public boolean equals( Object o ) { if ( this == o ) { return true; } if ( o == null || getClass() != o.getClass() ) { return false; } final ProteinHolder that = (ProteinHolder) o; if ( protein != null ? !protein.equals( that.protein ) : that.protein != null ) { return false; } if ( !proteinInteractor.equals( that.proteinInteractor ) ) { return false; } if ( spliceVariant != null ? !spliceVariant.equals( that.spliceVariant ) : that.spliceVariant != null ) { return false; } return true; }
/** * Get an Intact Protein out of a ProteinInteractorTag. * * @param proteinParticipant * * @return the IntAct Protein correcponding to the given ProteinParticipantTag. */ private static ProteinHolder getProtein( final ProteinParticipantTag proteinParticipant ) { final ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor(); OrganismTag organism = proteinInteractor.getOrganism(); BioSource bioSource = null; if ( organism != null ) { bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() ); } String proteinId = proteinInteractor.getPrimaryXref().getId(); String db = proteinInteractor.getPrimaryXref().getDb(); // System.out.println( "Search interactor (" + proteinInteractor.getShortlabel() + ") from cache(" + // proteinId + ", " + db + ", " + bioSource.getShortLabel() + ")" ); return ProteinInteractorChecker.getProtein( proteinId, db, bioSource ); } }
/** * a protein is from uniprot only if the attached ProteinInteractorTag answers true to that question. * @return */ public boolean isUniprot() { if( proteinInteractor != null ) { return proteinInteractor.hasUniProtXref(); } return false; }
String proteinId = proteinInteractor.getPrimaryXref().getId(); String db = proteinInteractor.getPrimaryXref().getDb(); if ( protein1.getBioSource().getTaxId().equals( proteinInteractor.getOrganism().getTaxId() ) ) { proteinInteractor.getOrganism().getTaxId() + ") and Xref: " + db + "(" + proteinId + "):"; String shortlabel = proteinInteractor.getShortlabel().toLowerCase(); BioSource bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() ); if ( bioSource == null ) { String message = "Could not find a BioSource using the definition: " + proteinInteractor.getOrganism(); createXref( protein, proteinInteractor.getPrimaryXref(), true ); Collection secondaryXrefs = proteinInteractor.getSecondaryXrefs(); for ( Iterator iterator = secondaryXrefs.iterator(); iterator.hasNext(); ) { XrefTag xrefTag = (XrefTag) iterator.next(); if ( proteinInteractor.getSequence() != null && proteinInteractor.getSequence().length() > 0 ) { protein.setSequence( proteinInteractor.getSequence() ); protein.setCrc64( Crc64.getCrc64( proteinInteractor.getSequence() ) ); proteinInteractor.getOrganism().getTaxId() + ") and Xref: " + db + "(" + proteinId + "). Reason: " + ie.getMessage(); ie.printStackTrace();
final BioSourceFactory bioSourceFactory ) { final OrganismTag organism = proteinInteractor.getOrganism(); String taxId = null; if ( organism != null ) { final String proteinId = proteinInteractor.getPrimaryXref().getId(); String db = proteinInteractor.getPrimaryXref().getDb(); if ( ! proteinInteractor.hasUniProtXref() ) { System.out.println( "########## PROTEIN WITH NO UNIPROT ID (" + proteinInteractor.getPrimaryXref().getId() + ") ##########" ); XrefTag primary = proteinInteractor.getPrimaryXref(); XrefChecker.check( primary ); Collection secondaries = proteinInteractor.getSecondaryXrefs(); for ( Iterator iterator = secondaries.iterator(); iterator.hasNext(); ) { XrefTag secondaryRef = (XrefTag) iterator.next(); final XrefTag uniprotDef = proteinInteractor.getPrimaryXref(); XrefChecker.check( uniprotDef );
public int hashCode() { int result; result = ( protein != null ? protein.hashCode() : 0 ); result = 29 * result + ( spliceVariant != null ? spliceVariant.hashCode() : 0 ); result = 29 * result + proteinInteractor.hashCode(); return result; }
Object o = (Object) iterator.next(); if ( o instanceof ProteinParticipantTag ) { uniprotID = ( (ProteinParticipantTag) o ).getProteinInteractor().getPrimaryXref().getId();
return proteinHolder.getProteinInteractor().getShortlabel();
lvb = new LabelValueBean( id, new ProteinInteractorTag( shortlabel, fullname, xref, secondaryXrefs, aliases, hostOrganism, sequence ) ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
String proteinId = proteinInteractor.getPrimaryXref().getId(); String db = proteinInteractor.getPrimaryXref().getDb(); if ( protein1.getBioSource().getTaxId().equals( proteinInteractor.getOrganism().getTaxId() ) ) { proteinInteractor.getOrganism().getTaxId() + ") and Xref: " + db + "(" + proteinId + "):"; String shortlabel = proteinInteractor.getShortlabel().toLowerCase(); BioSource bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() ); if ( bioSource == null ) { String message = "Could not find a BioSource using the definition: " + proteinInteractor.getOrganism(); createXref( protein, proteinInteractor.getPrimaryXref(), true ); Collection secondaryXrefs = proteinInteractor.getSecondaryXrefs(); for ( Iterator iterator = secondaryXrefs.iterator(); iterator.hasNext(); ) { XrefTag xrefTag = (XrefTag) iterator.next(); if ( proteinInteractor.getSequence() != null && proteinInteractor.getSequence().length() > 0 ) { protein.setSequence( proteinInteractor.getSequence() ); protein.setCrc64( Crc64.getCrc64( proteinInteractor.getSequence() ) ); proteinInteractor.getOrganism().getTaxId() + ") and Xref: " + db + "(" + proteinId + "). Reason: " + ie.getMessage(); ie.printStackTrace();
final BioSourceFactory bioSourceFactory ) { final OrganismTag organism = proteinInteractor.getOrganism(); String taxId = null; if ( organism != null ) { final String proteinId = proteinInteractor.getPrimaryXref().getId(); String db = proteinInteractor.getPrimaryXref().getDb(); if ( ! proteinInteractor.hasUniProtXref() ) { System.out.println( "########## PROTEIN WITH NO UNIPROT ID (" + proteinInteractor.getPrimaryXref().getId() + ") ##########" ); XrefTag primary = proteinInteractor.getPrimaryXref(); XrefChecker.check( primary ); Collection secondaries = proteinInteractor.getSecondaryXrefs(); for ( Iterator iterator = secondaries.iterator(); iterator.hasNext(); ) { XrefTag secondaryRef = (XrefTag) iterator.next(); final XrefTag uniprotDef = proteinInteractor.getPrimaryXref(); XrefChecker.check( uniprotDef );
public int hashCode() { int result; result = ( protein != null ? protein.hashCode() : 0 ); result = 29 * result + ( spliceVariant != null ? spliceVariant.hashCode() : 0 ); result = 29 * result + proteinInteractor.hashCode(); return result; }
Object o = (Object) iterator.next(); if ( o instanceof ProteinParticipantTag ) { uniprotID = ( (ProteinParticipantTag) o ).getProteinInteractor().getPrimaryXref().getId();
return proteinHolder.getProteinInteractor().getShortlabel();
lvb = new LabelValueBean( id, new ProteinInteractorTag( shortlabel, fullname, xref, secondaryXrefs, aliases, hostOrganism, sequence ) ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );
String proteinId = proteinInteractor.getPrimaryXref().getId(); String db = proteinInteractor.getPrimaryXref().getDb(); if ( protein1.getBioSource().getTaxId().equals( proteinInteractor.getOrganism().getTaxId() ) ) { proteinInteractor.getOrganism().getTaxId() + ") and Xref: " + db + "(" + proteinId + "):"; String shortlabel = proteinInteractor.getShortlabel().toLowerCase(); BioSource bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() ); if ( bioSource == null ) { String message = "Could not find a BioSource using the definition: " + proteinInteractor.getOrganism(); createXref( protein, proteinInteractor.getPrimaryXref(), true ); Collection secondaryXrefs = proteinInteractor.getSecondaryXrefs(); for ( Iterator iterator = secondaryXrefs.iterator(); iterator.hasNext(); ) { XrefTag xrefTag = (XrefTag) iterator.next(); if ( proteinInteractor.getSequence() != null && proteinInteractor.getSequence().length() > 0 ) { protein.setSequence( proteinInteractor.getSequence() ); protein.setCrc64( Crc64.getCrc64( proteinInteractor.getSequence() ) ); proteinInteractor.getOrganism().getTaxId() + ") and Xref: " + db + "(" + proteinId + "). Reason: " + ie.getMessage(); ie.printStackTrace();
/** * Get an Intact Protein out of a ProteinInteractorTag. * * @param proteinParticipant * * @return the IntAct Protein correcponding to the given ProteinParticipantTag. */ private static ProteinHolder getProtein( final ProteinParticipantTag proteinParticipant ) { final ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor(); OrganismTag organism = proteinInteractor.getOrganism(); BioSource bioSource = null; if ( organism != null ) { bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() ); } String proteinId = proteinInteractor.getPrimaryXref().getId(); String db = proteinInteractor.getPrimaryXref().getDb(); // System.out.println( "Search interactor (" + proteinInteractor.getShortlabel() + ") from cache(" + // proteinId + ", " + db + ", " + bioSource.getShortLabel() + ")" ); return ProteinInteractorChecker.getProtein( proteinId, db, bioSource ); } }
final BioSourceFactory bioSourceFactory ) { final OrganismTag organism = proteinInteractor.getOrganism(); String taxId = null; if ( organism != null ) { final String proteinId = proteinInteractor.getPrimaryXref().getId(); String db = proteinInteractor.getPrimaryXref().getDb(); if ( ! proteinInteractor.hasUniProtXref() ) { System.out.println( "########## PROTEIN WITH NO UNIPROT ID (" + proteinInteractor.getPrimaryXref().getId() + ") ##########" ); XrefTag primary = proteinInteractor.getPrimaryXref(); XrefChecker.check( primary ); Collection secondaries = proteinInteractor.getSecondaryXrefs(); for ( Iterator iterator = secondaries.iterator(); iterator.hasNext(); ) { XrefTag secondaryRef = (XrefTag) iterator.next(); final XrefTag uniprotDef = proteinInteractor.getPrimaryXref(); XrefChecker.check( uniprotDef );
public int hashCode() { int result; result = ( protein != null ? protein.hashCode() : 0 ); result = 29 * result + ( spliceVariant != null ? spliceVariant.hashCode() : 0 ); result = 29 * result + proteinInteractor.hashCode(); return result; }
/** * a protein is from uniprot only if the attached ProteinInteractorTag answers true to that question. * @return */ public boolean isUniprot() { if( proteinInteractor != null ) { return proteinInteractor.hasUniProtXref(); } return false; }