uk.ac.ebi.intact.application.dataConversion.psiUpload.util.report.MessageHolder.addParserMessage java code examples

Common ways to obtain MessageHolder

private void myMethod () {
 MessageHolder m =Conversion.psiUpload.util.report.MessageHolder messageHolder;messageHolder.getInstance()
Smart code suggestions by Codota
}

  private static XrefTag createXref( final Element xrefNode, final short type ) {

    XrefTag xref = null;
    try {
      String db = xrefNode.getAttribute( "db" );
      if ( db != null ) {
        db = db.toLowerCase();
      }

      xref = new XrefTag( type,
                xrefNode.getAttribute( "id" ),
                db,
                xrefNode.getAttribute( "secondary" ),
                xrefNode.getAttribute( "version" ) );

    } catch ( IllegalArgumentException e ) {
      MessageHolder.getInstance().addParserMessage( new Message( xrefNode, e.getMessage() ) );
    }

    return xref;
  }
}

  private static XrefTag createXref( final Element xrefNode, final short type ) {

    XrefTag xref = null;
    try {
      String db = xrefNode.getAttribute( "db" );
      if ( db != null ) {
        db = db.toLowerCase();
      }

      xref = new XrefTag( type,
                xrefNode.getAttribute( "id" ),
                db,
                xrefNode.getAttribute( "secondary" ),
                xrefNode.getAttribute( "version" ) );

    } catch ( IllegalArgumentException e ) {
      MessageHolder.getInstance().addParserMessage( new Message( xrefNode, e.getMessage() ) );
    }

    return xref;
  }
}

  private static XrefTag createXref( final Element xrefNode, final short type ) {

    XrefTag xref = null;
    try {
      String db = xrefNode.getAttribute( "db" );
      if ( db != null ) {
        db = db.toLowerCase();
      }

      xref = new XrefTag( type,
                xrefNode.getAttribute( "id" ),
                db,
                xrefNode.getAttribute( "secondary" ),
                xrefNode.getAttribute( "version" ) );

    } catch ( IllegalArgumentException e ) {
      MessageHolder.getInstance().addParserMessage( new Message( xrefNode, e.getMessage() ) );
    }

    return xref;
  }
}

  /**
   * Take &lt;featureList&gt; in parameter.
   *
   * @param element
   */
  public static Collection process( final Element element ) {

    Collection features = new ArrayList( 2 );

    final String name = element.getNodeName();
    if ( false == "featureList".equals( name ) ) {
      MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in a " +
                                        "featureList tag." ) );
      // TODO should we carry on here ? If the tag is not right ... the parsing can only fail !
    }

    final NodeList someFeatures = element.getElementsByTagName( "feature" );
    final int count = someFeatures.getLength();

    for ( int i = 0; i < count; i++ ) {
      final Node featureNode = someFeatures.item( i );

      final FeatureTag feature = FeatureParser.process( (Element) featureNode );

      features.add( feature );
    } // features

    return features;
  }
}

  /**
   * Take &lt;featureList&gt; in parameter.
   *
   * @param element
   */
  public static Collection process( final Element element ) {

    Collection features = new ArrayList( 2 );

    final String name = element.getNodeName();
    if ( false == "featureList".equals( name ) ) {
      MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in a " +
                                        "featureList tag." ) );
      // TODO should we carry on here ? If the tag is not right ... the parsing can only fail !
    }

    final NodeList someFeatures = element.getElementsByTagName( "feature" );
    final int count = someFeatures.getLength();

    for ( int i = 0; i < count; i++ ) {
      final Node featureNode = someFeatures.item( i );

      final FeatureTag feature = FeatureParser.process( (Element) featureNode );

      features.add( feature );
    } // features

    return features;
  }
}

  /**
   * Take &lt;featureList&gt; in parameter.
   *
   * @param element
   */
  public static Collection process( final Element element ) {

    Collection features = new ArrayList( 2 );

    final String name = element.getNodeName();
    if ( false == "featureList".equals( name ) ) {
      MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in a " +
                                        "featureList tag." ) );
      // TODO should we carry on here ? If the tag is not right ... the parsing can only fail !
    }

    final NodeList someFeatures = element.getElementsByTagName( "feature" );
    final int count = someFeatures.getLength();

    for ( int i = 0; i < count; i++ ) {
      final Node featureNode = someFeatures.item( i );

      final FeatureTag feature = FeatureParser.process( (Element) featureNode );

      features.add( feature );
    } // features

    return features;
  }
}

MessageHolder.getInstance().addParserMessage( new Message( entrySet, "ERROR - We should be in entrySet tag." ) );

MessageHolder.getInstance().addParserMessage( new Message( entrySet, "ERROR - We should be in entrySet tag." ) );

  /**
   * Process a &lt;cellType&gt; in an organism. <br> In order to map it to the IntAct data, we look for the psi-mi
   * <code>primaryRef</code>, and look-up in intact using its <code>id</code>.
   *
   * @param element &lt;cellType&gt;.
   *
   * @return a <code>CellTypeTag</code> if the XML contains a walid psi-mi descriptor.
   *
   * @see uk.ac.ebi.intact.application.dataConversion.psiUpload.model.CellTypeTag
   */
  public static ConfidenceTag process( final Element element ) {

    if ( false == "confidence".equals( element.getNodeName() ) ) {
      MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in confidence tag." ) );
    }

    String unit = element.getAttribute( "unit" );
    String value = element.getAttribute( "value" );

    ConfidenceTag confidenceTag = null;
    try {
      confidenceTag = new ConfidenceTag( unit, value );
    } catch ( IllegalArgumentException e ) {
      MessageHolder.getInstance().addParserMessage( new Message( element, e.getMessage() ) );
    }

    return confidenceTag;
  }
}

MessageHolder.getInstance().addParserMessage( new Message( entrySet, "ERROR - We should be in entrySet tag." ) );

  /**
   * Process a &lt;cellType&gt; in an organism. <br> In order to map it to the IntAct data, we look for the psi-mi
   * <code>primaryRef</code>, and look-up in intact using its <code>id</code>.
   *
   * @param element &lt;cellType&gt;.
   *
   * @return a <code>CellTypeTag</code> if the XML contains a walid psi-mi descriptor.
   *
   * @see uk.ac.ebi.intact.application.dataConversion.psiUpload.model.CellTypeTag
   */
  public static ConfidenceTag process( final Element element ) {

    if ( false == "confidence".equals( element.getNodeName() ) ) {
      MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in confidence tag." ) );
    }

    String unit = element.getAttribute( "unit" );
    String value = element.getAttribute( "value" );

    ConfidenceTag confidenceTag = null;
    try {
      confidenceTag = new ConfidenceTag( unit, value );
    } catch ( IllegalArgumentException e ) {
      MessageHolder.getInstance().addParserMessage( new Message( element, e.getMessage() ) );
    }

    return confidenceTag;
  }
}

  /**
   * Process a &lt;cellType&gt; in an organism. <br> In order to map it to the IntAct data, we look for the psi-mi
   * <code>primaryRef</code>, and look-up in intact using its <code>id</code>.
   *
   * @param element &lt;cellType&gt;.
   *
   * @return a <code>CellTypeTag</code> if the XML contains a walid psi-mi descriptor.
   *
   * @see uk.ac.ebi.intact.application.dataConversion.psiUpload.model.CellTypeTag
   */
  public static ConfidenceTag process( final Element element ) {

    if ( false == "confidence".equals( element.getNodeName() ) ) {
      MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in confidence tag." ) );
    }

    String unit = element.getAttribute( "unit" );
    String value = element.getAttribute( "value" );

    ConfidenceTag confidenceTag = null;
    try {
      confidenceTag = new ConfidenceTag( unit, value );
    } catch ( IllegalArgumentException e ) {
      MessageHolder.getInstance().addParserMessage( new Message( element, e.getMessage() ) );
    }

    return confidenceTag;
  }
}

/**
 * Extract Primary Xref.
 * <p/>
 * <pre>
 *   <xref>
 *       <primaryRef db="Swiss-Prot" id="P10912"/>
 *   </xref>
 * </pre>
 *
 * @return an intact Xref or null if something goes wrong.
 */
public static XrefTag processPrimaryRef( final Element root ) {
  XrefTag xref = null;
  final String nodeName = root.getNodeName();
  if ( false == "xref".equals( nodeName ) ) {
    MessageHolder.getInstance().addParserMessage( new Message( root, "ERROR - We should be in xref tag, <" + root.getNodeName() + "> instead." ) );
  }
  final Element xrefNode = DOMUtil.getFirstElement( root, "primaryRef" ); // and the secondary ?!
  try {
    xref = createXref( xrefNode, XrefTag.PRIMARY_REF );
  } catch ( IllegalArgumentException e ) {
    MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
  }
  return xref;
}

/**
 * Extract Primary Xref.
 * <p/>
 * <pre>
 *   <xref>
 *       <primaryRef db="Swiss-Prot" id="P10912"/>
 *   </xref>
 * </pre>
 *
 * @return an intact Xref or null if something goes wrong.
 */
public static XrefTag processPrimaryRef( final Element root ) {
  XrefTag xref = null;
  final String nodeName = root.getNodeName();
  if ( false == "xref".equals( nodeName ) ) {
    MessageHolder.getInstance().addParserMessage( new Message( root, "ERROR - We should be in xref tag, <" + root.getNodeName() + "> instead." ) );
  }
  final Element xrefNode = DOMUtil.getFirstElement( root, "primaryRef" ); // and the secondary ?!
  try {
    xref = createXref( xrefNode, XrefTag.PRIMARY_REF );
  } catch ( IllegalArgumentException e ) {
    MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
  }
  return xref;
}

/**
 * Extract Primary Xref.
 * <p/>
 * <pre>
 *   <xref>
 *       <primaryRef db="Swiss-Prot" id="P10912"/>
 *   </xref>
 * </pre>
 *
 * @return an intact Xref or null if something goes wrong.
 */
public static XrefTag processPrimaryRef( final Element root ) {
  XrefTag xref = null;
  final String nodeName = root.getNodeName();
  if ( false == "xref".equals( nodeName ) ) {
    MessageHolder.getInstance().addParserMessage( new Message( root, "ERROR - We should be in xref tag, <" + root.getNodeName() + "> instead." ) );
  }
  final Element xrefNode = DOMUtil.getFirstElement( root, "primaryRef" ); // and the secondary ?!
  try {
    xref = createXref( xrefNode, XrefTag.PRIMARY_REF );
  } catch ( IllegalArgumentException e ) {
    MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
  }
  return xref;
}

  MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in interactionType tag." ) );
  interactionType = new InteractionTypeTag( xref );
} catch ( IllegalArgumentException e ) {
  MessageHolder.getInstance().addParserMessage( new Message( element, e.getMessage() ) );

  MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in interactionType tag." ) );
  interactionType = new InteractionTypeTag( xref );
} catch ( IllegalArgumentException e ) {
  MessageHolder.getInstance().addParserMessage( new Message( element, e.getMessage() ) );

  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;
  }
}

  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;
  }
}

  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;
  }
}

Popular methods of MessageHolder

Popular in Java

Making http post requests using okhttp
requestLocationUpdates (LocationManager)
addToBackStack (FragmentTransaction)
onRequestPermissionsResult (Fragment)
Color (java.awt)
The Color class is used encapsulate colors in the default sRGB color space or colors in arbitrary co
PrintWriter (java.io)
Prints formatted representations of objects to a text-output stream. This class implements all of th
SocketException (java.net)
This SocketException may be thrown during socket creation or setting options, and is the superclass
Calendar (java.util)
Calendar is an abstract base class for converting between a Date object and a set of integer fields
LinkedList (java.util)
Doubly-linked list implementation of the List and Dequeinterfaces. Implements all optional list oper
Set (java.util)
A collection that contains no duplicate elements. More formally, sets contain no pair of elements e1

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

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

How to use
addParserMessage
method
in
uk.ac.ebi.intact.application.dataConversion.psiUpload.util.report.MessageHolder