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 bool HasReverseProteins(string revstring)
{
for (int i = 0; i < proteinIds.Length; i++)
{
if (T07SearchEngineEnhancement.IsReverseProtein(proteinIds[i], revstring))
{
return(true);
}
}
return(false);
}
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 MsmsHit(MascotPeptide[] peptides, int scanNumber, int fileIndex, MascotQueryType type,
int silacIndex, double elutionTime, double mz, double monoisotopicMz, ushort[] fixedMods,
HashSet <string> labelModificationSet, SilacType silacType, SilacLabel[] labels1, SilacLabel[] labels2)
{
rawFileIndex = fileIndex;
this.scanNumber = scanNumber;
this.silacIndex = silacIndex;
this.type = type;
pep = peptides[0].Pep;
score = peptides[0].MascotScore;
altScore = peptides[0].AltScore;
charge = (int)Math.Round(peptides[0].Mass / mz);
massErrorPpm = peptides[0].MassErrorPpm;
if (peptides.Length > 1)
{
deltaScoreAll = peptides[0].MascotScore - peptides[1].MascotScore;
}
else
{
deltaScoreAll = peptides[0].MascotScore;
}
int ind = -1;
for (int i = 1; i < peptides.Length; i++)
{
if (!peptides[i].Sequence.Equals(peptides[0].Sequence))
{
ind = i;
break;
}
}
if (ind != -1)
{
deltaScoreDifferentPep = peptides[0].MascotScore - peptides[ind].MascotScore;
}
else
{
deltaScoreDifferentPep = peptides[0].MascotScore;
}
labelModifications =
peptides[0].Modifications.GetLabelModifications(fixedMods, peptides[0].Sequence, labelModificationSet);
trueModifications = peptides[0].Modifications.GetTrueModifications(labelModificationSet);
this.elutionTime = elutionTime;
this.mz = mz;
this.monoisotopicMz = monoisotopicMz;
if (silacType == SilacType.Singlets)
{
this.silacIndex = 0;
}
else if (type != MascotQueryType.Silac)
{
AminoAcid[] allAas = T07SearchEngineEnhancement.CalcAllAas(silacType, labels1, labels2);
char[] allAaLetts = AminoAcid.GetSingleLetters(allAas);
for (int i = 0; i < allAaLetts.Length; i++)
{
this.silacIndex =
CalcSilacIndex(allAaLetts[i], labelModifications, peptides[0].Sequence, silacType, labels1,
labels2);
if (this.silacIndex != -1)
{
break;
}
}
}
}
private int GetSilacIndex(char aa, SilacType type, SilacLabel[] labels1, SilacLabel[] labels2)
{
if (type == SilacType.Singlets)
{
return(0);
}
int index = -1;
string seq = sequence;
for (int i = 0; i < seq.Length; i++)
{
if (seq[i] == aa)
{
index = i;
break;
}
}
if (index == -1)
{
return(-1);
}
Modification[] mods = T07SearchEngineEnhancement.GetModifiedVersions(aa, type, labels1, labels2);
ushort mod = modifications.GetModificationAt(index);
if (mod == ushort.MaxValue)
{
for (int i = 1; i < mods.Length; i++)
{
if (mods[i] == null)
{
return(-1);
}
}
return(0);
}
if (type == SilacType.Doublets)
{
if (mods[1] == null)
{
return(-1);
}
if (mods[1].Index == mod)
{
return(1);
}
return(-1);
}
if (mods[1] == mods[2])
{
return(-1);
}
if (mods[1] != null && mods[1].Index == mod)
{
return(1);
}
if (mods[2] != null && mods[2].Index == mod)
{
return(2);
}
return(-1);
}
