override public void ThreadProc(Object stateInfo)
{
int i, j;
i = (stateInfo as QAlInfo).i;
j = (stateInfo as QAlInfo).j;
QAlignment Align = new QAlignment(Peptides, Proteins, i, j);
Align.Run();
Align.Proteins.Sort(new ProteinPair.byIPI());
Align.Peptides.Sort(new PeptidePair.bySet());
//копирование итоговых значений в итоговые массивы
for (int k = 0; k < Peptides.Count; k++)
{
PeptidePair PP = Align.Peptides[k];
if (PP.Ratio == 0.0)
{
PeptideRatios[i, j][k] = 0.0;
}
else
{
PeptideRatios[i, j][k] = PP.Ratio;
}
}
for (int k = 0; k < Proteins.Count; k++)
{
ProteinPair PP = Align.Proteins[k];
ProteinMedians[i, j, k] = PP.Median;
ProteinSlopes[i, j, k] = PP.Slope;
ProteinDeltas[i, j, k] = PP.SlopeDelta;
}
lock (ForCountLock){
Count++;
}
}
public QAlignment(List <QPeptide> Peptides, List <QProtein> Proteins, int LeftIndex, int RightIndex)
{
Left = LeftIndex;
Right = RightIndex;
this.Peptides = new List <PeptidePair>();
for (int i = 0; i < Peptides.Count; i++)
{
this.Peptides.Add(new PeptidePair(Peptides[i], Left, Right));
}
this.Proteins = new List <ProteinPair>();
int j = 0;
for (int i = 0; i < Proteins.Count; i++)
{
ProteinPair PPair = new ProteinPair();
PPair.Protein = Proteins[i];
while (Proteins[i].ipi == Peptides[j].IPI)
{
if (Proteins[i] == this.Peptides[j].Peptide.PartOfProtein && this.Peptides[j].Exists)
{
PPair.Peptides.Add(this.Peptides[j]);
}
j++;
if (j >= Peptides.Count)
{
break;
}
}
this.Proteins.Add(PPair);
}
}
public string GetString(int MatchNumber, int RefMatchNumber /* if no refs =-1 */)
{
ProteinPair Pair;
if (Aligner != null)
{
Pair = Aligner.GetProtPair(this, MatchNumber, RefMatchNumber);
}
else
{
Pair = new ProteinPair();
//чего можем то заполним
for (int i = 0; i < Peptides.Count; i++)
{
if (Peptides[i].Matches[MatchNumber] != null)
{
Pair.LeftScore += Peptides[i].Matches[MatchNumber].Score;
Pair.NCount++;
}
}
Pair.RightScore = Pair.LeftScore;
}
string Res =
((ReportString[0] != '1')?"":String.Format("\"{0}\"\t", ipi)) +
((ReportString[1] != '1')?"":String.Format("{0:f4}\t", Pair.LeftScore)) +
((ReportString[2] != '1')?"":String.Format("{0:f4}\t", Pair.RightScore)) +
((ReportString[3] != '1')?"":String.Format("\"{0}\"\t", Desc)) +
((ReportString[4] != '1')?"":(Utils.IPIListtoString(ipis)) + "\t") +
((ReportString[5] != '1')?"":String.Format("{0}\t", Peptides.Count)) +
((ReportString[6] != '1')?"":String.Format("{0}\t", Pair.NCount)) +
((ReportString[7] != '1')?"":String.Format("{0:f4}\t", Pair.RSquare)) +
((ReportString[8] != '1')?"":String.Format("{0:f4}\t", Pair.Slope)) +
((ReportString[9] != '1')?"":String.Format("{0:f4}\t", Pair.Median)) +
((ReportString[10] != '1')?"":String.Format("{0:f4}\t", Pair.PrAverage)) +
((ReportString[11] != '1')?"":String.Format("{0:f4}\t", Pair.MinInterval)) +
((ReportString[12] != '1')?"":String.Format("{0:f4}\t", Pair.MaxInterval)) +
((ReportString[13] != '1')?"":String.Format("{0:e4}", Pair.PValue));
return(Res);
}
public QAlignment(List <QPeptide> Peptides, List <QProtein> Proteins, int LeftIndex, int RightIndex)
{
Left = LeftIndex;
Right = RightIndex;
this.Peptides = new List <PeptidePair>();
for (int i = 0; i < Peptides.Count; i++)
{
this.Peptides.Add(new PeptidePair(Peptides[i], Left, Right));
}
this.Proteins = new List <ProteinPair>();
for (int i = 0; i < Proteins.Count; i++)
{
ProteinPair PPair = new ProteinPair();
PPair.Protein = Proteins[i];
for (int j = 0; j < Peptides.Count; j++)
{
if (Proteins[i].Peptides.Contains(this.Peptides[j].Peptide) && this.Peptides[j].Exists)
{
PPair.Peptides.Add(this.Peptides[j]);
}
}
this.Proteins.Add(PPair);
}
}
public string GetSheetString(int RefNumber)
{
ProteinPair Pair;
if (Aligner != null)
{
Pair = Aligner.GetProtPair(this, RefNumber, RefNumber);
}
else
{
Pair = new ProteinPair();
Pair.RightScore = 0.0;
}
string Res =
((SheetReportString[0] != '1')?"":String.Format("{0}\t", ipi)) +
((SheetReportString[1] != '1')?"":String.Format("{0:f2}\t", Pair.RightScore)) +
((SheetReportString[2] != '1')?"":String.Format("{0}\t", Desc)) +
((SheetReportString[3] != '1')?"":(Utils.IPIListtoString(ipis)) + "\t") +
((SheetReportString[4] != '1')?"":String.Format("{0}\t", Peptides.Count));
for (int i = 0; i < FileList.Count; i++)
{
if (Aligner != null)
{
Pair = Aligner.GetProtPair(this, i, RefNumber);
}
else
{
break;
}
Res = Res +
((SheetReportString[5] != '1')?"":String.Format("{0:f5}\t", Pair.Median)) +
((SheetReportString[6] != '1')?"":String.Format("{0:f5}\t", Pair.Slope)) +
((SheetReportString[7] != '1')?"":String.Format("{0:f5}\t", Pair.PrAverage)) +
((SheetReportString[8] != '1')?"":String.Format("{0:f5}\t", Pair.MinInterval)) +
((SheetReportString[9] != '1')?"":String.Format("{0:f5}\t", Pair.MaxInterval)) +
((SheetReportString[10] != '1')?"":String.Format("{0:f5}\t", Pair.RSquare));
}
double[] RawScores = new double[FileList.Count];
if (SheetReportString[12] == '1' || SheetReportString[1] == '1')
{
for (int i = 0; i < FileList.Count; i++)
{
for (int j = 0; j < Peptides.Count; j++)
{
if (Peptides[j].Matches[i] != null &&
Peptides[j].Matches[i].Score > 0.0)
{
if (RefNumber < 0 || Peptides[j].Matches[RefNumber] != null)
{
RawScores[i] += Peptides[j].Matches[i].Score;
}
}
}
}
}
//ppm's
if (SheetReportString[12] == '1')
{
Res += "\t";
for (int i = 0; i < FileList.Count; i++)
{
double PPM = (RawScores[i] / FileFactors[i]) * 1000000.0;
Res += String.Format("{0:f5}\t", PPM);
}
}
//Raw values
if (SheetReportString[13] == '1')
{
Res += "\t";
for (int i = 0; i < FileList.Count; i++)
{
Res += String.Format("{0:f5}\t", RawScores[i]);
}
}
return(Res);
}
