public void writeEmptyResults(FastaSequence fasta) throws IOException {
FileWriter writer = new FileWriter(ouptutFile);
writer.write(fasta.getIdentifier());
writer.write(NEW_COLUMN);
writer.write(EMPTY);
writer.write(NEW_COLUMN);
writer.write(EMPTY);
writer.write(NEW_COLUMN);
writer.write(EMPTY);
writer.write(NEW_COLUMN);
writer.write(EMPTY);
writer.write(NEW_COLUMN);
writer.write(EMPTY);
writer.write(NEW_COLUMN);
writer.write(EMPTY);
writer.write(NEW_COLUMN);
writer.write(EMPTY);
writer.write(NEW_COLUMN);
writer.write(EMPTY);
writer.write(NEW_COLUMN);
writer.write(fasta.getSequence());
writer.write(NEW_COLUMN);
writer.write(EMPTY);
writer.write(NEW_COLUMN);
writer.write(EMPTY);
writer.write(NEW_LINE);
writer.flush();
writer.close();
}
private void writeBlastResults(
Writer writer, BlastResults blastResult, FastaSequence fastaSequence) throws IOException {
// candidate uniprot
writer.write(NEW_COLUMN);
writer.write(blastResult.getAccession());
// write identity
writer.write(NEW_COLUMN);
writer.write(Float.toString(blastResult.getIdentity()));
// write sequence coverages
writer.write(NEW_COLUMN);
writer.write(
Float.toString(getQueryCoveragePercentFor(blastResult, fastaSequence.getSequence())));
writer.write(NEW_COLUMN);
writer.write(Float.toString(getMatchCoveragePercentFor(blastResult)));
// write start/end
writer.write(NEW_COLUMN);
writer.write(Integer.toString(blastResult.getStartQuery()));
writer.write("-");
writer.write(Integer.toString(blastResult.getEndQuery()));
writer.write(NEW_COLUMN);
writer.write(Integer.toString(blastResult.getStartMatch()));
writer.write("-");
writer.write(Integer.toString(blastResult.getEndMatch()));
// write query sequence
writer.write(NEW_COLUMN);
writer.write(fastaSequence.getSequence());
// write alignment
writer.write(NEW_COLUMN);
writer.write(blastResult.getAlignment());
// write matching sequence
writer.write(NEW_COLUMN);
writer.write(blastResult.getSequence());
writer.write(NEW_LINE);
writer.flush();
}
private void writeEmpytBlastResults(Writer writer, FastaSequence fastaSequence)
throws IOException {
// candidate uniprot
writer.write(NEW_COLUMN);
writer.write(EMPTY);
// write identity
writer.write(NEW_COLUMN);
writer.write(EMPTY);
// write sequence coverages
writer.write(NEW_COLUMN);
writer.write(EMPTY);
writer.write(NEW_COLUMN);
writer.write(EMPTY);
// write start/end
writer.write(NEW_COLUMN);
writer.write(EMPTY);
writer.write(NEW_COLUMN);
writer.write(EMPTY);
// write query sequence
writer.write(NEW_COLUMN);
writer.write(fastaSequence.getSequence());
// write alignment
writer.write(NEW_COLUMN);
writer.write(EMPTY);
// write matching sequence
writer.write(NEW_COLUMN);
writer.write(EMPTY);
writer.write(NEW_LINE);
writer.flush();
}
