uk.ac.ebi.intact.application.dataConversion.psiUpload.model.ExperimentDescriptionTag java code examples

  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 );

Javadoc

That class reflects what is needed to create an IntAct Experiment (non including interactions).

 
<experimentDescription id="EBI-12"> 
<names> 
<shortLabel>gavin-2002</shortLabel> 
<fullName>Functional organization of the yeast 
proteome by systematic analysis of protein complexes.</fullName> 
</names> 
<bibref> 
<xref> 
<primaryRef db="pubmed" id="11805826" secondary="" version=""/> 
</xref> 
</bibref> 
<hostOrganism ncbiTaxId="4932"> 
<names> 
<shortLabel>s cerevisiae</shortLabel> 
<fullName>Saccharomyces cerevisiae</fullName> 
</names> 
</hostOrganism> 
<interactionDetection> 
<names> 
<shortLabel>tandem affinity puri</shortLabel> 
<fullName>tandem affinity purification</fullName> 
</names> 
<xref> 
<primaryRef db="pubmed" id="10504710" secondary="" version=""/> 
<secondaryRef db="psi-mi" id="MI:0109" secondary="" version=""/> 
</xref> 
</interactionDetection> 
<participantDetection> 
<names> 
<shortLabel>peptide massfingerpr</shortLabel> 
<fullName>peptide massfingerprinting</fullName> 
</names> 
<xref> 
<primaryRef db="pubmed" id="11752590" secondary="" version=""/> 
<secondaryRef db="psi-mi" id="MI:0082" secondary="" version=""/> 
<secondaryRef db="pubmed" id="10967324" secondary="" version=""/> 
</xref> 
</participantDetection> 
</experimentDescription>

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How to useExperimentDescriptionTag in uk.ac.ebi.intact.application.dataConversion.psiUpload.model

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How to use
ExperimentDescriptionTag
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uk.ac.ebi.intact.application.dataConversion.psiUpload.model