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

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private void myMethod () {
 OutputStreamWriter o =OutputStream out;new OutputStreamWriter(out)
OutputStream out;String charsetName;new OutputStreamWriter(out, charsetName)
HttpURLConnection connection;new OutputStreamWriter(connection.getOutputStream())
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}

/**
 * Load all global Experiment and Interaction succeptible to be used by the interactions described in the PSI data.
 *
 * @param entry
 */
private static void loadGlobalContext( Element entry ) {
  // process all eventual experiment (COULD BE EMPTY)
  globalExperiments = new ExperimentListParser();
  globalExperiments.process( entry );
  // process all eventual interactors (COULD BE EMPTY)
  globalParticipants = new ParticipantListParser();
  globalParticipants.process( entry );
}

/**
 * Collect all primary and secondary Xrefs.
 * <p/>
 * <pre>
 *   <xref>
 *       <primaryRef db="Swiss-Prot" id="P10912"/>
 * <p/>
 *       <secondaryRef db="Swiss-Prot" id="P11111"/>
 *       <secondaryRef db="Swiss-Prot" id="P22222"/>
 *       <secondaryRef db="Swiss-Prot" id="P33333"/>
 *   </xref>
 * </pre>
 *
 * @return an intact Xref collection. Empty collection if something goes wrong.
 */
public static Collection process( final Element root ) {
  Collection xrefs;
  xrefs = processSecondaryRef( root );
  XrefTag xref = processPrimaryRef( root );
  if ( xref != null ) {
    xrefs.add( xref );
  }
  return xrefs;
}

  public static EntryTag process( Element entry ) {

    loadGlobalContext( entry );

    // process all interactions
    InteractionListParser interactionList = new InteractionListParser( globalExperiments, globalParticipants );
    Collection interactions = interactionList.process( entry );


    EntryTag entryTag = null;
    try {
      entryTag = new EntryTag( globalExperiments.getExperiments(),
                   globalParticipants.getInteractors(),
                   interactions );
    } catch ( IllegalArgumentException e ) {
      MessageHolder.getInstance().addParserMessage( new Message( entry, e.getMessage() ) );
    }

    return entryTag;
  }
}

CellTypeTag cellType = null;
if ( null != cellTypeElement ) {
  cellType = CellTypeParser.process( cellTypeElement );
TissueTag tissue = null;
if ( null != tissueElement ) {
  tissue = TissueParser.process( tissueElement );

  /**
   * @param entry
   */
  public Collection process( final Element entry ) {

    final Element interactionList = DOMUtil.getFirstElement( entry, "interactionList" );
    final NodeList someInteractions = interactionList.getElementsByTagName( "interaction" );
    final int count = someInteractions.getLength();

    final Collection interactions = new ArrayList( count );

    for ( int i = 0; i < count; i++ ) {
      final Element interactionNode = (Element) someInteractions.item( i );
      final InteractionParser interaction = new InteractionParser( experimentList, participantList,
                                     interactionNode );
      InteractionTag interactionTag = interaction.process();

      if ( interactionTag != null ) {
        interactions.add( interactionTag );
      }
    } // interactions

    return interactions;
  }
}

  /**
   * 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
    }
  }
}

  public static EntryTag process( Element entry ) {

    loadGlobalContext( entry );

    // process all interactions
    InteractionListParser interactionList = new InteractionListParser( globalExperiments, globalParticipants );
    Collection interactions = interactionList.process( entry );


    EntryTag entryTag = null;
    try {
      entryTag = new EntryTag( globalExperiments.getExperiments(),
                   globalParticipants.getInteractors(),
                   interactions );
    } catch ( IllegalArgumentException e ) {
      MessageHolder.getInstance().addParserMessage( new Message( entry, e.getMessage() ) );
    }

    return entryTag;
  }
}

/**
 * Load all global Experiment and Interaction succeptible to be used by the interactions described in the PSI data.
 *
 * @param entry
 */
private static void loadGlobalContext( Element entry ) {
  // process all eventual experiment (COULD BE EMPTY)
  globalExperiments = new ExperimentListParser();
  globalExperiments.process( entry );
  // process all eventual interactors (COULD BE EMPTY)
  globalParticipants = new ParticipantListParser();
  globalParticipants.process( entry );
}

CellTypeTag cellType = null;
if ( null != cellTypeElement ) {
  cellType = CellTypeParser.process( cellTypeElement );
TissueTag tissue = null;
if ( null != tissueElement ) {
  tissue = TissueParser.process( tissueElement );

/**
 * Collect all primary and secondary Xrefs.
 * <p/>
 * <pre>
 *   <xref>
 *       <primaryRef db="Swiss-Prot" id="P10912"/>
 * <p/>
 *       <secondaryRef db="Swiss-Prot" id="P11111"/>
 *       <secondaryRef db="Swiss-Prot" id="P22222"/>
 *       <secondaryRef db="Swiss-Prot" id="P33333"/>
 *   </xref>
 * </pre>
 *
 * @return an intact Xref collection. Empty collection if something goes wrong.
 */
public static Collection process( final Element root ) {
  Collection xrefs;
  xrefs = processSecondaryRef( root );
  XrefTag xref = processPrimaryRef( root );
  if ( xref != null ) {
    xrefs.add( xref );
  }
  return xrefs;
}

  /**
   * @param entry
   */
  public Collection process( final Element entry ) {

    final Element interactionList = DOMUtil.getFirstElement( entry, "interactionList" );
    final NodeList someInteractions = interactionList.getElementsByTagName( "interaction" );
    final int count = someInteractions.getLength();

    final Collection interactions = new ArrayList( count );

    for ( int i = 0; i < count; i++ ) {
      final Element interactionNode = (Element) someInteractions.item( i );
      final InteractionParser interaction = new InteractionParser( experimentList, participantList,
                                     interactionNode );
      InteractionTag interactionTag = interaction.process();

      if ( interactionTag != null ) {
        interactions.add( interactionTag );
      }
    } // interactions

    return interactions;
  }
}

  /**
   * 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
    }
  }
}

  public static EntryTag process( Element entry ) {

    loadGlobalContext( entry );

    // process all interactions
    InteractionListParser interactionList = new InteractionListParser( globalExperiments, globalParticipants );
    Collection interactions = interactionList.process( entry );


    EntryTag entryTag = null;
    try {
      entryTag = new EntryTag( globalExperiments.getExperiments(),
                   globalParticipants.getInteractors(),
                   interactions );
    } catch ( IllegalArgumentException e ) {
      MessageHolder.getInstance().addParserMessage( new Message( entry, e.getMessage() ) );
    }

    return entryTag;
  }
}

/**
 * Load all global Experiment and Interaction succeptible to be used by the interactions described in the PSI data.
 *
 * @param entry
 */
private static void loadGlobalContext( Element entry ) {
  // process all eventual experiment (COULD BE EMPTY)
  globalExperiments = new ExperimentListParser();
  globalExperiments.process( entry );
  // process all eventual interactors (COULD BE EMPTY)
  globalParticipants = new ParticipantListParser();
  globalParticipants.process( entry );
}

CellTypeTag cellType = null;
if ( null != cellTypeElement ) {
  cellType = CellTypeParser.process( cellTypeElement );
TissueTag tissue = null;
if ( null != tissueElement ) {
  tissue = TissueParser.process( tissueElement );

/**
 * Collect all primary and secondary Xrefs.
 * <p/>
 * <pre>
 *   <xref>
 *       <primaryRef db="Swiss-Prot" id="P10912"/>
 * <p/>
 *       <secondaryRef db="Swiss-Prot" id="P11111"/>
 *       <secondaryRef db="Swiss-Prot" id="P22222"/>
 *       <secondaryRef db="Swiss-Prot" id="P33333"/>
 *   </xref>
 * </pre>
 *
 * @return an intact Xref collection. Empty collection if something goes wrong.
 */
public static Collection process( final Element root ) {
  Collection xrefs;
  xrefs = processSecondaryRef( root );
  XrefTag xref = processPrimaryRef( root );
  if ( xref != null ) {
    xrefs.add( xref );
  }
  return xrefs;
}

  /**
   * @param entry
   */
  public Collection process( final Element entry ) {

    final Element interactionList = DOMUtil.getFirstElement( entry, "interactionList" );
    final NodeList someInteractions = interactionList.getElementsByTagName( "interaction" );
    final int count = someInteractions.getLength();

    final Collection interactions = new ArrayList( count );

    for ( int i = 0; i < count; i++ ) {
      final Element interactionNode = (Element) someInteractions.item( i );
      final InteractionParser interaction = new InteractionParser( experimentList, participantList,
                                     interactionNode );
      InteractionTag interactionTag = interaction.process();

      if ( interactionTag != null ) {
        interactions.add( interactionTag );
      }
    } // interactions

    return interactions;
  }
}

CellTypeTag cellType = null;
if ( null != cellTypeElement ) {
  cellType = CellTypeParser.process( cellTypeElement );
TissueTag tissue = null;
if ( null != tissueElement ) {
  tissue = TissueParser.process( tissueElement );

CellTypeTag cellType = null;
if ( null != cellTypeElement ) {
  cellType = CellTypeParser.process( cellTypeElement );
TissueTag tissue = null;
if ( null != tissueElement ) {
  tissue = TissueParser.process( tissueElement );

CellTypeTag cellType = null;
if ( null != cellTypeElement ) {
  cellType = CellTypeParser.process( cellTypeElement );
TissueTag tissue = null;
if ( null != tissueElement ) {
  tissue = TissueParser.process( tissueElement );

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