xref = createXref( xrefNode, XrefTag.SECONDARY_REF ); if ( xref != null ) { xrefs.add( xref );
/** * 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; }
if ( bibref != null ) { final Element bibXrefElement = DOMUtil.getFirstElement( bibref, "xref" ); bibXref = XrefParser.processPrimaryRef( bibXrefElement ); secondaryBibXrefs = XrefParser.processSecondaryRef( bibXrefElement ); Collection xrefs = null; if ( xrefElement != null ) { primaryXref = XrefParser.processPrimaryRef( xrefElement ); secondaryXrefs = XrefParser.processSecondaryRef( xrefElement ); XrefTag interactionXref = XrefParser.getXrefByDb( interactionDetectionXrefElement, CvDatabase.PSI_MI ); try { XrefTag participantXref = XrefParser.getXrefByDb( participantDetectionXrefElement, CvDatabase.PSI_MI ); try {
Collection xrefs = null; if ( xrefElement != null ) { xrefs = XrefParser.process( xrefElement ); XrefTag typeXref = XrefParser.processPrimaryRef( typeXrefElement ); featureType = new FeatureTypeTag( typeXref ); if ( detectionElement != null ) { Element detectionXrefElement = DOMUtil.getFirstElement( detectionElement, "xref" ); XrefTag detectionXref = XrefParser.processPrimaryRef( detectionXrefElement );
final XrefTag xref = XrefParser.getXrefByDb( interactionTypeXref, CvDatabase.PSI_MI );
Collection xrefs = null; if ( xrefElement != null ) { xrefs = XrefParser.process( xrefElement );
if ( bibref != null ) { final Element bibXrefElement = DOMUtil.getFirstElement( bibref, "xref" ); bibXref = XrefParser.processPrimaryRef( bibXrefElement ); secondaryBibXrefs = XrefParser.processSecondaryRef( bibXrefElement ); Collection xrefs = null; if ( xrefElement != null ) { primaryXref = XrefParser.processPrimaryRef( xrefElement ); secondaryXrefs = XrefParser.processSecondaryRef( xrefElement ); XrefTag interactionXref = XrefParser.getXrefByDb( interactionDetectionXrefElement, CvDatabase.PSI_MI ); try { XrefTag participantXref = XrefParser.getXrefByDb( participantDetectionXrefElement, CvDatabase.PSI_MI ); try {
Collection xrefs = null; if ( xrefElement != null ) { xrefs = XrefParser.process( xrefElement ); XrefTag typeXref = XrefParser.processPrimaryRef( typeXrefElement ); featureType = new FeatureTypeTag( typeXref ); if ( detectionElement != null ) { Element detectionXrefElement = DOMUtil.getFirstElement( detectionElement, "xref" ); XrefTag detectionXref = XrefParser.processPrimaryRef( detectionXrefElement );
final XrefTag xref = XrefParser.getXrefByDb( interactionTypeXref, CvDatabase.PSI_MI );
Collection xrefs = null; if ( xrefElement != null ) { xrefs = XrefParser.process( xrefElement );
/** * 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; }
if ( bibref != null ) { final Element bibXrefElement = DOMUtil.getFirstElement( bibref, "xref" ); bibXref = XrefParser.processPrimaryRef( bibXrefElement ); secondaryBibXrefs = XrefParser.processSecondaryRef( bibXrefElement ); Collection xrefs = null; if ( xrefElement != null ) { primaryXref = XrefParser.processPrimaryRef( xrefElement ); secondaryXrefs = XrefParser.processSecondaryRef( xrefElement ); XrefTag interactionXref = XrefParser.getXrefByDb( interactionDetectionXrefElement, CvDatabase.PSI_MI ); try { XrefTag participantXref = XrefParser.getXrefByDb( participantDetectionXrefElement, CvDatabase.PSI_MI ); try {
Collection xrefs = null; if ( xrefElement != null ) { xrefs = XrefParser.process( xrefElement ); XrefTag typeXref = XrefParser.processPrimaryRef( typeXrefElement ); featureType = new FeatureTypeTag( typeXref ); if ( detectionElement != null ) { Element detectionXrefElement = DOMUtil.getFirstElement( detectionElement, "xref" ); XrefTag detectionXref = XrefParser.processPrimaryRef( detectionXrefElement );
final XrefTag xref = XrefParser.getXrefByDb( interactionTypeXref, CvDatabase.PSI_MI );
xref = createXref( xrefNode, XrefTag.SECONDARY_REF ); if ( xref != null ) { xrefs.add( xref );
Collection xrefs = null; if ( xrefElement != null ) { xrefs = XrefParser.process( xrefElement );
/** * 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; }
xref = XrefParser.getXrefByDb( cellTypeXref, CvDatabase.PSI_MI );
xref = createXref( xrefNode, XrefTag.SECONDARY_REF ); if ( xref != null ) { xrefs.add( xref );
XrefTag xref = XrefParser.processPrimaryRef( xrefElement ); if ( db.equalsIgnoreCase( xref.getDb() ) ) { interactionXref = xref; } else { final Collection interactionDetectionXrefs = XrefParser.processSecondaryRef( xrefElement ); for ( Iterator iterator = interactionDetectionXrefs.iterator(); iterator.hasNext(); ) { xref = (XrefTag) iterator.next();