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();
}
public String toString() {
StringBuilder buf = new StringBuilder();
try {
buf.append("sequence: " + resultPeptide.getFullModifiedPeptide());
} catch (ModifiedSequenceBuilderException e) {
buf.append("sequence: ERROR building full modified sequence: " + e.getMessage());
}
buf.append("\n");
buf.append("qvalue: " + qvalue);
buf.append("\n");
buf.append("score: " + score);
buf.append("\n");
if (proteins.size() == 0) buf.append("NO MATCHING PROTEINS\n");
else {
buf.append("Proteins:\n");
for (MsSearchResultProteinIn locus : proteins) {
buf.append(locus.getAccession() + "\n");
}
}
if (baristaPsmIds.size() == 0) buf.append("NO PSMs\n");
else {
buf.append("PSMs:\n");
for (Integer baristaPsmId : baristaPsmIds) {
buf.append(baristaPsmId + "\n");
}
}
buf.append("\n");
return buf.toString();
}
public PeptideTerminalAAResult calculateForRunSearchAnalysis(
int analysisId, int runSearchAnalysisId) {
if (lookAtUniqPeptides) {
if (this.peptides == null) {
peptides = new HashSet<String>();
}
}
PercolatorResultDAO percDao = DAOFactory.instance().getPercolatorResultDAO();
PercolatorResultFilterCriteria filterCriteria = new PercolatorResultFilterCriteria();
filterCriteria.setMaxQValue(scoreCutoff);
long s = System.currentTimeMillis();
PeptideTerminalAAResultBuilder builder = new PeptideTerminalAAResultBuilder(analysisId, enzyme);
builder.setScoreCutoff(this.scoreCutoff);
builder.setScoreType("PERC_PSM_QVAL");
int totalResults = 0;
List<Integer> percResultIds =
percDao.loadIdsForRunSearchAnalysis(runSearchAnalysisId, filterCriteria, null);
log.info(
"Found "
+ percResultIds.size()
+ " Percolator results at qvalue <= "
+ scoreCutoff
+ " for runSearchAnalysisID "
+ runSearchAnalysisId);
for (Integer percResultId : percResultIds) {
PercolatorResult pres = percDao.loadForPercolatorResultId(percResultId);
MsSearchResultPeptide peptide = pres.getResultPeptide();
String seq = peptide.getPeptideSequence();
if (this.lookAtUniqPeptides) {
String fullseq = peptide.getPreResidue() + "." + seq + "." + peptide.getPostResidue();
if (peptides.contains(fullseq)) continue;
else peptides.add(fullseq);
}
totalResults++;
char ntermMinusOne = peptide.getPreResidue(); // nterm - 1 residue
builder.addNtermMinusOneCount(ntermMinusOne);
char nterm = seq.charAt(0); // nterm residue
builder.addNtermCount(nterm);
char cterm = seq.charAt(seq.length() - 1); // cterm residue
builder.addCtermCount(cterm);
char ctermPlusOne = peptide.getPostResidue(); // cterm + 1 residue
builder.addCtermPlusOneCount(ctermPlusOne);
int numEnzTerm = 0;
if (this.rule != null)
numEnzTerm = rule.getNumEnzymaticTermini(seq, ntermMinusOne, ctermPlusOne);
builder.addEnzymaticTerminiCount(numEnzTerm);
}
long e = System.currentTimeMillis();
log.info(
"Time to get results for runSearchAnalysisId "
+ runSearchAnalysisId
+ " "
+ TimeUtils.timeElapsedSeconds(s, e)
+ " seconds");
log.info("# filtered results: " + totalResults);
builder.setTotalResultCount(totalResults);
return builder.getResult();
}