/** * {@inheritDoc} */ @Override public String toString() { final StringBuilder sb = new StringBuilder(); sb.append( "UniprotFeatureChain" ); sb.append( "{ id='" ).append( getPrimaryAc() ).append( '\'' ); sb.append( ", sequence='" ).append( getSequence() ).append( '\'' ); sb.append( ", organism=" ).append( getOrganism() ); sb.append( ", description=" ).append( description ); sb.append( ", start=" ).append( getStart() ); sb.append( ", end=" ).append( getEnd() ); sb.append( '}' ); return sb.toString(); } }
UniprotFeatureChain chain = new UniprotFeatureChain( id, protein.getOrganism(), chainSequence ); chain.setDescription( description ); chain.setStart( begin ); chain.setEnd( end );
public Collection<UniprotFeatureChain> retrieveFeatureChain( String ac ) { if (log.isDebugEnabled()) { log.debug("Retrieving feature chains from UniProt: "+ac); } Collection<UniprotFeatureChain> variants = new ArrayList<UniprotFeatureChain>(); Collection<UniprotProtein> proteins = new ArrayList<UniprotProtein>(); Iterator<UniProtEntry> it = getUniProtEntry( ac ); if ( !it.hasNext() ) { // we didn't find anything addError( ac, new UniprotServiceReport( "Could not find splice variants: " + ac ) ); } while ( it.hasNext() ) { UniProtEntry uniProtEntry = it.next(); UniprotProtein uniprotProtein = buildUniprotProtein( uniProtEntry, true ); proteins.add( uniprotProtein ); UniprotFeatureChain variant = retrieveUniprotFeatureChain(uniprotProtein, ac); if (variant != null) { variants.add(variant); variant.setMasterProtein(uniprotProtein); } } return variants; }
public UniprotFeatureChain retrieveUniprotFeatureChain( UniprotProtein uniProtEntry, String ac) { if (uniProtEntry != null && ac != null){ for (UniprotFeatureChain fc : uniProtEntry.getFeatureChains()){ String acFixed = ac; // if not of type primaryAc-PRO_xxxxx, it is not a feature chain. we have to build the feature chain ac if (ac.indexOf("-") == -1){ acFixed = uniProtEntry.getPrimaryAc() + "-" + ac; } if (acFixed.equals(fc.getPrimaryAc())){ return fc; } } } return null; } }
UniprotFeatureChain chain = new UniprotFeatureChain( id, protein.getOrganism(), chainSequence ); chain.setDescription( description ); chain.setStart( begin ); chain.setEnd( end );
variant.setMasterProtein(p); variant.setMasterProtein(uniprotProtein);
UniprotFeatureChain chain = new UniprotFeatureChain( id, protein.getOrganism(), chainSequence ); chain.setDescription( description ); chain.setStart( begin ); chain.setEnd( end );