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();
}
public void writeResults(
FastaSequence fastaSequence,
IdentificationResults<? extends MappingReport> identificationResults)
throws IOException {
if (identificationResults == null) {
throw new IllegalArgumentException("Identification results are expected");
}
if (fastaSequence == null) {
throw new IllegalArgumentException("A fast sequence is expected");
}
BufferedWriter writer = new BufferedWriter(new FileWriter(ouptutFile, true));
// PICR/swissprot remapping could identify one single uniprot id. We want to give the blast
// results of swissprot remapping if necessary
if (identificationResults.hasUniqueUniprotId()) {
// fast identifier
writer.write(fastaSequence.getIdentifier());
// we retrieved the uniprot id from PICR
writer.write(NEW_COLUMN);
writer.write(identificationResults.getFinalUniprotId());
// no other possible uniprot ids from PICR
writer.write(NEW_COLUMN);
writer.write(EMPTY);
// check if last report is not blast remapping to be reviewed
MappingReport report = identificationResults.getLastAction();
if (report != null
&& report.getStatusLabel().equals(StatusLabel.TO_BE_REVIEWED)
&& report.getName().equals(ActionName.BLAST_Swissprot_Remapping)) {
BlastReport<BlastResults> blastReport = (BlastReport<BlastResults>) report;
// we have one result that can match
Set<BlastResults> blastResults = blastReport.getBlastMatchingProteins();
if (blastResults.size() == 1) {
BlastResults blastResult = blastResults.iterator().next();
writeBlastResults(writer, blastResult, fastaSequence);
}
// we don't write the other results
else {
writeEmpytBlastResults(writer, fastaSequence);
}
}
// no swissprot remapping to review
else {
writeEmpytBlastResults(writer, fastaSequence);
}
} else {
// PICR sequence to be reviewed ? if yes, no blast to report
MappingReport report = identificationResults.getLastAction();
if (report != null
&& report.getStatusLabel().equals(StatusLabel.TO_BE_REVIEWED)
&& (report.getName().equals(ActionName.PICR_sequence_Swissprot)
|| report.getName().equals(ActionName.PICR_sequence_Trembl))) {
// fasta identifier
writer.write(fastaSequence.getIdentifier());
// no unique uniprot id
writer.write(NEW_COLUMN);
writer.write(EMPTY);
// possible uniprot from PICR
writer.write(NEW_COLUMN);
writer.write(StringUtils.join(report.getPossibleAccessions(), ", "));
writeEmpytBlastResults(writer, fastaSequence);
}
// for each blast to be reviewed, we need to write a line with blast results
else if (report != null
&& report.getStatusLabel().equals(StatusLabel.TO_BE_REVIEWED)
&& report instanceof BlastReport) {
BlastReport<BlastResults> blastReport = (BlastReport<BlastResults>) report;
if (blastReport.getBlastMatchingProteins().isEmpty()) {
writeEmptyResults(fastaSequence);
} else {
for (BlastResults blastResult : blastReport.getBlastMatchingProteins()) {
// fasta identifier
writer.write(fastaSequence.getIdentifier());
// no unique uniprot id
writer.write(NEW_COLUMN);
writer.write(EMPTY);
// no other possible uniprot ids from PICR
writer.write(NEW_COLUMN);
writer.write(EMPTY);
writeBlastResults(writer, blastResult, fastaSequence);
}
}
}
// no blast results
else {
writeEmptyResults(fastaSequence);
}
}
writer.flush();
writer.close();
}