public void convertToSqt(int runSearchId, String outputFile) throws IOException {
try {
outFile = new BufferedWriter(new FileWriter(outputFile));
SQTRunSearchDAO searchDao = DAOFactory.instance().getSqtRunSearchDAO();
SQTRunSearch runSearch = searchDao.loadRunSearch(runSearchId);
if (runSearch == null) {
System.err.println("No run search found with id: " + runSearchId);
return;
}
int searchDatabaseId = getSearchDatabaseId(runSearch.getSearchId());
printSqtHeader(runSearch);
outFile.write("\n");
SearchFileFormat origFileType = runSearch.getSearchFileFormat();
if (origFileType == SearchFileFormat.SQT_SEQ) {
printSequestSQTData(runSearch, searchDatabaseId, outFile);
} else if (origFileType == SearchFileFormat.SQT_PLUCID) {
// TODO
}
outFile.flush();
} finally {
if (outFile != null) outFile.close();
}
}
private void printSqtHeader(SQTRunSearch search) throws IOException {
SQTHeader sqtHeader = new SQTHeader();
List<SQTHeaderItem> headerList = search.getHeaders();
for (SQTHeaderItem header : headerList) {
try {
sqtHeader.addHeaderItem(header.getName(), header.getValue());
} catch (SQTParseException e) {
e.printStackTrace();
}
}
outFile.write(sqtHeader.toString());
}
private void printSequestSQTData(
SQTRunSearch runSearch, int searchDatabaseId, BufferedWriter outFile) throws IOException {
List<MsResidueModification> dynaResidueModsDb =
getDynaResidueModsForSearch(runSearch.getSearchId());
SQTSearchScanDAO scanDao = DAOFactory.instance().getSqtSpectrumDAO();
SequestSearchResultDAO resultDao = DAOFactory.instance().getSequestResultDAO();
List<Integer> resultIds = resultDao.loadResultIdsForRunSearch(runSearch.getId());
int currCharge = -1;
int currScanId = -1;
SearchScan currScan = null;
for (Integer resultId : resultIds) {
SequestSearchResult result = resultDao.load(resultId);
if (result.getScanId() != currScanId || result.getCharge() != currCharge) {
if (currScan != null) {
outFile.write(currScan.toString());
outFile.write("\n");
}
currScanId = result.getScanId();
currCharge = result.getCharge();
SQTSearchScan scanDb =
scanDao.load(runSearch.getId(), currScanId, currCharge, result.getObservedMass());
currScan = makeScanResult(scanDb);
}
List<MsResidueModificationIn> dynaResidueMods = new ArrayList<MsResidueModificationIn>();
for (MsResidueModification modDb : dynaResidueModsDb) {
dynaResidueMods.add(modDb);
}
SequestResult peptResult = new SequestResult();
peptResult.setResultPeptide(result.getResultPeptide());
SequestResultData data = result.getSequestResultData();
peptResult.setCharge(result.getCharge());
peptResult.setObservedMass(result.getObservedMass());
peptResult.setDeltaCN(data.getDeltaCN());
peptResult.setCalculatedMass(data.getCalculatedMass());
peptResult.setMatchingIons(data.getMatchingIons());
peptResult.setPredictedIons(data.getPredictedIons());
peptResult.setOriginalPeptideSequence(
reconstructSequestPeptideSequence(runSearch.getSearchId(), result));
peptResult.setScanNumber(currScan.getScanNumber());
peptResult.setSp(data.getSp());
peptResult.setSpRank(data.getSpRank());
peptResult.setValidationStatus(result.getValidationStatus().getStatusChar());
peptResult.setxCorr(data.getxCorr());
peptResult.setxCorrRank(data.getxCorrRank());
peptResult.setEvalue(data.getEvalue());
List<MsSearchResultProtein> proteins = getProteinsForResultId(resultId);
for (MsSearchResultProtein pr : proteins) {
peptResult.addMatchingLocus(pr.getAccession(), null);
}
// currScan.addPeptideResult(peptResult);
}
// print the last one
if (currScan != null) {
outFile.write(currScan.toString());
outFile.write("\n");
}
}
