/** * Get the protein sequence with user defined TranscriptEngine * @param engine * @return */ public ProteinSequence getProteinSequence(TranscriptionEngine engine) { DNASequence dnaCodingSequence = getDNACodingSequence(); RNASequence rnaCodingSequence = dnaCodingSequence.getRNASequence(engine); ProteinSequence proteinSequence = rnaCodingSequence.getProteinSequence(engine); proteinSequence.setAccession(new AccessionID(this.getAccession().getID())); return proteinSequence; }
/** Converts the DNA sequence to protein sequence. * * @param dnaSequence the DNA sequence * * @return the protein sequence */ public static ProteinSequence convertDNAtoProteinSequence(DNASequence dnaSequence) throws CompoundNotFoundException { RNASequence mRNA = dnaSequence.getRNASequence(); return mRNA.getProteinSequence(); } }
public StartCodonSequence(TranscriptSequence parentGeneSequence, int begin, int end){ this.parentGeneSequence = parentGeneSequence; setBioBegin(begin); setBioEnd(end); }
public Sequence<?> getSequenceFromString(String sequence) throws CompoundNotFoundException { if( isNucleotideSequence(sequence)) { return new DNASequence(sequence); } else { return new ProteinSequence(sequence); } }
static public LinkedHashMap<String, GeneSequence> getGeneSequences(Collection<ChromosomeSequence> chromosomeSequences) throws Exception { LinkedHashMap<String, GeneSequence> geneSequenceHashMap = new LinkedHashMap<String, GeneSequence>(); for (ChromosomeSequence chromosomeSequence : chromosomeSequences) { for (GeneSequence geneSequence : chromosomeSequence.getGeneSequences().values()) { geneSequenceHashMap.put(geneSequence.getAccession().getID(), geneSequence); } } return geneSequenceHashMap; }
static public LinkedHashMap<String, ChromosomeSequence> getChromosomeSequenceFromDNASequence(LinkedHashMap<String, DNASequence> dnaSequenceList) { LinkedHashMap<String, ChromosomeSequence> chromosomeSequenceList = new LinkedHashMap<String, ChromosomeSequence>(); for (String key : dnaSequenceList.keySet()) { DNASequence dnaSequence = dnaSequenceList.get(key); ChromosomeSequence chromosomeSequence = new ChromosomeSequence(dnaSequence.getProxySequenceReader()); //we want the underlying sequence but don't need storage chromosomeSequence.setAccession(dnaSequence.getAccession()); chromosomeSequenceList.put(key, chromosomeSequence); } return chromosomeSequenceList; }
/** * * @param sequence The Sequence from a String * @param index Currently not used * @return */ @Override public AbstractSequence<NucleotideCompound> getSequence(String sequence, long index) throws CompoundNotFoundException { return new DNASequence(sequence, compoundSet); } /**
/** * * @param proxyLoader * @param index not used in this implementation * @return */ @Override public AbstractSequence<AminoAcidCompound> getSequence( ProxySequenceReader<AminoAcidCompound> proxyLoader, long index) { return new ProteinSequence(proxyLoader, compoundSet); } }
/** * * @param sequence * @param index * @return * @throws CompoundNotFoundException */ @Override public AbstractSequence<NucleotideCompound> getSequence(String sequence, long index) throws CompoundNotFoundException { return new RNASequence(sequence, compoundSet); } /**
/** * @param startCodonSequence the startCodonSequence to set */ public void addStartCodonSequence(AccessionID accession, int begin, int end) { this.startCodonSequence = new StartCodonSequence(this, begin, end); startCodonSequence.setAccession(accession); }
public StopCodonSequence(TranscriptSequence parentGeneSequence, int begin, int end){ this.parentGeneSequence = parentGeneSequence; setBioBegin(begin); setBioEnd(end); }
/** * @return the strand */ public Strand getStrand() { return parentGeneSequence.getStrand(); }
/** * @param stopCodonSequence the stopCodonSequence to set */ public void addStopCodonSequence(AccessionID accession, int begin, int end) { this.stopCodonSequence = new StopCodonSequence(this, begin, end); stopCodonSequence.setAccession(accession); } }
/** * * @return get the strand */ public Strand getStrand() { return parentTranscriptSequence.getStrand(); }
/** * Delegates to {@link #getInverse() } for the reverse complement */ public SequenceView<NucleotideCompound> getReverseComplement() { return getInverse(); }
/** * Get the protein sequence with user defined TranscriptEngine * @param engine * @return */ public ProteinSequence getProteinSequence(TranscriptionEngine engine) { DNASequence dnaCodingSequence = getDNACodingSequence(); RNASequence rnaCodingSequence = dnaCodingSequence.getRNASequence(engine); ProteinSequence proteinSequence = rnaCodingSequence.getProteinSequence(engine); proteinSequence.setAccession(new AccessionID(this.getAccession().getID())); return proteinSequence; }
public Sequence<?> getSequenceFromString(String sequence) throws CompoundNotFoundException { if( isNucleotideSequence(sequence)) { return new DNASequence(sequence); } else { return new ProteinSequence(sequence); } }
/** * @param startCodonSequence the startCodonSequence to set */ public void addStartCodonSequence(AccessionID accession, int begin, int end) { this.startCodonSequence = new StartCodonSequence(this, begin, end); startCodonSequence.setAccession(accession); }
public StopCodonSequence(TranscriptSequence parentGeneSequence, int begin, int end){ this.parentGeneSequence = parentGeneSequence; setBioBegin(begin); setBioEnd(end); }