uk.ac.ebi.intact.application.dataConversion.psiUpload.persister java code examples

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private void myMethod () {
 List l =new LinkedList()
Collections.emptyList()
new ArrayList()
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}

  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;

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