uk.ac.ebi.intact.application.dataConversion.psiDownload.xmlGenerator.AbstractAnnotatedObject2xml java code examples

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private void myMethod () {
 Connection c =DataSource dataSource;dataSource.getConnection()
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IdentityDatabaseUtil.getDBConnection()
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}

/**
 * Generate an filled attributeList based upon the annotation of the given AnnotatedObject.
 *
 * @param session
 * @param parent  the Element to which we will attach the newly generated AttributeList.
 * @param object  the Annotated object from which we generate the attributes.
 *
 * @return a newly created attributeList or null if none were created.
 */
protected Element createAttributeList( UserSessionDownload session, Element parent, AnnotatedObject object ) {
  return createAttributeList( session, parent, object, null );
}

Collection interproXrefs = AbstractAnnotatedObject2xml.getXrefByDatabase( feature, CvDatabase.INTERPRO );

Collection identityXrefs = AbstractAnnotatedObject2xml.getXrefByQualifier( interactor, CvXrefQualifier.IDENTITY );
  identityXrefs = AbstractAnnotatedObject2xml.getXrefByQualifier( interactor, CvXrefQualifier.PRIMARY_REFERENCE );

Collection interproXrefs = AbstractAnnotatedObject2xml.getXrefByDatabase( feature, CvDatabase.INTERPRO );

Collection identityXrefs = AbstractAnnotatedObject2xml.getXrefByQualifier( protein, CvXrefQualifier.IDENTITY );
  identityXrefs = AbstractAnnotatedObject2xml.getXrefByQualifier( protein, CvXrefQualifier.PRIMARY_REFERENCE );

Collection interproXrefs = AbstractAnnotatedObject2xml.getXrefByDatabase( feature, CvDatabase.INTERPRO );

Collection identityXrefs = AbstractAnnotatedObject2xml.getXrefByQualifier( interactor, CvXrefQualifier.IDENTITY );
  identityXrefs = AbstractAnnotatedObject2xml.getXrefByQualifier( interactor, CvXrefQualifier.PRIMARY_REFERENCE );

/**
 * Generate an filled attributeList based upon the annotation of the given AnnotatedObject.
 *
 * @param session
 * @param parent  the Element to which we will attach the newly generated AttributeList.
 * @param object  the Annotated object from which we generate the attributes.
 *
 * @return a newly created attributeList or null if none were created.
 */
protected Element createAttributeList( UserSessionDownload session, Element parent, AnnotatedObject object ) {
  return createAttributeList( session, parent, object, null );
}

Collection uniprotXrefs = AbstractAnnotatedObject2xml.getXrefByDatabase( protein, CvDatabase.UNIPROT );

Collection identityXrefs = AbstractAnnotatedObject2xml.getXrefByQualifier( interactor, CvXrefQualifier.IDENTITY );
  identityXrefs = AbstractAnnotatedObject2xml.getXrefByQualifier( interactor, CvXrefQualifier.PRIMARY_REFERENCE );

/**
 * Generate an filled attributeList based upon the annotation of the given AnnotatedObject.
 *
 * @param session
 * @param parent  the Element to which we will attach the newly generated AttributeList.
 * @param object  the Annotated object from which we generate the attributes.
 *
 * @return a newly created attributeList or null if none were created.
 */
protected Element createAttributeList( UserSessionDownload session, Element parent, AnnotatedObject object ) {
  return createAttributeList( session, parent, object, null );
}

Collection uniprotXrefs = AbstractAnnotatedObject2xml.getXrefByDatabase( smallMolecule, CvDatabase.RESID );

Collection identityXrefs = AbstractAnnotatedObject2xml.getXrefByQualifier( protein, CvXrefQualifier.IDENTITY );
  identityXrefs = AbstractAnnotatedObject2xml.getXrefByQualifier( protein, CvXrefQualifier.PRIMARY_REFERENCE );

Collection uniprotXrefs = AbstractAnnotatedObject2xml.getXrefByDatabase( smallMolecule, CvDatabase.RESID );

Collection identityXrefs = AbstractAnnotatedObject2xml.getXrefByQualifier( protein, CvXrefQualifier.IDENTITY );
  identityXrefs = AbstractAnnotatedObject2xml.getXrefByQualifier( protein, CvXrefQualifier.PRIMARY_REFERENCE );

Collection uniprotXrefs = AbstractAnnotatedObject2xml.getXrefByDatabase( protein, CvDatabase.UNIPROT );

Collection uniprotXrefs = AbstractAnnotatedObject2xml.getXrefByDatabase( protein, CvDatabase.UNIPROT );

Collection uniprotXrefs = AbstractAnnotatedObject2xml.getXrefByDatabase( smallMolecule, CvDatabase.RESID );

Collection pubmedXrefs = AbstractAnnotatedObject2xml.getXrefByDatabase( experiment, CvDatabase.PUBMED );

Collection psiXrefs = AbstractAnnotatedObject2xml.getXrefByDatabase( cvObject, CvDatabase.PSI_MI );

Javadoc

Process common attributes of all AnnotatedObject. eg. shortlabel, fullname, Annotations, Xrefs

Most used methods

createAttributeList
Generate and fill an attributeList based upon the annotation of the given AnnotatedObject. We apply
getXrefByDatabase
Based upon the given database name (db), select all Xref of the given AnnotatedObject having that sp
getXrefByQualifier
Based upon the given CvXrefQualifier name (db), select all Xref of the given AnnotatedObject having

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How to useAbstractAnnotatedObject2xml in uk.ac.ebi.intact.application.dataConversion.psiDownload.xmlGenerator

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