public static EntryTag process( Element entry ) { loadGlobalContext( entry ); // process all interactions InteractionListParser interactionList = new InteractionListParser( globalExperiments, globalParticipants ); Collection interactions = interactionList.process( entry ); EntryTag entryTag = null; try { entryTag = new EntryTag( globalExperiments.getExperiments(), globalParticipants.getInteractors(), interactions ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( entry, e.getMessage() ) ); } return entryTag; } }
public static EntryTag process( Element entry ) { loadGlobalContext( entry ); // process all interactions InteractionListParser interactionList = new InteractionListParser( globalExperiments, globalParticipants ); Collection interactions = interactionList.process( entry ); EntryTag entryTag = null; try { entryTag = new EntryTag( globalExperiments.getExperiments(), globalParticipants.getInteractors(), interactions ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( entry, e.getMessage() ) ); } return entryTag; } }
public static EntryTag process( Element entry ) { loadGlobalContext( entry ); // process all interactions InteractionListParser interactionList = new InteractionListParser( globalExperiments, globalParticipants ); Collection interactions = interactionList.process( entry ); EntryTag entryTag = null; try { entryTag = new EntryTag( globalExperiments.getExperiments(), globalParticipants.getInteractors(), interactions ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( entry, e.getMessage() ) ); } return entryTag; } }
interactor = (ProteinInteractorTag) interactorList.getInteractors().get( id ); if ( interactor == null ) {
interactor = (ProteinInteractorTag) interactorList.getInteractors().get( id ); if ( interactor == null ) {
interactor = (ProteinInteractorTag) interactorList.getInteractors().get( id ); if ( interactor == null ) {
proteinInteractor = (ProteinInteractorTag) interactorList.getInteractors().get( id ); if ( proteinInteractor != null ) { final String msg = "WARNING - the protein id: " + id + " is defined several times. " +
proteinInteractor = (ProteinInteractorTag) interactorList.getInteractors().get( id ); if ( proteinInteractor != null ) { final String msg = "WARNING - the protein id: " + id + " is defined several times. " +
proteinInteractor = (ProteinInteractorTag) interactorList.getInteractors().get( id ); if ( proteinInteractor != null ) { final String msg = "WARNING - the protein id: " + id + " is defined several times. " +