private static boolean isAliasSearchable( Alias alias ) { return alias.getCvAliasType() != null; } }
public static Collection<Alias> getAliasByType(AnnotatedObject<?, ?> annotatedObject, String miOrLabel) { Collection<Alias> matchingAliases = new ArrayList<Alias>(); for (Alias alias : annotatedObject.getAliases()) { if (alias.getCvAliasType() != null && ( alias.getCvAliasType().getIdentifier().equals(miOrLabel) || alias.getCvAliasType().getShortLabel().equals(miOrLabel)) ) { matchingAliases.add(alias); } } return matchingAliases; }
public UpdatedAlias(Alias alias, UpdateStatus status){ super(); if (alias != null){ type = alias.getCvAliasType() != null ? alias.getCvAliasType().getAc() : null; this.name = alias.getName(); } else { this.type = null; this.name = null; } this.status = status != null ? status : UpdateStatus.none; this.parent = null; }
public static Collection<Alias> getAliasByType(AnnotatedObject<?, ?> annotatedObject, String miOrLabel) { Collection<Alias> matchingAliases = new ArrayList<Alias>(); for (Alias alias : annotatedObject.getAliases()) { if (alias.getCvAliasType() != null && ( alias.getCvAliasType().getIdentifier().equals(miOrLabel) || alias.getCvAliasType().getShortLabel().equals(miOrLabel)) ) { matchingAliases.add(alias); } } return matchingAliases; }
public static List<String> getSynonyms(InteractionImpl complex) { List<String> synosyms = new ArrayList<String>(); for (Alias alias : complex.getAliases()) { if (alias.getName() != null && alias.getCvAliasType() != null && alias.getCvAliasType().getIdentifier().equals(CvAliasType.COMPLEX_SYNONYM_NAME_MI_REF)) { synosyms.add(alias.getName()); } } return synosyms; }
public static List<String> getSynonyms(InteractionImpl complex) { List<String> synosyms = new ArrayList<String>(); for (Alias alias : complex.getAliases()) { if (alias.getName() != null && alias.getCvAliasType() != null && alias.getCvAliasType().getIdentifier().equals(CvAliasType.COMPLEX_SYNONYM_NAME_MI_REF)) { synosyms.add(alias.getName()); } } return synosyms; }
private static String getAlias(InteractionImpl complex, String id) { for (Alias alias : complex.getAliases()) { if (alias.getName() != null && alias.getCvAliasType() != null && alias.getCvAliasType().getIdentifier().equals(id)) { return alias.getName(); } } return null; }
private static String getAlias(InteractionImpl complex, String id) { for (Alias alias : complex.getAliases()) { if (alias.getName() != null && alias.getCvAliasType() != null && alias.getCvAliasType().getIdentifier().equals(id)) { return alias.getName(); } } return null; }
@Override public void visitAlias( Alias alias ) { final CvAliasType type = alias.getCvAliasType(); if( type != null ) { final String mi = type.getIdentifier(); if ( mi != null ) { final String key = createCvKey( type.getClass(), mi ); final CvAliasType oboTerm = ( CvAliasType ) mi2cv.get( key ); if ( oboTerm == null ) { log.warn( "Could not find alias " + type.getClass().getSimpleName() + "( " + type.getShortLabel() + " ) by MI: " + mi ); } else { alias.setCvAliasType( oboTerm ); } } } }
@Override public void visitAlias(Alias alias) { currentNode.setUserObject("Alias: "+alias.getName()+" / Type="+DebugUtil.cvObjectToSimpleString(alias.getCvAliasType())); }
private static SearchItem searchItemForAlias( Alias alias ) { return new SearchItem( alias.getParentAc(), alias.getName(), alias.getParent().getClass().getName(), alias.getCvAliasType().getShortLabel() ); }
@Override public void visitAlias(Alias alias) { currentNode.setUserObject("Alias: "+alias.getName()+" / Type="+DebugUtil.cvObjectToSimpleString(alias.getCvAliasType())); }
public static boolean sameAlias( Alias a1, Alias a2 ) { if (a1.getAc() != null && a2.getAc() != null) { return a1.getAc().equals(a2.getAc()); } if ( !same( a1.getName(), a2.getName() ) ) { return false; } if ( !CvObjectUtils.areEqual( a1.getCvAliasType(), a2.getCvAliasType() ) ) { return false; } return true; }
protected Alias cloneAlias(Alias alias) throws IntactClonerException { if (alias == null) return null; Class clazz = CgLibUtil.removeCglibEnhanced(alias.getClass()); Alias clone = null; try { final Constructor constructor = clazz.getConstructor(); clone = (Alias) constructor.newInstance(); clonerManager.addClone(alias, clone); clone.setCvAliasType(clone(alias.getCvAliasType())); clone.setName(alias.getName()); } catch (Exception e) { throw new IntactClonerException("An error occured upon building a " + clazz.getSimpleName(), e); } return clone; }
protected Alias cloneAlias(Alias alias) throws IntactClonerException { if (alias == null) return null; Class clazz = CgLibUtil.removeCglibEnhanced(alias.getClass()); Alias clone = null; try { final Constructor constructor = clazz.getConstructor(); clone = (Alias) constructor.newInstance(); clonerManager.addClone(alias, clone); clone.setCvAliasType(clone(alias.getCvAliasType())); clone.setName(alias.getName()); } catch (Exception e) { throw new IntactClonerException("An error occured upon building a " + clazz.getSimpleName(), e); } return clone; }
public static boolean sameAlias( Alias a1, Alias a2 ) { if (a1.getAc() != null && a2.getAc() != null) { return a1.getAc().equals(a2.getAc()); } if ( !same( a1.getName(), a2.getName() ) ) { return false; } if ( !CvObjectUtils.areEqual( a1.getCvAliasType(), a2.getCvAliasType() ) ) { return false; } return true; }
protected void traverseAlias(Alias alias, IntactVisitor... visitors) { if (alias == null) return; for (IntactVisitor visitor : visitors) { visitor.visitAlias(alias); } // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(alias)) { return; } traverse(alias.getCvAliasType(), visitors); traverse(alias.getOwner(), visitors); }
protected void traverseAlias(Alias alias, IntactVisitor... visitors) { if (alias == null) return; for (IntactVisitor visitor : visitors) { visitor.visitAlias(alias); } // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(alias)) { return; } traverse(alias.getCvAliasType(), visitors); traverse(alias.getOwner(), visitors); }
private Alias synchronizeAlias( Alias alias, AnnotatedObject parent ) { if (alias.getAc() != null) { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory() .getAliasDao().getByAc(alias.getAc()); } alias.setCvAliasType( synchronize( alias.getCvAliasType() ) ); alias.setParent(parent); if (alias.getAc() == null && parent.getAc() != null) { annotatedObjectsToPersist.put(keyBuilder.keyForAlias(alias), alias); } return alias; }
private Alias synchronizeAlias( Alias alias, AnnotatedObject parent ) { if (alias.getAc() != null) { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory() .getAliasDao().getByAc(alias.getAc()); } alias.setCvAliasType( synchronize( alias.getCvAliasType() ) ); alias.setParent(parent); if (alias.getAc() == null && parent.getAc() != null) { annotatedObjectsToPersist.put(keyBuilder.keyForAlias(alias), alias); } return alias; }