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 void Read()
{
if (!File.Exists(filePath))
{
return;
}
using (BinaryReader reader = FileUtil.GetBinaryReader(filePath)) {
int len = reader.ReadInt32();
scanNumbers = new int[len];
peptides = new MascotPeptide[len][];
fixedModifications = new ushort[len][];
for (int i = 0; i < scanNumbers.Length; i++)
{
scanNumbers[i] = reader.ReadInt32();
int l = reader.ReadInt32();
peptides[i] = new MascotPeptide[l];
for (int j = 0; j < peptides[i].Length; j++)
{
peptides[i][j] = new MascotPeptide(reader);
}
l = reader.ReadInt32();
fixedModifications[i] = new ushort[l];
for (int j = 0; j < fixedModifications[i].Length; j++)
{
fixedModifications[i][j] = reader.ReadUInt16();
}
}
byte x = reader.ReadByte();
switch (x)
{
case 0:
type = MascotQueryType.Silac;
break;
case 1:
type = MascotQueryType.Isotope;
break;
case 2:
type = MascotQueryType.Peak;
break;
}
reader.Close();
}
}
public void AddPeptide(int peptideNumber, MascotPeptide peptide)
{
peptides.Add(peptideNumber, peptide);
}
public string GetModificationClassification(int index, HashSet <string> labelModSet)
{
MascotPeptide p = GetPeptidesAt(index)[0];
return(p.GetModificationClassification(labelModSet));
}
public bool IsHighestScoringCorrect(int index, string revstring, IProteinSet proteinSet)
{
MascotPeptide p = GetPeptidesAt(index)[0];
return(!p.HasOnlyReverseHits(revstring, proteinSet));
}
