/** * * @param sequence * @param index not used in this implementation * @return * @throws CompoundNotFoundException */ @Override public AbstractSequence<AminoAcidCompound> getSequence(String sequence, long index) throws CompoundNotFoundException { return new ProteinSequence(sequence, compoundSet); } /**
private static boolean isProteinSequence(String str) { try { new ProteinSequence(str); } catch (CompoundNotFoundException e) { return false; } return true; }
/** * * @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 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 not used in this implementation * @return * @throws CompoundNotFoundException */ @Override public AbstractSequence<AminoAcidCompound> getSequence(String sequence, long index) throws CompoundNotFoundException { return new ProteinSequence(sequence, compoundSet); } /**
/** * Returns an AFPChain corresponding to the alignment between {@code structure1} and {@code structure2}, which is given by the gapped protein sequences {@code sequence1} and {@code sequence2}. The * sequences need not correspond to the entire structures, since local alignment is performed to match the sequences to structures. * @throws StructureException * @throws CompoundNotFoundException */ public static AFPChain fastaStringToAfpChain(String sequence1, String sequence2, Structure structure1, Structure structure2) throws StructureException, CompoundNotFoundException { ProteinSequence seq1 = new ProteinSequence(sequence1); ProteinSequence seq2 = new ProteinSequence(sequence2); return fastaToAfpChain(seq1, seq2, structure1, structure2); }
/** * Get the protein sequence of the Subunit. * * @return sequence ProteinSequence * @throws CompoundNotFoundException */ public ProteinSequence getProteinSequence() throws CompoundNotFoundException { if (sequence == null) sequence = new ProteinSequence(getProteinSequenceString()); return sequence; }
public static double getDistributionPosition(String sequence, ATTRIBUTE attribute, GROUPING group, DISTRIBUTION distribution) throws Exception{ return ProfeatProperties.getDistributionPosition(new ProteinSequence(sequence), attribute, group, distribution); }
public static Map<DISTRIBUTION, Double> getDistributionPosition(String sequence, ATTRIBUTE attribute, GROUPING group) throws Exception{ return ProfeatProperties.getDistributionPosition(new ProteinSequence(sequence), attribute, group); }
public static Map<ATTRIBUTE , Map<GROUPING, Map<DISTRIBUTION, Double>>> getDistributionPosition(String sequence) throws Exception{ return ProfeatProperties.getDistributionPosition(new ProteinSequence(sequence)); } }
public static double getComposition(String sequence, ATTRIBUTE attribute, GROUPING group) throws Exception{ return ProfeatProperties.getComposition(new ProteinSequence(sequence), attribute, group); }
public static Map<ATTRIBUTE, Map<GROUPING, Double>> getComposition(String sequence) throws Exception{ return ProfeatProperties.getComposition(new ProteinSequence(sequence)); }
public static void main(String[] args) throws Exception { ProteinSequence proteinSequence = new ProteinSequence("ARNDCEQGHILKMFPSTWYVBZJX"); logger.info("Protein Sequence: {}", proteinSequence.toString()); StringProxySequenceReader<AminoAcidCompound> sequenceStringProxyLoader = new StringProxySequenceReader<AminoAcidCompound>("XRNDCEQGHILKMFPSTWYVBZJA", AminoAcidCompoundSet.getAminoAcidCompoundSet()); ProteinSequence proteinSequenceFromProxy = new ProteinSequence(sequenceStringProxyLoader); logger.info("Protein Sequence from Proxy: {}", proteinSequenceFromProxy.toString()); } }
public static void main(String[] args) throws Exception { ProteinSequence proteinSequence = new ProteinSequence("ARNDCEQGHILKMFPSTWYVBZJX"); logger.info("Protein Sequence: {}", proteinSequence.toString()); StringProxySequenceReader<AminoAcidCompound> sequenceStringProxyLoader = new StringProxySequenceReader<AminoAcidCompound>("XRNDCEQGHILKMFPSTWYVBZJA", AminoAcidCompoundSet.getAminoAcidCompoundSet()); ProteinSequence proteinSequenceFromProxy = new ProteinSequence(sequenceStringProxyLoader); logger.info("Protein Sequence from Proxy: {}", proteinSequenceFromProxy.toString()); } }
public Sequence<?> getSequenceFromString(String sequence) throws CompoundNotFoundException { if( isNucleotideSequence(sequence)) { return new DNASequence(sequence); } else { return new ProteinSequence(sequence); } }
public Sequence<?> getSequenceFromString(String sequence) throws CompoundNotFoundException { if( isNucleotideSequence(sequence)) { return new DNASequence(sequence); } else { return new ProteinSequence(sequence); } }
public static AFPChain cpFastaToAfpChain(String first, String second, Structure structure, int cpSite) throws StructureException, CompoundNotFoundException { ProteinSequence s1 = new ProteinSequence(first); s1.setUserCollection(getAlignedUserCollection(first)); ProteinSequence s2 = new ProteinSequence(second); s2.setUserCollection(getAlignedUserCollection(second)); return cpFastaToAfpChain(s1, s2, structure, cpSite); }
public static void main(String[] args) { try { UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<AminoAcidCompound>("YA745_GIBZE", AminoAcidCompoundSet.getAminoAcidCompoundSet()); ProteinSequence proteinSequence = new ProteinSequence(uniprotSequence); logger.info("Accession: {}", proteinSequence.getAccession().getID()); logger.info("Sequence: {}", proteinSequence.getSequenceAsString()); } catch (Exception e) { logger.error("Exception: ", e); } }
public static void main(String[] args) { try { UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<AminoAcidCompound>("YA745_GIBZE", AminoAcidCompoundSet.getAminoAcidCompoundSet()); ProteinSequence proteinSequence = new ProteinSequence(uniprotSequence); logger.info("Accession: {}", proteinSequence.getAccession().getID()); logger.info("Sequence: {}", proteinSequence.getSequenceAsString()); } catch (Exception e) { logger.error("Exception: ", e); } }
/** * * @param list * @return */ @Override public AbstractSequence<AminoAcidCompound> getSequence( List<AminoAcidCompound> list) { ArrayListProxySequenceReader<AminoAcidCompound> store = new ArrayListProxySequenceReader<AminoAcidCompound>(); store.setCompoundSet(compoundSet); store.setContents(list); return new ProteinSequence(store); } /**