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OrganismTag
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OrganismTag
in
uk.ac.ebi.intact.application.dataConversion.psiUpload.model

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.psiUpload.model.OrganismTag (Showing top 20 results out of 315)

origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

if ( organism != null ? !organism.equals( proteinInteractorTag.organism ) : proteinInteractorTag.organism != null )
origin: uk.ac.ebi.intact.util/data-conversion

public static BioSource getBioSource( final OrganismTag organism ) {
  if ( organism == null ) {
    return null;
  }
  final String taxid = organism.getTaxId();
  final CellTypeTag cellType = organism.getCellType();
  final TissueTag tissue = organism.getTissue();
  return getBioSource( taxid, cellType, tissue );
}
origin: uk.ac.ebi.intact.util/data-conversion

public int hashCode() {
  int result;
  result = secondaryXrefs.hashCode();
  result = 29 * result + ( organism != null ? organism.hashCode() : 0 );
  result = 29 * result + ( shortlabel != null ? shortlabel.hashCode() : 0 );
  result = 29 * result + ( fullname != null ? fullname.hashCode() : 0 );
  result = 29 * result + ( primaryXref != null ? primaryXref.hashCode() : 0 );
  result = 29 * result + ( sequence != null ? sequence.hashCode() : 0 );
  result = 29 * result + aliases.hashCode();
  return result;
}
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

taxid = proteinInteractor.getOrganism().getTaxId();
origin: uk.ac.ebi.intact.util/data-conversion

  organismTag = new OrganismTag( taxid, cellType, tissue );
} catch ( IllegalArgumentException e ) {
  MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
origin: uk.ac.ebi.intact.app/data-conversion

taxid = proteinInteractor.getOrganism().getTaxId();
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

  organismTag = new OrganismTag( taxid, cellType, tissue );
} catch ( IllegalArgumentException e ) {
  MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
origin: uk.ac.ebi.intact.util/data-conversion

  public static void check( final OrganismTag organism,
               final BioSourceFactory bioSourceFactory ) {

    final String taxid = organism.getTaxId();
    final CellTypeTag cellType = organism.getCellType();
    final TissueTag tissue = organism.getTissue();
    check( taxid, cellType, tissue, bioSourceFactory );
  }
}
origin: uk.ac.ebi.intact.util/data-conversion

taxid = proteinInteractor.getOrganism().getTaxId();
origin: uk.ac.ebi.intact.app/data-conversion

  organismTag = new OrganismTag( taxid, cellType, tissue );
} catch ( IllegalArgumentException e ) {
  MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
origin: uk.ac.ebi.intact.app/data-conversion

public int hashCode() {
  int result;
  result = secondaryXrefs.hashCode();
  result = 29 * result + ( organism != null ? organism.hashCode() : 0 );
  result = 29 * result + ( shortlabel != null ? shortlabel.hashCode() : 0 );
  result = 29 * result + ( fullname != null ? fullname.hashCode() : 0 );
  result = 29 * result + ( primaryXref != null ? primaryXref.hashCode() : 0 );
  result = 29 * result + ( sequence != null ? sequence.hashCode() : 0 );
  result = 29 * result + aliases.hashCode();
  return result;
}
origin: uk.ac.ebi.intact.app/data-conversion

if ( organism != null ? !organism.equals( proteinInteractorTag.organism ) : proteinInteractorTag.organism != null )
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

public static BioSource getBioSource( final OrganismTag organism ) {
  if ( organism == null ) {
    return null;
  }
  final String taxid = organism.getTaxId();
  final CellTypeTag cellType = organism.getCellType();
  final TissueTag tissue = organism.getTissue();
  return getBioSource( taxid, cellType, tissue );
}
origin: uk.ac.ebi.intact.app/data-conversion

  taxid = proteinInteractor.getOrganism().getTaxId();
} else {
  taxid = "taxid not specified";
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

hostOrganism = new OrganismTag( defaultTaxid );
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

public int hashCode() {
  int result;
  result = secondaryXrefs.hashCode();
  result = 29 * result + ( organism != null ? organism.hashCode() : 0 );
  result = 29 * result + ( shortlabel != null ? shortlabel.hashCode() : 0 );
  result = 29 * result + ( fullname != null ? fullname.hashCode() : 0 );
  result = 29 * result + ( primaryXref != null ? primaryXref.hashCode() : 0 );
  result = 29 * result + ( sequence != null ? sequence.hashCode() : 0 );
  result = 29 * result + aliases.hashCode();
  return result;
}
origin: uk.ac.ebi.intact.util/data-conversion

if ( organism != null ? !organism.equals( proteinInteractorTag.organism ) : proteinInteractorTag.organism != null )
origin: uk.ac.ebi.intact.app/data-conversion

public static BioSource getBioSource( final OrganismTag organism ) {
  if ( organism == null ) {
    return null;
  }
  final String taxid = organism.getTaxId();
  final CellTypeTag cellType = organism.getCellType();
  final TissueTag tissue = organism.getTissue();
  return getBioSource( taxid, cellType, tissue );
}
origin: uk.ac.ebi.intact.util/data-conversion

  taxid = proteinInteractor.getOrganism().getTaxId();
} else {
  taxid = "taxid not specified";
origin: uk.ac.ebi.intact.util/data-conversion

hostOrganism = new OrganismTag( defaultTaxid );
uk.ac.ebi.intact.application.dataConversion.psiUpload.modelOrganismTag

Javadoc

That class reflects what is needed to create an IntAct BioSource.

 
<organism ncbiTaxId="4932"> 
<names> 
<shortLabel>s cerevisiae</shortLabel> 
<fullName>Saccharomyces cerevisiae</fullName> 
</names> 
<tissue> 
<xref> 
<primaryRef db="psi-mi" id="MI:xxx" secondary="" version=""/> 
</xref> 
</tissue> 
<cellType> 
<xref> 
<primaryRef db="psi-mi" id="MI:xxx" secondary="" version=""/> 
</xref> 
</cellType> 
</hostOrganism> 

Most used methods

  • <init>
  • equals
  • getCellType
  • getTaxId
  • getTissue
  • hashCode

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