Collection experiments = interaction.getExperiments(); for ( Iterator iterator = experiments.iterator(); iterator.hasNext(); ) { ExperimentDescriptionTag experimentDescription = (ExperimentDescriptionTag) iterator.next(); final Collection participants = interaction.getParticipants(); final InteractionTypeTag interactionType = interaction.getInteractionType(); InteractionTypeChecker.check( interactionType ); Collection xrefs = interaction.getXrefs(); for ( Iterator iterator = xrefs.iterator(); iterator.hasNext(); ) { XrefTag xref = (XrefTag) iterator.next(); final Collection annotations = interaction.getAnnotations(); int countKd = 0; for ( Iterator iterator = annotations.iterator(); iterator.hasNext(); ) {
System.out.println( "Compare interactions: " + psi + "\n and " + intactInteraction ); if ( psi.getParticipants().size() == intactInteraction.getComponents().size() ) { Collection psiExperiments = psi.getExperiments(); for ( Iterator iterator = psiExperiments.iterator(); iterator.hasNext(); ) { ExperimentDescriptionTag psiExperiment = (ExperimentDescriptionTag) iterator.next(); Collection psiComponents = psi.getParticipants(); boolean allComponentFound = true; for ( Iterator iterator2 = psiComponents.iterator(); iterator2.hasNext() && allComponentFound; ) sb.append( NEW_LINE ); sb.append( "and involving the following components: " ); for ( Iterator iterator2 = psi.getParticipants().iterator(); iterator2.hasNext(); ) { ProteinParticipantTag psiComponent = (ProteinParticipantTag) iterator2.next(); sb.append( NEW_LINE ).append( '[' );
Collection e = interactionTag.getExperiments(); Collection experiments = new ArrayList( e.size() ); for ( Iterator iterator = e.iterator(); iterator.hasNext(); ) { final Collection components = new ArrayList( interactionTag.getParticipants().size() ); final String cvInteractionTypeId = interactionTag.getInteractionType().getPsiDefinition().getId(); CvInteractionType cvInteractionType = InteractionTypeChecker.getCvInteractionType( cvInteractionTypeId ); interaction.setFullName( interactionTag.getFullname() ); Collection annotations = interactionTag.getAnnotations(); for ( Iterator iterator1 = annotations.iterator(); iterator1.hasNext(); ) { AnnotationTag annotationTag = (AnnotationTag) iterator1.next(); annotations = interactionTag.getAnnotations(); for ( Iterator iterator2 = annotations.iterator(); iterator2.hasNext(); ) { final AnnotationTag annotationTag = (AnnotationTag) iterator2.next(); Collection xrefs = interactionTag.getXrefs(); for ( Iterator iterator1 = xrefs.iterator(); iterator1.hasNext(); ) { final XrefTag xrefTag = (XrefTag) iterator1.next(); final ConfidenceTag confidence = interactionTag.getConfidence(); if ( confidence != null ) { final Collection participants = interactionTag.getParticipants(); for ( Iterator iterator4 = participants.iterator(); iterator4.hasNext(); ) { ProteinParticipantTag proteinParticipant = (ProteinParticipantTag) iterator4.next();
final InteractionTag interaction = (InteractionTag) iterator.next(); if ( guiEnabled ) { String name = interaction.getShortlabel(); if ( name == null ) { name = "no shortlabel specified";
final Collection proteins = interaction.getParticipants(); for ( Iterator iterator = proteins.iterator(); iterator.hasNext(); ) { ProteinParticipantTag proteinParticipant = (ProteinParticipantTag) iterator.next();
interactionTag = new InteractionTag( shortLabel, fullName, localExperiments,
Collection e = interactionTag.getExperiments(); Collection experiments = new ArrayList( e.size() ); for ( Iterator iterator = e.iterator(); iterator.hasNext(); ) { final Collection components = new ArrayList( interactionTag.getParticipants().size() ); final String cvInteractionTypeId = interactionTag.getInteractionType().getPsiDefinition().getId(); CvInteractionType cvInteractionType = InteractionTypeChecker.getCvInteractionType( cvInteractionTypeId ); interaction.setFullName( interactionTag.getFullname() ); Collection annotations = interactionTag.getAnnotations(); for ( Iterator iterator1 = annotations.iterator(); iterator1.hasNext(); ) { AnnotationTag annotationTag = (AnnotationTag) iterator1.next(); annotations = interactionTag.getAnnotations(); for ( Iterator iterator2 = annotations.iterator(); iterator2.hasNext(); ) { final AnnotationTag annotationTag = (AnnotationTag) iterator2.next(); Collection xrefs = interactionTag.getXrefs(); for ( Iterator iterator1 = xrefs.iterator(); iterator1.hasNext(); ) { final XrefTag xrefTag = (XrefTag) iterator1.next(); final ConfidenceTag confidence = interactionTag.getConfidence(); if ( confidence != null ) { final Collection participants = interactionTag.getParticipants(); for ( Iterator iterator4 = participants.iterator(); iterator4.hasNext(); ) { ProteinParticipantTag proteinParticipant = (ProteinParticipantTag) iterator4.next();
System.out.println( "Compare interactions: " + psi + "\n and " + intactInteraction ); if ( psi.getParticipants().size() == intactInteraction.getComponents().size() ) { Collection psiExperiments = psi.getExperiments(); for ( Iterator iterator = psiExperiments.iterator(); iterator.hasNext(); ) { ExperimentDescriptionTag psiExperiment = (ExperimentDescriptionTag) iterator.next(); Collection psiComponents = psi.getParticipants(); boolean allComponentFound = true; for ( Iterator iterator2 = psiComponents.iterator(); iterator2.hasNext() && allComponentFound; ) sb.append( NEW_LINE ); sb.append( "and involving the following components: " ); for ( Iterator iterator2 = psi.getParticipants().iterator(); iterator2.hasNext(); ) { ProteinParticipantTag psiComponent = (ProteinParticipantTag) iterator2.next(); sb.append( NEW_LINE ).append( '[' );
final InteractionTag interaction = (InteractionTag) iterator.next(); if ( guiEnabled ) { String name = interaction.getShortlabel(); if ( name == null ) { name = "no shortlabel specified";
final Collection proteins = interaction.getParticipants(); for ( Iterator iterator = proteins.iterator(); iterator.hasNext(); ) { ProteinParticipantTag proteinParticipant = (ProteinParticipantTag) iterator.next();
interactionTag = new InteractionTag( shortLabel, fullName, localExperiments,
Collection e = interactionTag.getExperiments(); Collection experiments = new ArrayList( e.size() ); for ( Iterator iterator = e.iterator(); iterator.hasNext(); ) { final Collection components = new ArrayList( interactionTag.getParticipants().size() ); final String cvInteractionTypeId = interactionTag.getInteractionType().getPsiDefinition().getId(); CvInteractionType cvInteractionType = InteractionTypeChecker.getCvInteractionType( cvInteractionTypeId ); interaction.setFullName( interactionTag.getFullname() ); Collection annotations = interactionTag.getAnnotations(); for ( Iterator iterator1 = annotations.iterator(); iterator1.hasNext(); ) { AnnotationTag annotationTag = (AnnotationTag) iterator1.next(); annotations = interactionTag.getAnnotations(); for ( Iterator iterator2 = annotations.iterator(); iterator2.hasNext(); ) { final AnnotationTag annotationTag = (AnnotationTag) iterator2.next(); Collection xrefs = interactionTag.getXrefs(); for ( Iterator iterator1 = xrefs.iterator(); iterator1.hasNext(); ) { final XrefTag xrefTag = (XrefTag) iterator1.next(); final ConfidenceTag confidence = interactionTag.getConfidence(); if ( confidence != null ) { final Collection participants = interactionTag.getParticipants(); for ( Iterator iterator4 = participants.iterator(); iterator4.hasNext(); ) { ProteinParticipantTag proteinParticipant = (ProteinParticipantTag) iterator4.next();
Collection experiments = interaction.getExperiments(); for ( Iterator iterator = experiments.iterator(); iterator.hasNext(); ) { ExperimentDescriptionTag experimentDescription = (ExperimentDescriptionTag) iterator.next(); final Collection participants = interaction.getParticipants(); final InteractionTypeTag interactionType = interaction.getInteractionType(); InteractionTypeChecker.check( interactionType ); Collection xrefs = interaction.getXrefs(); for ( Iterator iterator = xrefs.iterator(); iterator.hasNext(); ) { XrefTag xref = (XrefTag) iterator.next(); final Collection annotations = interaction.getAnnotations(); int countKd = 0; for ( Iterator iterator = annotations.iterator(); iterator.hasNext(); ) {
System.out.println( "Compare interactions: " + psi + "\n and " + intactInteraction ); if ( psi.getParticipants().size() == intactInteraction.getComponents().size() ) { Collection psiExperiments = psi.getExperiments(); for ( Iterator iterator = psiExperiments.iterator(); iterator.hasNext(); ) { ExperimentDescriptionTag psiExperiment = (ExperimentDescriptionTag) iterator.next(); Collection psiComponents = psi.getParticipants(); boolean allComponentFound = true; for ( Iterator iterator2 = psiComponents.iterator(); iterator2.hasNext() && allComponentFound; ) sb.append( NEW_LINE ); sb.append( "and involving the following components: " ); for ( Iterator iterator2 = psi.getParticipants().iterator(); iterator2.hasNext(); ) { ProteinParticipantTag psiComponent = (ProteinParticipantTag) iterator2.next(); sb.append( NEW_LINE ).append( '[' );
final InteractionTag interaction = (InteractionTag) iterator.next(); if ( guiEnabled ) { String name = interaction.getShortlabel(); if ( name == null ) { name = "no shortlabel specified";
final Collection proteins = interaction.getParticipants(); for ( Iterator iterator = proteins.iterator(); iterator.hasNext(); ) { ProteinParticipantTag proteinParticipant = (ProteinParticipantTag) iterator.next();
interactionTag = new InteractionTag( shortLabel, fullName, localExperiments,
Collection experiments = interaction.getExperiments(); for ( Iterator iterator = experiments.iterator(); iterator.hasNext(); ) { ExperimentDescriptionTag experimentDescription = (ExperimentDescriptionTag) iterator.next(); final Collection participants = interaction.getParticipants(); final InteractionTypeTag interactionType = interaction.getInteractionType(); InteractionTypeChecker.check( interactionType ); Collection xrefs = interaction.getXrefs(); for ( Iterator iterator = xrefs.iterator(); iterator.hasNext(); ) { XrefTag xref = (XrefTag) iterator.next(); final Collection annotations = interaction.getAnnotations(); int countKd = 0; for ( Iterator iterator = annotations.iterator(); iterator.hasNext(); ) {