Ejemplo n.º 1
0
  public static void main(String[] args) {
    ProteinSequence proteinSequence = new ProteinSequence("ARNDCEQGHILKMFPSTWYVBZJX");
    System.out.println(proteinSequence.toString());

    StringProxySequenceReader<AminoAcidCompound> sequenceStringProxyLoader =
        new StringProxySequenceReader<AminoAcidCompound>(
            "XRNDCEQGHILKMFPSTWYVBZJA", AminoAcidCompoundSet.getAminoAcidCompoundSet());
    ProteinSequence proteinSequenceFromProxy = new ProteinSequence(sequenceStringProxyLoader);
    System.out.println(proteinSequenceFromProxy.toString());
  }
Ejemplo n.º 2
0
  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);
    }
  }
Ejemplo n.º 3
0
 /**
  * A protein sequence where the storage of the sequence is somewhere else. Could be loaded from a
  * large Fasta file or via a Uniprot Proxy reader via Uniprot ID
  *
  * @param proxyLoader
  */
 public ProteinSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader) {
   this(proxyLoader, AminoAcidCompoundSet.getAminoAcidCompoundSet());
 }
Ejemplo n.º 4
0
 /**
  * Create a protein from a string
  *
  * @param seqString
  */
 public ProteinSequence(String seqString) {
   this(seqString, AminoAcidCompoundSet.getAminoAcidCompoundSet());
 }