repo stringlengths 7 58 | path stringlengths 12 218 | func_name stringlengths 3 140 | original_string stringlengths 73 34.1k | language stringclasses 1
value | code stringlengths 73 34.1k | code_tokens list | docstring stringlengths 3 16k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 105 339 | partition stringclasses 1
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Topic.java | Topic.getScores | public double getScores(int i) {
if (Topic_Type.featOkTst && ((Topic_Type)jcasType).casFeat_scores == null)
jcasType.jcas.throwFeatMissing("scores", "ch.epfl.bbp.uima.types.Topic");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Topic_Type)jcasType).casFeatCode_scores), i);
return jcasType.ll_cas.ll_getDoubleArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((Topic_Type)jcasType).casFeatCode_scores), i);} | java | public double getScores(int i) {
if (Topic_Type.featOkTst && ((Topic_Type)jcasType).casFeat_scores == null)
jcasType.jcas.throwFeatMissing("scores", "ch.epfl.bbp.uima.types.Topic");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Topic_Type)jcasType).casFeatCode_scores), i);
return jcasType.ll_cas.ll_getDoubleArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((Topic_Type)jcasType).casFeatCode_scores), i);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Topic.java | Topic.setScores | public void setScores(int i, double v) {
if (Topic_Type.featOkTst && ((Topic_Type)jcasType).casFeat_scores == null)
jcasType.jcas.throwFeatMissing("scores", "ch.epfl.bbp.uima.types.Topic");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Topic_Type)jcasType).casFeatCode_scores), i);
jcasType.ll_cas.ll_setDoubleArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((Topic_Type)jcasType).casFeatCode_scores), i, v);} | java | public void setScores(int i, double v) {
if (Topic_Type.featOkTst && ((Topic_Type)jcasType).casFeat_scores == null)
jcasType.jcas.throwFeatMissing("scores", "ch.epfl.bbp.uima.types.Topic");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Topic_Type)jcasType).casFeatCode_scores), i);
jcasType.ll_cas.ll_setDoubleArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((Topic_Type)jcasType).casFeatCode_scores), i, v);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Topic.java | Topic.getMostLikelyTopic | public int getMostLikelyTopic() {
if (Topic_Type.featOkTst && ((Topic_Type)jcasType).casFeat_mostLikelyTopic == null)
jcasType.jcas.throwFeatMissing("mostLikelyTopic", "ch.epfl.bbp.uima.types.Topic");
return jcasType.ll_cas.ll_getIntValue(addr, ((Topic_Type)jcasType).casFeatCode_mostLikelyTopic);} | java | public int getMostLikelyTopic() {
if (Topic_Type.featOkTst && ((Topic_Type)jcasType).casFeat_mostLikelyTopic == null)
jcasType.jcas.throwFeatMissing("mostLikelyTopic", "ch.epfl.bbp.uima.types.Topic");
return jcasType.ll_cas.ll_getIntValue(addr, ((Topic_Type)jcasType).casFeatCode_mostLikelyTopic);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/ch/epfl/bbp/uima/types/Topic.java | Topic.setMostLikelyTopic | public void setMostLikelyTopic(int v) {
if (Topic_Type.featOkTst && ((Topic_Type)jcasType).casFeat_mostLikelyTopic == null)
jcasType.jcas.throwFeatMissing("mostLikelyTopic", "ch.epfl.bbp.uima.types.Topic");
jcasType.ll_cas.ll_setIntValue(addr, ((Topic_Type)jcasType).casFeatCode_mostLikelyTopic, v);} | java | public void setMostLikelyTopic(int v) {
if (Topic_Type.featOkTst && ((Topic_Type)jcasType).casFeat_mostLikelyTopic == null)
jcasType.jcas.throwFeatMissing("mostLikelyTopic", "ch.epfl.bbp.uima.types.Topic");
jcasType.ll_cas.ll_setIntValue(addr, ((Topic_Type)jcasType).casFeatCode_mostLikelyTopic, v);} | [
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/abbvGapsHmm/AbbvGapsHMMEvaluator.java | AbbvGapsHMMEvaluator.updateOutgoingEdgesStateM | protected void updateOutgoingEdgesStateM(
int currS, int currL,
int prevS, int prevL,
Emissions emission
){
updateOutgoingEdges(currS, currL, States.M, prevS, prevL, States.DL, Transitions.t_DL_to_M, emission);
updateOutgoingEdges(currS, currL, States.M, prevS, prevL, States.M, Transitions.t_M_in, emission);
updateOutgoingEdges(currS, currL, States.M, prevS, prevL, States.D, Transitions.t_D_to_M, emission);
updateOutgoingEdges(currS, currL, States.M, prevS, prevL, States.S, Transitions.t_S_to_M, emission);
} | java | protected void updateOutgoingEdgesStateM(
int currS, int currL,
int prevS, int prevL,
Emissions emission
){
updateOutgoingEdges(currS, currL, States.M, prevS, prevL, States.DL, Transitions.t_DL_to_M, emission);
updateOutgoingEdges(currS, currL, States.M, prevS, prevL, States.M, Transitions.t_M_in, emission);
updateOutgoingEdges(currS, currL, States.M, prevS, prevL, States.D, Transitions.t_D_to_M, emission);
updateOutgoingEdges(currS, currL, States.M, prevS, prevL, States.S, Transitions.t_S_to_M, emission);
} | [
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/abbvGapsHmm/AbbvGapsHMMEvaluator.java | AbbvGapsHMMEvaluator.updateOutgoingEdgesStateD | protected void updateOutgoingEdgesStateD(
int currS, int currL,
int prevS, int prevL,
Emissions emission
){
updateOutgoingEdges(currS, currL, States.D, prevS, prevL, States.D, Transitions.t_D_in, emission);
updateOutgoingEdges(currS, currL, States.D, prevS, prevL, States.M, Transitions.t_M_to_D, emission);
} | java | protected void updateOutgoingEdgesStateD(
int currS, int currL,
int prevS, int prevL,
Emissions emission
){
updateOutgoingEdges(currS, currL, States.D, prevS, prevL, States.D, Transitions.t_D_in, emission);
updateOutgoingEdges(currS, currL, States.D, prevS, prevL, States.M, Transitions.t_M_to_D, emission);
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/abbvGapsHmm/AbbvGapsHMMEvaluator.java | AbbvGapsHMMEvaluator.updateOutgoingEdgesStateDL | protected void updateOutgoingEdgesStateDL(
int currS, int currL,
int prevS, int prevL,
Emissions emission
){
updateOutgoingEdges(currS, currL, States.DL, prevS, prevL, States.DL, Transitions.t_DL_in, emission);
updateOutgoingEdges(currS, currL, States.DL, prevS, prevL, States.S, Transitions.t_S_to_DL, emission);
} | java | protected void updateOutgoingEdgesStateDL(
int currS, int currL,
int prevS, int prevL,
Emissions emission
){
updateOutgoingEdges(currS, currL, States.DL, prevS, prevL, States.DL, Transitions.t_DL_in, emission);
updateOutgoingEdges(currS, currL, States.DL, prevS, prevL, States.S, Transitions.t_S_to_DL, emission);
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/abbvGapsHmm/AbbvGapsHMMEvaluator.java | AbbvGapsHMMEvaluator.updateOutgoingEdgesStateEND | protected void updateOutgoingEdgesStateEND(
int currS, int currL,
int prevS, int prevL,
Emissions emission
){
updateOutgoingEdges(currS, currL, States.END, prevS, prevL, States.D, Transitions.t_D_to_END, emission);
updateOutgoingEdges(currS, currL, States.END, prevS, prevL, States.M, Transitions.t_M_to_END, emission);
} | java | protected void updateOutgoingEdgesStateEND(
int currS, int currL,
int prevS, int prevL,
Emissions emission
){
updateOutgoingEdges(currS, currL, States.END, prevS, prevL, States.D, Transitions.t_D_to_END, emission);
updateOutgoingEdges(currS, currL, States.END, prevS, prevL, States.M, Transitions.t_M_to_END, emission);
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/Clause.java | Clause.getRule | public String getRule() {
if (Clause_Type.featOkTst && ((Clause_Type)jcasType).casFeat_rule == null)
jcasType.jcas.throwFeatMissing("rule", "com.digitalpebble.rasp.Clause");
return jcasType.ll_cas.ll_getStringValue(addr, ((Clause_Type)jcasType).casFeatCode_rule);} | java | public String getRule() {
if (Clause_Type.featOkTst && ((Clause_Type)jcasType).casFeat_rule == null)
jcasType.jcas.throwFeatMissing("rule", "com.digitalpebble.rasp.Clause");
return jcasType.ll_cas.ll_getStringValue(addr, ((Clause_Type)jcasType).casFeatCode_rule);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/Clause.java | Clause.setRule | public void setRule(String v) {
if (Clause_Type.featOkTst && ((Clause_Type)jcasType).casFeat_rule == null)
jcasType.jcas.throwFeatMissing("rule", "com.digitalpebble.rasp.Clause");
jcasType.ll_cas.ll_setStringValue(addr, ((Clause_Type)jcasType).casFeatCode_rule, v);} | java | public void setRule(String v) {
if (Clause_Type.featOkTst && ((Clause_Type)jcasType).casFeat_rule == null)
jcasType.jcas.throwFeatMissing("rule", "com.digitalpebble.rasp.Clause");
jcasType.ll_cas.ll_setStringValue(addr, ((Clause_Type)jcasType).casFeatCode_rule, v);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/Clause.java | Clause.getSubclauses | public FSArray getSubclauses() {
if (Clause_Type.featOkTst && ((Clause_Type)jcasType).casFeat_subclauses == null)
jcasType.jcas.throwFeatMissing("subclauses", "com.digitalpebble.rasp.Clause");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((Clause_Type)jcasType).casFeatCode_subclauses)));} | java | public FSArray getSubclauses() {
if (Clause_Type.featOkTst && ((Clause_Type)jcasType).casFeat_subclauses == null)
jcasType.jcas.throwFeatMissing("subclauses", "com.digitalpebble.rasp.Clause");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((Clause_Type)jcasType).casFeatCode_subclauses)));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/Clause.java | Clause.setSubclauses | public void setSubclauses(FSArray v) {
if (Clause_Type.featOkTst && ((Clause_Type)jcasType).casFeat_subclauses == null)
jcasType.jcas.throwFeatMissing("subclauses", "com.digitalpebble.rasp.Clause");
jcasType.ll_cas.ll_setRefValue(addr, ((Clause_Type)jcasType).casFeatCode_subclauses, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setSubclauses(FSArray v) {
if (Clause_Type.featOkTst && ((Clause_Type)jcasType).casFeat_subclauses == null)
jcasType.jcas.throwFeatMissing("subclauses", "com.digitalpebble.rasp.Clause");
jcasType.ll_cas.ll_setRefValue(addr, ((Clause_Type)jcasType).casFeatCode_subclauses, jcasType.ll_cas.ll_getFSRef(v));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/Clause.java | Clause.getSubclauses | public Annotation getSubclauses(int i) {
if (Clause_Type.featOkTst && ((Clause_Type)jcasType).casFeat_subclauses == null)
jcasType.jcas.throwFeatMissing("subclauses", "com.digitalpebble.rasp.Clause");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Clause_Type)jcasType).casFeatCode_subclauses), i);
return (Annotation)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((Clause_Type)jcasType).casFeatCode_subclauses), i)));} | java | public Annotation getSubclauses(int i) {
if (Clause_Type.featOkTst && ((Clause_Type)jcasType).casFeat_subclauses == null)
jcasType.jcas.throwFeatMissing("subclauses", "com.digitalpebble.rasp.Clause");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Clause_Type)jcasType).casFeatCode_subclauses), i);
return (Annotation)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((Clause_Type)jcasType).casFeatCode_subclauses), i)));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/Clause.java | Clause.setSubclauses | public void setSubclauses(int i, Annotation v) {
if (Clause_Type.featOkTst && ((Clause_Type)jcasType).casFeat_subclauses == null)
jcasType.jcas.throwFeatMissing("subclauses", "com.digitalpebble.rasp.Clause");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Clause_Type)jcasType).casFeatCode_subclauses), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((Clause_Type)jcasType).casFeatCode_subclauses), i, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setSubclauses(int i, Annotation v) {
if (Clause_Type.featOkTst && ((Clause_Type)jcasType).casFeat_subclauses == null)
jcasType.jcas.throwFeatMissing("subclauses", "com.digitalpebble.rasp.Clause");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((Clause_Type)jcasType).casFeatCode_subclauses), i);
jcasType.ll_cas.ll_setRefArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((Clause_Type)jcasType).casFeatCode_subclauses), i, jcasType.ll_cas.ll_getFSRef(v));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/EventTrigger.java | EventTrigger.getProbability | public String getProbability() {
if (EventTrigger_Type.featOkTst && ((EventTrigger_Type)jcasType).casFeat_probability == null)
jcasType.jcas.throwFeatMissing("probability", "de.julielab.jules.types.EventTrigger");
return jcasType.ll_cas.ll_getStringValue(addr, ((EventTrigger_Type)jcasType).casFeatCode_probability);} | java | public String getProbability() {
if (EventTrigger_Type.featOkTst && ((EventTrigger_Type)jcasType).casFeat_probability == null)
jcasType.jcas.throwFeatMissing("probability", "de.julielab.jules.types.EventTrigger");
return jcasType.ll_cas.ll_getStringValue(addr, ((EventTrigger_Type)jcasType).casFeatCode_probability);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/EventTrigger.java | EventTrigger.setProbability | public void setProbability(String v) {
if (EventTrigger_Type.featOkTst && ((EventTrigger_Type)jcasType).casFeat_probability == null)
jcasType.jcas.throwFeatMissing("probability", "de.julielab.jules.types.EventTrigger");
jcasType.ll_cas.ll_setStringValue(addr, ((EventTrigger_Type)jcasType).casFeatCode_probability, v);} | java | public void setProbability(String v) {
if (EventTrigger_Type.featOkTst && ((EventTrigger_Type)jcasType).casFeat_probability == null)
jcasType.jcas.throwFeatMissing("probability", "de.julielab.jules.types.EventTrigger");
jcasType.ll_cas.ll_setStringValue(addr, ((EventTrigger_Type)jcasType).casFeatCode_probability, v);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/EventTrigger.java | EventTrigger.getSpecifity | public String getSpecifity() {
if (EventTrigger_Type.featOkTst && ((EventTrigger_Type)jcasType).casFeat_specifity == null)
jcasType.jcas.throwFeatMissing("specifity", "de.julielab.jules.types.EventTrigger");
return jcasType.ll_cas.ll_getStringValue(addr, ((EventTrigger_Type)jcasType).casFeatCode_specifity);} | java | public String getSpecifity() {
if (EventTrigger_Type.featOkTst && ((EventTrigger_Type)jcasType).casFeat_specifity == null)
jcasType.jcas.throwFeatMissing("specifity", "de.julielab.jules.types.EventTrigger");
return jcasType.ll_cas.ll_getStringValue(addr, ((EventTrigger_Type)jcasType).casFeatCode_specifity);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/EventTrigger.java | EventTrigger.setSpecifity | public void setSpecifity(String v) {
if (EventTrigger_Type.featOkTst && ((EventTrigger_Type)jcasType).casFeat_specifity == null)
jcasType.jcas.throwFeatMissing("specifity", "de.julielab.jules.types.EventTrigger");
jcasType.ll_cas.ll_setStringValue(addr, ((EventTrigger_Type)jcasType).casFeatCode_specifity, v);} | java | public void setSpecifity(String v) {
if (EventTrigger_Type.featOkTst && ((EventTrigger_Type)jcasType).casFeat_specifity == null)
jcasType.jcas.throwFeatMissing("specifity", "de.julielab.jules.types.EventTrigger");
jcasType.ll_cas.ll_setStringValue(addr, ((EventTrigger_Type)jcasType).casFeatCode_specifity, v);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/EventTrigger.java | EventTrigger.getImportance | public String getImportance() {
if (EventTrigger_Type.featOkTst && ((EventTrigger_Type)jcasType).casFeat_importance == null)
jcasType.jcas.throwFeatMissing("importance", "de.julielab.jules.types.EventTrigger");
return jcasType.ll_cas.ll_getStringValue(addr, ((EventTrigger_Type)jcasType).casFeatCode_importance);} | java | public String getImportance() {
if (EventTrigger_Type.featOkTst && ((EventTrigger_Type)jcasType).casFeat_importance == null)
jcasType.jcas.throwFeatMissing("importance", "de.julielab.jules.types.EventTrigger");
return jcasType.ll_cas.ll_getStringValue(addr, ((EventTrigger_Type)jcasType).casFeatCode_importance);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/EventTrigger.java | EventTrigger.setImportance | public void setImportance(String v) {
if (EventTrigger_Type.featOkTst && ((EventTrigger_Type)jcasType).casFeat_importance == null)
jcasType.jcas.throwFeatMissing("importance", "de.julielab.jules.types.EventTrigger");
jcasType.ll_cas.ll_setStringValue(addr, ((EventTrigger_Type)jcasType).casFeatCode_importance, v);} | java | public void setImportance(String v) {
if (EventTrigger_Type.featOkTst && ((EventTrigger_Type)jcasType).casFeat_importance == null)
jcasType.jcas.throwFeatMissing("importance", "de.julielab.jules.types.EventTrigger");
jcasType.ll_cas.ll_setStringValue(addr, ((EventTrigger_Type)jcasType).casFeatCode_importance, v);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/muc7/MUC7Header.java | MUC7Header.getStoryID | public String getStoryID() {
if (MUC7Header_Type.featOkTst && ((MUC7Header_Type)jcasType).casFeat_storyID == null)
jcasType.jcas.throwFeatMissing("storyID", "de.julielab.jules.types.muc7.MUC7Header");
return jcasType.ll_cas.ll_getStringValue(addr, ((MUC7Header_Type)jcasType).casFeatCode_storyID);} | java | public String getStoryID() {
if (MUC7Header_Type.featOkTst && ((MUC7Header_Type)jcasType).casFeat_storyID == null)
jcasType.jcas.throwFeatMissing("storyID", "de.julielab.jules.types.muc7.MUC7Header");
return jcasType.ll_cas.ll_getStringValue(addr, ((MUC7Header_Type)jcasType).casFeatCode_storyID);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/muc7/MUC7Header.java | MUC7Header.setStoryID | public void setStoryID(String v) {
if (MUC7Header_Type.featOkTst && ((MUC7Header_Type)jcasType).casFeat_storyID == null)
jcasType.jcas.throwFeatMissing("storyID", "de.julielab.jules.types.muc7.MUC7Header");
jcasType.ll_cas.ll_setStringValue(addr, ((MUC7Header_Type)jcasType).casFeatCode_storyID, v);} | java | public void setStoryID(String v) {
if (MUC7Header_Type.featOkTst && ((MUC7Header_Type)jcasType).casFeat_storyID == null)
jcasType.jcas.throwFeatMissing("storyID", "de.julielab.jules.types.muc7.MUC7Header");
jcasType.ll_cas.ll_setStringValue(addr, ((MUC7Header_Type)jcasType).casFeatCode_storyID, v);} | [
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/Level2.java | Level2.explainScore | public String explainScore(StringWrapper s, StringWrapper t)
{
StringBuffer buf = new StringBuffer();
BagOfTokens sBag = asBagOfTokens(s);
BagOfTokens tBag = asBagOfTokens(t);
double sumOverI = 0;
for (Iterator i = sBag.tokenIterator(); i.hasNext(); ) {
Token tokenI = (Token)i.next();
buf.append("token="+tokenI);
double maxOverJ = -Double.MAX_VALUE;
Token closestToI = null;
for (Iterator j = tBag.tokenIterator(); j.hasNext(); ) {
Token tokenJ = (Token)j.next();
double scoreItoJ = tokenDistance.score( tokenI.getValue(), tokenJ.getValue() );
buf.append(" dist("+tokenJ.getValue()+")="+scoreItoJ);
if (scoreItoJ >= maxOverJ) {
maxOverJ = scoreItoJ;
closestToI = tokenJ;
}
}
sumOverI += maxOverJ;
buf.append(" match="+closestToI+" score="+maxOverJ+"\n");
}
buf.append("total: "+sumOverI+"/"+sBag.size()+" = "+score(s,t)+"\n");
return buf.toString();
} | java | public String explainScore(StringWrapper s, StringWrapper t)
{
StringBuffer buf = new StringBuffer();
BagOfTokens sBag = asBagOfTokens(s);
BagOfTokens tBag = asBagOfTokens(t);
double sumOverI = 0;
for (Iterator i = sBag.tokenIterator(); i.hasNext(); ) {
Token tokenI = (Token)i.next();
buf.append("token="+tokenI);
double maxOverJ = -Double.MAX_VALUE;
Token closestToI = null;
for (Iterator j = tBag.tokenIterator(); j.hasNext(); ) {
Token tokenJ = (Token)j.next();
double scoreItoJ = tokenDistance.score( tokenI.getValue(), tokenJ.getValue() );
buf.append(" dist("+tokenJ.getValue()+")="+scoreItoJ);
if (scoreItoJ >= maxOverJ) {
maxOverJ = scoreItoJ;
closestToI = tokenJ;
}
}
sumOverI += maxOverJ;
buf.append(" match="+closestToI+" score="+maxOverJ+"\n");
}
buf.append("total: "+sumOverI+"/"+sBag.size()+" = "+score(s,t)+"\n");
return buf.toString();
} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_abbreviations/src/main/java/com/wcohen/ss/Level2.java#L49-L74 | train |
BlueBrain/bluima | modules/bluima_opennlp/src/main/java/ch/epfl/bbp/shaded/opennlp/maxent/io/OldFormatGISModelReader.java | OldFormatGISModelReader.main | public static void main (String[] args) throws IOException {
if (args.length < 1) {
System.out.println("Usage: java opennlp.maxent.io.OldFormatGISModelReader model_name_prefix (new_model_name)");
System.exit(0);
}
int nameIndex = 0;
String infilePrefix = args[nameIndex];
String outfile;
if (args.length > nameIndex)
outfile = args[nameIndex+1];
else
outfile = infilePrefix + ".bin.gz";
GISModelReader reader = new OldFormatGISModelReader(infilePrefix);
new SuffixSensitiveGISModelWriter(reader.getModel(),
new File(outfile)).persist();
} | java | public static void main (String[] args) throws IOException {
if (args.length < 1) {
System.out.println("Usage: java opennlp.maxent.io.OldFormatGISModelReader model_name_prefix (new_model_name)");
System.exit(0);
}
int nameIndex = 0;
String infilePrefix = args[nameIndex];
String outfile;
if (args.length > nameIndex)
outfile = args[nameIndex+1];
else
outfile = infilePrefix + ".bin.gz";
GISModelReader reader = new OldFormatGISModelReader(infilePrefix);
new SuffixSensitiveGISModelWriter(reader.getModel(),
new File(outfile)).persist();
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/lookup/SoftTFIDFDictionary.java | SoftTFIDFDictionary.put | public void put(String string,Object value)
{
if (frozen) throw new IllegalStateException("can't add new values to a frozen dictionary");
Set valset = (Set)valueMap.get(string);
if (valset==null) valueMap.put(string, (valset=new HashSet()));
valset.add( value );
} | java | public void put(String string,Object value)
{
if (frozen) throw new IllegalStateException("can't add new values to a frozen dictionary");
Set valset = (Set)valueMap.get(string);
if (valset==null) valueMap.put(string, (valset=new HashSet()));
valset.add( value );
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/lookup/SoftTFIDFDictionary.java | SoftTFIDFDictionary.freeze | public void freeze()
{
if (frozen) return;
// train the TFIDF distance on all strings seen
trainDistances();
// now, compute the maxScore of each token, and create an inverted index
if (DEBUG) System.out.println("computing maxScore of "+tokenizer.maxTokenIndex()+" tokens");
invertedIndex = new Set[ tokenizer.maxTokenIndex()+1 ];
maxTFIDFScore = new double[ tokenizer.maxTokenIndex()+1 ];
for (Iterator i=valueMap.keySet().iterator(); i.hasNext(); ) {
String s = (String)i.next();
tfidfDistance.prepare( s );
Token[] tokens = tfidfDistance.getTokens();
for (int j=0; j<tokens.length; j++) {
Token tok = tokens[j];
double w = tfidfDistance.getWeight( tok );
maxTFIDFScore[ tok.getIndex() ] = Math.max( maxTFIDFScore[tok.getIndex()], w );
Set ii = invertedIndex[ tok.getIndex() ];
if (ii==null) ii = invertedIndex[ tok.getIndex() ] = new HashSet();
ii.add( s );
//if (DEBUG) System.out.println("adjust maxscore, invertedIndex for "+tok);
}
}
// find out which tokens are similar to which other tokens
if (DEBUG) System.out.println("computing similar-tokens for "+tokenizer.maxTokenIndex()+" tokens, window="+windowSize);
allTokens = new Token[tokenizer.maxTokenIndex()] ;
numTokens=0;
for (Iterator i=tokenizer.tokenIterator(); i.hasNext(); ) {
Token toki = (Token)i.next();
allTokens[numTokens++] = toki;
}
Arrays.sort(allTokens,LEXICAL_ORDER_FOR_TOKENS);
similarTokens = new Token[tokenizer.maxTokenIndex()+1][];
for (int i=0; i<numTokens; i++) {
Token toki = allTokens[i];
Set likeTokI = findSimilarTokens( toki.getValue(), i );
similarTokens[ toki.getIndex() ] = new Token[ likeTokI.size() ];
int k = 0;
for (Iterator j=likeTokI.iterator(); j.hasNext(); ) {
Token tokj = (Token)j.next();
similarTokens[toki.getIndex()][ k++ ] = tokj;
}
}
frozen = true;
} | java | public void freeze()
{
if (frozen) return;
// train the TFIDF distance on all strings seen
trainDistances();
// now, compute the maxScore of each token, and create an inverted index
if (DEBUG) System.out.println("computing maxScore of "+tokenizer.maxTokenIndex()+" tokens");
invertedIndex = new Set[ tokenizer.maxTokenIndex()+1 ];
maxTFIDFScore = new double[ tokenizer.maxTokenIndex()+1 ];
for (Iterator i=valueMap.keySet().iterator(); i.hasNext(); ) {
String s = (String)i.next();
tfidfDistance.prepare( s );
Token[] tokens = tfidfDistance.getTokens();
for (int j=0; j<tokens.length; j++) {
Token tok = tokens[j];
double w = tfidfDistance.getWeight( tok );
maxTFIDFScore[ tok.getIndex() ] = Math.max( maxTFIDFScore[tok.getIndex()], w );
Set ii = invertedIndex[ tok.getIndex() ];
if (ii==null) ii = invertedIndex[ tok.getIndex() ] = new HashSet();
ii.add( s );
//if (DEBUG) System.out.println("adjust maxscore, invertedIndex for "+tok);
}
}
// find out which tokens are similar to which other tokens
if (DEBUG) System.out.println("computing similar-tokens for "+tokenizer.maxTokenIndex()+" tokens, window="+windowSize);
allTokens = new Token[tokenizer.maxTokenIndex()] ;
numTokens=0;
for (Iterator i=tokenizer.tokenIterator(); i.hasNext(); ) {
Token toki = (Token)i.next();
allTokens[numTokens++] = toki;
}
Arrays.sort(allTokens,LEXICAL_ORDER_FOR_TOKENS);
similarTokens = new Token[tokenizer.maxTokenIndex()+1][];
for (int i=0; i<numTokens; i++) {
Token toki = allTokens[i];
Set likeTokI = findSimilarTokens( toki.getValue(), i );
similarTokens[ toki.getIndex() ] = new Token[ likeTokI.size() ];
int k = 0;
for (Iterator j=likeTokI.iterator(); j.hasNext(); ) {
Token tokj = (Token)j.next();
similarTokens[toki.getIndex()][ k++ ] = tokj;
}
}
frozen = true;
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/lookup/SoftTFIDFDictionary.java | SoftTFIDFDictionary.findSimilarTokens | private Set findSimilarTokens(String s,int i)
{
Set likeTokI = new HashSet();
for (int j=Math.max(0,i-windowSize); j<Math.min(i+windowSize,numTokens); j++) {
if (i!=j) {
Token tokj = allTokens[j];
double d = jaroWinklerDistance.score( s, tokj.getValue() );
if (d>=minTokenSimilarity) likeTokI.add( tokj );
}
}
return likeTokI;
} | java | private Set findSimilarTokens(String s,int i)
{
Set likeTokI = new HashSet();
for (int j=Math.max(0,i-windowSize); j<Math.min(i+windowSize,numTokens); j++) {
if (i!=j) {
Token tokj = allTokens[j];
double d = jaroWinklerDistance.score( s, tokj.getValue() );
if (d>=minTokenSimilarity) likeTokI.add( tokj );
}
}
return likeTokI;
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/lookup/SoftTFIDFDictionary.java | SoftTFIDFDictionary.slowLookup | public int slowLookup(double minScore,String toFind)
{
if (!frozen) freeze();
long start = System.currentTimeMillis();
StringWrapper wa = softTFIDFDistance.prepare( toFind );
result = new ArrayList();
for (Iterator i=valueMap.keySet().iterator(); i.hasNext(); ) {
String found = (String)i.next();
StringWrapper wb = softTFIDFDistance.prepare( found );
double d = softTFIDFDistance.score( wa, wb );
if (d>=minScore) {
Set valset = (Set)valueMap.get(found);
for (Iterator j=valset.iterator(); j.hasNext(); ) {
String valj=(String)j.next();
result.add(new LookupResult(found,valj,d));
}
}
}
Collections.sort( result );
lookupTime = (System.currentTimeMillis()-start) / 1000.0;
return result.size();
} | java | public int slowLookup(double minScore,String toFind)
{
if (!frozen) freeze();
long start = System.currentTimeMillis();
StringWrapper wa = softTFIDFDistance.prepare( toFind );
result = new ArrayList();
for (Iterator i=valueMap.keySet().iterator(); i.hasNext(); ) {
String found = (String)i.next();
StringWrapper wb = softTFIDFDistance.prepare( found );
double d = softTFIDFDistance.score( wa, wb );
if (d>=minScore) {
Set valset = (Set)valueMap.get(found);
for (Iterator j=valset.iterator(); j.hasNext(); ) {
String valj=(String)j.next();
result.add(new LookupResult(found,valj,d));
}
}
}
Collections.sort( result );
lookupTime = (System.currentTimeMillis()-start) / 1000.0;
return result.size();
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/lookup/SoftTFIDFDictionary.java | SoftTFIDFDictionary.storeUpperBound | private void storeUpperBound(Token tok, Token simTok, List usefulTokens, Map upperBoundOnWeight, double sim)
{
double upperBound = tfidfDistance.getWeight(tok)*maxTFIDFScore[simTok.getIndex()]*sim;
if (DEBUG) System.out.println("upper-bounding tok "+simTok+" sim="+sim+" to "+tok+" upperBound "+upperBound);
if (DEBUG) System.out.println("upperBound = "+tfidfDistance.getWeight(tok)+"*"+maxTFIDFScore[simTok.getIndex()]+"*"+sim);
usefulTokens.add( simTok );
upperBoundOnWeight.put( simTok, new Double(upperBound) );
} | java | private void storeUpperBound(Token tok, Token simTok, List usefulTokens, Map upperBoundOnWeight, double sim)
{
double upperBound = tfidfDistance.getWeight(tok)*maxTFIDFScore[simTok.getIndex()]*sim;
if (DEBUG) System.out.println("upper-bounding tok "+simTok+" sim="+sim+" to "+tok+" upperBound "+upperBound);
if (DEBUG) System.out.println("upperBound = "+tfidfDistance.getWeight(tok)+"*"+maxTFIDFScore[simTok.getIndex()]+"*"+sim);
usefulTokens.add( simTok );
upperBoundOnWeight.put( simTok, new Double(upperBound) );
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BlueBrain/bluima | utils/blue_commons/src/main/java/ch/epfl/bbp/io/TextFileWriter.java | TextFileWriter.addLine | public void addLine(String line) {
try {
writer.append(line);
writer.newLine();
} catch (IOException e) {
e.printStackTrace();
}
} | java | public void addLine(String line) {
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BlueBrain/bluima | utils/blue_commons/src/main/java/ch/epfl/bbp/io/TextFileWriter.java | TextFileWriter.addText | public void addText(String text) {
try {
writer.append(text);
} catch (IOException e) {
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} | java | public void addText(String text) {
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/MultiStringDistance.java | MultiStringDistance.multiScore | private double[] multiScore(MultiStringWrapper ms,MultiStringWrapper mt)
{
if (ms.size() != mt.size()) {
throw new IllegalArgumentException("inputs have different numbers of fields");
}
int n = ms.size();
double scores[] = new double[n];
for (int i=0; i<n; i++) {
scores[i] = getDistance(i).score(ms.get(i), mt.get(i));
}
return scores;
} | java | private double[] multiScore(MultiStringWrapper ms,MultiStringWrapper mt)
{
if (ms.size() != mt.size()) {
throw new IllegalArgumentException("inputs have different numbers of fields");
}
int n = ms.size();
double scores[] = new double[n];
for (int i=0; i<n; i++) {
scores[i] = getDistance(i).score(ms.get(i), mt.get(i));
}
return scores;
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/MultiStringDistance.java | MultiStringDistance.score | final public double score(String s, String t) {
return score(prepare(s), prepare(t));
} | java | final public double score(String s, String t) {
return score(prepare(s), prepare(t));
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/MultiStringDistance.java | MultiStringDistance.explainScore | final public String explainScore(String s, String t) {
return explainScore(prepare(s),prepare(t));
} | java | final public String explainScore(String s, String t) {
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/MultiStringDistance.java | MultiStringDistance.prepare | final public StringWrapper prepare(String s) {
MultiStringWrapper ms = new MultiStringWrapper(s,delim);
if (!isLegalMultiStringWrapperSize(ms.size())) {
throw new IllegalArgumentException("string has invalid number of fields");
}
for (int i=0; i<ms.size(); i++) {
ms.set(i, getDistance(i).prepare( ms.get(i).unwrap() ));
}
return ms;
} | java | final public StringWrapper prepare(String s) {
MultiStringWrapper ms = new MultiStringWrapper(s,delim);
if (!isLegalMultiStringWrapperSize(ms.size())) {
throw new IllegalArgumentException("string has invalid number of fields");
}
for (int i=0; i<ms.size(); i++) {
ms.set(i, getDistance(i).prepare( ms.get(i).unwrap() ));
}
return ms;
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/MultiStringDistance.java | MultiStringDistance.doMain | final protected static void doMain(StringDistance d,String[] argv)
{
if (argv.length!=2) {
System.out.println("usage: string1 string2");
} else {
System.out.println(d.explainScore(argv[0],argv[1]));
}
} | java | final protected static void doMain(StringDistance d,String[] argv)
{
if (argv.length!=2) {
System.out.println("usage: string1 string2");
} else {
System.out.println(d.explainScore(argv[0],argv[1]));
}
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/ApproxNeedlemanWunsch.java | ApproxNeedlemanWunsch.getAlignedChar | public int getAlignedChar(int iMinusOne,boolean preferHigherIndices)
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int i = iMinusOne+1;
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double bestScore = -Double.MAX_VALUE;
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double score = mat.get(i,j);
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bestScore = score; bestJ = j;
}
}
// convert back to the usual 0...N-1 Java convention
return bestJ-1;
} | java | public int getAlignedChar(int iMinusOne,boolean preferHigherIndices)
{
// internally to this package, strings are indexed 1...N, so
// we need to convert from the usual 0...N-1 Java convention
int i = iMinusOne+1;
int bestJ = -1;
double bestScore = -Double.MAX_VALUE;
for (int j=mat.getFirstStoredEntryInRow(i); j<=mat.getLastStoredEntryInRow(i); j++) {
if (mat.outOfRange(i,j)) log.error("out of range: "+i+","+j);
double score = mat.get(i,j);
if ((score>bestScore) || (score==bestScore && preferHigherIndices)) {
bestScore = score; bestJ = j;
}
}
// convert back to the usual 0...N-1 Java convention
return bestJ-1;
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Header.java | Header.getCopyright | public String getCopyright() {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Header.java | Header.setCopyright | public void setCopyright(String v) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Header.java | Header.getTruncated | public boolean getTruncated() {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Header.java | Header.setTruncated | public void setTruncated(boolean v) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Header.java | Header.getAuthors | public FSArray getAuthors() {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Header.java | Header.setAuthors | public void setAuthors(FSArray v) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Header.java | Header.getAuthors | public AuthorInfo getAuthors(int i) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Header.java | Header.setAuthors | public void setAuthors(int i, AuthorInfo v) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Header.java | Header.getPubTypeList | public FSArray getPubTypeList() {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Header.java | Header.setPubTypeList | public void setPubTypeList(FSArray v) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Header.java | Header.getPubTypeList | public PubType getPubTypeList(int i) {
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jcasType.jcas.throwFeatMissing("pubTypeList", "de.julielab.jules.types.Header");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Header.java | Header.setPubTypeList | public void setPubTypeList(int i, PubType v) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Header.java | Header.getLanguage | public String getLanguage() {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Header.java | Header.setLanguage | public void setLanguage(String v) {
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jcasType.jcas.throwFeatMissing("language", "de.julielab.jules.types.Header");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Header.java | Header.getDoi | public String getDoi() {
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jcasType.jcas.throwFeatMissing("doi", "de.julielab.jules.types.Header");
return jcasType.ll_cas.ll_getStringValue(addr, ((Header_Type)jcasType).casFeatCode_doi);} | java | public String getDoi() {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Header.java | Header.setDoi | public void setDoi(String v) {
if (Header_Type.featOkTst && ((Header_Type)jcasType).casFeat_doi == null)
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jcasType.ll_cas.ll_setStringValue(addr, ((Header_Type)jcasType).casFeatCode_doi, v);} | java | public void setDoi(String v) {
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jcasType.jcas.throwFeatMissing("doi", "de.julielab.jules.types.Header");
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/SourcedTFIDF.java | SourcedTFIDF.getDocumentFrequency | public int getDocumentFrequency(Token token)
{
Integer df = (Integer)documentFrequency.get(token);
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} | java | public int getDocumentFrequency(Token token)
{
Integer df = (Integer)documentFrequency.get(token);
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/PronounFeats.java | PronounFeats.setGender | public void setGender(String v) {
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jcasType.jcas.throwFeatMissing("gender", "de.julielab.jules.types.PronounFeats");
jcasType.ll_cas.ll_setStringValue(addr, ((PronounFeats_Type)jcasType).casFeatCode_gender, v);} | java | public void setGender(String v) {
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jcasType.jcas.throwFeatMissing("gender", "de.julielab.jules.types.PronounFeats");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/PronounFeats.java | PronounFeats.getCase | public String getCase() {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/PronounFeats.java | PronounFeats.setCase | public void setCase(String v) {
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jcasType.jcas.throwFeatMissing("case", "de.julielab.jules.types.PronounFeats");
jcasType.ll_cas.ll_setStringValue(addr, ((PronounFeats_Type)jcasType).casFeatCode_case, v);} | java | public void setCase(String v) {
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jcasType.jcas.throwFeatMissing("case", "de.julielab.jules.types.PronounFeats");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/PronounFeats.java | PronounFeats.getNumber | public String getNumber() {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/PronounFeats.java | PronounFeats.setNumber | public void setNumber(String v) {
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BlueBrain/bluima | modules/bluima_xml/src/main/java/ch/epfl/bbp/uima/xml/archivearticle3/Th.java | Th.getHeaders | public java.util.List<Object> getHeaders() {
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headers = new ArrayList<Object>();
}
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} | java | public java.util.List<Object> getHeaders() {
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<p>
This accessor method returns a reference to the live list,
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This is why there is not a <CODE>set</CODE> method for the headers property.
<p>
For example, to add a new item, do as follows:
<pre>
getHeaders().add(newItem);
</pre>
<p>
Objects of the following type(s) are allowed in the list
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Annotation.java | Annotation.getComponentId | public String getComponentId() {
if (Annotation_Type.featOkTst && ((Annotation_Type)jcasType).casFeat_componentId == null)
jcasType.jcas.throwFeatMissing("componentId", "de.julielab.jules.types.Annotation");
return jcasType.ll_cas.ll_getStringValue(addr, ((Annotation_Type)jcasType).casFeatCode_componentId);} | java | public String getComponentId() {
if (Annotation_Type.featOkTst && ((Annotation_Type)jcasType).casFeat_componentId == null)
jcasType.jcas.throwFeatMissing("componentId", "de.julielab.jules.types.Annotation");
return jcasType.ll_cas.ll_getStringValue(addr, ((Annotation_Type)jcasType).casFeatCode_componentId);} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Annotation.java | Annotation.setComponentId | public void setComponentId(String v) {
if (Annotation_Type.featOkTst && ((Annotation_Type)jcasType).casFeat_componentId == null)
jcasType.jcas.throwFeatMissing("componentId", "de.julielab.jules.types.Annotation");
jcasType.ll_cas.ll_setStringValue(addr, ((Annotation_Type)jcasType).casFeatCode_componentId, v);} | java | public void setComponentId(String v) {
if (Annotation_Type.featOkTst && ((Annotation_Type)jcasType).casFeat_componentId == null)
jcasType.jcas.throwFeatMissing("componentId", "de.julielab.jules.types.Annotation");
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BlueBrain/bluima | modules/bluima_banner/src/main/java/banner/tagging/DictionaryTagger.java | DictionaryTagger.add | public void add(String text, MentionType type)
{
MentionType previousType = entities.add(process(text), type);
if (previousType != null && !previousType.equals(type))
throw new IllegalArgumentException("Text is already associated with a different tag: " + text);
} | java | public void add(String text, MentionType type)
{
MentionType previousType = entities.add(process(text), type);
if (previousType != null && !previousType.equals(type))
throw new IllegalArgumentException("Text is already associated with a different tag: " + text);
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BlueBrain/bluima | utils/blue_commons/src/main/java/ch/epfl/bbp/triechar/TrieCnt.java | TrieCnt.toFrequencyFile | public void toFrequencyFile(String filePath) throws IOException {
BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(
new FileOutputStream(filePath), "UTF-8"));
for (TrieNodeCnt child : root.children.values()) {
child.writeFrequencies(writer, new char[0]);// recursive
}
writer.close();
} | java | public void toFrequencyFile(String filePath) throws IOException {
BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(
new FileOutputStream(filePath), "UTF-8"));
for (TrieNodeCnt child : root.children.values()) {
child.writeFrequencies(writer, new char[0]);// recursive
}
writer.close();
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EntityAttribute.java | EntityAttribute.getNames | public FSArray getNames() {
if (EntityAttribute_Type.featOkTst && ((EntityAttribute_Type)jcasType).casFeat_names == null)
jcasType.jcas.throwFeatMissing("names", "de.julielab.jules.types.ace.EntityAttribute");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((EntityAttribute_Type)jcasType).casFeatCode_names)));} | java | public FSArray getNames() {
if (EntityAttribute_Type.featOkTst && ((EntityAttribute_Type)jcasType).casFeat_names == null)
jcasType.jcas.throwFeatMissing("names", "de.julielab.jules.types.ace.EntityAttribute");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EntityAttribute.java | EntityAttribute.setNames | public void setNames(FSArray v) {
if (EntityAttribute_Type.featOkTst && ((EntityAttribute_Type)jcasType).casFeat_names == null)
jcasType.jcas.throwFeatMissing("names", "de.julielab.jules.types.ace.EntityAttribute");
jcasType.ll_cas.ll_setRefValue(addr, ((EntityAttribute_Type)jcasType).casFeatCode_names, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setNames(FSArray v) {
if (EntityAttribute_Type.featOkTst && ((EntityAttribute_Type)jcasType).casFeat_names == null)
jcasType.jcas.throwFeatMissing("names", "de.julielab.jules.types.ace.EntityAttribute");
jcasType.ll_cas.ll_setRefValue(addr, ((EntityAttribute_Type)jcasType).casFeatCode_names, jcasType.ll_cas.ll_getFSRef(v));} | [
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EntityAttribute.java | EntityAttribute.getNames | public Name getNames(int i) {
if (EntityAttribute_Type.featOkTst && ((EntityAttribute_Type)jcasType).casFeat_names == null)
jcasType.jcas.throwFeatMissing("names", "de.julielab.jules.types.ace.EntityAttribute");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((EntityAttribute_Type)jcasType).casFeatCode_names), i);
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if (EntityAttribute_Type.featOkTst && ((EntityAttribute_Type)jcasType).casFeat_names == null)
jcasType.jcas.throwFeatMissing("names", "de.julielab.jules.types.ace.EntityAttribute");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/ace/EntityAttribute.java | EntityAttribute.setNames | public void setNames(int i, Name v) {
if (EntityAttribute_Type.featOkTst && ((EntityAttribute_Type)jcasType).casFeat_names == null)
jcasType.jcas.throwFeatMissing("names", "de.julielab.jules.types.ace.EntityAttribute");
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if (EntityAttribute_Type.featOkTst && ((EntityAttribute_Type)jcasType).casFeat_names == null)
jcasType.jcas.throwFeatMissing("names", "de.julielab.jules.types.ace.EntityAttribute");
jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((EntityAttribute_Type)jcasType).casFeatCode_names), i);
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BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/TableExtractor.java | TableExtractor.judgeHTMLCode | private boolean judgeHTMLCode(ArrayList<ArrayList<TextPiece>> wordsByPage) {
ArrayList<TextPiece> wordsOfPageOne = wordsByPage.get(0);
boolean isHTMLCode = true;
int i = 0;
/*
* do not have to check all words, Checking 10 words is enough
*/
while (i < Math.min(20, wordsOfPageOne.size())) {
TextPiece currentWord = wordsOfPageOne.get(i);
String thisText = currentWord.getText();
if ((thisText.length() % 2 != 0)
&& (thisText.matches("([A-Z]([A-Z]|[0-9]))*") == false)) {
isHTMLCode = false;
break;
}
i++;
}
// if (isHTMLCode)
// System.out.println("This document is coded in HTML code!");
return isHTMLCode;
} | java | private boolean judgeHTMLCode(ArrayList<ArrayList<TextPiece>> wordsByPage) {
ArrayList<TextPiece> wordsOfPageOne = wordsByPage.get(0);
boolean isHTMLCode = true;
int i = 0;
/*
* do not have to check all words, Checking 10 words is enough
*/
while (i < Math.min(20, wordsOfPageOne.size())) {
TextPiece currentWord = wordsOfPageOne.get(i);
String thisText = currentWord.getText();
if ((thisText.length() % 2 != 0)
&& (thisText.matches("([A-Z]([A-Z]|[0-9]))*") == false)) {
isHTMLCode = false;
break;
}
i++;
}
// if (isHTMLCode)
// System.out.println("This document is coded in HTML code!");
return isHTMLCode;
} | [
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@param wordsByPage
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@return A boolean value: true/false | [
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BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/TableExtractor.java | TableExtractor.extractFiguresFromAPage | private void extractFiguresFromAPage(ArrayList<TextPiece> linesOfAPage,
ArrayList<TextPiece> wordsOfAPage, int i, File pdfFile,
ArrayList<ArrayList<TextPiece>> linesByPage) {
if (linesOfAPage.size() > 30) { // if this page is very short, it
// usually does not contain tables
/*
* Checks for table keyword
*/
boolean figureKwdExist = false;
int prevTableEndIndex = 0;
int k = -1;
for (TextPiece t : linesOfAPage) {
k++;
String textWithoutSpace = t.getText().replace(" ", "");
TextPiece prevLine = (k == 0) ? null : linesOfAPage.get(k - 1);
if (getMatchedFigureKeyword(textWithoutSpace) != null) {
figureKwdExist = true;
String figKwd = getMatchedFigureKeyword(textWithoutSpace);
System.out.println("In page " + (i + 1) + ": "
+ textWithoutSpace);
}
}
} else {
/*
* Impossible to contain tables because of few texts in the page
*/
}
} | java | private void extractFiguresFromAPage(ArrayList<TextPiece> linesOfAPage,
ArrayList<TextPiece> wordsOfAPage, int i, File pdfFile,
ArrayList<ArrayList<TextPiece>> linesByPage) {
if (linesOfAPage.size() > 30) { // if this page is very short, it
// usually does not contain tables
/*
* Checks for table keyword
*/
boolean figureKwdExist = false;
int prevTableEndIndex = 0;
int k = -1;
for (TextPiece t : linesOfAPage) {
k++;
String textWithoutSpace = t.getText().replace(" ", "");
TextPiece prevLine = (k == 0) ? null : linesOfAPage.get(k - 1);
if (getMatchedFigureKeyword(textWithoutSpace) != null) {
figureKwdExist = true;
String figKwd = getMatchedFigureKeyword(textWithoutSpace);
System.out.println("In page " + (i + 1) + ": "
+ textWithoutSpace);
}
}
} else {
/*
* Impossible to contain tables because of few texts in the page
*/
}
} | [
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@param linesOfAPage
the list of lines of one page
@param wordsOfAPage
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@param i
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@param linesByPage
the list of lines of the document | [
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BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/TableExtractor.java | TableExtractor.extractOneTable | private int extractOneTable(int lineNumber,
ArrayList<TextPiece> linesOfAPage, String keyword,
TableCandidate tc, ArrayList<TextPiece> wordsOfAPage, int i,
int prevTableEndIndex, ArrayList<ArrayList<TextPiece>> linesByPage) {
TextPiece line = linesOfAPage.get(lineNumber);
if (line.getX() < 0 && line.getWidth() == 0.0) {
System.out
.println("\n This is a reversed table, currently we do not support such tables!");
lineNumber++;
tc.setValid(false);
} else {
lineNumber = findCaptionBoundary(lineNumber, linesOfAPage, tc);
if (tc.isValid()) {
tc.setPageId_thisTable(i);
// getReferenceTableTexts(tc, linesByPage);
isWideTable(tc);
Vector distinctY = new Vector();
Vector piecesEachY = new Vector();
distinctY = getDistinctSortedY(distinctY, piecesEachY,
wordsOfAPage, tc);
boolean aboveCaption = judgeCaptionLocation(linesOfAPage, tc,
distinctY, wordsOfAPage);
lineNumber = findBodyBoundary(lineNumber, linesOfAPage, tc,
aboveCaption, prevTableEndIndex);
getReferenceTableTexts(tc, linesByPage);
// System.out.println(tc.getRefText());
}
tc.setHighLevelMeta(i);
if (tc.isValid()) {
organizeCells(linesOfAPage, tc);
}
if (tc.isValid()) {
findFootnoteBeginRow(tc);
}
if (tc.isValid()) {
determineFootnoteHeading(tc);
getColumnBoundaryWithoutHeading(tc);
}
int cc = tc.getColumnNum_thisTable();
if (cc > 20) {
tc.setValid(false);
} else {
// if((cc>=2) && (tc.getMaxColumnNumber()<cc*2) ) { //if we
// treat each line as the possible table beginning without
// considering the table keyword, we need use this
if (cc >= 2) {
getTableStructure(cc, tc, wordsOfAPage);
// if (tc.isValid()) parameters.tableNum++;
} else {
tc.setEmptyMetadataStructureLevel(tc.getRows().size(), cc,
wordsOfAPage, m_docInfo);
}
}
}
return lineNumber;
} | java | private int extractOneTable(int lineNumber,
ArrayList<TextPiece> linesOfAPage, String keyword,
TableCandidate tc, ArrayList<TextPiece> wordsOfAPage, int i,
int prevTableEndIndex, ArrayList<ArrayList<TextPiece>> linesByPage) {
TextPiece line = linesOfAPage.get(lineNumber);
if (line.getX() < 0 && line.getWidth() == 0.0) {
System.out
.println("\n This is a reversed table, currently we do not support such tables!");
lineNumber++;
tc.setValid(false);
} else {
lineNumber = findCaptionBoundary(lineNumber, linesOfAPage, tc);
if (tc.isValid()) {
tc.setPageId_thisTable(i);
// getReferenceTableTexts(tc, linesByPage);
isWideTable(tc);
Vector distinctY = new Vector();
Vector piecesEachY = new Vector();
distinctY = getDistinctSortedY(distinctY, piecesEachY,
wordsOfAPage, tc);
boolean aboveCaption = judgeCaptionLocation(linesOfAPage, tc,
distinctY, wordsOfAPage);
lineNumber = findBodyBoundary(lineNumber, linesOfAPage, tc,
aboveCaption, prevTableEndIndex);
getReferenceTableTexts(tc, linesByPage);
// System.out.println(tc.getRefText());
}
tc.setHighLevelMeta(i);
if (tc.isValid()) {
organizeCells(linesOfAPage, tc);
}
if (tc.isValid()) {
findFootnoteBeginRow(tc);
}
if (tc.isValid()) {
determineFootnoteHeading(tc);
getColumnBoundaryWithoutHeading(tc);
}
int cc = tc.getColumnNum_thisTable();
if (cc > 20) {
tc.setValid(false);
} else {
// if((cc>=2) && (tc.getMaxColumnNumber()<cc*2) ) { //if we
// treat each line as the possible table beginning without
// considering the table keyword, we need use this
if (cc >= 2) {
getTableStructure(cc, tc, wordsOfAPage);
// if (tc.isValid()) parameters.tableNum++;
} else {
tc.setEmptyMetadataStructureLevel(tc.getRows().size(), cc,
wordsOfAPage, m_docInfo);
}
}
}
return lineNumber;
} | [
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BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/TableExtractor.java | TableExtractor.isWideTable | private void isWideTable(TableCandidate tc) {
float docWidth = m_docInfo.getMaxX() - m_docInfo.getMinX();
if ((((tc.getCaptionX() > ((docWidth - 30) / (float) 4.0)
+ m_docInfo.getMinX())) && (tc.getCaptionX() < docWidth / 2.5))
|| (tc.getCaptonEndX() - tc.getCaptionX() > docWidth
/ (float) 1.85)) {
tc.setWideTable(true);
// System.out.println();
// System.out.println("This is a wide table? " + tc.isWideTable());
} else {
// System.out.println();
// System.out.println("This is a single-doc-column table!");
}
} | java | private void isWideTable(TableCandidate tc) {
float docWidth = m_docInfo.getMaxX() - m_docInfo.getMinX();
if ((((tc.getCaptionX() > ((docWidth - 30) / (float) 4.0)
+ m_docInfo.getMinX())) && (tc.getCaptionX() < docWidth / 2.5))
|| (tc.getCaptonEndX() - tc.getCaptionX() > docWidth
/ (float) 1.85)) {
tc.setWideTable(true);
// System.out.println();
// System.out.println("This is a wide table? " + tc.isWideTable());
} else {
// System.out.println();
// System.out.println("This is a single-doc-column table!");
}
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BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/TableExtractor.java | TableExtractor.organizeCells | private void organizeCells(ArrayList<TextPiece> linesOfAPage,
TableCandidate tc) {
float captionY = linesOfAPage.get(tc.getCaptionStartLine()).getY();
float captionEndY = linesOfAPage.get(tc.getCaptionEndLine()).getEndY();
ArrayList<TextPiece> rawCells = new ArrayList<TextPiece>();
/*
* Copy & sort
*/
for (int i = tc.getBodyStartLine(); i <= tc.getBodyEndLine(); i++) {
rawCells.add(linesOfAPage.get(i));
}
Collections.sort(rawCells);
assert rawCells.size() >= 4; // due to previous check
TableRow currentRow = null; // creates first row
for (TextPiece cell : rawCells) {
/*
* Skips lines beyond caption //TODO: remove the far Y
*/
if (tc.isTopCaption() && (cell.getY() < captionY))
continue;
if (!tc.isTopCaption() && (cell.getEndY() > captionEndY))
continue;
/*
* Lines too close to each other are treated as a single line
*/
if (currentRow != null
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currentRow.addCell(cell);
else {
/*
* Creates a new row
*/
currentRow = new TableRow();
currentRow.setY(cell.getY());
if (cell.isSuperScriptBeginning())
currentRow.setSuperScriptRow(true);
currentRow.addCell(cell);
tc.addRow(currentRow);
}
}
if (tc.getRows().size() < 2)
tc.setValid(false);
} | java | private void organizeCells(ArrayList<TextPiece> linesOfAPage,
TableCandidate tc) {
float captionY = linesOfAPage.get(tc.getCaptionStartLine()).getY();
float captionEndY = linesOfAPage.get(tc.getCaptionEndLine()).getEndY();
ArrayList<TextPiece> rawCells = new ArrayList<TextPiece>();
/*
* Copy & sort
*/
for (int i = tc.getBodyStartLine(); i <= tc.getBodyEndLine(); i++) {
rawCells.add(linesOfAPage.get(i));
}
Collections.sort(rawCells);
assert rawCells.size() >= 4; // due to previous check
TableRow currentRow = null; // creates first row
for (TextPiece cell : rawCells) {
/*
* Skips lines beyond caption //TODO: remove the far Y
*/
if (tc.isTopCaption() && (cell.getY() < captionY))
continue;
if (!tc.isTopCaption() && (cell.getEndY() > captionEndY))
continue;
/*
* Lines too close to each other are treated as a single line
*/
if (currentRow != null
&& cell.getY() - currentRow.getY() < m_docInfo
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currentRow.addCell(cell);
else {
/*
* Creates a new row
*/
currentRow = new TableRow();
currentRow.setY(cell.getY());
if (cell.isSuperScriptBeginning())
currentRow.setSuperScriptRow(true);
currentRow.addCell(cell);
tc.addRow(currentRow);
}
}
if (tc.getRows().size() < 2)
tc.setValid(false);
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BlueBrain/bluima | modules/bluima_pdf/src/main/java/edu/psu/seersuite/extractors/tableextractor/extraction/TableExtractor.java | TableExtractor.getRowHeadingBasedOnCells | public void getRowHeadingBasedOnCells(TableCandidate tc) {
String rowHeadingThisTable = "";
int footnoteLineIndex = tc.getFootnoteBeginRow();
String[][] cells = tc.getCells();
// if (cells[0][0].length()==0 ) {
for (int j = 0; j < footnoteLineIndex; j++) {
if (cells[j][0].length() > 0)
rowHeadingThisTable = rowHeadingThisTable + cells[j][0] + "; ";
}
// }
rowHeadingThisTable = tc
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tc.setHeadingRows(rowHeadingThisTable);
} | java | public void getRowHeadingBasedOnCells(TableCandidate tc) {
String rowHeadingThisTable = "";
int footnoteLineIndex = tc.getFootnoteBeginRow();
String[][] cells = tc.getCells();
// if (cells[0][0].length()==0 ) {
for (int j = 0; j < footnoteLineIndex; j++) {
if (cells[j][0].length() > 0)
rowHeadingThisTable = rowHeadingThisTable + cells[j][0] + "; ";
}
// }
rowHeadingThisTable = tc
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tc.setHeadingRows(rowHeadingThisTable);
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/Dependency.java | Dependency.getDeptype | public String getDeptype() {
if (Dependency_Type.featOkTst && ((Dependency_Type)jcasType).casFeat_deptype == null)
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/Dependency.java | Dependency.setDeptype | public void setDeptype(String v) {
if (Dependency_Type.featOkTst && ((Dependency_Type)jcasType).casFeat_deptype == null)
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jcasType.ll_cas.ll_setStringValue(addr, ((Dependency_Type)jcasType).casFeatCode_deptype, v);} | java | public void setDeptype(String v) {
if (Dependency_Type.featOkTst && ((Dependency_Type)jcasType).casFeat_deptype == null)
jcasType.jcas.throwFeatMissing("deptype", "com.digitalpebble.rasp.Dependency");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/Dependency.java | Dependency.getSubtype | public String getSubtype() {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/Dependency.java | Dependency.setSubtype | public void setSubtype(String v) {
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/Dependency.java | Dependency.getDep | public WordForm getDep() {
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if (Dependency_Type.featOkTst && ((Dependency_Type)jcasType).casFeat_dep == null)
jcasType.jcas.throwFeatMissing("dep", "com.digitalpebble.rasp.Dependency");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/Dependency.java | Dependency.setDep | public void setDep(WordForm v) {
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if (Dependency_Type.featOkTst && ((Dependency_Type)jcasType).casFeat_dep == null)
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/Lemma.java | Lemma.setValue | public void setValue(String v) {
if (Lemma_Type.featOkTst && ((Lemma_Type)jcasType).casFeat_value == null)
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jcasType.ll_cas.ll_setStringValue(addr, ((Lemma_Type)jcasType).casFeatCode_value, v);} | java | public void setValue(String v) {
if (Lemma_Type.featOkTst && ((Lemma_Type)jcasType).casFeat_value == null)
jcasType.jcas.throwFeatMissing("value", "de.julielab.jules.types.Lemma");
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BlueBrain/bluima | modules/bluima_abbreviations/src/main/java/com/wcohen/ss/abbvGapsHmm/AbbvGapsHMM.java | AbbvGapsHMM.trainCorpus | protected boolean trainCorpus(List<List<Acronym>> corpus, List<Map<String, String>> trueLabels){
boolean converge = false;
// Unsupervised
trueLabels = null;
initModelParamsAndCounters();
int n = corpus.size();
int c = 1;
Double change;
LOG.debug("Training abbreviations...");
while(!converge){
for (int i = 0; i < n; i++) {
List<Acronym> docAcronyms = corpus.get(i);
Map<String, String> docTrueLabels = null;
if(trueLabels != null)
docTrueLabels = trueLabels.get(i);
int m = docAcronyms.size();
for (int j = 0; j < m; j++) {
Acronym currAcronym = docAcronyms.get(j);
if(trueLabels != null)
expectationStep(currAcronym, docTrueLabels.get(currAcronym._shortForm));
else
expectationStep(currAcronym, null);
}
}
change = maximizationStep();
LOG.debug("step {}...",c);
c++;
if(c > MAX_ITERATIONS){
System.out.println("\n\tTraining stopped after "+(c-1)+" iterations with final change: "+change);
converge = true;
}
if(change.compareTo(CHANGE_THRESHOLD) < 0){
LOG.debug("Training converged in "+(c-1)+" iterations.");
converge = true;
}
}
saveModelParams();
return true;
} | java | protected boolean trainCorpus(List<List<Acronym>> corpus, List<Map<String, String>> trueLabels){
boolean converge = false;
// Unsupervised
trueLabels = null;
initModelParamsAndCounters();
int n = corpus.size();
int c = 1;
Double change;
LOG.debug("Training abbreviations...");
while(!converge){
for (int i = 0; i < n; i++) {
List<Acronym> docAcronyms = corpus.get(i);
Map<String, String> docTrueLabels = null;
if(trueLabels != null)
docTrueLabels = trueLabels.get(i);
int m = docAcronyms.size();
for (int j = 0; j < m; j++) {
Acronym currAcronym = docAcronyms.get(j);
if(trueLabels != null)
expectationStep(currAcronym, docTrueLabels.get(currAcronym._shortForm));
else
expectationStep(currAcronym, null);
}
}
change = maximizationStep();
LOG.debug("step {}...",c);
c++;
if(c > MAX_ITERATIONS){
System.out.println("\n\tTraining stopped after "+(c-1)+" iterations with final change: "+change);
converge = true;
}
if(change.compareTo(CHANGE_THRESHOLD) < 0){
LOG.debug("Training converged in "+(c-1)+" iterations.");
converge = true;
}
}
saveModelParams();
return true;
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BlueBrain/bluima | modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/cleanup/LigaturesRemover.java | LigaturesRemover.remove | public String remove(String txt) {
for (Pattern p : patterns.keySet()) {
System.out.println("p: "+p);
System.out.println("b: "+txt);
txt = p.matcher(txt).replaceAll(patterns.get(p));
System.out.println("a: "+txt);
}
return txt;
} | java | public String remove(String txt) {
for (Pattern p : patterns.keySet()) {
System.out.println("p: "+p);
System.out.println("b: "+txt);
txt = p.matcher(txt).replaceAll(patterns.get(p));
System.out.println("a: "+txt);
}
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/DiscontinuousAnnotation.java | DiscontinuousAnnotation.getValue | public FSArray getValue() {
if (DiscontinuousAnnotation_Type.featOkTst && ((DiscontinuousAnnotation_Type)jcasType).casFeat_value == null)
jcasType.jcas.throwFeatMissing("value", "de.julielab.jules.types.DiscontinuousAnnotation");
return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((DiscontinuousAnnotation_Type)jcasType).casFeatCode_value)));} | java | public FSArray getValue() {
if (DiscontinuousAnnotation_Type.featOkTst && ((DiscontinuousAnnotation_Type)jcasType).casFeat_value == null)
jcasType.jcas.throwFeatMissing("value", "de.julielab.jules.types.DiscontinuousAnnotation");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/DiscontinuousAnnotation.java | DiscontinuousAnnotation.setValue | public void setValue(FSArray v) {
if (DiscontinuousAnnotation_Type.featOkTst && ((DiscontinuousAnnotation_Type)jcasType).casFeat_value == null)
jcasType.jcas.throwFeatMissing("value", "de.julielab.jules.types.DiscontinuousAnnotation");
jcasType.ll_cas.ll_setRefValue(addr, ((DiscontinuousAnnotation_Type)jcasType).casFeatCode_value, jcasType.ll_cas.ll_getFSRef(v));} | java | public void setValue(FSArray v) {
if (DiscontinuousAnnotation_Type.featOkTst && ((DiscontinuousAnnotation_Type)jcasType).casFeat_value == null)
jcasType.jcas.throwFeatMissing("value", "de.julielab.jules.types.DiscontinuousAnnotation");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/DiscontinuousAnnotation.java | DiscontinuousAnnotation.getValue | public Annotation getValue(int i) {
if (DiscontinuousAnnotation_Type.featOkTst && ((DiscontinuousAnnotation_Type)jcasType).casFeat_value == null)
jcasType.jcas.throwFeatMissing("value", "de.julielab.jules.types.DiscontinuousAnnotation");
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if (DiscontinuousAnnotation_Type.featOkTst && ((DiscontinuousAnnotation_Type)jcasType).casFeat_value == null)
jcasType.jcas.throwFeatMissing("value", "de.julielab.jules.types.DiscontinuousAnnotation");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/de/julielab/jules/types/DiscontinuousAnnotation.java | DiscontinuousAnnotation.setValue | public void setValue(int i, Annotation v) {
if (DiscontinuousAnnotation_Type.featOkTst && ((DiscontinuousAnnotation_Type)jcasType).casFeat_value == null)
jcasType.jcas.throwFeatMissing("value", "de.julielab.jules.types.DiscontinuousAnnotation");
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if (DiscontinuousAnnotation_Type.featOkTst && ((DiscontinuousAnnotation_Type)jcasType).casFeat_value == null)
jcasType.jcas.throwFeatMissing("value", "de.julielab.jules.types.DiscontinuousAnnotation");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/org/apache/uima/examples/SourceDocumentInformation.java | SourceDocumentInformation.getDocumentSize | public int getDocumentSize() {
if (SourceDocumentInformation_Type.featOkTst && ((SourceDocumentInformation_Type)jcasType).casFeat_documentSize == null)
jcasType.jcas.throwFeatMissing("documentSize", "org.apache.uima.examples.SourceDocumentInformation");
return jcasType.ll_cas.ll_getIntValue(addr, ((SourceDocumentInformation_Type)jcasType).casFeatCode_documentSize);} | java | public int getDocumentSize() {
if (SourceDocumentInformation_Type.featOkTst && ((SourceDocumentInformation_Type)jcasType).casFeat_documentSize == null)
jcasType.jcas.throwFeatMissing("documentSize", "org.apache.uima.examples.SourceDocumentInformation");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/org/apache/uima/examples/SourceDocumentInformation.java | SourceDocumentInformation.setDocumentSize | public void setDocumentSize(int v) {
if (SourceDocumentInformation_Type.featOkTst && ((SourceDocumentInformation_Type)jcasType).casFeat_documentSize == null)
jcasType.jcas.throwFeatMissing("documentSize", "org.apache.uima.examples.SourceDocumentInformation");
jcasType.ll_cas.ll_setIntValue(addr, ((SourceDocumentInformation_Type)jcasType).casFeatCode_documentSize, v);} | java | public void setDocumentSize(int v) {
if (SourceDocumentInformation_Type.featOkTst && ((SourceDocumentInformation_Type)jcasType).casFeat_documentSize == null)
jcasType.jcas.throwFeatMissing("documentSize", "org.apache.uima.examples.SourceDocumentInformation");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/org/apache/uima/examples/SourceDocumentInformation.java | SourceDocumentInformation.getLastSegment | public boolean getLastSegment() {
if (SourceDocumentInformation_Type.featOkTst && ((SourceDocumentInformation_Type)jcasType).casFeat_lastSegment == null)
jcasType.jcas.throwFeatMissing("lastSegment", "org.apache.uima.examples.SourceDocumentInformation");
return jcasType.ll_cas.ll_getBooleanValue(addr, ((SourceDocumentInformation_Type)jcasType).casFeatCode_lastSegment);} | java | public boolean getLastSegment() {
if (SourceDocumentInformation_Type.featOkTst && ((SourceDocumentInformation_Type)jcasType).casFeat_lastSegment == null)
jcasType.jcas.throwFeatMissing("lastSegment", "org.apache.uima.examples.SourceDocumentInformation");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/org/apache/uima/examples/SourceDocumentInformation.java | SourceDocumentInformation.setLastSegment | public void setLastSegment(boolean v) {
if (SourceDocumentInformation_Type.featOkTst && ((SourceDocumentInformation_Type)jcasType).casFeat_lastSegment == null)
jcasType.jcas.throwFeatMissing("lastSegment", "org.apache.uima.examples.SourceDocumentInformation");
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jcasType.jcas.throwFeatMissing("lastSegment", "org.apache.uima.examples.SourceDocumentInformation");
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BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/WordForm.java | WordForm.getLemma | public String getLemma() {
if (WordForm_Type.featOkTst && ((WordForm_Type)jcasType).casFeat_lemma == null)
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if (WordForm_Type.featOkTst && ((WordForm_Type)jcasType).casFeat_lemma == null)
jcasType.jcas.throwFeatMissing("lemma", "com.digitalpebble.rasp.WordForm");
return jcasType.ll_cas.ll_getStringValue(addr, ((WordForm_Type)jcasType).casFeatCode_lemma);} | [
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... | getter for lemma - gets lemma of the 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/com/digitalpebble/rasp/WordForm.java#L86-L89 | train |
BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/WordForm.java | WordForm.setLemma | public void setLemma(String v) {
if (WordForm_Type.featOkTst && ((WordForm_Type)jcasType).casFeat_lemma == null)
jcasType.jcas.throwFeatMissing("lemma", "com.digitalpebble.rasp.WordForm");
jcasType.ll_cas.ll_setStringValue(addr, ((WordForm_Type)jcasType).casFeatCode_lemma, v);} | java | public void setLemma(String v) {
if (WordForm_Type.featOkTst && ((WordForm_Type)jcasType).casFeat_lemma == null)
jcasType.jcas.throwFeatMissing("lemma", "com.digitalpebble.rasp.WordForm");
jcasType.ll_cas.ll_setStringValue(addr, ((WordForm_Type)jcasType).casFeatCode_lemma, v);} | [
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"(",... | setter for lemma - sets lemma of the Form
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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/com/digitalpebble/rasp/WordForm.java#L95-L98 | train |
BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/WordForm.java | WordForm.getPOS | public String getPOS() {
if (WordForm_Type.featOkTst && ((WordForm_Type)jcasType).casFeat_POS == null)
jcasType.jcas.throwFeatMissing("POS", "com.digitalpebble.rasp.WordForm");
return jcasType.ll_cas.ll_getStringValue(addr, ((WordForm_Type)jcasType).casFeatCode_POS);} | java | public String getPOS() {
if (WordForm_Type.featOkTst && ((WordForm_Type)jcasType).casFeat_POS == null)
jcasType.jcas.throwFeatMissing("POS", "com.digitalpebble.rasp.WordForm");
return jcasType.ll_cas.ll_getStringValue(addr, ((WordForm_Type)jcasType).casFeatCode_POS);} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/WordForm.java#L108-L111 | train |
BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/WordForm.java | WordForm.setPOS | public void setPOS(String v) {
if (WordForm_Type.featOkTst && ((WordForm_Type)jcasType).casFeat_POS == null)
jcasType.jcas.throwFeatMissing("POS", "com.digitalpebble.rasp.WordForm");
jcasType.ll_cas.ll_setStringValue(addr, ((WordForm_Type)jcasType).casFeatCode_POS, v);} | java | public void setPOS(String v) {
if (WordForm_Type.featOkTst && ((WordForm_Type)jcasType).casFeat_POS == null)
jcasType.jcas.throwFeatMissing("POS", "com.digitalpebble.rasp.WordForm");
jcasType.ll_cas.ll_setStringValue(addr, ((WordForm_Type)jcasType).casFeatCode_POS, v);} | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/WordForm.java#L117-L120 | train |
BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/WordForm.java | WordForm.getSuffix | public String getSuffix() {
if (WordForm_Type.featOkTst && ((WordForm_Type)jcasType).casFeat_suffix == null)
jcasType.jcas.throwFeatMissing("suffix", "com.digitalpebble.rasp.WordForm");
return jcasType.ll_cas.ll_getStringValue(addr, ((WordForm_Type)jcasType).casFeatCode_suffix);} | java | public String getSuffix() {
if (WordForm_Type.featOkTst && ((WordForm_Type)jcasType).casFeat_suffix == null)
jcasType.jcas.throwFeatMissing("suffix", "com.digitalpebble.rasp.WordForm");
return jcasType.ll_cas.ll_getStringValue(addr, ((WordForm_Type)jcasType).casFeatCode_suffix);} | [
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"\"suffix\""... | getter for suffix - gets
@generated
@return value of the feature | [
"getter",
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"-",
"gets"
] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/WordForm.java#L152-L155 | train |
BlueBrain/bluima | modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/WordForm.java | WordForm.setSuffix | public void setSuffix(String v) {
if (WordForm_Type.featOkTst && ((WordForm_Type)jcasType).casFeat_suffix == null)
jcasType.jcas.throwFeatMissing("suffix", "com.digitalpebble.rasp.WordForm");
jcasType.ll_cas.ll_setStringValue(addr, ((WordForm_Type)jcasType).casFeatCode_suffix, v);} | java | public void setSuffix(String v) {
if (WordForm_Type.featOkTst && ((WordForm_Type)jcasType).casFeat_suffix == null)
jcasType.jcas.throwFeatMissing("suffix", "com.digitalpebble.rasp.WordForm");
jcasType.ll_cas.ll_setStringValue(addr, ((WordForm_Type)jcasType).casFeatCode_suffix, v);} | [
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"(... | setter for suffix - sets
@generated
@param v value to set into the feature | [
"setter",
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"-",
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_typesystem/src/main/java/com/digitalpebble/rasp/WordForm.java#L161-L164 | train |
BlueBrain/bluima | modules/bluima_pdf/src/main/java/ch/epfl/bbp/uima/pdf/cr/PdfCollectionReader.java | PdfCollectionReader.serializeXMLDocument | public static void serializeXMLDocument (Document doc, Writer output) throws TransformerException {
// serialize XML document using identity transformation
Transformer trans = TransformerFactory.newInstance().newTransformer();
DOMSource source = new DOMSource(doc);
StreamResult result = new StreamResult(output);
trans.transform(source, result);
} | java | public static void serializeXMLDocument (Document doc, Writer output) throws TransformerException {
// serialize XML document using identity transformation
Transformer trans = TransformerFactory.newInstance().newTransformer();
DOMSource source = new DOMSource(doc);
StreamResult result = new StreamResult(output);
trans.transform(source, result);
} | [
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BlueBrain/bluima | modules/bluima_jsre/src/main/java/org/itc/irst/tcc/sre/CompareExampleSet.java | CompareExampleSet.createFeatureIndex | private FeatureIndex[] createFeatureIndex(int subspaceCount) // throws
// Exception
{
logger.info("create feature index");
FeatureIndex[] index = new FeatureIndex[subspaceCount];
for (int i = 0; i < subspaceCount; i++)
index[i] = new FeatureIndex(false, 1);
return index;
} | java | private FeatureIndex[] createFeatureIndex(int subspaceCount) // throws
// Exception
{
logger.info("create feature index");
FeatureIndex[] index = new FeatureIndex[subspaceCount];
for (int i = 0; i < subspaceCount; i++)
index[i] = new FeatureIndex(false, 1);
return index;
} | [
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"... | create feature index | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_jsre/src/main/java/org/itc/irst/tcc/sre/CompareExampleSet.java#L166-L176 | train |
BlueBrain/bluima | modules/bluima_corpora/src/main/java/ch/epfl/bbp/uima/cr/GeniaCorpusCollectionReader.java | GeniaCorpusCollectionReader.annotatateContent | private static String annotatateContent(JCas jcas, Object contentObj,
int start) {
LOG.trace("annotate: " + reflectionToString(contentObj));
int end = start;
StringBuilder internalSb = new StringBuilder();
if (contentObj instanceof String) {
String c = (String) contentObj;
internalSb.append(c);
end += c.length();
} else if (contentObj instanceof Cons) {
Cons cons = (Cons) contentObj;
for (Object o : cons.getContent()) {
String parse = annotatateContent(jcas, o, end);
end += parse.length();
internalSb.append(parse);
}
BioEntityMention entity = new BioEntityMention(jcas, start, end);
entity.setSpecificType(cons.getSem());
entity.setComponentId(GeniaCorpusCollectionReader.COMPONENT_ID);
entity.setTextualRepresentation(cons.getLex());
entity.addToIndexes();
}
return internalSb.toString();
} | java | private static String annotatateContent(JCas jcas, Object contentObj,
int start) {
LOG.trace("annotate: " + reflectionToString(contentObj));
int end = start;
StringBuilder internalSb = new StringBuilder();
if (contentObj instanceof String) {
String c = (String) contentObj;
internalSb.append(c);
end += c.length();
} else if (contentObj instanceof Cons) {
Cons cons = (Cons) contentObj;
for (Object o : cons.getContent()) {
String parse = annotatateContent(jcas, o, end);
end += parse.length();
internalSb.append(parse);
}
BioEntityMention entity = new BioEntityMention(jcas, start, end);
entity.setSpecificType(cons.getSem());
entity.setComponentId(GeniaCorpusCollectionReader.COMPONENT_ID);
entity.setTextualRepresentation(cons.getLex());
entity.addToIndexes();
}
return internalSb.toString();
} | [
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... | Recursive, since annotations can overlap | [
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] | 793ea3f46761dce72094e057a56cddfa677156ae | https://github.com/BlueBrain/bluima/blob/793ea3f46761dce72094e057a56cddfa677156ae/modules/bluima_corpora/src/main/java/ch/epfl/bbp/uima/cr/GeniaCorpusCollectionReader.java#L115-L144 | train |
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