private String reconstructSequestPeptideSequence(int searchId, SequestSearchResult resultDb) {
// dynamic modifications for the search
MsSearchResultPeptide peptideSeq = resultDb.getResultPeptide();
List<MsResultResidueMod> resultMods = peptideSeq.getResultDynamicResidueModifications();
Collections.sort(
resultMods,
new Comparator<MsResultResidueMod>() {
public int compare(MsResultResidueMod o1, MsResultResidueMod o2) {
return new Integer(o1.getModifiedPosition())
.compareTo(new Integer(o2.getModifiedPosition()));
}
});
String justSeq = peptideSeq.getPeptideSequence();
StringBuilder fullSeq = new StringBuilder();
fullSeq.append(peptideSeq.getPreResidue() + ".");
int lastIdx = 0;
for (MsResultResidueMod mod : resultMods) {
int pos = mod.getModifiedPosition();
fullSeq.append(justSeq.substring(lastIdx, pos + 1));
fullSeq.append(mod.getModificationSymbol());
lastIdx = pos + 1;
}
if (lastIdx < justSeq.length()) {
fullSeq.append(justSeq.substring(lastIdx, justSeq.length()));
}
fullSeq.append("." + peptideSeq.getPostResidue());
return fullSeq.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");
}
}