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());
}
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);
}
}
/**
* 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());
}
/**
* Create a protein from a string
*
* @param seqString
*/
public ProteinSequence(String seqString) {
this(seqString, AminoAcidCompoundSet.getAminoAcidCompoundSet());
}