/** @generated * @param jcas JCas to which this Feature Structure belongs * @param begin offset to the begin spot in the SofA * @param end offset to the end spot in the SofA */ public MedicationMention(JCas jcas, int begin, int end) { super(jcas); setBegin(begin); setEnd(end); readObject(); }
MedicationEventMention medEventMention = (MedicationEventMention) original; MedicationMention medMention = (MedicationMention) mention; JCas jcas = medMention.getCAS().getJCas(); if (medEventMention.getStartDate()!=null) { Date date = medEventMention.getStartDate(); TimeMention timeMention = new TimeMention(jcas); timeMention.setDate(date); medMention.setStartDate(timeMention); TimeMention timeMention = new TimeMention(jcas); timeMention.setDate(date); medMention.setEndDate(timeMention); medDosageModifier.setNormalizedForm(dosage); medDosageModifier.setCategory(dosage.getValue()); medMention.setMedicationDosage(medDosageModifier); medDurationModifier.setNormalizedForm(duration); medDurationModifier.setCategory(duration.getValue()); medMention.setMedicationDuration(medDurationModifier); medFormModifier.setNormalizedForm(form); medFormModifier.setCategory(form.getValue()); medMention.setMedicationForm(medFormModifier); medFrequencyModifier.setNormalizedForm(frequency); medFrequencyModifier.setCategory(frequency.getNumber() + frequency.getUnit()); medMention.setMedicationFrequency(medFrequencyModifier);
modifier.setCategory(dosage.getValue()); medicationMention.setMedicationDosage(modifier); modifier.setCategory(duration.getValue()); medicationMention.setMedicationDuration(modifier); modifier.setCategory(sc.getValue()); medicationMention.setMedicationStatusChange(modifier); modifier.setCategory(form.getValue()); medicationMention.setMedicationForm(modifier); modifier.setCategory(fromAnnotation.getFrequency() + fromAnnotation.getFrequencyUnit()); medicationMention.setMedicationFrequency(modifier); medicationMention.setMedicationRoute(modifier); medicationMention.setMedicationStrength(modifier); if (d!=null) medicationMention.setStartDate(timeMention); medicationMention.setConfidence(fromAnnotation.getConfidence());
IdentifiedAnnotation neAnnot = new MedicationMention( jcas ); // medication NEs are EventMention neAnnot.setTypeID( CONST.NE_TYPE_ID_DRUG ); neAnnot.setBegin( neBegin );
FSArray ocArr = tokenAnt.getOntologyConceptArr(); if (ocArr != null) int holdRightEnd = end + 1; int holdLeftStart = begin; drugTokenAnt = new DrugMentionAnnotation(jcas, tokenAnt.getBegin(), tokenAnt.getEnd()); tokenAnt.setTypeID(NERTypeIdentifier); holdDrugNERArr.add(drugTokenAnt); } else if (sub.getBegin() > tokenAnt.getEnd()) holdRightEnd = tokenAnt.getBegin(); if (ssid.getSubSectionBodyBegin() <= tokenAnt.getBegin() && ssid.getSubSectionBodyEnd() >= tokenAnt.getEnd()) ca.setSentenceID(tokenAnt.getSentenceID()); MedicationMention mem = new MedicationMention(jcas, globalDrugNER.get(i).getBegin(), globalDrugNER.get(i).getEnd()); addMedicationSpecificAttributes(jcas, globalDrugNER.get(i), mem); mem.addToIndexes(jcas);
/** Internal - constructor used by generator * @generated * @param addr low level Feature Structure reference * @param type the type of this Feature Structure */ public MedicationMention(int addr, TOP_Type type) { super(addr, type); readObject(); }
int originalEndSpan = endSpan; int originalBeginSpan = beginSpan; MedicationMention neAnnot = new MedicationMention(jcas, tokenDrugNER.getBegin(), tokenDrugNER.getEnd()); int beginChunk = drugChangeStatus.getEnd(); neAnnot.setTypeID(NERTypeIdentifier); int [] updatedSpan = {beginSpan, endSpan}; NewlineToken.type, neAnnot.getBegin(), beginChunk); if (!findLF.hasNext())
modifier.setCategory(dosage.getValue()); medicationMention.setMedicationDosage(modifier); modifier.setCategory(duration.getValue()); medicationMention.setMedicationDuration(modifier); modifier.setCategory(sc.getValue()); medicationMention.setMedicationStatusChange(modifier); modifier.setCategory(form.getValue()); medicationMention.setMedicationForm(modifier); modifier.setCategory(fromAnnotation.getFrequency() + fromAnnotation.getFrequencyUnit()); medicationMention.setMedicationFrequency(modifier); medicationMention.setMedicationRoute(modifier); medicationMention.setMedicationStrength(modifier); if (d!=null) medicationMention.setStartDate(timeMention); medicationMention.setConfidence(fromAnnotation.getConfidence());
IdentifiedAnnotation neAnnot = new MedicationMention( jcas ); // medication NEs are EventMention neAnnot.setTypeID( CONST.NE_TYPE_ID_DRUG ); neAnnot.setBegin( neBegin );
FSArray ocArr = tokenAnt.getOntologyConceptArr(); if (ocArr != null) int holdRightEnd = end + 1; int holdLeftStart = begin; drugTokenAnt = new DrugMentionAnnotation(jcas, tokenAnt.getBegin(), tokenAnt.getEnd()); tokenAnt.setTypeID(NERTypeIdentifier); holdDrugNERArr.add(drugTokenAnt); } else if (sub.getBegin() > tokenAnt.getEnd()) holdRightEnd = tokenAnt.getBegin(); if (ssid.getSubSectionBodyBegin() <= tokenAnt.getBegin() && ssid.getSubSectionBodyEnd() >= tokenAnt.getEnd()) ca.setSentenceID(tokenAnt.getSentenceID()); MedicationMention mem = new MedicationMention(jcas, globalDrugNER.get(i).getBegin(), globalDrugNER.get(i).getEnd()); addMedicationSpecificAttributes(jcas, globalDrugNER.get(i), mem); mem.addToIndexes(jcas);
/** Internal - constructor used by generator * @generated * @param addr low level Feature Structure reference * @param type the type of this Feature Structure */ public MedicationMention(int addr, TOP_Type type) { super(addr, type); readObject(); }
int originalEndSpan = endSpan; int originalBeginSpan = beginSpan; MedicationMention neAnnot = new MedicationMention(jcas, tokenDrugNER.getBegin(), tokenDrugNER.getEnd()); int beginChunk = drugChangeStatus.getEnd(); neAnnot.setTypeID(NERTypeIdentifier); int [] updatedSpan = {beginSpan, endSpan}; NewlineToken.type, neAnnot.getBegin(), beginChunk); if (!findLF.hasNext())
/** @generated * @param jcas JCas to which this Feature Structure belongs * @param begin offset to the begin spot in the SofA * @param end offset to the end spot in the SofA */ public MedicationMention(JCas jcas, int begin, int end) { super(jcas); setBegin(begin); setEnd(end); readObject(); }
final int conceptKey = conceptEntry.getKey(); if ( conceptKey == CONST.NE_TYPE_ID_DRUG ) { neAnnot = new MedicationMention( jcas ); } else if ( conceptKey == CONST.NE_TYPE_ID_ANATOMICAL_SITE ) { neAnnot = new AnatomicalSiteMention( jcas );
/** Internal - constructor used by generator * @generated * @param addr low level Feature Structure reference * @param type the type of this Feature Structure */ public MedicationMention(int addr, TOP_Type type) { super(addr, type); readObject(); }
/** @generated * @param jcas JCas to which this Feature Structure belongs * @param begin offset to the begin spot in the SofA * @param end offset to the end spot in the SofA */ public MedicationMention(JCas jcas, int begin, int end) { super(jcas); setBegin(begin); setEnd(end); readObject(); }
final int conceptKey = conceptEntry.getKey(); if ( conceptKey == CONST.NE_TYPE_ID_DRUG ) { neAnnot = new MedicationMention( jcas ); } else if ( conceptKey == CONST.NE_TYPE_ID_ANATOMICAL_SITE ) { neAnnot = new AnatomicalSiteMention( jcas );
/** @generated * @param jcas JCas to which this Feature Structure belongs */ public MedicationMention(JCas jcas) { super(jcas); readObject(); }
/** @generated * @param jcas JCas to which this Feature Structure belongs * @param begin offset to the begin spot in the SofA * @param end offset to the end spot in the SofA */ public MedicationMention(JCas jcas, int begin, int end) { super(jcas); setBegin(begin); setEnd(end); readObject(); }
mention = new MedicationMention(jcas); mapToMentions.put(original, mention); setAttributesFromOriginal(mention, original);