaGroupOrChemStructWrap == null) {
dispFormulaOrDispFormulaGroupOrChemStructWrap = new ArrayList<Object>();
}
return this.dispFormulaOrDispFormulaGroupOrChemStructWrap;
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140,668 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/SupplementaryMaterial.java | SupplementaryMaterial.getAttribOrPermissions | public java.util.List<Object> getAttribOrPermissions() {
if (attribOrPermissions == null) {
attribOrPermissions = new ArrayList<Object>();
}
return this.attribOrPermissions;
} | java | public java.util.List<Object> getAttribOrPermissions() {
if (attribOrPermissions == null) {
attribOrPermissions = new ArrayList<Object>();
}
return this.attribOrPermissions;
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140,669 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Constituent.java | Constituent.getParent | public Constituent getParent() {
if (Constituent_Type.featOkTst && ((Constituent_Type)jcasType).casFeat_parent == null)
jcasType.jcas.throwFeatMissing("parent", "de.julielab.jules.types.Constituent");
return (Constituent)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((Constituent_Type)jcasType).casFeatCode_parent)));} | java | public Constituent getParent() {
if (Constituent_Type.featOkTst && ((Constituent_Type)jcasType).casFeat_parent == null)
jcasType.jcas.throwFeatMissing("parent", "de.julielab.jules.types.Constituent");
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140,670 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Constituent.java | Constituent.setParent | public void setParent(Constituent v) {
if (Constituent_Type.featOkTst && ((Constituent_Type)jcasType).casFeat_parent == null)
jcasType.jcas.throwFeatMissing("parent", "de.julielab.jules.types.Constituent");
jcasType.ll_cas.ll_setRefValue(addr, ((Constituent_Type)jcasType).casFeatCode_parent, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setParent(Constituent v) {
if (Constituent_Type.featOkTst && ((Constituent_Type)jcasType).casFeat_parent == null)
jcasType.jcas.throwFeatMissing("parent", "de.julielab.jules.types.Constituent");
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140,671 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/CombinedStringDistanceLearner.java | CombinedStringDistanceLearner.hasNextQuery | public boolean hasNextQuery() {
for (int i=0; i<innerLearners.length; i++) {
if (innerLearners[i].hasNextQuery()) return true;
}
return comboHasNextQuery();
} | java | public boolean hasNextQuery() {
for (int i=0; i<innerLearners.length; i++) {
if (innerLearners[i].hasNextQuery()) return true;
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140,672 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/CombinedStringDistanceLearner.java | CombinedStringDistanceLearner.nextQuery | public DistanceInstance nextQuery() {
// need to save out the i-th field, if it's been prepared.
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// index innerLearners.length is the comboLearner
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} else if (innerLearners[k].hasNextQuery()) {
return innerLearners[k].nextQuery();
}
}
throw new IllegalStateException("someone seems to have forgotten they want a query");
} | java | public DistanceInstance nextQuery() {
// need to save out the i-th field, if it's been prepared.
// poll sublearners in random order, to be fair
// indices [0,innerLearners.length-1] are the inner learners,
// index innerLearners.length is the comboLearner
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for (int i=0; i<indices.size(); i++) indices.set(i, new Integer(i) );
Collections.shuffle(indices);
for (int i=0; i<indices.size(); i++) {
int k = ((Integer)indices.get(i)).intValue();
if ( k==innerLearners.length && comboHasNextQuery() ) {
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} else if (innerLearners[k].hasNextQuery()) {
return innerLearners[k].nextQuery();
}
}
throw new IllegalStateException("someone seems to have forgotten they want a query");
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_abbreviations/src/main/java/com/wcohen/ss/CombinedStringDistanceLearner.java#L111-L128 |
140,673 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/CombinedStringDistanceLearner.java | CombinedStringDistanceLearner.addExample | public void addExample(DistanceInstance answeredQuery) {
MyMultiDistanceInstance di = asMultiDistanceInstance( answeredQuery );
for (int i=0; i<innerLearners.length; i++) {
innerLearners[i].addExample( di.get(i) );
}
comboAddExample( di );
} | java | public void addExample(DistanceInstance answeredQuery) {
MyMultiDistanceInstance di = asMultiDistanceInstance( answeredQuery );
for (int i=0; i<innerLearners.length; i++) {
innerLearners[i].addExample( di.get(i) );
}
comboAddExample( di );
} | [
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140,674 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/CombinedStringDistanceLearner.java | CombinedStringDistanceLearner.prepare | public StringWrapperIterator prepare(StringWrapperIterator it)
{
List multiWrappers = asMultiStringWrapperList(it);
if (multiWrappers.size()==0) return new BasicStringWrapperIterator( Collections.EMPTY_SET.iterator() );
MultiStringWrapper prototype = (MultiStringWrapper)multiWrappers.get(0);
for (int i=0; i<prototype.size(); i++) {
int j = prototype.getDistanceLearnerIndex(i);
StringDistanceLearner learner = innerLearners[j];
StringWrapperIterator prepped = learner.prepare( new JthStringWrapperValueIterator( j, multiWrappers.iterator() ) );
for (int k=0; k<multiWrappers.size(); k++) {
MultiStringWrapper msw = (MultiStringWrapper)multiWrappers.get(k);
StringWrapper w = prepped.nextStringWrapper();
msw.set( i, w );
}
}
return new BasicStringWrapperIterator( multiWrappers.iterator() );
} | java | public StringWrapperIterator prepare(StringWrapperIterator it)
{
List multiWrappers = asMultiStringWrapperList(it);
if (multiWrappers.size()==0) return new BasicStringWrapperIterator( Collections.EMPTY_SET.iterator() );
MultiStringWrapper prototype = (MultiStringWrapper)multiWrappers.get(0);
for (int i=0; i<prototype.size(); i++) {
int j = prototype.getDistanceLearnerIndex(i);
StringDistanceLearner learner = innerLearners[j];
StringWrapperIterator prepped = learner.prepare( new JthStringWrapperValueIterator( j, multiWrappers.iterator() ) );
for (int k=0; k<multiWrappers.size(); k++) {
MultiStringWrapper msw = (MultiStringWrapper)multiWrappers.get(k);
StringWrapper w = prepped.nextStringWrapper();
msw.set( i, w );
}
}
return new BasicStringWrapperIterator( multiWrappers.iterator() );
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140,675 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/CombinedStringDistanceLearner.java | CombinedStringDistanceLearner.prepare | public DistanceInstanceIterator prepare(DistanceInstanceIterator it)
{
List multiDistances = asMultiDistanceInstanceList(it);
return new BasicDistanceInstanceIterator( multiDistances.iterator() );
} | java | public DistanceInstanceIterator prepare(DistanceInstanceIterator it)
{
List multiDistances = asMultiDistanceInstanceList(it);
return new BasicDistanceInstanceIterator( multiDistances.iterator() );
} | [
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140,676 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/CombinedStringDistanceLearner.java | CombinedStringDistanceLearner.prepareForLearner | private StringWrapper prepareForLearner(StringWrapper w,StringDistanceLearner learner) {
StringWrapperIterator it = new BasicStringWrapperIterator( Collections.singleton(w).iterator() );
return learner.prepare(it).nextStringWrapper();
} | java | private StringWrapper prepareForLearner(StringWrapper w,StringDistanceLearner learner) {
StringWrapperIterator it = new BasicStringWrapperIterator( Collections.singleton(w).iterator() );
return learner.prepare(it).nextStringWrapper();
} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_abbreviations/src/main/java/com/wcohen/ss/CombinedStringDistanceLearner.java#L197-L200 |
140,677 | BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/CombinedStringDistanceLearner.java | CombinedStringDistanceLearner.getInnerDistances | protected StringDistance[] getInnerDistances()
{
StringDistance[] innerDistances = new StringDistance[ innerLearners.length ];
for (int j=0; j<innerLearners.length; j++) {
innerDistances[j] = innerLearners[j].getDistance();
}
return innerDistances;
} | java | protected StringDistance[] getInnerDistances()
{
StringDistance[] innerDistances = new StringDistance[ innerLearners.length ];
for (int j=0; j<innerLearners.length; j++) {
innerDistances[j] = innerLearners[j].getDistance();
}
return innerDistances;
} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_abbreviations/src/main/java/com/wcohen/ss/CombinedStringDistanceLearner.java#L271-L278 |
140,678 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/neuroner/NeuroNER/Developmental.java | Developmental.getOntologyId | public String getOntologyId() {
if (Developmental_Type.featOkTst && ((Developmental_Type)jcasType).casFeat_ontologyId == null)
jcasType.jcas.throwFeatMissing("ontologyId", "neuroner.NeuroNER.Developmental");
return jcasType.ll_cas.ll_getStringValue(addr, ((Developmental_Type)jcasType).casFeatCode_ontologyId);} | java | public String getOntologyId() {
if (Developmental_Type.featOkTst && ((Developmental_Type)jcasType).casFeat_ontologyId == null)
jcasType.jcas.throwFeatMissing("ontologyId", "neuroner.NeuroNER.Developmental");
return jcasType.ll_cas.ll_getStringValue(addr, ((Developmental_Type)jcasType).casFeatCode_ontologyId);} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/neuroner/NeuroNER/Developmental.java#L105-L108 |
140,679 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/BatchExtractor.java | BatchExtractor.showUsage | private static void showUsage()
{
System.out.println("BatchExtractor <pdf-dir-path> <output-dir-path> <parser>");
System.out.println("BatchExtractor <pdf-dir-path> <output-dir-path> <parser> --debug");
System.out.println("BatchExtractor <pdf-dir-path> <output-dir-path> <parser> --small");
System.out.println("\tparser= pdfbox | tet");
} | java | private static void showUsage()
{
System.out.println("BatchExtractor <pdf-dir-path> <output-dir-path> <parser>");
System.out.println("BatchExtractor <pdf-dir-path> <output-dir-path> <parser> --debug");
System.out.println("BatchExtractor <pdf-dir-path> <output-dir-path> <parser> --small");
System.out.println("\tparser= pdfbox | tet");
} | [
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140,680 | BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/pubmed/PubDate.java | PubDate.getYearOrMonthOrDayOrSeasonOrMedlineDate | public List<java.lang.Object> getYearOrMonthOrDayOrSeasonOrMedlineDate() {
if (yearOrMonthOrDayOrSeasonOrMedlineDate == null) {
yearOrMonthOrDayOrSeasonOrMedlineDate = new ArrayList<java.lang.Object>();
}
return this.yearOrMonthOrDayOrSeasonOrMedlineDate;
} | java | public List<java.lang.Object> getYearOrMonthOrDayOrSeasonOrMedlineDate() {
if (yearOrMonthOrDayOrSeasonOrMedlineDate == null) {
yearOrMonthOrDayOrSeasonOrMedlineDate = new ArrayList<java.lang.Object>();
}
return this.yearOrMonthOrDayOrSeasonOrMedlineDate;
} | [
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140,681 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/ngram/NGramFactory.java | NGramFactory.createNGram | public NGram createNGram(List words) {
int[] nums = new int[words.size()]; //ngram needs it own copy of this array so keep making a unique one for each instance.
for (int wi=0;wi<nums.length;wi++) {
nums[wi] = wordMap.getIndex(words.get(wi));
if (nums[wi] == -1) {
return null;
}
}
return new NGram(nums);
} | java | public NGram createNGram(List words) {
int[] nums = new int[words.size()]; //ngram needs it own copy of this array so keep making a unique one for each instance.
for (int wi=0;wi<nums.length;wi++) {
nums[wi] = wordMap.getIndex(words.get(wi));
if (nums[wi] == -1) {
return null;
}
}
return new NGram(nums);
} | [
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140,682 | BlueBrain/bluima | modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/cleanup/HyphenRemover.java | HyphenRemover.shouldDehyphenate | private static boolean shouldDehyphenate(String w1, String w2) {
boolean dehyphenate = true;
String rule = "DH"; // choice by default, dehyphenate
if (w1.length() <= 1) {
// w1 has only one char
dehyphenate = false;
rule = "N11";
} else if (w2.length() <= 1) {
// w2 has only one char
dehyphenate = false;
rule = "N12";
} else if (numberEnd.matcher(w1).find()) {
// number at the end of w1
dehyphenate = false;
rule = "N21";
} else if (numberStart.matcher(w2).find()) {
// number at the beginning of w2
dehyphenate = false;
rule = "N22";
} else if (greekEnd.matcher(w1).find()) {
// greek letter at the end of w1
dehyphenate = false;
rule = "N31";
} else if (greekStart.matcher(w2).find()) {
// greek letter at the beginning of w2
dehyphenate = false;
rule = "N32";
}
if (dehyphenate) {
String word = w1.substring(0, w1.length() - 1) + w2;
LOG.debug("\"" + w1 + "\",\"" + w2 + "\",\"" + rule + "\",\""
+ word + "\"\n");
} else {
LOG.debug("\"" + w1 + "\",\"" + w2 + "\",\"" + rule + "\",\"" + w1
+ w2 + "\"\n");
}
return dehyphenate;
} | java | private static boolean shouldDehyphenate(String w1, String w2) {
boolean dehyphenate = true;
String rule = "DH"; // choice by default, dehyphenate
if (w1.length() <= 1) {
// w1 has only one char
dehyphenate = false;
rule = "N11";
} else if (w2.length() <= 1) {
// w2 has only one char
dehyphenate = false;
rule = "N12";
} else if (numberEnd.matcher(w1).find()) {
// number at the end of w1
dehyphenate = false;
rule = "N21";
} else if (numberStart.matcher(w2).find()) {
// number at the beginning of w2
dehyphenate = false;
rule = "N22";
} else if (greekEnd.matcher(w1).find()) {
// greek letter at the end of w1
dehyphenate = false;
rule = "N31";
} else if (greekStart.matcher(w2).find()) {
// greek letter at the beginning of w2
dehyphenate = false;
rule = "N32";
}
if (dehyphenate) {
String word = w1.substring(0, w1.length() - 1) + w2;
LOG.debug("\"" + w1 + "\",\"" + w2 + "\",\"" + rule + "\",\""
+ word + "\"\n");
} else {
LOG.debug("\"" + w1 + "\",\"" + w2 + "\",\"" + rule + "\",\"" + w1
+ w2 + "\"\n");
}
return dehyphenate;
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@param w1
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@return returns true if the word should be dehyphenated | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/cleanup/HyphenRemover.java#L65-L105 |
140,683 | BlueBrain/bluima | modules/bluima_utils/src/main/java/ds/tree/RadixTreeImpl.java | RadixTreeImpl.visit | public <R> void visit(String key, Visitor<T, R> visitor) {
if (root != null) {
visit(key, visitor, null, root);
}
} | java | public <R> void visit(String key, Visitor<T, R> visitor) {
if (root != null) {
visit(key, visitor, null, root);
}
} | [
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140,684 | BlueBrain/bluima | modules/bluima_utils/src/main/java/ds/tree/RadixTreeImpl.java | RadixTreeImpl.visit | private <R> void visit(String prefix, Visitor<T, R> visitor,
RadixTreeNode<T> parent, RadixTreeNode<T> node) {
int numberOfMatchingCharacters = node.getNumberOfMatchingCharacters(prefix);
// if the node key and prefix match, we found a match!
if (numberOfMatchingCharacters == prefix.length() && numberOfMatchingCharacters == node.getKey().length()) {
visitor.visit(prefix, parent, node);
} else if (node.getKey().equals("") == true // either we are at the
// root
|| (numberOfMatchingCharacters < prefix.length() && numberOfMatchingCharacters >= node.getKey().length())) { // OR we need to
// traverse the childern
String newText = prefix.substring(numberOfMatchingCharacters, prefix.length());
for (RadixTreeNode<T> child : node.getChildern()) {
// recursively search the child nodes
if (child.getKey().startsWith(newText.charAt(0) + "")) {
visit(newText, visitor, node, child);
break;
}
}
}
} | java | private <R> void visit(String prefix, Visitor<T, R> visitor,
RadixTreeNode<T> parent, RadixTreeNode<T> node) {
int numberOfMatchingCharacters = node.getNumberOfMatchingCharacters(prefix);
// if the node key and prefix match, we found a match!
if (numberOfMatchingCharacters == prefix.length() && numberOfMatchingCharacters == node.getKey().length()) {
visitor.visit(prefix, parent, node);
} else if (node.getKey().equals("") == true // either we are at the
// root
|| (numberOfMatchingCharacters < prefix.length() && numberOfMatchingCharacters >= node.getKey().length())) { // OR we need to
// traverse the childern
String newText = prefix.substring(numberOfMatchingCharacters, prefix.length());
for (RadixTreeNode<T> child : node.getChildern()) {
// recursively search the child nodes
if (child.getKey().startsWith(newText.charAt(0) + "")) {
visit(newText, visitor, node, child);
break;
}
}
}
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@param prefix
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@param visitor
The Visitor that will be called if a node with "key" as its
key is found
@param node
The Node from where onward to search | [
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140,685 | BlueBrain/bluima | modules/bluima_utils/src/main/java/ds/tree/RadixTreeImpl.java | RadixTreeImpl.formatNodeTo | private void formatNodeTo(Formatter f, int level, RadixTreeNode<T> node) {
for (int i = 0; i < level; i++) {
f.format(" ");
}
f.format("|");
for (int i = 0; i < level; i++) {
f.format("-");
}
if (node.isReal() == true)
f.format("%s[%s]*%n", node.getKey(), node.getValue());
else
f.format("%s%n", node.getKey());
for (RadixTreeNode<T> child : node.getChildern()) {
formatNodeTo(f, level + 1, child);
}
} | java | private void formatNodeTo(Formatter f, int level, RadixTreeNode<T> node) {
for (int i = 0; i < level; i++) {
f.format(" ");
}
f.format("|");
for (int i = 0; i < level; i++) {
f.format("-");
}
if (node.isReal() == true)
f.format("%s[%s]*%n", node.getKey(), node.getValue());
else
f.format("%s%n", node.getKey());
for (RadixTreeNode<T> child : node.getChildern()) {
formatNodeTo(f, level + 1, child);
}
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140,686 | BlueBrain/bluima | modules/bluima_utils/src/main/java/ds/tree/RadixTreeImpl.java | RadixTreeImpl.formatTo | @Override
public void formatTo(Formatter formatter, int flags, int width, int precision) {
formatNodeTo(formatter, 0, root);
} | java | @Override
public void formatTo(Formatter formatter, int flags, int width, int precision) {
formatNodeTo(formatter, 0, root);
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140,687 | BlueBrain/bluima | modules/bluima_protein_concentrations/src/main/java/ch/epfl/bbp/nlp/ie/proteinconc/normalizer/ConcentrationNormalizer.java | ConcentrationNormalizer.normalizeSpecialCases | private ValueUnitWrapper normalizeSpecialCases(double value, String unit)
throws UnknownUnitException {
if (unit.equals("mol/dm3")) {
return new ValueUnitWrapper(value, MOLAR_NORMALIZED_UNIT);
} else {
throw new UnknownUnitException(unit);
}
} | java | private ValueUnitWrapper normalizeSpecialCases(double value, String unit)
throws UnknownUnitException {
if (unit.equals("mol/dm3")) {
return new ValueUnitWrapper(value, MOLAR_NORMALIZED_UNIT);
} else {
throw new UnknownUnitException(unit);
}
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140,688 | BlueBrain/bluima | modules/bluima_protein_concentrations/src/main/java/ch/epfl/bbp/nlp/ie/proteinconc/normalizer/ConcentrationNormalizer.java | ConcentrationNormalizer.normalizeMassUnit | private ValueUnitWrapper normalizeMassUnit(final double value, final String unit)
throws UnknownUnitException {
Matcher matcher = mMassUnitPatter.matcher(unit);
if (matcher.find()) {
double normalizationFactor = 1.0;
String numeratorSIPrefix = matcher.group(1);
Double numeratorFactor = getSIFactor(numeratorSIPrefix);
if (numeratorFactor != null) {
normalizationFactor *= numeratorFactor;
}
String denominatorSIPrefix = matcher.group(3);
String denominatorUnit = matcher.group(4);
Double denominatorFactor = getSIFactor(denominatorSIPrefix);
if (denominatorFactor != null) {
int power = (denominatorUnit.endsWith("3")) ? 3 : 1;
normalizationFactor /= Math.pow(denominatorFactor, power);
}
if (denominatorUnit.equals("l") || denominatorUnit.equals("L")) {
normalizationFactor *= 1000;
}
assert mSIPrefixes.get("kilo") != null : "kilo seems not to be in the table !";
double normalizedValue = (normalizationFactor * value) / mSIPrefixes.get("kilo");
return new ValueUnitWrapper(normalizedValue, MASS_NORMALIZED_UNIT);
} else {
throw new UnknownUnitException(unit);
}
} | java | private ValueUnitWrapper normalizeMassUnit(final double value, final String unit)
throws UnknownUnitException {
Matcher matcher = mMassUnitPatter.matcher(unit);
if (matcher.find()) {
double normalizationFactor = 1.0;
String numeratorSIPrefix = matcher.group(1);
Double numeratorFactor = getSIFactor(numeratorSIPrefix);
if (numeratorFactor != null) {
normalizationFactor *= numeratorFactor;
}
String denominatorSIPrefix = matcher.group(3);
String denominatorUnit = matcher.group(4);
Double denominatorFactor = getSIFactor(denominatorSIPrefix);
if (denominatorFactor != null) {
int power = (denominatorUnit.endsWith("3")) ? 3 : 1;
normalizationFactor /= Math.pow(denominatorFactor, power);
}
if (denominatorUnit.equals("l") || denominatorUnit.equals("L")) {
normalizationFactor *= 1000;
}
assert mSIPrefixes.get("kilo") != null : "kilo seems not to be in the table !";
double normalizedValue = (normalizationFactor * value) / mSIPrefixes.get("kilo");
return new ValueUnitWrapper(normalizedValue, MASS_NORMALIZED_UNIT);
} else {
throw new UnknownUnitException(unit);
}
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_protein_concentrations/src/main/java/ch/epfl/bbp/nlp/ie/proteinconc/normalizer/ConcentrationNormalizer.java#L83-L115 |
140,689 | BlueBrain/bluima | modules/bluima_protein_concentrations/src/main/java/ch/epfl/bbp/nlp/ie/proteinconc/normalizer/ConcentrationNormalizer.java | ConcentrationNormalizer.normalizeMolarUnit | private ValueUnitWrapper normalizeMolarUnit(final double value, final String unit)
throws UnknownUnitException {
Matcher matcher = mMolarUnitPattern.matcher(unit);
if (matcher.find()) {
String siPrefix = matcher.group(1);
Double convFactor = getSIFactor(siPrefix);
if (convFactor == null) {
throw new UnknownUnitException(unit);
} else {
double normalizedValue = convFactor * value;
return new ValueUnitWrapper(normalizedValue, MOLAR_NORMALIZED_UNIT);
}
} else {
throw new UnknownUnitException(unit);
}
} | java | private ValueUnitWrapper normalizeMolarUnit(final double value, final String unit)
throws UnknownUnitException {
Matcher matcher = mMolarUnitPattern.matcher(unit);
if (matcher.find()) {
String siPrefix = matcher.group(1);
Double convFactor = getSIFactor(siPrefix);
if (convFactor == null) {
throw new UnknownUnitException(unit);
} else {
double normalizedValue = convFactor * value;
return new ValueUnitWrapper(normalizedValue, MOLAR_NORMALIZED_UNIT);
}
} else {
throw new UnknownUnitException(unit);
}
} | [
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140,690 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/FeatureTokens.java | FeatureTokens.getTokens | public StringArray getTokens() {
if (FeatureTokens_Type.featOkTst && ((FeatureTokens_Type)jcasType).casFeat_tokens == null)
jcasType.jcas.throwFeatMissing("tokens", "ch.epfl.bbp.uima.types.FeatureTokens");
return (StringArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((FeatureTokens_Type)jcasType).casFeatCode_tokens)));} | java | public StringArray getTokens() {
if (FeatureTokens_Type.featOkTst && ((FeatureTokens_Type)jcasType).casFeat_tokens == null)
jcasType.jcas.throwFeatMissing("tokens", "ch.epfl.bbp.uima.types.FeatureTokens");
return (StringArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((FeatureTokens_Type)jcasType).casFeatCode_tokens)));} | [
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] | getter for tokens - gets
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/FeatureTokens.java#L88-L91 |
140,691 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/FeatureTokens.java | FeatureTokens.setTokens | public void setTokens(StringArray v) {
if (FeatureTokens_Type.featOkTst && ((FeatureTokens_Type)jcasType).casFeat_tokens == null)
jcasType.jcas.throwFeatMissing("tokens", "ch.epfl.bbp.uima.types.FeatureTokens");
jcasType.ll_cas.ll_setRefValue(addr, ((FeatureTokens_Type)jcasType).casFeatCode_tokens, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setTokens(StringArray v) {
if (FeatureTokens_Type.featOkTst && ((FeatureTokens_Type)jcasType).casFeat_tokens == null)
jcasType.jcas.throwFeatMissing("tokens", "ch.epfl.bbp.uima.types.FeatureTokens");
jcasType.ll_cas.ll_setRefValue(addr, ((FeatureTokens_Type)jcasType).casFeatCode_tokens, jcasType.ll_cas.ll_getFSRef(v));} | [
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] | setter for tokens - sets
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@param v value to set into the feature | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/FeatureTokens.java#L97-L100 |
140,692 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/FeatureTokens.java | FeatureTokens.getTokens | public String getTokens(int i) {
if (FeatureTokens_Type.featOkTst && ((FeatureTokens_Type)jcasType).casFeat_tokens == null)
jcasType.jcas.throwFeatMissing("tokens", "ch.epfl.bbp.uima.types.FeatureTokens");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((FeatureTokens_Type)jcasType).casFeatCode_tokens), i);
return jcasType.ll_cas.ll_getStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((FeatureTokens_Type)jcasType).casFeatCode_tokens), i);} | java | public String getTokens(int i) {
if (FeatureTokens_Type.featOkTst && ((FeatureTokens_Type)jcasType).casFeat_tokens == null)
jcasType.jcas.throwFeatMissing("tokens", "ch.epfl.bbp.uima.types.FeatureTokens");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((FeatureTokens_Type)jcasType).casFeatCode_tokens), i);
return jcasType.ll_cas.ll_getStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((FeatureTokens_Type)jcasType).casFeatCode_tokens), i);} | [
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] | indexed getter for tokens - gets an indexed value -
@generated
@param i index in the array to get
@return value of the element at index i | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/FeatureTokens.java#L107-L111 |
140,693 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/FeatureTokens.java | FeatureTokens.setTokens | public void setTokens(int i, String v) {
if (FeatureTokens_Type.featOkTst && ((FeatureTokens_Type)jcasType).casFeat_tokens == null)
jcasType.jcas.throwFeatMissing("tokens", "ch.epfl.bbp.uima.types.FeatureTokens");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((FeatureTokens_Type)jcasType).casFeatCode_tokens), i);
jcasType.ll_cas.ll_setStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((FeatureTokens_Type)jcasType).casFeatCode_tokens), i, v);} | java | public void setTokens(int i, String v) {
if (FeatureTokens_Type.featOkTst && ((FeatureTokens_Type)jcasType).casFeat_tokens == null)
jcasType.jcas.throwFeatMissing("tokens", "ch.epfl.bbp.uima.types.FeatureTokens");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((FeatureTokens_Type)jcasType).casFeatCode_tokens), i);
jcasType.ll_cas.ll_setStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((FeatureTokens_Type)jcasType).casFeatCode_tokens), i, v);} | [
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] | indexed setter for tokens - sets an indexed value -
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@param i index in the array to set
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/FeatureTokens.java#L118-L122 |
140,694 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/org/apache/uima/conceptMapper/DictTerm.java | DictTerm.getDictCanon | public String getDictCanon() {
if (DictTerm_Type.featOkTst && ((DictTerm_Type)jcasType).casFeat_DictCanon == null)
jcasType.jcas.throwFeatMissing("DictCanon", "org.apache.uima.conceptMapper.DictTerm");
return jcasType.ll_cas.ll_getStringValue(addr, ((DictTerm_Type)jcasType).casFeatCode_DictCanon);} | java | public String getDictCanon() {
if (DictTerm_Type.featOkTst && ((DictTerm_Type)jcasType).casFeat_DictCanon == null)
jcasType.jcas.throwFeatMissing("DictCanon", "org.apache.uima.conceptMapper.DictTerm");
return jcasType.ll_cas.ll_getStringValue(addr, ((DictTerm_Type)jcasType).casFeatCode_DictCanon);} | [
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] | getter for DictCanon - gets canonical form
@generated
@return value of the feature | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/org/apache/uima/conceptMapper/DictTerm.java#L88-L91 |
140,695 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/org/apache/uima/conceptMapper/DictTerm.java | DictTerm.setDictCanon | public void setDictCanon(String v) {
if (DictTerm_Type.featOkTst && ((DictTerm_Type)jcasType).casFeat_DictCanon == null)
jcasType.jcas.throwFeatMissing("DictCanon", "org.apache.uima.conceptMapper.DictTerm");
jcasType.ll_cas.ll_setStringValue(addr, ((DictTerm_Type)jcasType).casFeatCode_DictCanon, v);} | java | public void setDictCanon(String v) {
if (DictTerm_Type.featOkTst && ((DictTerm_Type)jcasType).casFeat_DictCanon == null)
jcasType.jcas.throwFeatMissing("DictCanon", "org.apache.uima.conceptMapper.DictTerm");
jcasType.ll_cas.ll_setStringValue(addr, ((DictTerm_Type)jcasType).casFeatCode_DictCanon, 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/conceptMapper/DictTerm.java#L97-L100 |
140,696 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/org/apache/uima/conceptMapper/DictTerm.java | DictTerm.setMatchedTokens | public void setMatchedTokens(FSArray v) {
if (DictTerm_Type.featOkTst && ((DictTerm_Type)jcasType).casFeat_matchedTokens == null)
jcasType.jcas.throwFeatMissing("matchedTokens", "org.apache.uima.conceptMapper.DictTerm");
jcasType.ll_cas.ll_setRefValue(addr, ((DictTerm_Type)jcasType).casFeatCode_matchedTokens, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setMatchedTokens(FSArray v) {
if (DictTerm_Type.featOkTst && ((DictTerm_Type)jcasType).casFeat_matchedTokens == null)
jcasType.jcas.throwFeatMissing("matchedTokens", "org.apache.uima.conceptMapper.DictTerm");
jcasType.ll_cas.ll_setRefValue(addr, ((DictTerm_Type)jcasType).casFeatCode_matchedTokens, jcasType.ll_cas.ll_getFSRef(v));} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/org/apache/uima/conceptMapper/DictTerm.java#L163-L166 |
140,697 | BlueBrain/bluima | modules/bluima_typesystem/src/main/java/org/apache/uima/conceptMapper/DictTerm.java | DictTerm.getMatchedTokens | public TOP getMatchedTokens(int i) {
if (DictTerm_Type.featOkTst && ((DictTerm_Type)jcasType).casFeat_matchedTokens == null)
jcasType.jcas.throwFeatMissing("matchedTokens", "org.apache.uima.conceptMapper.DictTerm");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((DictTerm_Type)jcasType).casFeatCode_matchedTokens), i);
return (TOP)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((DictTerm_Type)jcasType).casFeatCode_matchedTokens), i)));} | java | public TOP getMatchedTokens(int i) {
if (DictTerm_Type.featOkTst && ((DictTerm_Type)jcasType).casFeat_matchedTokens == null)
jcasType.jcas.throwFeatMissing("matchedTokens", "org.apache.uima.conceptMapper.DictTerm");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((DictTerm_Type)jcasType).casFeatCode_matchedTokens), i);
return (TOP)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((DictTerm_Type)jcasType).casFeatCode_matchedTokens), i)));} | [
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@generated
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@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/org/apache/uima/conceptMapper/DictTerm.java#L173-L177 |
140,698 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/tools/util/CountedNumberedSet.java | CountedNumberedSet.setCount | public void setCount(Object o,int c) {
int[] nums = (int[]) cset.get(o);
if (nums != null) {
nums[0] = c;
}
else {
cset.put(o,new int[]{c,1});
}
} | java | public void setCount(Object o,int c) {
int[] nums = (int[]) cset.get(o);
if (nums != null) {
nums[0] = c;
}
else {
cset.put(o,new int[]{c,1});
}
} | [
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140,699 | BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/maxent/io/GISModelReader.java | GISModelReader.getParameters | protected Context[] getParameters (int[][] outcomePatterns) throws java.io.IOException {
Context[] params = new Context[NUM_PREDS];
int pid=0;
for (int i=0; i<outcomePatterns.length; i++) {
//construct outcome pattern
int[] outcomePattern = new int[outcomePatterns[i].length-1];
for (int k=1; k<outcomePatterns[i].length; k++) {
outcomePattern[k-1] = outcomePatterns[i][k];
}
//populate parameters for each context which uses this outcome pattern.
for (int j=0; j<outcomePatterns[i][0]; j++) {
double[] contextParameters = new double[outcomePatterns[i].length-1];
for (int k=1; k<outcomePatterns[i].length; k++) {
contextParameters[k-1] = readDouble();
}
params[pid] = new Context(outcomePattern,contextParameters);
pid++;
}
}
return params;
} | java | protected Context[] getParameters (int[][] outcomePatterns) throws java.io.IOException {
Context[] params = new Context[NUM_PREDS];
int pid=0;
for (int i=0; i<outcomePatterns.length; i++) {
//construct outcome pattern
int[] outcomePattern = new int[outcomePatterns[i].length-1];
for (int k=1; k<outcomePatterns[i].length; k++) {
outcomePattern[k-1] = outcomePatterns[i][k];
}
//populate parameters for each context which uses this outcome pattern.
for (int j=0; j<outcomePatterns[i][0]; j++) {
double[] contextParameters = new double[outcomePatterns[i].length-1];
for (int k=1; k<outcomePatterns[i].length; k++) {
contextParameters[k-1] = readDouble();
}
params[pid] = new Context(outcomePattern,contextParameters);
pid++;
}
}
return params;
} | [
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@param outcomePatterns The outcomes patterns for the model. The first index refers to which
outcome pattern (a set of outcomes that occurs with a context) is being specified. The
second index specifies the number of contexts which use this pattern at index 0, and the
index of each outcomes which make up this pattern in indicies 1-n.
@return An array of context objects.
@throws java.io.IOException when the model file does not match the outcome patterns or can not be read. | [
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