private TMHMMMatch createNewTmhmmMatch(TMHMMSignature prediction, Set<TMHMMMatch.TMHMMLocation> locations) { Signature signature = new Signature.Builder(prediction.getAccession()). description(prediction.getShortDesc()). signatureLibraryRelease(signatureLibraryRelease). build(); String signatureModel = signature.getAccession(); return new TMHMMMatch(signature, signatureModel, locations); }
private TMHMMMatch.TMHMMLocation buildTmhmmLocation(int start, int end, TMHMMSignature prediction, float currentScore) { return new TMHMMMatch.TMHMMLocation.Builder(start, end) .prediction(prediction.toString()) .score(currentScore) .build(); }
/** * Utility method to add a List of cross references * * @param accessions */ public void addCrossReferences(String... accessions) { for (String accession : accessions) { addCrossReference(new ProteinXref(accession)); } }
private void setException(String exception) { this.exception = exception; List<String> chunks = CHUNKER.chunkIntoList(exception); this.exceptionFirstChunk = CHUNKER.firstChunk(chunks); this.exceptionChunks = CHUNKER.latterChunks(chunks); }
private String getDomainRegion(LocationFragment locationFragment){ String domainRegion = locationFragment.getStart() + "-" + locationFragment.getEnd() + "-" + locationFragment.getDcStatus().getSymbol(); return domainRegion; }
public MobiDBFilteredMatchDAO(SignatureLibraryRelease release) { super(MobiDBMatch.class); this.release = release; this.mobidbReleaseVersion = release.getVersion(); }
private void setSequenceObject(Sequence sequence) { setSequence(sequence.getSequence()); setMd5(sequence.getMd5()); }
private void setSequenceObject(Sequence sequence) { setSequence(sequence.getSequence()); setMd5(sequence.getMd5()); }
private void setSequenceAndMd5(String sequence) { setSequence(sequence); setMd5(Md5Helper.calculateMd5(sequence)); }
public Model(String accession, String name, String description) { setAccession(accession); setName(name); setDescription(description); }
private TMHMMMatch createNewTmhmmMatch(TMHMMSignature prediction, Set<TMHMMMatch.TMHMMLocation> locations) { Signature signature = new Signature.Builder(prediction.getAccession()). description(prediction.getShortDesc()). signatureLibraryRelease(signatureLibraryRelease). build(); String signatureModel = signature.getAccession(); return new TMHMMMatch(signature, signatureModel, locations); } }
private TMHMMMatch.TMHMMLocation buildTmhmmLocation(int start, int end, TMHMMSignature prediction, float currentScore) { return new TMHMMMatch.TMHMMLocation.Builder(start, end) .prediction(prediction.toString()) .score(currentScore) .build(); }
private void setDefinition(String definition) { this.definition = definition; List<String> chunks = CHUNKER.chunkIntoList(definition); definitionFirstChunk = CHUNKER.firstChunk(chunks); definitionChunks = CHUNKER.latterChunks(chunks); }
private TMHMMMatch createNewTmhmmMatch(TMHMMSignature prediction, Set<TMHMMMatch.TMHMMLocation> locations) { Signature signature = new Signature.Builder(prediction.getAccession()). description(prediction.getShortDesc()). signatureLibraryRelease(signatureLibraryRelease). build(); return new TMHMMMatch(signature, locations); } }
private TMHMMMatch.TMHMMLocation buildTmhmmLocation(int start, int end, TMHMMSignature prediction) { return new TMHMMMatch.TMHMMLocation.Builder(start, end) .prediction(prediction.toString()) .build(); }
private TMHMMMatch createNewTmhmmMatch(TMHMMSignature prediction, Set<TMHMMMatch.TMHMMLocation> locations) { Signature signature = new Signature.Builder(prediction.getAccession()). description(prediction.getShortDesc()). signatureLibraryRelease(signatureLibraryRelease). build(); return new TMHMMMatch(signature, locations); }
private TMHMMMatch.TMHMMLocation buildTmhmmLocation(int start, int end, TMHMMSignature prediction) { return new TMHMMMatch.TMHMMLocation.Builder(start, end) .prediction(prediction.toString()) .build(); }