/** * Fairly important constructor given the size of a ChromsomeSequence where the * ProxySequenceReader could load from disk via RandomAccessFile so that the sequence * doesn't need to be kept in memory. Could also be a NCBI proxy to load sequence * data as needed from remote web server. * @param proxyLoader */ public ChromosomeSequence(SequenceReader<NucleotideCompound> proxyLoader) { super(proxyLoader, DNACompoundSet.getDNACompoundSet()); }
public DNACompoundSet() { addNucleotideCompound("A", "T"); addNucleotideCompound("T", "A"); addNucleotideCompound("G", "C"); addNucleotideCompound("C", "G"); addNucleotideCompound("N", "N"); addNucleotideCompound("-", "-"); }
Compound gapSymbol = DNACompoundSet.getDNACompoundSet().getCompoundForString("-");
@Override public NucleotideCompound newNucleotideCompound(String base, String complement, String... equivalents) { if(equivalents.length == 0) { return new NucleotideCompound(base, this, complement); } else { NucleotideCompound[] compounds = new NucleotideCompound[equivalents.length]; for(int i=0; i<compounds.length; i++) { compounds[i] = getCompoundForString(equivalents[i]); } return new NucleotideCompound(base, this, complement, compounds); } } }
@Override public NucleotideCompound newNucleotideCompound(String base, String complement, String... equivalents) { if(equivalents.length == 0) { return new NucleotideCompound(base, this, complement); } else { NucleotideCompound[] compounds = new NucleotideCompound[equivalents.length]; for(int i=0; i<compounds.length; i++) { compounds[i] = getCompoundForString(equivalents[i]); } return new NucleotideCompound(base, this, complement, compounds); } } }
/** * String is king and assume DNA * @param seqString * @throws CompoundNotFoundException */ public ChromosomeSequence(String seqString) throws CompoundNotFoundException { super(seqString, DNACompoundSet.getDNACompoundSet()); }
public DNACompoundSet() { addNucleotideCompound("A", "T"); addNucleotideCompound("T", "A"); addNucleotideCompound("G", "C"); addNucleotideCompound("C", "G"); addNucleotideCompound("N", "N"); addNucleotideCompound("-", "-"); }
/** * String is king and assume DNA * @param seqString * @throws CompoundNotFoundException */ public ChromosomeSequence(String seqString) throws CompoundNotFoundException { super(seqString, DNACompoundSet.getDNACompoundSet()); }
/** * String is king and create a sequence from DNA with default DNA compound set * @param seqString * @throws CompoundNotFoundException */ public DNASequence(String seqString) throws CompoundNotFoundException { super(seqString, DNACompoundSet.getDNACompoundSet()); }
/** * Create a sequence where the actual storage of the sequence data is somewhere else * @param proxyLoader */ public DNASequence(SequenceReader<NucleotideCompound> proxyLoader) { super(proxyLoader, DNACompoundSet.getDNACompoundSet()); }
/** * Fairly important constructor given the size of a ChromsomeSequence where the * ProxySequenceReader could load from disk via RandomAccessFile so that the sequence * doesn't need to be kept in memory. Could also be a NCBI proxy to load sequence * data as needed from remote web server. * @param proxyLoader */ public ChromosomeSequence(SequenceReader<NucleotideCompound> proxyLoader) { super(proxyLoader, DNACompoundSet.getDNACompoundSet()); }
/** * String is king and create a sequence from DNA with default DNA compound set * @param seqString * @throws CompoundNotFoundException */ public DNASequence(String seqString) throws CompoundNotFoundException { super(seqString, DNACompoundSet.getDNACompoundSet()); }
/** * Create a sequence where the actual storage of the sequence data is somewhere else * @param proxyLoader */ public DNASequence(SequenceReader<NucleotideCompound> proxyLoader) { super(proxyLoader, DNACompoundSet.getDNACompoundSet()); }
private Sequence getSequence(String gappedSequenceString){ if (gappedSequenceString == null) return null; Sequence returnSeq = null; String sequenceString = gappedSequenceString.replace("-", ""); try { if (sequenceString.matches("^[ACTG]+$")) returnSeq = new DNASequence(sequenceString, DNACompoundSet.getDNACompoundSet()); else if (sequenceString.matches("^[ACUG]+$")) returnSeq = new RNASequence(sequenceString, DNACompoundSet.getDNACompoundSet()); else returnSeq = new ProteinSequence(sequenceString, AminoAcidCompoundSet.getAminoAcidCompoundSet()); } catch (CompoundNotFoundException ex) { logger.error("Unexpected error, could not find compound when creating Sequence object from Hsp", ex); } return returnSeq; }
private Sequence getSequence(String gappedSequenceString){ if (gappedSequenceString == null) return null; Sequence returnSeq = null; String sequenceString = gappedSequenceString.replace("-", ""); try { if (sequenceString.matches("^[ACTG]+$")) returnSeq = new DNASequence(sequenceString, DNACompoundSet.getDNACompoundSet()); else if (sequenceString.matches("^[ACUG]+$")) returnSeq = new RNASequence(sequenceString, DNACompoundSet.getDNACompoundSet()); else returnSeq = new ProteinSequence(sequenceString, AminoAcidCompoundSet.getAminoAcidCompoundSet()); } catch (CompoundNotFoundException ex) { logger.error("Unexpected error, could not find compound when creating Sequence object from Hsp", ex); } return returnSeq; }
/** * Determines GCG type * @param cs compound set of sequences * @return GCG type */ public static <C extends Compound> String getGCGType(CompoundSet<C> cs) { return (cs == DNACompoundSet.getDNACompoundSet() || cs == AmbiguityDNACompoundSet.getDNACompoundSet()) ? "D" : (cs == RNACompoundSet.getRNACompoundSet() || cs == AmbiguityRNACompoundSet.getRNACompoundSet()) ? "R" : "P"; }
public static void main(String[] args) throws Exception { DNASequence dnaSequence = new DNASequence("ATCG"); logger.info("DNA Sequence: {}", dnaSequence.toString()); StringProxySequenceReader<NucleotideCompound> sequenceStringProxyLoader = new StringProxySequenceReader<NucleotideCompound>("GCTA", DNACompoundSet.getDNACompoundSet()); DNASequence dnaSequenceFromProxy = new DNASequence(sequenceStringProxyLoader); logger.info("DNA Sequence from Proxy: {}", dnaSequenceFromProxy.toString()); } }
public static void main(String[] args) throws Exception { DNASequence dnaSequence = new DNASequence("ATCG"); logger.info("DNA Sequence: {}", dnaSequence.toString()); StringProxySequenceReader<NucleotideCompound> sequenceStringProxyLoader = new StringProxySequenceReader<NucleotideCompound>("GCTA", DNACompoundSet.getDNACompoundSet()); DNASequence dnaSequenceFromProxy = new DNASequence(sequenceStringProxyLoader); logger.info("DNA Sequence from Proxy: {}", dnaSequenceFromProxy.toString()); } }
/** * Determines GCG type * @param cs compound set of sequences * @return GCG type */ public static <C extends Compound> String getGCGType(CompoundSet<C> cs) { return (cs == DNACompoundSet.getDNACompoundSet() || cs == AmbiguityDNACompoundSet.getDNACompoundSet()) ? "D" : (cs == RNACompoundSet.getRNACompoundSet() || cs == AmbiguityRNACompoundSet.getRNACompoundSet()) ? "R" : "P"; }
/** * * @param parentSequence * @param bioBegin * @param bioEnd * @param phase */ public CDSSequence(TranscriptSequence parentSequence, int bioBegin, int bioEnd, int phase) { parentTranscriptSequence = parentSequence; this.setParentSequence(parentTranscriptSequence); setBioBegin(bioBegin); setBioEnd(bioEnd); this.phase = phase; this.setCompoundSet(DNACompoundSet.getDNACompoundSet()); }