/** * {@inheritDoc} */ @Override public String toString() { final StringBuilder sb = new StringBuilder(); sb.append( "SpliceVariant" ); sb.append( "{primaryAC='" ).append( getPrimaryAc() ).append( '\'' ); sb.append( ",secondaryAcs=" ).append( secondaryAcs ); sb.append( ",sequence='" ).append( getSequence() ).append( '\'' ); sb.append( ", start=" ).append( getStart() ); sb.append( ", end=" ).append( getEnd() ); sb.append( ", note='" ).append( note ).append( '\'' ); sb.append( '}' ); return sb.toString(); } }
public UniprotSpliceVariant retrieveUniprotSpliceVariant( UniprotProtein uniProtEntry, String ac) { if (uniProtEntry != null && ac != null){ for (UniprotSpliceVariant sv : uniProtEntry.getSpliceVariants()){ if (ac.equals(sv.getPrimaryAc())){ return sv; } else if (sv.getSecondaryAcs().contains(ac)){ return sv; } } } return null; }
public Collection<UniprotSpliceVariant> retrieveSpliceVariant( String ac ) { if (log.isDebugEnabled()) { log.debug("Retrieving splice variants from UniProt: "+ac); } Collection<UniprotSpliceVariant> variants = new ArrayList<UniprotSpliceVariant>(); Collection<String> variantAcProcessed = new ArrayList<String>(); Collection<UniprotProtein> proteins = getFromCache( ac ); if ( proteins == null ) { proteins = service.retrieve( ac ); storeInCache( proteins, ac ); } for (UniprotProtein p : proteins){ UniprotSpliceVariant variant = super.retrieveUniprotSpliceVariant(p, ac); if (!variantAcProcessed.contains(variant.getPrimaryAc())){ variants.add(variant); variantAcProcessed.add(variant.getPrimaryAc()); } } return variants; }
public Collection<UniprotSpliceVariant> retrieveSpliceVariant( String ac ) { if (log.isDebugEnabled()) { log.debug("Retrieving splice variants from UniProt: "+ac); } Collection<UniprotSpliceVariant> variants = new ArrayList<UniprotSpliceVariant>(); Collection<String> variantAcProcessed = new ArrayList<String>(); 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 ); UniprotSpliceVariant variant = retrieveUniprotSpliceVariant(uniprotProtein, ac); if (variant != null){ if (!variantAcProcessed.contains(variant.getPrimaryAc())){ variants.add(variant); variantAcProcessed.add(variant.getPrimaryAc()); variant.setMasterProtein(uniprotProtein); } } } return variants; }
UniprotSpliceVariant variant = retrieveUniprotSpliceVariant(p, ac); if (variant != null && !variantAcProcessed.contains(variant.getPrimaryAc())){ variants.add(variant); variantAcProcessed.add(variant.getPrimaryAc()); variant.setMasterProtein(p); if (!variantAcProcessed.contains(variant.getPrimaryAc())){ variants.add(variant); variantAcProcessed.add(variant.getPrimaryAc()); variant.setMasterProtein(uniprotProtein);
if (uniprotSpliceVariant.getPrimaryAc().equals(spliceVarId)) { sequence = uniprotSpliceVariant.getSequence(); break;