public boolean equals( Object o ) { if ( this == o ) { return true; } if ( !( o instanceof FeatureTypeTag ) ) { return false; } final FeatureTypeTag featureTypeTag = (FeatureTypeTag) o; if ( psiDefinition != null ? !psiDefinition.equals( featureTypeTag.psiDefinition ) : featureTypeTag.psiDefinition != null ) { return false; } return true; }
public InteractionTypeTag( final XrefTag psiDefinition ) { if ( psiDefinition == null ) { throw new IllegalArgumentException( "You must give a non null psi definition for an interactionType" ); } if ( !CvDatabase.PSI_MI.equals( psiDefinition.getDb() ) ) { throw new IllegalArgumentException( "You must give a psi-mi Xref, not " + psiDefinition.getDb() + " for an InteractionType" ); } this.psiDefinition = psiDefinition; }
public int hashCode() { return psiDefinition.hashCode(); }
private static void createXref( Protein protein, XrefTag xrefTag, boolean identity ) throws IntactException { CvXrefQualifier qualifier = null; if ( identity ) { qualifier = ControlledVocabularyRepository.getIdentityQualifier(); } CvDatabase database = XrefChecker.getCvDatabase( xrefTag.getDb() ); if ( database == null ) { // failed to find the database, skip the Xref creation } else { InteractorXref xref = new InteractorXref( IntactContext.getCurrentInstance().getInstitution(), database, xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), qualifier ); protein.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref ); } }
if ( Constants.UNIPROT_DB_SHORTLABEL.equals( primaryXref.getDb() ) ) { this.primaryXref = new XrefTag( primaryXref.getType(), primaryXref.getId(), primaryXref.getSecondary(), primaryXref.getVersion() ); } else if ( CvDatabase.UNIPROT.equals( primaryXref.getDb() ) ) { this.primaryXref = new XrefTag( primaryXref.getType(), primaryXref.getId(), primaryXref.getSecondary(), primaryXref.getVersion() );
/** * Get from a feature object the primaryId of an Xref having the given database. * * @param feature * @param database * * @return the primaryId of null if we can't find it. */ private String getFeatureId( FeatureTag feature, String database ) { for ( Iterator iterator = feature.getXrefs().iterator(); iterator.hasNext(); ) { XrefTag xref = (XrefTag) iterator.next(); if ( xref.getDb().equalsIgnoreCase( database ) ) { return xref.getId(); } } return null; }
public String toString() { final StringBuffer buf = new StringBuffer(); buf.append( "HostOrganismTag" ); buf.append( "{taxId=" ).append( taxId ); buf.append( ", tissue=" ); if ( null == tissue || tissue.getPsiDefinition() == null) { buf.append( '-' ); } else { buf.append( tissue.getPsiDefinition().getId() ); } buf.append( ", cellType=" ); if ( null == cellType || cellType.getPsiDefinition() == null) { buf.append( '-' ); } else { buf.append( cellType.getPsiDefinition().getId() ); } buf.append( '}' ); return buf.toString(); } }
private static XrefTag createXref( final Element xrefNode, final short type ) { XrefTag xref = null; try { String db = xrefNode.getAttribute( "db" ); if ( db != null ) { db = db.toLowerCase(); } xref = new XrefTag( type, xrefNode.getAttribute( "id" ), db, xrefNode.getAttribute( "secondary" ), xrefNode.getAttribute( "version" ) ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( xrefNode, e.getMessage() ) ); } return xref; } }
private static void createXref( Protein protein, XrefTag xrefTag, boolean identity ) throws IntactException { CvXrefQualifier qualifier = null; if ( identity ) { qualifier = ControlledVocabularyRepository.getIdentityQualifier(); } CvDatabase database = XrefChecker.getCvDatabase( xrefTag.getDb() ); if ( database == null ) { // failed to find the database, skip the Xref creation } else { InteractorXref xref = new InteractorXref( IntactContext.getCurrentInstance().getInstitution(), database, xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), qualifier ); protein.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref ); } }
if ( Constants.UNIPROT_DB_SHORTLABEL.equals( primaryXref.getDb() ) ) { this.primaryXref = new XrefTag( primaryXref.getType(), primaryXref.getId(), primaryXref.getSecondary(), primaryXref.getVersion() ); } else if ( CvDatabase.UNIPROT.equals( primaryXref.getDb() ) ) { this.primaryXref = new XrefTag( primaryXref.getType(), primaryXref.getId(), primaryXref.getSecondary(), primaryXref.getVersion() );
/** * Get from a feature object the primaryId of an Xref having the given database. * * @param feature * @param database * * @return the primaryId of null if we can't find it. */ private String getFeatureId( FeatureTag feature, String database ) { for ( Iterator iterator = feature.getXrefs().iterator(); iterator.hasNext(); ) { XrefTag xref = (XrefTag) iterator.next(); if ( xref.getDb().equalsIgnoreCase( database ) ) { return xref.getId(); } } return null; }
public String toString() { final StringBuffer buf = new StringBuffer(); buf.append( "HostOrganismTag" ); buf.append( "{taxId=" ).append( taxId ); buf.append( ", tissue=" ); if ( null == tissue || tissue.getPsiDefinition() == null) { buf.append( '-' ); } else { buf.append( tissue.getPsiDefinition().getId() ); } buf.append( ", cellType=" ); if ( null == cellType || cellType.getPsiDefinition() == null) { buf.append( '-' ); } else { buf.append( cellType.getPsiDefinition().getId() ); } buf.append( '}' ); return buf.toString(); } }
private static XrefTag createXref( final Element xrefNode, final short type ) { XrefTag xref = null; try { String db = xrefNode.getAttribute( "db" ); if ( db != null ) { db = db.toLowerCase(); } xref = new XrefTag( type, xrefNode.getAttribute( "id" ), db, xrefNode.getAttribute( "secondary" ), xrefNode.getAttribute( "version" ) ); } catch ( IllegalArgumentException e ) { MessageHolder.getInstance().addParserMessage( new Message( xrefNode, e.getMessage() ) ); } return xref; } }
private static void createXref( Protein protein, XrefTag xrefTag, boolean identity ) throws IntactException { CvXrefQualifier qualifier = null; if ( identity ) { qualifier = ControlledVocabularyRepository.getIdentityQualifier(); } CvDatabase database = XrefChecker.getCvDatabase( xrefTag.getDb() ); if ( database == null ) { // failed to find the database, skip the Xref creation } else { InteractorXref xref = new InteractorXref( IntactContext.getCurrentInstance().getInstitution(), database, xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), qualifier ); protein.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref ); } }
if ( Constants.UNIPROT_DB_SHORTLABEL.equals( primaryXref.getDb() ) ) { this.primaryXref = new XrefTag( primaryXref.getType(), primaryXref.getId(), primaryXref.getSecondary(), primaryXref.getVersion() ); } else if ( CvDatabase.UNIPROT.equals( primaryXref.getDb() ) ) { this.primaryXref = new XrefTag( primaryXref.getType(), primaryXref.getId(), primaryXref.getSecondary(), primaryXref.getVersion() );
/** * Get from a feature object the primaryId of an Xref having the given database. * * @param feature * @param database * * @return the primaryId of null if we can't find it. */ private String getFeatureId( FeatureTag feature, String database ) { for ( Iterator iterator = feature.getXrefs().iterator(); iterator.hasNext(); ) { XrefTag xref = (XrefTag) iterator.next(); if ( xref.getDb().equalsIgnoreCase( database ) ) { return xref.getId(); } } return null; }
public boolean equals( Object o ) { if ( this == o ) { return true; } if ( !( o instanceof FeatureDetectionTag ) ) { return false; } final FeatureDetectionTag featureDetectionTag = (FeatureDetectionTag) o; if ( psiDefinition != null ? !psiDefinition.equals( featureDetectionTag.psiDefinition ) : featureDetectionTag.psiDefinition != null ) { return false; } return true; }
public int hashCode() { return psiDefinition.hashCode(); }
public FeatureTypeTag( final XrefTag psiDefinition ) { if ( psiDefinition == null ) { throw new IllegalArgumentException( "You must give a non null psi definition for an feature type" ); } if ( !CvDatabase.PSI_MI.equals( psiDefinition.getDb() ) ) { throw new IllegalArgumentException( "You must give a psi-mi Xref, not " + psiDefinition.getDb() + " for a FeatureType" ); } this.psiDefinition = psiDefinition; }
public String toString() { final StringBuffer buf = new StringBuffer(); buf.append( "HostOrganismTag" ); buf.append( "{taxId=" ).append( taxId ); buf.append( ", tissue=" ); if ( null == tissue || tissue.getPsiDefinition() == null) { buf.append( '-' ); } else { buf.append( tissue.getPsiDefinition().getId() ); } buf.append( ", cellType=" ); if ( null == cellType || cellType.getPsiDefinition() == null) { buf.append( '-' ); } else { buf.append( cellType.getPsiDefinition().getId() ); } buf.append( '}' ); return buf.toString(); } }