public int compare(X o1, X o2) { return o1.getPrimaryId().compareTo(o2.getPrimaryId()); } };
public int compare(X o1, X o2) { return o1.getPrimaryId().compareTo(o2.getPrimaryId()); } };
private Collection<String> getIds(Collection<CvObjectXref> xrefs) { List<String> ids = new ArrayList<String>(xrefs.size()); for (Xref xref : xrefs) { ids.add(xref.getPrimaryId()); } return ids; }
private Collection<String> getIds(Collection<CvObjectXref> xrefs) { List<String> ids = new ArrayList<String>(xrefs.size()); for (Xref xref : xrefs) { ids.add(xref.getPrimaryId()); } return ids; }
/** * @return The GO id, which belongs to this unique CvGoNode Object */ @Transient public String getGoId() { Collection<CvObjectXref> someXrefs = this.getXrefs(); if ( someXrefs.size() != 1 ) { System.out.println( "warning: a CvGoNode can only have one specific Xref" ); } Xref xref = someXrefs.iterator().next(); return xref.getPrimaryId(); }
public static String getPsiReference( CvObject cv ) { if ( cv == null ) { throw new IllegalArgumentException( "the given CvObject must not be null." ); } for ( Iterator iterator = cv.getXrefs().iterator(); iterator.hasNext(); ) { Xref xref = (Xref) iterator.next(); if ( CvDatabase.PSI_MI.equals( xref.getCvDatabase().getShortLabel() ) ) { return xref.getPrimaryId(); } } return null; } }
public static String getPsiReference( CvObject cv ) { if ( cv == null ) { throw new IllegalArgumentException( "the given CvObject must not be null." ); } for ( Iterator iterator = cv.getXrefs().iterator(); iterator.hasNext(); ) { Xref xref = (Xref) iterator.next(); if ( CvDatabase.PSI_MI.equals( xref.getCvDatabase().getShortLabel() ) ) { return xref.getPrimaryId(); } } return null; } }
public static String getPsiReference( CvObject cv ) { if ( cv == null ) { throw new IllegalArgumentException( "the given CvObject must not be null." ); } for ( Iterator iterator = cv.getXrefs().iterator(); iterator.hasNext(); ) { Xref xref = (Xref) iterator.next(); if ( CvDatabase.PSI_MI.equals( xref.getCvDatabase().getShortLabel() ) ) { return xref.getPrimaryId(); } } return null; } }
private boolean hasPsiXref( AnnotatedObject annotatedObject, String psiId ) { boolean hasIt = false; if ( psiId == null ) { return false; } for ( Iterator iterator = annotatedObject.getXrefs().iterator(); iterator.hasNext() && false == hasIt; ) { Xref xref = (Xref) iterator.next(); if ( xref.getCvDatabase().getShortLabel().equals( CvDatabase.PSI_MI ) ) { if ( psiId.equals( xref.getPrimaryId() ) ) { hasIt = true; } } } return hasIt; }
private boolean hasPsiXref( AnnotatedObject annotatedObject, String psiId ) { boolean hasIt = false; if ( psiId == null ) { return false; } for ( Iterator iterator = annotatedObject.getXrefs().iterator(); iterator.hasNext() && false == hasIt; ) { Xref xref = (Xref) iterator.next(); if ( xref.getCvDatabase().getShortLabel().equals( CvDatabase.PSI_MI ) ) { if ( psiId.equals( xref.getPrimaryId() ) ) { hasIt = true; } } } return hasIt; }
private static SearchItem searchItemForXref( Xref xref ) { return new SearchItem( xref.getParentAc(), xref.getPrimaryId(), xref.getParent().getClass().getName(), "xref" ); }
private void insertSearchItemForXref( Xref xref ) { if ( log.isDebugEnabled() ) { log.debug( "Inserting SearchItems for Xref: " + xref.getPrimaryId() + " (" + xref.getAc() + "); Parent AC: " + xref.getParentAc() ); } SearchItem searchItem = searchItemForXref( xref ); if ( log.isDebugEnabled() ) { log.debug( "\t" + searchItem ); } IntactContext.getCurrentInstance().getDataContext().getDaoFactory() .getSearchItemDao().persist( searchItem ); }
@Override public void visitXref(Xref xref) { ps.println(indentation()+"Xref: "+xref.getPrimaryId()+" (db: "+xref.getCvDatabase().getShortLabel()+", qual: "+xref.getCvXrefQualifier().getShortLabel()+")"); }
@Override public void visitXref(Xref xref) { ps.println(indentation()+"Xref: "+xref.getPrimaryId()+" (db: "+xref.getCvDatabase().getShortLabel()+", qual: "+xref.getCvXrefQualifier().getShortLabel()+")"); }
public Key keyForXref(Xref xref) { return new Key(keyFor(xref.getParent()).getUniqueString() + "::" + xref.getPrimaryId()); }
public Key keyForXref(Xref xref) { return new Key(keyFor(xref.getParent()).getUniqueString() + "::" + xref.getPrimaryId()); }
private void deleteSearchItemForXref( Xref xref ) { if ( log.isDebugEnabled() ) { log.debug( "Deleting SearchItems for Xref: " + xref.getPrimaryId() + " (" + xref.getAc() + "); Parent AC: " + xref.getParentAc() ); } SearchItem searchItem = searchItemForXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory() .getSearchItemDao().delete( searchItem ); }
@Override public void visitXref(Xref xref) { currentNode.setUserObject("Xref: "+xref.getPrimaryId()+" / Database="+ DebugUtil.cvObjectToSimpleString(xref.getCvDatabase())+ ", Qualifier="+DebugUtil.cvObjectToSimpleString(xref.getCvXrefQualifier())); }
@Override public void visitXref(Xref xref) { currentNode.setUserObject("Xref: "+xref.getPrimaryId()+" / Database="+ DebugUtil.cvObjectToSimpleString(xref.getCvDatabase())+ ", Qualifier="+DebugUtil.cvObjectToSimpleString(xref.getCvXrefQualifier())); }
private String getMiReference( CvObject cv ) { for ( Xref xref : cv.getXrefs() ) { if ( getPsi().equals( xref.getCvDatabase() ) ) { if ( getIdentity().equals( xref.getCvXrefQualifier() ) ) { return xref.getPrimaryId(); } } } return null; }