/** * Process a <interactorList> * * @param entry a <interactorList> Element */ public void process( final Element entry ) { final Element proteinsList = DOMUtil.getFirstElement( entry, "interactorList" ); if ( proteinsList != null ) { final NodeList someProteins = proteinsList.getElementsByTagName( "proteinInteractor" ); for ( int i = 0; i < someProteins.getLength(); i++ ) { final Node interactor = someProteins.item( i ); final ProteinInteractorParser proteinInteractor = new ProteinInteractorParser( this, (Element) interactor ); final LabelValueBean lvb = proteinInteractor.process(); if ( lvb != null ) { interactors.put( lvb.getLabel(), lvb.getValue() ); } } // interactors } } }
&& false == "interaction".equals( name ) ) { MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in either " + "entry or interaction tag." ) ); experiments.put( lvb.getLabel(), lvb.getValue() );
MessageHolder.getInstance().addParserMessage( new Message( root, "We should be in proteinInteractor tag." ) ); final String msg = "WARNING - the protein id: " + id + " is defined several times. " + "The global definition will be used instead."; MessageHolder.getInstance().addParserMessage( new Message( root, msg ) ); return new LabelValueBean( id, proteinInteractor ); } else { if ( CommandLineOptions.getInstance().hasDefaultInteractorTaxid() ) { final String defaultTaxid = CommandLineOptions.getInstance().getDefaultInteractorTaxid(); hostOrganism = new OrganismTag( defaultTaxid ); lvb = new LabelValueBean( id, new ProteinInteractorTag( shortlabel, fullname, xref, secondaryXrefs, aliases, hostOrganism, sequence ) ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
MessageHolder.getInstance().addParserMessage( new Message( root, "ERROR - We should be in interaction tag." ) ); localExperiments.add( e ); } else { MessageHolder.getInstance().addParserMessage( new Message( experimentListElement, "Experiment reference is unknown: " + ref ) ); expressedInAnnotations.add( new ExpressedInTag( annotation ) ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) ); MessageHolder.getInstance().addParserMessage( new Message( participantElement, msg ) ); final LabelValueBean lvb = proteinInteractor.process(); if ( lvb != null ) { interactor = (ProteinInteractorTag) lvb.getValue(); id = lvb.getLabel(); MessageHolder.getInstance().addParserMessage( new Message( root, msg ) ); } else { final String msg = "ERROR - No role found under that participant, abort that interaction."; MessageHolder.getInstance().addParserMessage( new Message( root, msg ) ); isOverexpressedProtein ) ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) ); if ( CommandLineOptions.getInstance().hasDefaultInteractionType() ) {
MessageHolder.getInstance().addParserMessage( new Message( root, "ERROR - We should be in experimentDescription tag." ) ); final String msg = "WARNING - the experiment id: " + id + "is defined several times. " + "The global definition will be used instead."; MessageHolder.getInstance().addParserMessage( new Message( root, msg ) ); return new LabelValueBean( id, experiment ); MessageHolder.getInstance().addParserMessage( new Message( root, msg ) ); MessageHolder.getInstance().addParserMessage( new Message( root, msg ) ); interactionDetection = new InteractionDetectionTag( interactionXref ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( interactionDetectionXrefElement, e.getMessage() ) ); participantDetection = new ParticipantDetectionTag( participantXref ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( participantDetectionXrefElement, e.getMessage() ) ); participantDetection ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) ); return new LabelValueBean( id, experiment );
boolean guiEnabled = CommandLineOptions.getInstance().isGuiEnabled(); Monitor monitor = null; if ( guiEnabled ) {
MessageHolder.getInstance().addParserMessage( new Message( root, "ERROR - We should be in interaction tag." ) ); localExperiments.add( e ); } else { MessageHolder.getInstance().addParserMessage( new Message( experimentListElement, "Experiment reference is unknown: " + ref ) ); expressedInAnnotations.add( new ExpressedInTag( annotation ) ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) ); MessageHolder.getInstance().addParserMessage( new Message( participantElement, msg ) ); final LabelValueBean lvb = proteinInteractor.process(); if ( lvb != null ) { interactor = (ProteinInteractorTag) lvb.getValue(); id = lvb.getLabel(); MessageHolder.getInstance().addParserMessage( new Message( root, msg ) ); } else { final String msg = "ERROR - No role found under that participant, abort that interaction."; MessageHolder.getInstance().addParserMessage( new Message( root, msg ) ); isOverexpressedProtein ) ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) ); if ( CommandLineOptions.getInstance().hasDefaultInteractionType() ) {
MessageHolder.getInstance().addParserMessage( new Message( root, "We should be in proteinInteractor tag." ) ); final String msg = "WARNING - the protein id: " + id + " is defined several times. " + "The global definition will be used instead."; MessageHolder.getInstance().addParserMessage( new Message( root, msg ) ); return new LabelValueBean( id, proteinInteractor ); } else { if ( CommandLineOptions.getInstance().hasDefaultInteractorTaxid() ) { final String defaultTaxid = CommandLineOptions.getInstance().getDefaultInteractorTaxid(); hostOrganism = new OrganismTag( defaultTaxid ); lvb = new LabelValueBean( id, new ProteinInteractorTag( shortlabel, fullname, xref, secondaryXrefs, aliases, hostOrganism, sequence ) ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
&& false == "interaction".equals( name ) ) { MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in either " + "entry or interaction tag." ) ); experiments.put( lvb.getLabel(), lvb.getValue() );
MessageHolder.getInstance().addParserMessage( new Message( root, "ERROR - We should be in experimentDescription tag." ) ); final String msg = "WARNING - the experiment id: " + id + "is defined several times. " + "The global definition will be used instead."; MessageHolder.getInstance().addParserMessage( new Message( root, msg ) ); return new LabelValueBean( id, experiment ); MessageHolder.getInstance().addParserMessage( new Message( root, msg ) ); MessageHolder.getInstance().addParserMessage( new Message( root, msg ) ); interactionDetection = new InteractionDetectionTag( interactionXref ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( interactionDetectionXrefElement, e.getMessage() ) ); participantDetection = new ParticipantDetectionTag( participantXref ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( participantDetectionXrefElement, e.getMessage() ) ); participantDetection ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) ); return new LabelValueBean( id, experiment );
boolean guiEnabled = CommandLineOptions.getInstance().isGuiEnabled(); Monitor monitor = null; if ( guiEnabled ) {
/** * Process a <interactorList> * * @param entry a <interactorList> Element */ public void process( final Element entry ) { final Element proteinsList = DOMUtil.getFirstElement( entry, "interactorList" ); if ( proteinsList != null ) { final NodeList someProteins = proteinsList.getElementsByTagName( "proteinInteractor" ); for ( int i = 0; i < someProteins.getLength(); i++ ) { final Node interactor = someProteins.item( i ); final ProteinInteractorParser proteinInteractor = new ProteinInteractorParser( this, (Element) interactor ); final LabelValueBean lvb = proteinInteractor.process(); if ( lvb != null ) { interactors.put( lvb.getLabel(), lvb.getValue() ); } } // interactors } } }
MessageHolder.getInstance().addParserMessage( new Message( root, "ERROR - We should be in interaction tag." ) ); localExperiments.add( e ); } else { MessageHolder.getInstance().addParserMessage( new Message( experimentListElement, "Experiment reference is unknown: " + ref ) ); expressedInAnnotations.add( new ExpressedInTag( annotation ) ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) ); MessageHolder.getInstance().addParserMessage( new Message( participantElement, msg ) ); final LabelValueBean lvb = proteinInteractor.process(); if ( lvb != null ) { interactor = (ProteinInteractorTag) lvb.getValue(); id = lvb.getLabel(); MessageHolder.getInstance().addParserMessage( new Message( root, msg ) ); } else { final String msg = "ERROR - No role found under that participant, abort that interaction."; MessageHolder.getInstance().addParserMessage( new Message( root, msg ) ); isOverexpressedProtein ) ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) ); if ( CommandLineOptions.getInstance().hasDefaultInteractionType() ) {
MessageHolder.getInstance().addParserMessage( new Message( root, "We should be in proteinInteractor tag." ) ); final String msg = "WARNING - the protein id: " + id + " is defined several times. " + "The global definition will be used instead."; MessageHolder.getInstance().addParserMessage( new Message( root, msg ) ); return new LabelValueBean( id, proteinInteractor ); } else { if ( CommandLineOptions.getInstance().hasDefaultInteractorTaxid() ) { final String defaultTaxid = CommandLineOptions.getInstance().getDefaultInteractorTaxid(); hostOrganism = new OrganismTag( defaultTaxid ); lvb = new LabelValueBean( id, new ProteinInteractorTag( shortlabel, fullname, xref, secondaryXrefs, aliases, hostOrganism, sequence ) ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
&& false == "interaction".equals( name ) ) { MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in either " + "entry or interaction tag." ) ); experiments.put( lvb.getLabel(), lvb.getValue() );
boolean guiEnabled = CommandLineOptions.getInstance().isGuiEnabled(); Monitor monitor = null; if ( guiEnabled ) {
/** * Process a <interactorList> * * @param entry a <interactorList> Element */ public void process( final Element entry ) { final Element proteinsList = DOMUtil.getFirstElement( entry, "interactorList" ); if ( proteinsList != null ) { final NodeList someProteins = proteinsList.getElementsByTagName( "proteinInteractor" ); for ( int i = 0; i < someProteins.getLength(); i++ ) { final Node interactor = someProteins.item( i ); final ProteinInteractorParser proteinInteractor = new ProteinInteractorParser( this, (Element) interactor ); final LabelValueBean lvb = proteinInteractor.process(); if ( lvb != null ) { interactors.put( lvb.getLabel(), lvb.getValue() ); } } // interactors } } }
boolean guiEnabled = CommandLineOptions.getInstance().isGuiEnabled(); Monitor monitor = null; boolean displayProgressBar = guiEnabled && keys.size() > 0;
boolean guiEnabled = CommandLineOptions.getInstance().isGuiEnabled(); Monitor monitor = null; boolean displayProgressBar = guiEnabled && keys.size() > 0;
boolean guiEnabled = CommandLineOptions.getInstance().isGuiEnabled(); Monitor monitor = null; boolean displayProgressBar = guiEnabled && keys.size() > 0;