public void ExcelOut(List <MatchedData> lst, string sFileName)
{
System.Reflection.Missing miss = System.Reflection.Missing.Value;
MatchedData matchecdData = new MatchedData();
Excel.Application excelApplication = new Excel.Application();
Excel.Workbook excelWorkbook = excelApplication.Workbooks.Add();
excelApplication.UserControl = true;
excelApplication.Application.DisplayAlerts = false;
Excel.Worksheet excelWorksheet = (Excel.Worksheet)excelWorkbook.Sheets.Add(miss, miss, miss, miss);
excelWorksheet.Name = "Protein";
int iRow = 0;
try
{
for (int i = excelWorkbook.Sheets.Count; i >= 1; i--)
{
Excel.Worksheet excelWorksheetTemp = (Excel.Worksheet)excelWorkbook.Sheets[i];
if (excelWorksheetTemp.Name != "Protein")
{
excelWorksheetTemp.Delete();
}
}
//Header
iRow = 1;
excelWorksheet.Cells[iRow, 1] = "Index";
excelWorksheet.Cells[iRow, 2] = "ID";
excelWorksheet.Cells[iRow, 3] = "MOD_RES";
excelWorksheet.Cells[iRow, 4] = "PTM_Score";
excelWorksheet.Cells[iRow, 5] = "TotalPTM_Score";
excelWorksheet.Cells[iRow, 6] = "Z";
excelWorksheet.Cells[iRow, 7] = "DatasetFile";
excelWorksheet.Cells[iRow, 8] = "Database";
excelWorksheet.Cells[iRow, 9] = "Repository";
excelWorksheet.Cells[iRow, 10] = "ScreeningApproach";
excelWorksheet.Cells[iRow, 11] = "ExpMZ";
excelWorksheet.Cells[iRow, 12] = "TheoMZ";
excelWorksheet.Cells[iRow, 13] = "Error_PPM";
excelWorksheet.Cells[iRow, 14] = "AccessionNumber";
excelWorksheet.Cells[iRow, 15] = "ProteinName";
excelWorksheet.Cells[iRow, 16] = "Length";
excelWorksheet.Cells[iRow, 17] = "Function";
excelWorksheet.Cells[iRow, 18] = "Sequence";
excelWorksheet.Cells[iRow, 19] = "NMFs";
excelWorksheet.Cells[iRow, 20] = "Actual_PMFs";
//Value
iRow = 2;
for (int i = 0; i < lst.Count; i++)
{
matchecdData = lst[i];
excelWorksheet.Cells[iRow, 1] = matchecdData.Index;
excelWorksheet.Cells[iRow, 2] = matchecdData.ID;
excelWorksheet.Cells[iRow, 3] = matchecdData.MOD_RES.Replace(";", "").Replace(",", "");
excelWorksheet.Cells[iRow, 4] = matchecdData.DataBase_PTM_SCORE;
excelWorksheet.Cells[iRow, 5] = matchecdData.Total_PTM_Score;
excelWorksheet.Cells[iRow, 6] = matchecdData.Z;
excelWorksheet.Cells[iRow, 7] = matchecdData.DatasetFile;
excelWorksheet.Cells[iRow, 8] = matchecdData.Database;
excelWorksheet.Cells[iRow, 9] = matchecdData.Repository;
excelWorksheet.Cells[iRow, 10] = matchecdData.ScreeningApproach;
excelWorksheet.Cells[iRow, 11] = matchecdData.ExpMZ;
excelWorksheet.Cells[iRow, 12] = matchecdData.TheoMZ;
excelWorksheet.Cells[iRow, 13] = matchecdData.Error_PPM;
excelWorksheet.Cells[iRow, 14] = matchecdData.AccessionNumber;
excelWorksheet.Cells[iRow, 15] = matchecdData.ProteinName;
excelWorksheet.Cells[iRow, 16] = matchecdData.Length;
excelWorksheet.Cells[iRow, 17] = matchecdData.Function;
excelWorksheet.Cells[iRow, 18] = matchecdData.Sequence;
excelWorksheet.Cells[iRow, 19] = matchecdData.NMFS;
excelWorksheet.Cells[iRow, 20] = matchecdData.Actualpmfs;
iRow++;
}
excelWorkbook.SaveAs(sFileName, miss, miss, miss, miss, miss, Excel.XlSaveAsAccessMode.xlNoChange, miss, miss, miss, miss, miss);
excelWorkbook.Close(false, miss, miss);
}
catch (Exception ex)
{
throw ex;
}
finally
{
matchecdData = null;
if (excelApplication != null)
{
excelApplication.Workbooks.Close();
excelApplication.Quit();
System.Runtime.InteropServices.Marshal.ReleaseComObject(excelApplication.Workbooks);
System.Runtime.InteropServices.Marshal.ReleaseComObject(excelApplication);
System.GC.Collect();
}
if (excelApplication != null)
{
IntPtr t = new IntPtr(excelApplication.Hwnd);
int k = 0;
GetWindowThreadProcessId(t, out k);
System.Diagnostics.Process p = System.Diagnostics.Process.GetProcessById(k);
p.Kill();
}
excelApplication = null;
GC.Collect();
}
}
private void SetMSChart(MatchedData MatchData,string sFileName)
{
double[] expX = MatchData.MatchedMsDataExp.Select(md => md.Mass).ToArray<double>();
double[] expY = MatchData.MatchedMsDataExp.Select(md => md.IntensityPercentage * 100).ToArray<double>();
double[] theoX = MatchData.MatchedMsDataTheo.Select(md => md.Mass).ToArray<double>();
double[] theoY = MatchData.MatchedMsDataTheo.Select(md => md.Intensity * 100).ToArray<double>();
double[] iPAD = MatchData.MatchedMsDataExp.Select(md => md.IPAD_R).ToArray<double>();
double[] iPMD = MatchData.MatchedMsDataExp.Select(md => md.IPMD_R).ToArray<double>();
double minexpX = 0d;
double maxexpX = 0d;
double mintheoX = 0d;
double maxtheoX = 0d;
if (MatchData.MatchedMsDataExp.Count != 0)
{
minexpX = MatchData.MatchedMsDataExp.Min(md => SetMinValue(md.Mass));
maxexpX = MatchData.MatchedMsDataExp.Max(md => SetMaxValue(md.Mass));
}
if (MatchData.MatchedMsDataTheo.Count != 0)
{
mintheoX = MatchData.MatchedMsDataTheo.Min(md => SetMinValue(md.Mass));
maxtheoX = MatchData.MatchedMsDataTheo.Max(md => SetMaxValue(md.Mass));
}
if (minexpX == 0)
minexpX = mintheoX;
ChartCommon chart = new ChartCommon();
if (iPAD.Length != 0)
{
string chartAreasTopName = "chartAreasTop";
chart.CreateChartAreas(chartAreasTopName);
chart.SetChartAreasSetting(chartAreasTopName);
chart.SetChartAreasX(chartAreasTopName, Math.Min(minexpX, mintheoX), Math.Max(maxexpX, maxtheoX));
chart.SetChartAreasYInterval(chartAreasTopName, 100);
chart.SetChartAreasXInterval(chartAreasTopName, 0.5);
chart.ChartE.ChartAreas[chartAreasTopName].Position.Height = 20;
chart.ChartE.ChartAreas[chartAreasTopName].Position.Width = 100;
chart.ChartE.ChartAreas[chartAreasTopName].Position.X = 0;
chart.ChartE.ChartAreas[chartAreasTopName].Position.Y = 0;
chart.ChartE.ChartAreas[chartAreasTopName].AxisX.MajorGrid.Enabled = true;
chart.ChartE.ChartAreas[chartAreasTopName].AxisX.MajorGrid.LineColor = Color.Transparent;
chart.ChartE.ChartAreas[chartAreasTopName].AxisX.MajorTickMark.Enabled = true;
chart.ChartE.ChartAreas[chartAreasTopName].AxisX.MajorTickMark.LineColor = Color.Transparent;
chart.ChartE.ChartAreas[chartAreasTopName].AxisX.LabelStyle.Enabled = true;
chart.ChartE.ChartAreas[chartAreasTopName].AxisX.LineColor = Color.Transparent;
chart.ChartE.ChartAreas[chartAreasTopName].AxisX.LabelStyle.ForeColor = Color.Transparent;
chart.ChartE.ChartAreas[chartAreasTopName].AxisY.MajorGrid.Enabled = true;
chart.ChartE.ChartAreas[chartAreasTopName].AxisY.MajorGrid.LineColor = Color.Transparent;
chart.ChartE.ChartAreas[chartAreasTopName].AxisY.MajorTickMark.Enabled = true;
chart.ChartE.ChartAreas[chartAreasTopName].AxisY.MajorTickMark.LineColor = Color.Transparent;
chart.ChartE.ChartAreas[chartAreasTopName].AxisY.LabelStyle.Enabled = true;
chart.ChartE.ChartAreas[chartAreasTopName].AxisY.LineColor = Color.Transparent;
chart.ChartE.ChartAreas[chartAreasTopName].AxisY.LabelStyle.ForeColor = Color.Transparent;
chart.SetChartAreasYTitle(chartAreasTopName, "Relative Abundance (%)");
chart.ChartE.ChartAreas[chartAreasTopName].AxisY.TitleForeColor = Color.Transparent;
string seriesNamePMD_PAD = "iPMD_iPAD";
chart.CreateSeries(seriesNamePMD_PAD, chartAreasTopName, SeriesChartType.Spline, "", Color.Red);
chart.ChartE.Series[seriesNamePMD_PAD].IsVisibleInLegend = false;
chart.ChartE.Series[seriesNamePMD_PAD].Color = Color.Transparent;
if (theoX.Length > 1)
{
chart.ChartE.Series[seriesNamePMD_PAD].Points.AddXY(theoX[0] - (theoX[1] - theoX[0]), 0);
chart.ChartE.Series[seriesNamePMD_PAD].Points[0].Label = "IPAD" + "\n" + "IPMD";
}
else
{
chart.ChartE.Series[seriesNamePMD_PAD].Points.AddXY(theoX[0] - 5, 0);
chart.ChartE.Series[seriesNamePMD_PAD].Points[0].Label = "IPAD" + "\n" + "IPMD";
}
for (int x = 0; x < theoX.Length; x++)
{
chart.ChartE.Series[seriesNamePMD_PAD].Points.AddXY(theoX[x], 0);
if (iPMD[x] > -10000)
chart.ChartE.Series[seriesNamePMD_PAD].Points[x + 1].Label = ((int)iPAD[x]).ToString() + "\n" + ((int)iPMD[x]).ToString();
else
chart.ChartE.Series[seriesNamePMD_PAD].Points[x + 1].Label = "".ToString() + "\n" + "".ToString();
}
}
string chartAreasName = "chartAreas";
chart.CreateChartAreas(chartAreasName);
chart.SetChartAreasSetting(chartAreasName);
if (MatchData.MatchedMsDataExp.Count != 0)
chart.SetChartAreasX(chartAreasName, Math.Min(minexpX, mintheoX), Math.Max(maxexpX, maxtheoX));
else
chart.SetChartAreasX(chartAreasName, mintheoX, maxtheoX);
chart.SetChartAreasY(chartAreasName, 0, 100);
chart.SetChartAreasSetting(chartAreasName);
chart.SetChartAreasXInterval(chartAreasName, 0.5);
chart.SetChartAreasYInterval(chartAreasName, 20);
chart.SetChartAreasXTitle(chartAreasName, "m/z");
chart.SetChartAreasYTitle(chartAreasName, "Relative Abundance (%)");
chart.SetChartAreasXMajorTickMark(chartAreasName, true);
chart.SetChartAreasYMajorTickMark(chartAreasName, true);
chart.ChartE.ChartAreas[chartAreasName].Position.Height = 80;
chart.ChartE.ChartAreas[chartAreasName].Position.Width = 100;
chart.ChartE.ChartAreas[chartAreasName].Position.Y = 20;
string legendName = "legend";
chart.CreateLegend(legendName);
if (MatchData.MatchedMsDataExp.Count != 0)
{
string seriesNameExp = "exp";
chart.CreateSeries(seriesNameExp, chartAreasName, SeriesChartType.Candlestick, legendName, Color.Black);
chart.SetSeriesAddPoint(seriesNameExp, expX, expY);
chart.SetSeriesAddLegendText(seriesNameExp, "Experimental");
}
if (MatchData.MatchedMsDataTheo.Count != 0)
{
string seriesNameTheo = "theo";
chart.CreateSeries(seriesNameTheo, chartAreasName, SeriesChartType.Point, legendName, Color.Red);
chart.SetSeriesAddPoint(seriesNameTheo, theoX, theoY);
chart.SetSeriesAddLegendText(seriesNameTheo, "Theoretical");
}
chart.ChartE.Size = size;
chart.ChartE.SaveImage(sFileName, ChartImageFormat.Jpeg);
}
public List<MatchedData> getMSMatchs(MassScan msScan2)
{
testParameter.IPMD = ParameterModel.MS_IPMD;
testParameter.IPACO = ParameterModel.MS_IPACO;
testParameter.IPAD = ParameterModel.MS_IPAD;
testParameter.IPADOM = ParameterModel.MS_IPADOM;
testParameter.IPMDOM = ParameterModel.MS_IPMDOM;
testParameter.IPADO = ParameterModel.MS_IPADO;
testParameter.IPMDO = ParameterModel.MS_IPMDO;
if (testParameter.IPMD > testParameter.IPMDOM)
testParameter.IPMDOM = testParameter.IPMD;
if (testParameter.IPAD > testParameter.IPADOM)
testParameter.IPADOM = testParameter.IPAD;
//testParameter.Window = 5;
testParameter.PAT = ParameterModel.MS_PAT;
List<MatchedData> matchedDataList = new List<MatchedData>();
List<ModResModel> modResFromDB = peptideModResDAL.getPmFromDB(testParameter.IPACO);
MatchedData matchedData = null;
List<MassPoint> msFromDB = null;
for (int k = 0; k < modResFromDB.Count; k++)
{
msFromDB = modResFromDB[k].Mass_Point;
matchedData = new MatchedData();
//matchedData.MatchedMsDataExp = msReturn.ToList();
matchedData.MatchedMsDataExp = new List<MassPoint>();
//matchedData.MatchedMsDataExp = msReturn.ToList();
matchedData.MatchedMsDataTheo = msFromDB;
matchedData.ID = modResFromDB[k].ID;
matchedData.MOD_RES = modResFromDB[k].Mod_Res;
matchedData.Z = modResFromDB[k].Z;
matchedData.Z = 15;
matchedData.Repository = "";
matchedData.TheoMZ = modResFromDB[k].M_Z.ToString(); matchedData.NMFS = "";
matchedData.Sequence = modResFromDB[k].Sequence;
matchedData.Actualpmfs = "";
//matchedData.Index = 1;
matchedDataList.Add(matchedData);
}
if (matchedDataList.Count > 0)
{
for (int j = 0; j < matchedDataList.Count; j++)
{
matchedData = matchedDataList[j];
if (ParameterModel.MS2_SA == 1)
{
getMS2MatchsTopDown(msScan2, matchedData);
matchedDataList[j].ScreeningApproach = "TopDown";
}
else
{
getMS2MatchsTargeted(msScan2, matchedData);
matchedDataList[j].ScreeningApproach = "Targeted";
}
try
{
matchedDataList[j].NMFS = matchedDataList[j].MatchedMs2.Count().ToString();
}
catch
{
matchedDataList[j].NMFS = "0";
}
matchedData.Index = "1";
//Console.WriteLine("matched MS2:\t" + matchedData.MatchedMs2.Count.ToString());
}
}
return matchedDataList;
}
public List<MatchedData> getMSMatchs(MassScan msScan, MassScan msScan2)
{
List<MatchedData> matchedDataList = new List<MatchedData>();
testParameter.IPMD = ParameterModel.MS_IPMD;
testParameter.IPACO = ParameterModel.MS_IPACO;
testParameter.IPAD = ParameterModel.MS_IPAD;
testParameter.IPADOM = ParameterModel.MS_IPADOM;
testParameter.IPMDOM = ParameterModel.MS_IPMDOM;
testParameter.IPADO = ParameterModel.MS_IPADO;
testParameter.IPMDO = ParameterModel.MS_IPMDO;
if (testParameter.IPMD > testParameter.IPMDOM)
testParameter.IPMDOM = testParameter.IPMD;
if (testParameter.IPAD > testParameter.IPADOM)
testParameter.IPADOM = testParameter.IPAD;
testParameter.Window = Convert.ToInt16(ParameterModel.MS_WINDOW / 2);
testParameter.PAT = ParameterModel.MS_PAT;
double ms2Point = msScan2.PrecursorMz;
double maxInten = msScan.BasePeakIntensity;
MatchedData matchedData = new MatchedData();
//Console.WriteLine("scanMS.Index Begin2 " + DateTime.Now);
//Console.WriteLine("scanMS.Index Begin3 " + DateTime.Now);
List<MassPoint> msFromFile;
List<MassPoint> msFromDB = null;
//���ļ�ȡ��MS��ͼ
msFromFile = Base64Convert.CalcMz(msScan.Peaks, msScan.PeaksCount);
Console.WriteLine("scanMS.Index Begin4 " + DateTime.Now);
//����MS2����
List<MassPoint> msFromFileOpenWindow = getOpenWindowFromFile(msFromFile, testParameter.Window, ms2Point);
//List<MassPoint> msFromFileOpenWindow = msFromFile;
Console.WriteLine("scanMS.Index Begin5 " + DateTime.Now);
//���˵�5%���µķ�
List<MassPoint> msFromFileReal = getRealMS2FromFile(msFromFileOpenWindow, testParameter.PAT, maxInten);
// Console.WriteLine("scanMS.Index Begin6 " + DateTime.Now);
//List<MassPoint> msFromFileReal = msFromFileOpenWindow;
int timesFlag = 0;
int maxMZIndex = 0;
while (timesFlag < 1000)
{
//ȡ����ߵ�1
maxMZIndex = getMaxMZ(msFromFileReal);
//Console.WriteLine("maxMZIndex.ToString()maxMZIndex.ToString()maxMZIndex.ToString()maxMZIndex.ToString() " + maxMZIndex.ToString());
if (maxMZIndex == -1)
{
break;
}
else
{
timesFlag = timesFlag + 1;
}
//����ƫ��
double deviationInten = msFromFileReal[maxMZIndex].Mass - msFromFileReal[maxMZIndex].Mass / (testParameter.IPMD / 1000000.0 + 1.0);
//MS��ߵ���DBƥ�� �������㴦��
//Console.WriteLine("scanMS.Index Begin7 " + DateTime.Now);
List<ModResModel> modResFromDB = peptideModResDAL.getPmFromDB(msFromFileReal[maxMZIndex].Mass, deviationInten, testParameter.IPACO);
//Console.WriteLine("scanMS.Index Begin8 " + DateTime.Now);
msFromFileReal[maxMZIndex].IsSearch = false;
if (modResFromDB.Count == 0)
{
//û��ƥ����
continue;
}
else
{
//����ƥ��������߷������ƥ���ϵ��б��
bool compareFlag = false;
string Forumla = "";
List<MassPoint> msReturn = new List<MassPoint>(); ;
for (int k = 0; k < modResFromDB.Count; k++)
{
msFromDB = modResFromDB[k].Mass_Point;
if (Forumla == modResFromDB[k].Forumla && compareFlag == true)
{
matchedData = new MatchedData();
//matchedData.MatchedMsDataExp = msReturn.ToList();
matchedData.MatchedMsDataExp = new List<MassPoint>();
foreach (MassPoint item in msReturn)
{
MassPoint cloneMasspoint = new MassPoint();
cloneMasspoint.Index = item.Index;
cloneMasspoint.Intensity = item.Intensity;
cloneMasspoint.IntensityPercentage = item.IntensityPercentage;
cloneMasspoint.IPAD_R = item.IPAD_R;
cloneMasspoint.IPADOM_R = item.IPADOM_R;
cloneMasspoint.IPMD_R = item.IPMD_R;
cloneMasspoint.IPMDOM_R = item.IPMDOM_R;
cloneMasspoint.Mass = item.Mass;
cloneMasspoint.MatchIndex = item.MatchIndex;
matchedData.MatchedMsDataExp.Add(cloneMasspoint);
}
//matchedData.MatchedMsDataExp = msReturn.ToList();
matchedData.MatchedMsDataTheo = msFromDB;
matchedData.ID = modResFromDB[k].ID;
matchedData.MOD_RES = modResFromDB[k].Mod_Res;
matchedData.Z = modResFromDB[k].Z;
matchedData.Repository = "";
matchedData.ExpMZ = (msFromFileReal[maxMZIndex].Mass).ToString();
matchedData.TheoMZ = modResFromDB[k].M_Z.ToString();
matchedData.Error_PPM = Convert.ToString(((msFromFileReal[maxMZIndex].Mass - modResFromDB[k].M_Z) / modResFromDB[k].M_Z) * 1000000);
matchedData.Index = msScan2.Index.ToString();
matchedData.ExpMass_DA = Convert.ToString(((msFromFileReal[maxMZIndex].Mass - modResFromDB[k].M_Z) / modResFromDB[k].M_Z) * 1000000);
matchedData.NMFS = "";
matchedData.Actualpmfs = "";
matchedData.Sequence = modResFromDB[k].Sequence;
matchedDataList.Add(matchedData);
continue;
}
Forumla = modResFromDB[k].Forumla;
// MZ_FromDB = modResFromDB[0].M;
compareFlag = false;
int maxMZindex_DB = Convert.ToInt16(modResFromDB[k].M);
//��һƥ����ͼ
msReturn = comparePMAll(msFromFileReal, maxMZIndex, maxMZindex_DB, msFromDB); //��֤ƥ������ƥ��
if (getComparePercentage(msReturn, maxMZindex_DB, msFromDB))
{
compareFlag = true;
matchedData = new MatchedData();
//matchedData.MatchedMsDataExp = new List<MassPoint>();
matchedData.MatchedMsDataExp = new List<MassPoint>();
foreach (MassPoint item in msReturn)
{
MassPoint cloneMasspoint = new MassPoint();
cloneMasspoint.Index = item.Index;
cloneMasspoint.Intensity = item.Intensity;
cloneMasspoint.IntensityPercentage = item.IntensityPercentage;
cloneMasspoint.IPAD_R = item.IPAD_R;
cloneMasspoint.IPADOM_R = item.IPADOM_R;
cloneMasspoint.IPMD_R = item.IPMD_R;
cloneMasspoint.IPMDOM_R = item.IPMDOM_R;
cloneMasspoint.Mass = item.Mass;
cloneMasspoint.MatchIndex = item.MatchIndex;
matchedData.MatchedMsDataExp.Add(cloneMasspoint);
}
matchedData.MatchedMsDataTheo = msFromDB;
matchedData.ID = modResFromDB[k].ID;
matchedData.MOD_RES = modResFromDB[k].Mod_Res;
matchedData.Z = modResFromDB[k].Z;
matchedData.Index = msScan2.Index.ToString();
matchedData.Repository = "";
matchedData.ExpMZ = (msFromFileReal[maxMZIndex].Mass).ToString();
matchedData.TheoMZ = modResFromDB[k].M_Z.ToString();
matchedData.Error_PPM = Convert.ToString(((msFromFileReal[maxMZIndex].Mass - modResFromDB[k].M_Z) / modResFromDB[k].M_Z) * 1000000);
matchedData.ExpMass_DA = Convert.ToString(((msFromFileReal[maxMZIndex].Mass - modResFromDB[k].M_Z) / modResFromDB[k].M_Z) * 1000000);
matchedData.NMFS = "";
matchedData.Actualpmfs = "";
matchedData.Sequence = modResFromDB[k].Sequence;
matchedDataList.Add(matchedData);
//break;
for (int i = 0; i < msFromFileReal.Count; i++)
{
double baseIntens = 0.0;
for (int j = 0; j < msReturn.Count; j++)
{
baseIntens = msFromFileReal[j].Intensity / msReturn[j].IntensityPercentage;
msFromFileReal[msReturn[j].MatchIndex].Intensity =
msFromFileReal[msReturn[j].MatchIndex].Intensity - (baseIntens * msFromDB[j].Intensity);
}
}
}
}
if (matchedData != null)
break;
}
}
if (matchedDataList.Count > 0)
{
for (int j = 0; j < matchedDataList.Count; j++)
{
matchedData = matchedDataList[j];
if (ParameterModel.MS2_SA == 1)
{
getMS2MatchsTopDown(msScan2, matchedData);
matchedDataList[j].ScreeningApproach = "TopDown";
}
else
{
getMS2MatchsTargeted(msScan2, matchedData);
matchedDataList[j].ScreeningApproach = "Targeted";
}
if (matchedDataList[j].MatchedMs2 == null)
matchedDataList[j].NMFS = "0";
else
matchedDataList[j].NMFS = matchedDataList[j].MatchedMs2.Count().ToString();
//Console.WriteLine("matched MS2:\t" + matchedData.MatchedMs2.Count.ToString());
}
}
return matchedDataList;
}
public void getMS2MatchsTopDown(MassScan msScan2, MatchedData matchedData)
{
testParameter.IPMD = ParameterModel.MS2_IPMD;
testParameter.IPACO = ParameterModel.MS2_IPACO;
testParameter.IPAD = ParameterModel.MS2_IPAD;
testParameter.IPADOM = ParameterModel.MS2_IPADOM;
testParameter.IPMDOM = ParameterModel.MS2_IPMDOM;
testParameter.IPADO = ParameterModel.MS2_IPADO;
testParameter.IPMDO = ParameterModel.MS2_IPMDO;
if (testParameter.IPMD > testParameter.IPMDOM)
testParameter.IPMDOM = testParameter.IPMD;
if (testParameter.IPAD > testParameter.IPADOM)
testParameter.IPADOM = testParameter.IPAD;
//testParameter.Window = 5;
testParameter.PAT = ParameterModel.MS2_FAT;
List<MassPoint> ms2FromFile = null;
List<MassPoint> msFromDB = null;
//ModResModel ms2Matched = new ModResModel();
List<ModResModel> MatchedMs2 = new List<ModResModel>();
double maxInten = msScan2.BasePeakIntensity;
//���˵�5%���µķ�
ms2FromFile = Base64Convert.CalcMz(msScan2.Peaks, msScan2.PeaksCount);
List<MassPoint> msFromFileReal = getRealMS2FromFile(ms2FromFile, testParameter.PAT, maxInten);
List<string[]> fmValue = peptideModResDAL.getFmFromDB(matchedData.ID, matchedData.MOD_RES, msScan2.ScanType, matchedData.Sequence);
if (fmValue.Count == 0)
{
return;
}
while (true)
{
//ȡ����ߵ�1
int maxMZIndex = getMaxMZ(msFromFileReal);
if (maxMZIndex == -1)
{
break;
}
if (maxMZIndex == 157)
{
maxMZIndex = 157;
}
//����ƫ��
double deviationInten = msFromFileReal[maxMZIndex].Mass - msFromFileReal[maxMZIndex].Mass / (testParameter.IPMD / 1000000.0 + 1.0);
//MS��ߵ���DBƥ�� �������㴦��
List<ModResModel> modResFromDB = getFMPointInfo(msFromFileReal[maxMZIndex].Mass, deviationInten, fmValue, matchedData.Z, testParameter.IPACO);
msFromFileReal[maxMZIndex].IsSearch = false;
if (modResFromDB == null)
{
//û��ƥ����
continue;
}
else
{
for (int k = 0; k < modResFromDB.Count; k++)
{
msFromDB = modResFromDB[k].Mass_Point;
int maxMZindex_DB = Convert.ToInt16(modResFromDB[k].M_Z);
//��һƥ����ͼ
List<MassPoint> msReturn = comparePMAll(msFromFileReal, maxMZIndex, maxMZindex_DB, msFromDB);
if (modResFromDB[k].ID == "B5")
{
modResFromDB[k].ID = "B5";
}
//��֤ƥ������ƥ��
if (getComparePercentage(msReturn, maxMZindex_DB, msFromDB))
{
ModResModel ms2Matched = new ModResModel();
double baseIntens = msFromFileReal[maxMZIndex].Intensity;
ms2Matched.Mass_Point = new List<MassPoint>(msFromDB.ToArray());
ms2Matched.Mass_Point_FromFile = new List<MassPoint>();
for (int j = 0; j < msReturn.Count; j++)
{
MassPoint massPoint = new MassPoint();
massPoint.Index = msReturn[j].Index;
//massPoint.Intensity = new Double();
massPoint.Intensity = msReturn[j].Intensity;
massPoint.IPAD_R = msReturn[j].IPAD_R;
massPoint.IPADOM_R = msReturn[j].IPADOM_R;
massPoint.IPMD_R = msReturn[j].IPMD_R;
massPoint.IPMDOM_R = msReturn[j].IPMDOM_R;
massPoint.Mass = msReturn[j].Mass;
massPoint.Index = msReturn[j].Index;
massPoint.IntensityPercentage = msReturn[j].IntensityPercentage;
ms2Matched.Mass_Point_FromFile.Add(massPoint);
}
ms2Matched.Z = modResFromDB[k].Z;
ms2Matched.ID = modResFromDB[k].ID;
MatchedMs2.Add(ms2Matched);
//matchedData.MatchedMs2DataExp = ms2Matched;
for (int j = 0; j < msReturn.Count; j++)
{
baseIntens = msFromFileReal[j].Intensity / msReturn[j].IntensityPercentage;
msFromFileReal[msReturn[j].MatchIndex].Intensity =
msFromFileReal[msReturn[j].MatchIndex].Intensity - (baseIntens * msFromDB[j].Intensity);
}
}
}
}
}
matchedData.MatchedMs2 = MatchedMs2;
}
public void getMS2MatchsTargeted(MassScan msScan2, MatchedData matchedData)
{
//testParameter.IPMD = 10;
//testParameter.IPACO = 5;
//testParameter.IPAD = 50;
//testParameter.IPADOM = 100;
//testParameter.IPMDOM = 30;
//testParameter.IPADO = 20;
//testParameter.IPMDO = 20;
//testParameter.Window = 5;
//testParameter.PAT = 0.2;
testParameter.IPMD = ParameterModel.MS2_IPMD;
testParameter.IPACO = ParameterModel.MS2_IPACO;
testParameter.IPAD = ParameterModel.MS2_IPAD;
testParameter.IPADOM = ParameterModel.MS2_IPADOM;
testParameter.IPMDOM = ParameterModel.MS2_IPMDOM;
testParameter.IPADO = ParameterModel.MS2_IPADO;
testParameter.IPMDO = ParameterModel.MS2_IPMDO;
if (testParameter.IPMD > testParameter.IPMDOM)
testParameter.IPMDOM = testParameter.IPMD;
if (testParameter.IPAD > testParameter.IPADOM)
testParameter.IPADOM = testParameter.IPAD;
//testParameter.Window = 5;
testParameter.PAT = ParameterModel.MS2_FAT;
//if (msScan2.ScanType == "CID")
//{
// return;
//}
List<MassPoint> ms2FromFile = null;
List<MassPoint> msFromDB = null;
//ModResModel ms2Matched = new ModResModel();
List<ModResModel> MatchedMs2 = new List<ModResModel>();
double maxInten = msScan2.BasePeakIntensity;
//���˵�5%���µķ�
ms2FromFile = Base64Convert.CalcMz(msScan2.Peaks, msScan2.PeaksCount);
List<MassPoint> msFromFileReal = getRealMS2FromFile(ms2FromFile, testParameter.PAT, maxInten);
List<string[]> fmValue = peptideModResDAL.getFmFromDB(matchedData.ID, matchedData.MOD_RES, msScan2.ScanType, matchedData.Sequence);
if (fmValue.Count == 0)
{
return;
}
//msFromDB = getFMDataPoints(fmValue);
for (int i = 0; i < fmValue[0].Count(); i++)
{
//��һƥ����ͼ
List<ModResModel> modResFromDB = comparePMFromDB(fmValue[0][i], fmValue[1][i], fmValue[2][i], msFromFileReal, matchedData.Z, testParameter.IPACO);
if (modResFromDB.Count > 1)
{
//modResFromDB = null;
}
for (int m = 0; m < modResFromDB.Count; m++)
{
if (modResFromDB[m].ID == "Y40")
{
modResFromDB[m].ID = "Y40";
}
msFromDB = modResFromDB[m].Mass_Point;
int maxMZIndex = Convert.ToInt16(modResFromDB[m].M);//��ʱʹ��
int maxMZindex_DB = Convert.ToInt16(modResFromDB[m].M_Z);
//��һƥ����ͼ
List<MassPoint> msReturn = comparePMAll(msFromFileReal, maxMZIndex, maxMZindex_DB, msFromDB);
//��֤ƥ������ƥ��
if (getComparePercentage(msReturn, maxMZindex_DB, msFromDB))
{
ModResModel ms2Matched = new ModResModel();
double baseIntens = msFromFileReal[maxMZIndex].Intensity;
ms2Matched.Mass_Point = new List<MassPoint>(msFromDB.ToArray());
ms2Matched.Mass_Point_FromFile = new List<MassPoint>();
for (int j = 0; j < msReturn.Count; j++)
{
MassPoint massPoint = new MassPoint();
massPoint.Index = msReturn[j].Index;
//massPoint.Intensity = new Double();
massPoint.Intensity = msReturn[j].Intensity;
massPoint.IPAD_R = msReturn[j].IPAD_R;
massPoint.IPADOM_R = msReturn[j].IPADOM_R;
massPoint.IPMD_R = msReturn[j].IPMD_R;
massPoint.IPMDOM_R = msReturn[j].IPMDOM_R;
massPoint.Mass = msReturn[j].Mass;
massPoint.Index = msReturn[j].Index;
massPoint.IntensityPercentage = msReturn[j].IntensityPercentage;
ms2Matched.Mass_Point_FromFile.Add(massPoint);
}
//matchedData.ID = modResFromDB[0].ID;
//matchedData.MOD_RES = modResFromDB[0].Mod_Res;
//matchedData.Z = modResFromDB[0].Z;
ms2Matched.Z = modResFromDB[m].Z;
ms2Matched.ID = modResFromDB[m].ID;
MatchedMs2.Add(ms2Matched);
//matchedData.MatchedMs2DataExp = ms2Matched;
for (int j = 0; j < msReturn.Count; j++)
{
//ms2Matched.Mass_Point_FromFile[j].Intensity = new Double();
//ms2Matched.Mass_Point_FromFile[j].Intensity = msFromFileReal[msReturn[j].MatchIndex].Intensity;
baseIntens = msFromFileReal[j].Intensity / msReturn[j].IntensityPercentage;
msFromFileReal[msReturn[j].MatchIndex].Intensity =
msFromFileReal[msReturn[j].MatchIndex].Intensity - (baseIntens * msFromDB[j].Intensity);
//if (maxInten * testParameter.IPACO / 100 > msFromFileReal[msReturn[j].MatchIndex].Intensity)
//{
// msFromFileReal[msReturn[j].MatchIndex].Intensity = 0;
//}
}
}
}
}
matchedData.MatchedMs2 = MatchedMs2;
//for (int i = 0; i < MatchedMs2.Count; i++)
//{
// Console.WriteLine("Ion: " + MatchedMs2[i].ID + "\t" + "Z: " + MatchedMs2[i].Z);
// for (int j = 0; j < MatchedMs2[i].Mass_Point.Count; j++)
// {
// Console.WriteLine("Mass: \t " + MatchedMs2[i].Mass_Point[j].Mass + "\t" + MatchedMs2[i].Mass_Point_FromFile[j].Mass + "\tIntensity: \t" + MatchedMs2[i].Mass_Point[j].Intensity + "\t" + MatchedMs2[i].Mass_Point_FromFile[j].IntensityPercentage + "\t" + MatchedMs2[i].Mass_Point_FromFile[j].IPAD_R);
// }
//}
}
