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 writeProteinSequence(ProteinSequence sequence, DataOutput out)
throws IOException {
String string = sequence.getSequenceAsString();
out.writeInt(string.length());
for (int i = 0; i < string.length(); i += 3) {
String substring = string.substring(i, Math.min(i + 3, string.length()));
int value = 0;
for (int j = 0; j < 3; j++) {
value += (j < substring.length() ? getSerializedAminoAcid(substring.charAt(j)) : 0);
if (j != 2) {
value <<= 5;
}
}
out.writeShort(value);
}
}