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

Add the Codota plugin to your IDE and get smart completions

private void myMethod () {
 Connection c =DataSource dataSource;dataSource.getConnection()
String url;DriverManager.getConnection(url)
IdentityDatabaseUtil.getDBConnection()
Smart code suggestions by Codota
}

/**
 * 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;
}

/**
 * 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;
}

/**
 * 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;
}

XrefTag xref = XrefParser.processPrimaryRef( xrefElement );
if ( db.equalsIgnoreCase( xref.getDb() ) ) {
  interactionXref = xref;

XrefTag xref = XrefParser.processPrimaryRef( xrefElement );
if ( db.equalsIgnoreCase( xref.getDb() ) ) {
  interactionXref = xref;

XrefTag xref = XrefParser.processPrimaryRef( xrefElement );
if ( db.equalsIgnoreCase( xref.getDb() ) ) {
  interactionXref = xref;

    XrefTag typeXref = XrefParser.processPrimaryRef( typeXrefElement );
    featureType = new FeatureTypeTag( typeXref );
if ( detectionElement != null ) {
  Element detectionXrefElement = DOMUtil.getFirstElement( detectionElement, "xref" );
  XrefTag detectionXref = XrefParser.processPrimaryRef( detectionXrefElement );

    XrefTag typeXref = XrefParser.processPrimaryRef( typeXrefElement );
    featureType = new FeatureTypeTag( typeXref );
if ( detectionElement != null ) {
  Element detectionXrefElement = DOMUtil.getFirstElement( detectionElement, "xref" );
  XrefTag detectionXref = XrefParser.processPrimaryRef( detectionXrefElement );

    XrefTag typeXref = XrefParser.processPrimaryRef( typeXrefElement );
    featureType = new FeatureTypeTag( typeXref );
if ( detectionElement != null ) {
  Element detectionXrefElement = DOMUtil.getFirstElement( detectionElement, "xref" );
  XrefTag detectionXref = XrefParser.processPrimaryRef( detectionXrefElement );

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 );

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 );

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 );

Collection secondaryXrefs = null;
if( xrefElement != null ) {
  xref = XrefParser.processPrimaryRef( xrefElement );
  secondaryXrefs = XrefParser.processSecondaryRef( xrefElement );
} else {

Collection secondaryXrefs = null;
if( xrefElement != null ) {
  xref = XrefParser.processPrimaryRef( xrefElement );
  secondaryXrefs = XrefParser.processSecondaryRef( xrefElement );
} else {

Collection secondaryXrefs = null;
if( xrefElement != null ) {
  xref = XrefParser.processPrimaryRef( xrefElement );
  secondaryXrefs = XrefParser.processSecondaryRef( xrefElement );
} else {

Javadoc

Extract Primary Xref.

Popular methods of XrefParser

createXref
getXrefByDb
Method accesible within the package.
process
Collect all primary and secondary Xrefs.
processSecondaryRef
Extract data from an xref Element and produce an Intact Xref

Popular in Java

Making http requests using okhttp
getContentResolver (Context)
getSupportFragmentManager (FragmentActivity)
Return the FragmentManager for interacting with fragments associated with this activity.
setContentView (Activity)
Kernel (java.awt.image)
Stack (java.util)
The Stack class represents a last-in-first-out (LIFO) stack of objects. It extends class Vector with
TimeZone (java.util)
TimeZone represents a time zone offset, and also figures out daylight savings. Typically, you get a
StringUtils (org.apache.commons.lang)
Operations on java.lang.String that arenull safe. * IsEmpty/IsBlank - checks if a String contains
Logger (org.apache.log4j)
This is the central class in the log4j package. Most logging operations, except configuration, are d
LoggerFactory (org.slf4j)
The LoggerFactory is a utility class producing Loggers for various logging APIs, most notably for lo

How to use processPrimaryRefmethodin uk.ac.ebi.intact.application.dataConversion.psiUpload.parser.XrefParser

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.psiUpload.parser.XrefParser.processPrimaryRef (Showing top 15 results out of 315)

How to use
processPrimaryRef
method
in
uk.ac.ebi.intact.application.dataConversion.psiUpload.parser.XrefParser