uk.ac.ebi.intact.application.dataConversion.psiDownload.PsiDocumentFactory java code examples

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private void myMethod () {
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}

/**
 * Return a PSI document. Create a new wmpty one if it doesn't exists yet.
 *
 * @return a PSI document.
 */
public Document getPsiDocument() {
  if ( psiDocument == null ) {
    psiDocument = PsiDocumentFactory.buildPsiDocument( this );
  }
  return psiDocument;
}

document = buildPsiVersion1(session, source);
document = buildPsiVersion2(session, source);
document = buildPsiVersion25(session, source);

/**
 * Builds an empty PSI document version 2.
 *
 * @param institution the source of that PSI Document.
 *
 * @return an empty PSI document version 2.
 */
private static Document buildPsiVersion2( UserSessionDownload session, Institution institution ) {
  DOMImplementationImpl impl = new DOMImplementationImpl();
  Document document = impl.createDocument( "net:sf:psidev:mi", "entrySet", null );  //doctype only used by DTDs !
  Element psiEntrySet = document.getDocumentElement();
  psiEntrySet.setAttribute( "xmlns", "net:sf:psidev:mi" );
  psiEntrySet.setAttribute( "xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance" );
  psiEntrySet.setAttribute( "xsi:schemaLocation",
               "net:sf:psidev:mi " + URL_SCHEMA_VERSION_2 );
  psiEntrySet.setAttribute( "level", "1" );
  psiEntrySet.setAttribute( "version", "2" );
  Element entry = document.createElement( "entry" );
  psiEntrySet.appendChild( entry );
  Element source = createSource( session, document, institution );
  entry.appendChild( source );
  return document;
}

source.setAttribute( "releaseDate", getReleaseDate() );

document = buildPsiVersion1( session, source );
document = buildPsiVersion2( session, source );
document = buildPsiVersion25( session, source );

/**
 * Builds an empty PSI document version 3.
 *
 * @param institution the source of that PSI Document.
 *
 * @return an empty PSI document version 3.
 */
private static Document buildPsiVersion25(UserSessionDownload session,
    Institution institution) {
  DOMImplementationImpl impl = new DOMImplementationImpl();
  Document document = impl.createDocument("net:sf:psidev:mi", "entrySet",
      null); //doctype only used by DTDs !
  Element psiEntrySet = document.getDocumentElement();
  psiEntrySet.setAttribute("xmlns", "net:sf:psidev:mi");
  psiEntrySet.setAttribute("xmlns:xsi",
      "http://www.w3.org/2001/XMLSchema-instance");
  psiEntrySet.setAttribute("xsi:schemaLocation", "net:sf:psidev:mi "
      + URL_SCHEMA_VERSION_25);
  // values fixed by the schema
  psiEntrySet.setAttribute("level", "2");
  psiEntrySet.setAttribute("version", "5");
  psiEntrySet.setAttribute("minorVersion", "3");
  Element entry = document.createElement("entry");
  psiEntrySet.appendChild(entry);
  Element source = createSource(session, document, institution);
  entry.appendChild(source);
  return document;
}

source.setAttribute( "releaseDate", getReleaseDate() );

document = buildPsiVersion1( session, source );
document = buildPsiVersion2( session, source );
document = buildPsiVersion25( session, source );

/**
 * Builds an empty PSI document version 1.
 *
 * @param institution the source of that PSI Document.
 *
 * @return an empty PSI document version 1.
 */
private static Document buildPsiVersion1( UserSessionDownload session, Institution institution ) {
  DOMImplementationImpl impl = new DOMImplementationImpl();
  Document document = impl.createDocument( "net:sf:psidev:mi", "entrySet", null );  //doctype only used by DTDs !
  Element psiEntrySet = document.getDocumentElement();
  psiEntrySet.setAttribute( "xmlns", "net:sf:psidev:mi" );
  psiEntrySet.setAttribute( "xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance" );
  psiEntrySet.setAttribute( "xsi:schemaLocation",
               "net:sf:psidev:mi " + URL_SCHEMA_VERSION_1 );
  psiEntrySet.setAttribute( "level", "1" );
  psiEntrySet.setAttribute( "version", "1" );
  Element entry = document.createElement( "entry" );
  psiEntrySet.appendChild( entry );
  Element source = createSource( session, document, institution );
  entry.appendChild( source );
  return document;
}

public UserSessionDownload( PsiVersion psiVersion, Institution source ) {
  this.psiVersion = psiVersion;
  this.source = source;
  psiDocument = PsiDocumentFactory.buildPsiDocument( this, source );
}

source.setAttribute("releaseDate", getReleaseDate());

/**
 * Builds an empty PSI document version 1.
 *
 * @param institution the source of that PSI Document.
 *
 * @return an empty PSI document version 1.
 */
private static Document buildPsiVersion1( UserSessionDownload session, Institution institution ) {
  DOMImplementationImpl impl = new DOMImplementationImpl();
  Document document = impl.createDocument( "net:sf:psidev:mi", "entrySet", null );  //doctype only used by DTDs !
  Element psiEntrySet = document.getDocumentElement();
  psiEntrySet.setAttribute( "xmlns", "net:sf:psidev:mi" );
  psiEntrySet.setAttribute( "xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance" );
  psiEntrySet.setAttribute( "xsi:schemaLocation",
               "net:sf:psidev:mi " + URL_SCHEMA_VERSION_1 );
  psiEntrySet.setAttribute( "level", "1" );
  psiEntrySet.setAttribute( "version", "1" );
  Element entry = document.createElement( "entry" );
  psiEntrySet.appendChild( entry );
  Element source = createSource( session, document, institution );
  entry.appendChild( source );
  return document;
}

/**
 * Return a PSI document. Create a new wmpty one if it doesn't exists yet.
 *
 * @return a PSI document.
 */
public Document getPsiDocument() {
  if ( psiDocument == null ) {
    psiDocument = PsiDocumentFactory.buildPsiDocument( this );
  }
  return psiDocument;
}

/**
 * Builds an empty PSI document version 2.
 *
 * @param institution the source of that PSI Document.
 *
 * @return an empty PSI document version 2.
 */
private static Document buildPsiVersion2( UserSessionDownload session, Institution institution ) {
  DOMImplementationImpl impl = new DOMImplementationImpl();
  Document document = impl.createDocument( "net:sf:psidev:mi", "entrySet", null );  //doctype only used by DTDs !
  Element psiEntrySet = document.getDocumentElement();
  psiEntrySet.setAttribute( "xmlns", "net:sf:psidev:mi" );
  psiEntrySet.setAttribute( "xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance" );
  psiEntrySet.setAttribute( "xsi:schemaLocation",
               "net:sf:psidev:mi " + URL_SCHEMA_VERSION_2 );
  psiEntrySet.setAttribute( "level", "1" );
  psiEntrySet.setAttribute( "version", "2" );
  Element entry = document.createElement( "entry" );
  psiEntrySet.appendChild( entry );
  Element source = createSource( session, document, institution );
  entry.appendChild( source );
  return document;
}

/**
 * Builds an empty PSI document of the specified version.
 *
 * @param session The user session that contains the requested PSI version.
 *
 * @return a XML Document representing an empty PSI document.
 */
public static Document buildPsiDocument( UserSessionDownload session ) {
  return buildPsiDocument( session, null );
}

/**
 * Builds an empty PSI document version 3.
 *
 * @param institution the source of that PSI Document.
 *
 * @return an empty PSI document version 3.
 */
private static Document buildPsiVersion25( UserSessionDownload session, Institution institution ) {
  DOMImplementationImpl impl = new DOMImplementationImpl();
  Document document = impl.createDocument( "net:sf:psidev:mi", "entrySet", null );  //doctype only used by DTDs !
  Element psiEntrySet = document.getDocumentElement();
  psiEntrySet.setAttribute( "xmlns", "net:sf:psidev:mi" );
  psiEntrySet.setAttribute( "xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance" );
  psiEntrySet.setAttribute( "xsi:schemaLocation",
               "net:sf:psidev:mi " + URL_SCHEMA_VERSION_25 );
  // values fixed by the schema
  psiEntrySet.setAttribute( "level", "2" );
  psiEntrySet.setAttribute( "version", "5" );
  psiEntrySet.setAttribute( "minorVersion", "3" );
  Element entry = document.createElement( "entry" );
  psiEntrySet.appendChild( entry );
  Element source = createSource( session, document, institution );
  entry.appendChild( source );
  return document;
}

public UserSessionDownload( PsiVersion psiVersion, Institution source ) {
  this.psiVersion = psiVersion;
  this.source = source;
  psiDocument = PsiDocumentFactory.buildPsiDocument( this, source );
}

/**
 * Builds an empty PSI document version 3.
 *
 * @param institution the source of that PSI Document.
 *
 * @return an empty PSI document version 3.
 */
private static Document buildPsiVersion25( UserSessionDownload session, Institution institution ) {
  DOMImplementationImpl impl = new DOMImplementationImpl();
  Document document = impl.createDocument( "net:sf:psidev:mi", "entrySet", null );  //doctype only used by DTDs !
  Element psiEntrySet = document.getDocumentElement();
  psiEntrySet.setAttribute( "xmlns", "net:sf:psidev:mi" );
  psiEntrySet.setAttribute( "xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance" );
  psiEntrySet.setAttribute( "xsi:schemaLocation",
               "net:sf:psidev:mi " + URL_SCHEMA_VERSION_25 );
  // values fixed by the schema
  psiEntrySet.setAttribute( "level", "2" );
  psiEntrySet.setAttribute( "version", "5" );
  psiEntrySet.setAttribute( "minorVersion", "3" );
  Element entry = document.createElement( "entry" );
  psiEntrySet.appendChild( entry );
  Element source = createSource( session, document, institution );
  entry.appendChild( source );
  return document;
}

/**
 * Builds an empty PSI document of the specified version.
 *
 * @param session The user session that contains the requested PSI version.
 *
 * @return a XML Document representing an empty PSI document.
 */
public static Document buildPsiDocument(UserSessionDownload session) {
  return buildPsiDocument(session, null);
}

Element source = PsiDocumentFactory.createSource( this, root, this.source );
entry.appendChild( source );

Javadoc

TODO document this ;o)

Most used methods

buildPsiDocument
Builds an empty PSI document of the specified version.
buildPsiVersion1
Builds an empty PSI document version 1.
buildPsiVersion2
Builds an empty PSI document version 2.
buildPsiVersion25
Builds an empty PSI document version 3.
createSource
generate the source of a PSI document.
getReleaseDate
Create today's date

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How to usePsiDocumentFactory in uk.ac.ebi.intact.application.dataConversion.psiDownload

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uk.ac.ebi.intact.application.dataConversion.psiDownload