public String toString() { return "ExperimentWrapper{" + "experiment=" + experiment.getShortlabel() + ", shortlabel='" + shortlabel + "'" + "}"; } }
public static void check( final ExperimentDescriptionTag experimentDescription, final BioSourceFactory bioSourceFactory ) { final String shortlabel = experimentDescription.getShortlabel(); if ( cache.get( shortlabel ) == null ) { final HostOrganismTag hostOrganism = experimentDescription.getHostOrganism(); HostOrganismChecker.check( hostOrganism, bioSourceFactory ); final InteractionDetectionTag interactionDetection = experimentDescription.getInteractionDetection(); InteractionDetectionChecker.check( interactionDetection ); final ParticipantDetectionTag participantDetection = experimentDescription.getParticipantDetection(); ParticipantDetectionChecker.check( participantDetection ); XrefChecker.check( experimentDescription.getBibRef() ); Collection additionalBibRef = experimentDescription.getAdditionalBibRef(); for ( Iterator iterator = additionalBibRef.iterator(); iterator.hasNext(); ) { XrefTag bibRef = (XrefTag) iterator.next(); final Collection xrefs = experimentDescription.getXrefs(); for ( Iterator iterator = xrefs.iterator(); iterator.hasNext(); ) { XrefTag xref = (XrefTag) iterator.next(); final Collection annotations = experimentDescription.getAnnotations(); for ( Iterator iterator = annotations.iterator(); iterator.hasNext(); ) { AnnotationTag annotation = (AnnotationTag) iterator.next();
psiExperiment.getShortlabel() + ") and intact(" + intactExperiment.getShortLabel() + ")" ); if ( intactExperiment.getShortLabel().equals( psiExperiment.getShortlabel() ) ) { for ( Iterator iterator2 = experiments.iterator(); iterator2.hasNext() && !found; ) { experimentWrapper = (ExperimentWrapper) iterator2.next(); if ( experimentWrapper.getExperiment().equals( psiExperiment ) ) { found = true;
experiment = new ExperimentDescriptionTag( shortLabel, fullName, bibXref,
public static void check( final ExperimentDescriptionTag experimentDescription, final BioSourceFactory bioSourceFactory ) { final String shortlabel = experimentDescription.getShortlabel(); if ( cache.get( shortlabel ) == null ) { final HostOrganismTag hostOrganism = experimentDescription.getHostOrganism(); HostOrganismChecker.check( hostOrganism, bioSourceFactory ); final InteractionDetectionTag interactionDetection = experimentDescription.getInteractionDetection(); InteractionDetectionChecker.check( interactionDetection ); final ParticipantDetectionTag participantDetection = experimentDescription.getParticipantDetection(); ParticipantDetectionChecker.check( participantDetection ); XrefChecker.check( experimentDescription.getBibRef() ); Collection additionalBibRef = experimentDescription.getAdditionalBibRef(); for ( Iterator iterator = additionalBibRef.iterator(); iterator.hasNext(); ) { XrefTag bibRef = (XrefTag) iterator.next(); final Collection xrefs = experimentDescription.getXrefs(); for ( Iterator iterator = xrefs.iterator(); iterator.hasNext(); ) { XrefTag xref = (XrefTag) iterator.next(); final Collection annotations = experimentDescription.getAnnotations(); for ( Iterator iterator = annotations.iterator(); iterator.hasNext(); ) { AnnotationTag annotation = (AnnotationTag) iterator.next();
psiExperiment.getShortlabel() + ") and intact(" + intactExperiment.getShortLabel() + ")" ); if ( intactExperiment.getShortLabel().equals( psiExperiment.getShortlabel() ) ) { for ( Iterator iterator2 = experiments.iterator(); iterator2.hasNext() && !found; ) { experimentWrapper = (ExperimentWrapper) iterator2.next(); if ( experimentWrapper.getExperiment().equals( psiExperiment ) ) { found = true;
experiment = new ExperimentDescriptionTag( shortLabel, fullName, bibXref,
public static void check( final ExperimentDescriptionTag experimentDescription, final BioSourceFactory bioSourceFactory ) { final String shortlabel = experimentDescription.getShortlabel(); if ( cache.get( shortlabel ) == null ) { final HostOrganismTag hostOrganism = experimentDescription.getHostOrganism(); HostOrganismChecker.check( hostOrganism, bioSourceFactory ); final InteractionDetectionTag interactionDetection = experimentDescription.getInteractionDetection(); InteractionDetectionChecker.check( interactionDetection ); final ParticipantDetectionTag participantDetection = experimentDescription.getParticipantDetection(); ParticipantDetectionChecker.check( participantDetection ); XrefChecker.check( experimentDescription.getBibRef() ); Collection additionalBibRef = experimentDescription.getAdditionalBibRef(); for ( Iterator iterator = additionalBibRef.iterator(); iterator.hasNext(); ) { XrefTag bibRef = (XrefTag) iterator.next(); final Collection xrefs = experimentDescription.getXrefs(); for ( Iterator iterator = xrefs.iterator(); iterator.hasNext(); ) { XrefTag xref = (XrefTag) iterator.next(); final Collection annotations = experimentDescription.getAnnotations(); for ( Iterator iterator = annotations.iterator(); iterator.hasNext(); ) { AnnotationTag annotation = (AnnotationTag) iterator.next();
psiExperiment.getShortlabel() + ") and intact(" + intactExperiment.getShortLabel() + ")" ); if ( intactExperiment.getShortLabel().equals( psiExperiment.getShortlabel() ) ) { for ( Iterator iterator2 = experiments.iterator(); iterator2.hasNext() && !found; ) { experimentWrapper = (ExperimentWrapper) iterator2.next(); if ( experimentWrapper.getExperiment().equals( psiExperiment ) ) { found = true;
public String toString() { return "ExperimentWrapper{" + "experiment=" + experiment.getShortlabel() + ", shortlabel='" + shortlabel + "'" + "}"; } }
experiment = new ExperimentDescriptionTag( shortLabel, fullName, bibXref,
final String shortlabel = experimentDescription.getShortlabel(); final BioSource biosource = HostOrganismChecker.getBioSource( experimentDescription.getHostOrganism() ); experiment.setFullName( experimentDescription.getFullname() ); final String participantDetectionId = experimentDescription.getParticipantDetection().getPsiDefinition().getId(); final CvIdentification cvIdentification = ParticipantDetectionChecker.getCvIdentification( participantDetectionId ); experiment.setCvIdentification( cvIdentification ); final String interactionDetectionId = experimentDescription.getInteractionDetection().getPsiDefinition().getId(); final CvInteraction cvInteraction = InteractionDetectionChecker.getCvInteraction( interactionDetectionId ); experiment.setCvInteraction( cvInteraction ); final XrefTag bibRef = experimentDescription.getBibRef(); final ExperimentXref primaryXref = new ExperimentXref( institution, XrefChecker.getCvDatabase( bibRef.getDb() ), final Collection secondaryPubmedXrefs = experimentDescription.getAdditionalBibRef(); for ( Iterator iterator = secondaryPubmedXrefs.iterator(); iterator.hasNext(); ) { XrefTag xrefTag = (XrefTag) iterator.next(); final Collection annotations = experimentDescription.getAnnotations(); for ( Iterator iterator = annotations.iterator(); iterator.hasNext(); ) { final AnnotationTag annotationTag = (AnnotationTag) iterator.next(); final Collection xrefs = experimentDescription.getXrefs(); for ( Iterator iterator = xrefs.iterator(); iterator.hasNext(); ) { XrefTag xrefTag = (XrefTag) iterator.next();
public String toString() { return "ExperimentWrapper{" + "experiment=" + experiment.getShortlabel() + ", shortlabel='" + shortlabel + "'" + "}"; } }
final String shortlabel = experimentDescription.getShortlabel(); final BioSource biosource = HostOrganismChecker.getBioSource( experimentDescription.getHostOrganism() ); experiment.setFullName( experimentDescription.getFullname() ); final String participantDetectionId = experimentDescription.getParticipantDetection().getPsiDefinition().getId(); final CvIdentification cvIdentification = ParticipantDetectionChecker.getCvIdentification( participantDetectionId ); experiment.setCvIdentification( cvIdentification ); final String interactionDetectionId = experimentDescription.getInteractionDetection().getPsiDefinition().getId(); final CvInteraction cvInteraction = InteractionDetectionChecker.getCvInteraction( interactionDetectionId ); experiment.setCvInteraction( cvInteraction ); final XrefTag bibRef = experimentDescription.getBibRef(); final ExperimentXref primaryXref = new ExperimentXref( institution, XrefChecker.getCvDatabase( bibRef.getDb() ), final Collection secondaryPubmedXrefs = experimentDescription.getAdditionalBibRef(); for ( Iterator iterator = secondaryPubmedXrefs.iterator(); iterator.hasNext(); ) { XrefTag xrefTag = (XrefTag) iterator.next(); final Collection annotations = experimentDescription.getAnnotations(); for ( Iterator iterator = annotations.iterator(); iterator.hasNext(); ) { final AnnotationTag annotationTag = (AnnotationTag) iterator.next(); final Collection xrefs = experimentDescription.getXrefs(); for ( Iterator iterator = xrefs.iterator(); iterator.hasNext(); ) { XrefTag xrefTag = (XrefTag) iterator.next();
oneExperimentHasAlreadyBeenUpdated = true; if ( DEBUG ) { System.out.println( "Experiment " + experimentWrapper.getExperiment().getShortlabel() + " has been given the interaction shortlabel: " + label );
final String shortlabel = experimentDescription.getShortlabel(); final BioSource biosource = HostOrganismChecker.getBioSource( experimentDescription.getHostOrganism() ); experiment.setFullName( experimentDescription.getFullname() ); final String participantDetectionId = experimentDescription.getParticipantDetection().getPsiDefinition().getId(); final CvIdentification cvIdentification = ParticipantDetectionChecker.getCvIdentification( participantDetectionId ); experiment.setCvIdentification( cvIdentification ); final String interactionDetectionId = experimentDescription.getInteractionDetection().getPsiDefinition().getId(); final CvInteraction cvInteraction = InteractionDetectionChecker.getCvInteraction( interactionDetectionId ); experiment.setCvInteraction( cvInteraction ); final XrefTag bibRef = experimentDescription.getBibRef(); final ExperimentXref primaryXref = new ExperimentXref( institution, XrefChecker.getCvDatabase( bibRef.getDb() ), final Collection secondaryPubmedXrefs = experimentDescription.getAdditionalBibRef(); for ( Iterator iterator = secondaryPubmedXrefs.iterator(); iterator.hasNext(); ) { XrefTag xrefTag = (XrefTag) iterator.next(); final Collection annotations = experimentDescription.getAnnotations(); for ( Iterator iterator = annotations.iterator(); iterator.hasNext(); ) { final AnnotationTag annotationTag = (AnnotationTag) iterator.next(); final Collection xrefs = experimentDescription.getXrefs(); for ( Iterator iterator = xrefs.iterator(); iterator.hasNext(); ) { XrefTag xrefTag = (XrefTag) iterator.next();
oneExperimentHasAlreadyBeenUpdated = true; if ( DEBUG ) { System.out.println( "Experiment " + experimentWrapper.getExperiment().getShortlabel() + " has been given the interaction shortlabel: " + label );
oneExperimentHasAlreadyBeenUpdated = true; if ( DEBUG ) { System.out.println( "Experiment " + experimentWrapper.getExperiment().getShortlabel() + " has been given the interaction shortlabel: " + label );