public static String getSimpleElementText( final Element node, final String name ) { final Element namedElement = getFirstElement( node, name ); if ( namedElement == null ) { return null; } return getSimpleElementText( namedElement ); }
public static String getSimpleElementText( final Element node, final String name ) { final Element namedElement = getFirstElement( node, name ); if ( namedElement == null ) { return null; } return getSimpleElementText( namedElement ); }
public static String getSimpleElementText( final Element node, final String name ) { final Element namedElement = getFirstElement( node, name ); if ( namedElement == null ) { return null; } return getSimpleElementText( namedElement ); }
/** * @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; } }
/** * @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; } }
/** * @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 <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 } } }
/** * 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 } } }
/** * 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 } } }
final Element experimentList = DOMUtil.getFirstElement( element, "experimentList" );
final Element experimentList = DOMUtil.getFirstElement( element, "experimentList" );
final Element experimentList = DOMUtil.getFirstElement( element, "experimentList" );
final Element cellTypeElement = DOMUtil.getFirstElement( root, "cellType" ); CellTypeTag cellType = null; if ( null != cellTypeElement ) { final Element tissueElement = DOMUtil.getFirstElement( root, "tissue" ); TissueTag tissue = null; if ( null != tissueElement ) {
/** * 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; }
final Element names = DOMUtil.getFirstElement( element, "names" ); String shortLabel = null; if ( names != null ) { final Element cellTypeXref = DOMUtil.getFirstElement( element, "xref" );
final Element interactionTypeXref = DOMUtil.getFirstElement( element, "xref" );
final Element interactionTypeXref = DOMUtil.getFirstElement( element, "xref" );
final Element interactionTypeXref = DOMUtil.getFirstElement( element, "xref" );