public void Correct(string prefix, IProteinSet proteinSet)
{
int count = 0;
for (int i = 0; i < proteinIndex.Length; i++)
{
if (T07SearchEngineEnhancement.IsReverseProtein(proteinSet.GetName(proteinIndex[i]), prefix))
{
count++;
}
}
if (count == 0 || count == proteinIndex.Length)
{
return;
}
List <int> result = new List <int>();
for (int i = 0; i < proteinIndex.Length; i++)
{
if (!proteinSet.GetName(proteinIndex[i]).StartsWith(prefix))
{
result.Add(proteinIndex[i]);
}
}
proteinIndex = result.ToArray();
}
public void FillProteinToPepTable(Dictionary <string, HashSet <string> > protIdToPepSeqs, IProteinSet proteinSet)
{
if (peptides == null)
{
Read();
}
for (int i = 0; i < peptides.Length; i++)
{
MascotPeptide p = peptides[i][0];
int[] proteinIndex = p.ProteinIndex;
if (!T07SearchEngineEnhancement.ValidPeptide(p.Sequence))
{
continue;
}
foreach (int pi in proteinIndex)
{
string protId = proteinSet.GetName(pi);
if (!protIdToPepSeqs.ContainsKey(protId))
{
protIdToPepSeqs.Add(protId, new HashSet <string>());
}
string key = p.Sequence;
if (!protIdToPepSeqs[protId].Contains(key))
{
protIdToPepSeqs[protId].Add(key);
}
}
}
}
public string[] GetProteinIds(IProteinSet proteinSet)
{
string[] result = new string[proteinIndex.Length];
for (int i = 0; i < result.Length; i++)
{
result[i] = proteinSet.GetName(proteinIndex[i]);
}
return(result);
}
public bool HasOnlyReverseHits(string reverseStr, IProteinSet proteinSet)
{
for (int i = 0; i < proteinIndex.Length; i++)
{
if (!T07SearchEngineEnhancement.IsReverseProtein(proteinSet.GetName(proteinIndex[i]), reverseStr))
{
return(false);
}
}
return(true);
}
public void ProcessPeptides(int fileIndex, Dictionary <string, int> proteinIdToGroupIndex, IPeakList peakList,
MsmsData msmsData, IIdentifiedPeptide[] identifiedPeptides, string[] peptideSequences,
ReQuantitationResult reQuantitationResult, bool reQuantify,
HashSet <string> labelModificationSet, IProteinSet proteinSet,
SilacType silacType, SilacLabel[] labels1, SilacLabel[] labels2, double ms2Tol,
string ms2TolUnit, int topx, string[] fixedMods)
{
if (peptides == null)
{
Read();
}
double[] monoIsoMz = peakList.MS2MonoisotopicMz;
for (int i = 0; i < peptides.Length; i++)
{
MascotPeptide[] p = peptides[i];
int scanNumber = scanNumbers[i];
int ms2ind = peakList.GetMs2IndexFromScanNumber(scanNumber);
double mz = peakList.GetMs2Mz(ms2ind);
double monotopicMz = monoIsoMz[ms2ind];
double time = peakList.GetMs2Rt(ms2ind);
int silacId = -1;
int isotopeId = -1;
int silacIndex = -1;
SilacCluster silacCluster = null;
IsotopeCluster isotopeCluster = null;
if (type == MascotQueryType.Silac)
{
int[] silacInfo = peakList.GetSilacInfoForMsmsScanNumber(scanNumber);
silacId = silacInfo[0];
silacIndex = silacInfo[1];
silacCluster = peakList.GetSilacCluster(silacId);
}
else if (type == MascotQueryType.Isotope)
{
isotopeId = peakList.GetIsotopeIndexForMsmsScanNumber(scanNumber);
isotopeCluster = peakList.GetIsotopeCluster(isotopeId);
}
int index = Array.BinarySearch(peptideSequences, p[0].Sequence);
if (index < 0)
{
continue;
}
HashSet <int> tmpGroupInds = new HashSet <int>();
foreach (int pi in p[0].ProteinIndex)
{
string protId = proteinSet.GetName(pi);
if (!proteinIdToGroupIndex.ContainsKey(protId))
{
continue;
}
int groupInd = proteinIdToGroupIndex[protId];
if (!tmpGroupInds.Contains(groupInd))
{
tmpGroupInds.Add(groupInd);
}
}
double[] specMasses;
float[] specIntensities;
bool uniqueProtein = (p[0].ProteinIndex.Length == 1);
bool uniqueGroup = (tmpGroupInds.Count == 1);
msmsData.GetSpectrumFromScanNumber(scanNumber, out specMasses, out specIntensities);
identifiedPeptides[index].AddMascotPeptideHit(p, scanNumber, fileIndex, type, silacId, silacIndex, isotopeId,
silacCluster, isotopeCluster, time, peakList, mz, monotopicMz,
fixedModifications[i], specMasses, specIntensities,
reQuantitationResult, reQuantify, labelModificationSet, silacType,
labels1, labels2, ms2Tol, ms2TolUnit, topx, fixedMods);
identifiedPeptides[index].UniqueProtein = uniqueProtein;
identifiedPeptides[index].UniqueGroup = uniqueGroup;
}
}
