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uk.ac.ebi.intact.application.dataConversion.psiUpload.util
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How to use uk.ac.ebi.intact.application.dataConversion.psiUpload.util

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.psiUpload.util (Showing top 20 results out of 315)

origin: uk.ac.ebi.intact.util/data-conversion

  /**
   * Process a <interactorList>
   *
   * @param entry a <interactorList> Element
   */
  public void process( final Element entry ) {

    final Element proteinsList = DOMUtil.getFirstElement( entry, "interactorList" );
    if ( proteinsList != null ) {
      final NodeList someProteins = proteinsList.getElementsByTagName( "proteinInteractor" );
      for ( int i = 0; i < someProteins.getLength(); i++ ) {
        final Node interactor = someProteins.item( i );
        final ProteinInteractorParser proteinInteractor = new ProteinInteractorParser( this, (Element) interactor );

        final LabelValueBean lvb = proteinInteractor.process();
        if ( lvb != null ) {
          interactors.put( lvb.getLabel(), lvb.getValue() );
        }
      } // interactors
    }
  }
}
origin: uk.ac.ebi.intact.app/data-conversion

 &&
 false == "interaction".equals( name ) ) {
MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in either " +
                                  "entry or interaction tag." ) );
    experiments.put( lvb.getLabel(), lvb.getValue() );
origin: uk.ac.ebi.intact.util/data-conversion

  MessageHolder.getInstance().addParserMessage( new Message( root, "We should be in proteinInteractor tag." ) );
    final String msg = "WARNING - the protein id: " + id + " is defined several times. " +
              "The global definition will be used instead.";
    MessageHolder.getInstance().addParserMessage( new Message( root, msg ) );
    return new LabelValueBean( id, proteinInteractor );
} else {
  if ( CommandLineOptions.getInstance().hasDefaultInteractorTaxid() ) {
    final String defaultTaxid = CommandLineOptions.getInstance().getDefaultInteractorTaxid();
    hostOrganism = new OrganismTag( defaultTaxid );
  lvb = new LabelValueBean( id, new ProteinInteractorTag( shortlabel, fullname, xref, secondaryXrefs, aliases, hostOrganism, sequence ) );
} catch ( IllegalArgumentException e ) {
  MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
origin: uk.ac.ebi.intact.util/data-conversion

MessageHolder.getInstance().addParserMessage( new Message( root, "ERROR - We should be in interaction tag." ) );
  localExperiments.add( e );
} else {
  MessageHolder.getInstance().addParserMessage( new Message( experimentListElement,
                                "Experiment reference is unknown: " + ref ) );
        expressedInAnnotations.add( new ExpressedInTag( annotation ) );
      } catch ( IllegalArgumentException e ) {
        MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
    MessageHolder.getInstance().addParserMessage( new Message( participantElement, msg ) );
    final LabelValueBean lvb = proteinInteractor.process();
    if ( lvb != null ) {
      interactor = (ProteinInteractorTag) lvb.getValue();
      id = lvb.getLabel();
  MessageHolder.getInstance().addParserMessage( new Message( root, msg ) );
} else {
  final String msg = "ERROR - No role found under that participant, abort that interaction.";
  MessageHolder.getInstance().addParserMessage( new Message( root, msg ) );
                         isOverexpressedProtein ) );
} catch ( IllegalArgumentException e ) {
  MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
if ( CommandLineOptions.getInstance().hasDefaultInteractionType() ) {
origin: uk.ac.ebi.intact.util/data-conversion

  MessageHolder.getInstance().addParserMessage( new Message( root, "ERROR - We should be in experimentDescription tag." ) );
    final String msg = "WARNING - the experiment id: " + id + "is defined several times. " +
              "The global definition will be used instead.";
    MessageHolder.getInstance().addParserMessage( new Message( root, msg ) );
    return new LabelValueBean( id, experiment );
  MessageHolder.getInstance().addParserMessage( new Message( root, msg ) );
  MessageHolder.getInstance().addParserMessage( new Message( root, msg ) );
      interactionDetection = new InteractionDetectionTag( interactionXref );
    } catch ( IllegalArgumentException e ) {
      MessageHolder.getInstance().addParserMessage( new Message( interactionDetectionXrefElement,
                                    e.getMessage() ) );
      participantDetection = new ParticipantDetectionTag( participantXref );
    } catch ( IllegalArgumentException e ) {
      MessageHolder.getInstance().addParserMessage( new Message( participantDetectionXrefElement,
                                    e.getMessage() ) );
                        participantDetection );
} catch ( IllegalArgumentException e ) {
  MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
return new LabelValueBean( id, experiment );
origin: uk.ac.ebi.intact.app/data-conversion

boolean guiEnabled = CommandLineOptions.getInstance().isGuiEnabled();
Monitor monitor = null;
if ( guiEnabled ) {
origin: uk.ac.ebi.intact.app/data-conversion

MessageHolder.getInstance().addParserMessage( new Message( root, "ERROR - We should be in interaction tag." ) );
  localExperiments.add( e );
} else {
  MessageHolder.getInstance().addParserMessage( new Message( experimentListElement,
                                "Experiment reference is unknown: " + ref ) );
        expressedInAnnotations.add( new ExpressedInTag( annotation ) );
      } catch ( IllegalArgumentException e ) {
        MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
    MessageHolder.getInstance().addParserMessage( new Message( participantElement, msg ) );
    final LabelValueBean lvb = proteinInteractor.process();
    if ( lvb != null ) {
      interactor = (ProteinInteractorTag) lvb.getValue();
      id = lvb.getLabel();
  MessageHolder.getInstance().addParserMessage( new Message( root, msg ) );
} else {
  final String msg = "ERROR - No role found under that participant, abort that interaction.";
  MessageHolder.getInstance().addParserMessage( new Message( root, msg ) );
                         isOverexpressedProtein ) );
} catch ( IllegalArgumentException e ) {
  MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
if ( CommandLineOptions.getInstance().hasDefaultInteractionType() ) {
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

  MessageHolder.getInstance().addParserMessage( new Message( root, "We should be in proteinInteractor tag." ) );
    final String msg = "WARNING - the protein id: " + id + " is defined several times. " +
              "The global definition will be used instead.";
    MessageHolder.getInstance().addParserMessage( new Message( root, msg ) );
    return new LabelValueBean( id, proteinInteractor );
} else {
  if ( CommandLineOptions.getInstance().hasDefaultInteractorTaxid() ) {
    final String defaultTaxid = CommandLineOptions.getInstance().getDefaultInteractorTaxid();
    hostOrganism = new OrganismTag( defaultTaxid );
  lvb = new LabelValueBean( id, new ProteinInteractorTag( shortlabel, fullname, xref, secondaryXrefs, aliases, hostOrganism, sequence ) );
} catch ( IllegalArgumentException e ) {
  MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
origin: uk.ac.ebi.intact.util/data-conversion

 &&
 false == "interaction".equals( name ) ) {
MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in either " +
                                  "entry or interaction tag." ) );
    experiments.put( lvb.getLabel(), lvb.getValue() );
origin: uk.ac.ebi.intact.app/data-conversion

  MessageHolder.getInstance().addParserMessage( new Message( root, "ERROR - We should be in experimentDescription tag." ) );
    final String msg = "WARNING - the experiment id: " + id + "is defined several times. " +
              "The global definition will be used instead.";
    MessageHolder.getInstance().addParserMessage( new Message( root, msg ) );
    return new LabelValueBean( id, experiment );
  MessageHolder.getInstance().addParserMessage( new Message( root, msg ) );
  MessageHolder.getInstance().addParserMessage( new Message( root, msg ) );
      interactionDetection = new InteractionDetectionTag( interactionXref );
    } catch ( IllegalArgumentException e ) {
      MessageHolder.getInstance().addParserMessage( new Message( interactionDetectionXrefElement,
                                    e.getMessage() ) );
      participantDetection = new ParticipantDetectionTag( participantXref );
    } catch ( IllegalArgumentException e ) {
      MessageHolder.getInstance().addParserMessage( new Message( participantDetectionXrefElement,
                                    e.getMessage() ) );
                        participantDetection );
} catch ( IllegalArgumentException e ) {
  MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
return new LabelValueBean( id, experiment );
origin: uk.ac.ebi.intact.util/data-conversion

boolean guiEnabled = CommandLineOptions.getInstance().isGuiEnabled();
Monitor monitor = null;
if ( guiEnabled ) {
origin: uk.ac.ebi.intact.app/data-conversion

  /**
   * Process a &lt;interactorList&gt;
   *
   * @param entry a &lt;interactorList&gt; Element
   */
  public void process( final Element entry ) {

    final Element proteinsList = DOMUtil.getFirstElement( entry, "interactorList" );
    if ( proteinsList != null ) {
      final NodeList someProteins = proteinsList.getElementsByTagName( "proteinInteractor" );
      for ( int i = 0; i < someProteins.getLength(); i++ ) {
        final Node interactor = someProteins.item( i );
        final ProteinInteractorParser proteinInteractor = new ProteinInteractorParser( this, (Element) interactor );

        final LabelValueBean lvb = proteinInteractor.process();
        if ( lvb != null ) {
          interactors.put( lvb.getLabel(), lvb.getValue() );
        }
      } // interactors
    }
  }
}
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

MessageHolder.getInstance().addParserMessage( new Message( root, "ERROR - We should be in interaction tag." ) );
  localExperiments.add( e );
} else {
  MessageHolder.getInstance().addParserMessage( new Message( experimentListElement,
                                "Experiment reference is unknown: " + ref ) );
        expressedInAnnotations.add( new ExpressedInTag( annotation ) );
      } catch ( IllegalArgumentException e ) {
        MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
    MessageHolder.getInstance().addParserMessage( new Message( participantElement, msg ) );
    final LabelValueBean lvb = proteinInteractor.process();
    if ( lvb != null ) {
      interactor = (ProteinInteractorTag) lvb.getValue();
      id = lvb.getLabel();
  MessageHolder.getInstance().addParserMessage( new Message( root, msg ) );
} else {
  final String msg = "ERROR - No role found under that participant, abort that interaction.";
  MessageHolder.getInstance().addParserMessage( new Message( root, msg ) );
                         isOverexpressedProtein ) );
} catch ( IllegalArgumentException e ) {
  MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
if ( CommandLineOptions.getInstance().hasDefaultInteractionType() ) {
origin: uk.ac.ebi.intact.app/data-conversion

  MessageHolder.getInstance().addParserMessage( new Message( root, "We should be in proteinInteractor tag." ) );
    final String msg = "WARNING - the protein id: " + id + " is defined several times. " +
              "The global definition will be used instead.";
    MessageHolder.getInstance().addParserMessage( new Message( root, msg ) );
    return new LabelValueBean( id, proteinInteractor );
} else {
  if ( CommandLineOptions.getInstance().hasDefaultInteractorTaxid() ) {
    final String defaultTaxid = CommandLineOptions.getInstance().getDefaultInteractorTaxid();
    hostOrganism = new OrganismTag( defaultTaxid );
  lvb = new LabelValueBean( id, new ProteinInteractorTag( shortlabel, fullname, xref, secondaryXrefs, aliases, hostOrganism, sequence ) );
} catch ( IllegalArgumentException e ) {
  MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

 &&
 false == "interaction".equals( name ) ) {
MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in either " +
                                  "entry or interaction tag." ) );
    experiments.put( lvb.getLabel(), lvb.getValue() );
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

boolean guiEnabled = CommandLineOptions.getInstance().isGuiEnabled();
Monitor monitor = null;
if ( guiEnabled ) {
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

  /**
   * Process a &lt;interactorList&gt;
   *
   * @param entry a &lt;interactorList&gt; Element
   */
  public void process( final Element entry ) {

    final Element proteinsList = DOMUtil.getFirstElement( entry, "interactorList" );
    if ( proteinsList != null ) {
      final NodeList someProteins = proteinsList.getElementsByTagName( "proteinInteractor" );
      for ( int i = 0; i < someProteins.getLength(); i++ ) {
        final Node interactor = someProteins.item( i );
        final ProteinInteractorParser proteinInteractor = new ProteinInteractorParser( this, (Element) interactor );

        final LabelValueBean lvb = proteinInteractor.process();
        if ( lvb != null ) {
          interactors.put( lvb.getLabel(), lvb.getValue() );
        }
      } // interactors
    }
  }
}
origin: uk.ac.ebi.intact.app/data-conversion

boolean guiEnabled = CommandLineOptions.getInstance().isGuiEnabled();
Monitor monitor = null;
boolean displayProgressBar = guiEnabled && keys.size() > 0;
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

boolean guiEnabled = CommandLineOptions.getInstance().isGuiEnabled();
Monitor monitor = null;
boolean displayProgressBar = guiEnabled && keys.size() > 0;
origin: uk.ac.ebi.intact.util/data-conversion

boolean guiEnabled = CommandLineOptions.getInstance().isGuiEnabled();
Monitor monitor = null;
boolean displayProgressBar = guiEnabled && keys.size() > 0;
uk.ac.ebi.intact.application.dataConversion.psiUpload.util

Most used classes

  • CommandLineOptions
  • LabelValueBean
    That class is used internally to return a mapping id -> created object
  • Message
    That class .
  • MessageHolder
    That class hold messages created during the Paring and checking process.
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