private Synonym createSynonym( String shortLabel, String shortLabelId ) { Synonym syn = new SynonymImpl(); syn.setText( shortLabel ); SynonymType synCat = new SynonymTypeImpl(); synCat.setID(shortLabelId); syn.setSynonymType( synCat ); syn.setScope( 1 ); return syn; }
String synVal = safeTrim(aSyn.getText()); if (synVal != null) { if (aSyn.getSynonymType() != null) { logger.debug("using user-defined synonym type: " + aSyn.getSynonymType().getName()); Term synTrm = ontologyTerms.get(aSyn.getSynonymType().getID()); if (synTrm != null) { tsb.setSynonymType(synTrm); throw new IllegalStateException( "Attempting to use user-defined synonym type that has not been initialized in common objects: " + aSyn.getSynonymType().getID() ); switch (aSyn.getScope()) { case Synonym.EXACT_SYNONYM: tsb.setSynonymType(EXACT); Collection<Dbxref> oboSynXrefs = aSyn.getXrefs(); if (oboSynXrefs != null) { Collection<DbXref> xrefs = new HashSet<DbXref>();
SynonymType synCat = synonym.getSynonymType(); shortLabel = synonym.getText();
String synVal = safeTrim(aSyn.getText()); if (synVal != null) { if (aSyn.getSynonymType() != null) { logger.debug("using user-defined synonym type: " + aSyn.getSynonymType().getName()); Term synTrm = ontologyTerms.get(aSyn.getSynonymType().getID()); if (synTrm != null) { tsb.setSynonymType(synTrm); throw new IllegalStateException( "Attempting to use user-defined synonym type that has not been initialized in common objects: " + aSyn.getSynonymType().getID() ); switch (aSyn.getScope()) { case Synonym.EXACT_SYNONYM: tsb.setSynonymType(EXACT); Collection<Dbxref> oboSynXrefs = aSyn.getXrefs(); if (oboSynXrefs != null) { Collection<DbXref> xrefs = new HashSet<DbXref>();
CvObjectAlias alias_; for ( Synonym aSyn : syn ) { SynonymType synCat = aSyn.getSynonymType(); if ( synCat != null && synCat.getID() != null && synCat.getID().equalsIgnoreCase( CvObjectOntologyBuilder.ALIAS_IDENTIFIER ) ) { String aliasName = aSyn.getText(); alias_ = ( CvObjectAlias ) toAlias( cvObject, aliasName ); cvObject.addAlias( alias_ );
String synVal = safeTrim(aSyn.getText(), true); if (synVal != null) { if (aSyn.getSynonymType() != null) { logger.debug("using user-defined synonym type: " + aSyn.getSynonymType().getName()); Term synTrm = ontologyTerms.get(aSyn.getSynonymType().getID()); if (synTrm != null) { tsb.setSynonymType(synTrm); throw new IllegalStateException( "Attempting to use user-defined synonym type that has not been initialized in common objects: " + aSyn.getSynonymType().getID() ); switch (aSyn.getScope()) { case Synonym.EXACT_SYNONYM: tsb.setSynonymType(EXACT); Collection<Dbxref> oboSynXrefs = aSyn.getXrefs(); if (oboSynXrefs != null) { Collection<DbXref> xrefs = new HashSet<DbXref>();
private void addPsimiShortSyn(OBOClass oboObj, String synonym) { Synonym syn = new SynonymImpl(); syn.setText( synonym ); SynonymType synCat = new SynonymTypeImpl(); synCat.setID(synonym); syn.setSynonymType( synCat ); syn.setScope( 1 ); oboObj.addSynonym( syn ); }
private Synonym createAlias( CvObjectAlias cvAlias, String aliasId ) { Synonym syn = new SynonymImpl(); syn.setText( cvAlias.getName() ); SynonymType synCat = new SynonymTypeImpl(); synCat.setID(aliasId); syn.setSynonymType( synCat ); syn.setScope( 1 ); return syn; }