public static void persist( final EntrySetTag entrySet ) throws IntactException { final Collection entries = entrySet.getEntries(); for ( Iterator iterator = entries.iterator(); iterator.hasNext(); ) { final EntryTag entry = (EntryTag) iterator.next(); EntryPersister.persist( entry ); } } }
ProteinParticipantTag proteinParticipant = (ProteinParticipantTag) iterator.next(); final String role = proteinParticipant.getRole(); final ProteinHolder proteinHolder = getProtein( proteinParticipant ); final String geneName = getGeneName( proteinHolder ); Arrays.sort( _geneNames, new GeneNameIgnoreCaseComparator() ); baitShortlabel = getLabelFromCollection( baits, true ); // fail on error preyShortlabel = getLabelFromCollection( preys, false ); // don't fail on error if ( preyShortlabel == null ) { preyShortlabel = getLabelFromCollection( neutrals, true ); // fail on error createInteractionShortLabels( interaction, experiments, baitShortlabel, preyShortlabel );
Arrays.sort( _geneNames, new GeneNameIgnoreCaseComparator() ); shortlabel = (String) _geneNames[ 0 ]; break;
for ( Iterator iterator = e.iterator(); iterator.hasNext(); ) { ExperimentDescriptionTag experimentDescription = (ExperimentDescriptionTag) iterator.next(); experiments.add( new ExperimentWrapper( experimentDescription ) ); createShortlabel( interactionTag, experiments ); ExperimentWrapper experimentWrapper = (ExperimentWrapper) iterator.next(); ExperimentDescriptionTag psiExperiment = experimentWrapper.getExperiment(); Experiment intactExperiment = ExperimentDescriptionPersister.persist( psiExperiment ); final String shortlabel = experimentWrapper.getShortlabel(); Annotation annotation = searchIntactAnnotation( annotationTag ); for ( Iterator iterator4 = participants.iterator(); iterator4.hasNext(); ) { ProteinParticipantTag proteinParticipant = (ProteinParticipantTag) iterator4.next(); ProteinParticipantPersister.persist( proteinParticipant, interaction );
if ( !experimentWrapper.hasShortlabel() ) { atLeastOneInteractionWithoutShortlabel = true; // exit the loop. if ( DEBUG ) { if ( !experimentWrapper.hasShortlabel() ) { experimentWrapper.setShortlabel( label ); oneExperimentHasAlreadyBeenUpdated = true; if ( DEBUG ) { System.out.println( "Experiment " + experimentWrapper.getExperiment().getShortlabel() + " has been given the interaction shortlabel: " + label ); alreadyExistsInIntact( psiInteraction, experiments, intactInteraction ); // update experiments !
final ExperimentDescriptionTag experimentDescription = (ExperimentDescriptionTag) experimentDescriptions.get( key ); ExperimentDescriptionPersister.persist( experimentDescription ); final InteractionTag interaction = (InteractionTag) iterator.next(); try { Collection createdInteractions = InteractionPersister.persist( interaction );
FeatureTag featureTag = (FeatureTag) iterator.next(); FeaturePersister.persist( featureTag, component, protein );
for ( Iterator iterator = e.iterator(); iterator.hasNext(); ) { ExperimentDescriptionTag experimentDescription = (ExperimentDescriptionTag) iterator.next(); experiments.add( new ExperimentWrapper( experimentDescription ) ); createShortlabel( interactionTag, experiments ); ExperimentWrapper experimentWrapper = (ExperimentWrapper) iterator.next(); ExperimentDescriptionTag psiExperiment = experimentWrapper.getExperiment(); Experiment intactExperiment = ExperimentDescriptionPersister.persist( psiExperiment ); final String shortlabel = experimentWrapper.getShortlabel(); Annotation annotation = searchIntactAnnotation( annotationTag ); for ( Iterator iterator4 = participants.iterator(); iterator4.hasNext(); ) { ProteinParticipantTag proteinParticipant = (ProteinParticipantTag) iterator4.next(); ProteinParticipantPersister.persist( proteinParticipant, interaction );
ProteinParticipantTag proteinParticipant = (ProteinParticipantTag) iterator.next(); final String role = proteinParticipant.getRole(); final ProteinHolder proteinHolder = getProtein( proteinParticipant ); final String geneName = getGeneName( proteinHolder ); Arrays.sort( _geneNames, new GeneNameIgnoreCaseComparator() ); baitShortlabel = getLabelFromCollection( baits, true ); // fail on error preyShortlabel = getLabelFromCollection( preys, false ); // don't fail on error if ( preyShortlabel == null ) { preyShortlabel = getLabelFromCollection( neutrals, true ); // fail on error createInteractionShortLabels( interaction, experiments, baitShortlabel, preyShortlabel );
if ( !experimentWrapper.hasShortlabel() ) { atLeastOneInteractionWithoutShortlabel = true; // exit the loop. if ( DEBUG ) { if ( !experimentWrapper.hasShortlabel() ) { experimentWrapper.setShortlabel( label ); oneExperimentHasAlreadyBeenUpdated = true; if ( DEBUG ) { System.out.println( "Experiment " + experimentWrapper.getExperiment().getShortlabel() + " has been given the interaction shortlabel: " + label ); alreadyExistsInIntact( psiInteraction, experiments, intactInteraction ); // update experiments !
final ExperimentDescriptionTag experimentDescription = (ExperimentDescriptionTag) experimentDescriptions.get( key ); ExperimentDescriptionPersister.persist( experimentDescription ); final InteractionTag interaction = (InteractionTag) iterator.next(); try { Collection createdInteractions = InteractionPersister.persist( interaction );
public static void persist( final EntrySetTag entrySet ) throws IntactException { final Collection entries = entrySet.getEntries(); for ( Iterator iterator = entries.iterator(); iterator.hasNext(); ) { final EntryTag entry = (EntryTag) iterator.next(); EntryPersister.persist( entry ); } } }
Arrays.sort( _geneNames, new GeneNameIgnoreCaseComparator() ); shortlabel = (String) _geneNames[ 0 ]; break;
FeatureTag featureTag = (FeatureTag) iterator.next(); FeaturePersister.persist( featureTag, component, protein );
for ( Iterator iterator = e.iterator(); iterator.hasNext(); ) { ExperimentDescriptionTag experimentDescription = (ExperimentDescriptionTag) iterator.next(); experiments.add( new ExperimentWrapper( experimentDescription ) ); createShortlabel( interactionTag, experiments ); ExperimentWrapper experimentWrapper = (ExperimentWrapper) iterator.next(); ExperimentDescriptionTag psiExperiment = experimentWrapper.getExperiment(); Experiment intactExperiment = ExperimentDescriptionPersister.persist( psiExperiment ); final String shortlabel = experimentWrapper.getShortlabel(); Annotation annotation = searchIntactAnnotation( annotationTag ); for ( Iterator iterator4 = participants.iterator(); iterator4.hasNext(); ) { ProteinParticipantTag proteinParticipant = (ProteinParticipantTag) iterator4.next(); ProteinParticipantPersister.persist( proteinParticipant, interaction );
ProteinParticipantTag proteinParticipant = (ProteinParticipantTag) iterator.next(); final String role = proteinParticipant.getRole(); final ProteinHolder proteinHolder = getProtein( proteinParticipant ); final String geneName = getGeneName( proteinHolder ); Arrays.sort( _geneNames, new GeneNameIgnoreCaseComparator() ); baitShortlabel = getLabelFromCollection( baits, true ); // fail on error preyShortlabel = getLabelFromCollection( preys, false ); // don't fail on error if ( preyShortlabel == null ) { preyShortlabel = getLabelFromCollection( neutrals, true ); // fail on error createInteractionShortLabels( interaction, experiments, baitShortlabel, preyShortlabel );
if ( !experimentWrapper.hasShortlabel() ) { atLeastOneInteractionWithoutShortlabel = true; // exit the loop. if ( DEBUG ) { if ( !experimentWrapper.hasShortlabel() ) { experimentWrapper.setShortlabel( label ); oneExperimentHasAlreadyBeenUpdated = true; if ( DEBUG ) { System.out.println( "Experiment " + experimentWrapper.getExperiment().getShortlabel() + " has been given the interaction shortlabel: " + label ); alreadyExistsInIntact( psiInteraction, experiments, intactInteraction ); // update experiments !
final ExperimentDescriptionTag experimentDescription = (ExperimentDescriptionTag) experimentDescriptions.get( key ); ExperimentDescriptionPersister.persist( experimentDescription ); final InteractionTag interaction = (InteractionTag) iterator.next(); try { Collection createdInteractions = InteractionPersister.persist( interaction );
public static void persist( final EntrySetTag entrySet ) throws IntactException { final Collection entries = entrySet.getEntries(); for ( Iterator iterator = entries.iterator(); iterator.hasNext(); ) { final EntryTag entry = (EntryTag) iterator.next(); EntryPersister.persist( entry ); } } }
Arrays.sort( _geneNames, new GeneNameIgnoreCaseComparator() ); shortlabel = (String) _geneNames[ 0 ]; break;