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ProteinInteractorChecker.isSpliceVariant
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How to use
isSpliceVariant
method
in
uk.ac.ebi.intact.application.dataConversion.psiUpload.checker.ProteinInteractorChecker

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.psiUpload.checker.ProteinInteractorChecker.isSpliceVariant (Showing top 3 results out of 315)

origin: uk.ac.ebi.intact.app/data-conversion

CvXrefQualifier identity = ControlledVocabularyRepository.getIdentityQualifier();
if ( isSpliceVariant( id ) ) {
  if ( DEBUG ) {
    System.out.println( "is splice variant ID" );
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

CvXrefQualifier identity = IntactContext.getCurrentInstance().getCvContext().getByMiRef(CvXrefQualifier.class, CvXrefQualifier.IDENTITY_MI_REF);
if ( isSpliceVariant( id ) ) {
  if ( DEBUG ) {
    System.out.println( "is splice variant ID" );
origin: uk.ac.ebi.intact.util/data-conversion

CvXrefQualifier identity = IntactContext.getCurrentInstance().getCvContext().getByMiRef(CvXrefQualifier.class, CvXrefQualifier.IDENTITY_MI_REF);
if ( isSpliceVariant( id ) ) {
  if ( DEBUG ) {
    System.out.println( "is splice variant ID" );
uk.ac.ebi.intact.application.dataConversion.psiUpload.checkerProteinInteractorCheckerisSpliceVariant

Javadoc

Answer the question: is that protein a Splice Variant ? One (quick) way is to check if the shortlabel match the pattern: XXXXXX-#

Popular methods of ProteinInteractorChecker

  • buildID
    Build an identifier for the cache
  • check
  • checkCvInteractorType
  • createXref
  • filterByTaxid
    Remove from a collection of Protein all those that are not related to the given taxid.
  • getIntactProtein
    Get Protein from IntAct from its ID. If this is ID refers to (1) a protein, we send back a Protein o
  • getOrCreateNonUniprotProtein
    In case of Non uniprot protein, we check if it already exist in IntAct (based on biosource, primaryi
  • getProtein
    Search a protein in the cache
  • hasMultipleBioSource
    Check if the set of proteins is related to more than one biosource.

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