public List <ModResModel> getPmFromDB(double ipaco)
{
StringBuilder sb = new StringBuilder();
sb.Append("SELECT max(z) MAXZ,Parent_ions.* FROM Parent_ions group by seq,mod_res");
//sb.Append(" WHERE ABS(MZ - " + pmFromFile.ToString() + ") < " + deviation + "order by FORUMLA");
DataSet ds = sqlHelper.Query(sb.ToString());
int count = ds.Tables[0].Rows.Count;
List <ModResModel> lst = new List <ModResModel>();
ModResModel model = new ModResModel();
for (int i = 0; i < count; i++)
{
//if (model.Forumla == ds.Tables[0].Rows[i]["FORUMLA"].ToString())
//{
//continue;
//}
model = new ModResModel();
model.ID = ds.Tables[0].Rows[i]["ID"].ToString();
model.Mod_Res = ds.Tables[0].Rows[i]["MOD_RES"].ToString();
model.Z = int.Parse(ds.Tables[0].Rows[i]["MAXZ"].ToString());
model.Sequence = ds.Tables[0].Rows[i]["SEQ"].ToString();
model.M_Z = double.Parse(ds.Tables[0].Rows[i]["MZ"].ToString());
model.Forumla = ds.Tables[0].Rows[i]["FORUMLA"].ToString();
model.M_Z_ALL = ds.Tables[0].Rows[i]["MZ_ALL"].ToString().Split(',').Select(ms => double.Parse(ms)).ToList();
model.M_ALL = ds.Tables[0].Rows[i]["Relative_Abundance_ALL"].ToString().Split(',').Select(ms => double.Parse(ms)).ToList();
List <MassPoint> lstMassPoint = new List <MassPoint>();
for (int j = 0; j < model.M_Z_ALL.Count; j++)
{
MassPoint mp = new MassPoint();
mp.Mass = Convert.ToDouble(model.M_Z_ALL[j]);
mp.Intensity = Convert.ToDouble(model.M_ALL[j]);
if (Convert.ToDouble(model.M_ALL[j]) * 100 > ipaco)
{
if (Convert.ToDouble(model.M_ALL[j]) == 1.000)
{
model.M = lstMassPoint.Count;
}
lstMassPoint.Add(mp);
}
}
model.Mass_Point = lstMassPoint;
lst.Add(model);
}
return(lst);
}
public List <ModResModel> getPmFromDB(double pmFromFile, double deviation, double ipaco)
{
StringBuilder sb = new StringBuilder();
//sb.AppendFormat("SELECT * FROM {0}", sTableName);
//sb.AppendFormat(" WHERE ABS(MZ - {0}) < {1}", pmFromFile, deviation);
//sb.Append(" ORDER BY FORUMLA");
sb.AppendFormat("SELECT * FROM {0}", sTableName);
sb.AppendFormat(" WHERE MZ < {0} + {1} AND MZ > {2}", pmFromFile, deviation, pmFromFile);
sb.AppendFormat(" OR MZ < {0} AND MZ > {1} - {2}", pmFromFile, pmFromFile, deviation);
sb.Append(" ORDER BY FORUMLA");
DataSet ds = sqlHelper.Query(sb.ToString());
List <ModResModel> lst = new List <ModResModel>();
ModResModel model;
for (int i = 0; i < ds.Tables[0].Rows.Count; i++)
{
model = new ModResModel();
model.ID = ds.Tables[0].Rows[i]["ID"].ToString();
model.Mod_Res = ds.Tables[0].Rows[i]["MOD_RES"].ToString();
model.Z = int.Parse(ds.Tables[0].Rows[i]["Z"].ToString());
model.Sequence = ds.Tables[0].Rows[i]["SEQ"].ToString();
model.M_Z = double.Parse(ds.Tables[0].Rows[i]["MZ"].ToString());
model.Forumla = ds.Tables[0].Rows[i]["FORUMLA"].ToString();
model.M_Z_ALL = ds.Tables[0].Rows[i]["MZ_ALL"].ToString().Split(',').Select(ms => double.Parse(ms)).ToList();
model.M_ALL = ds.Tables[0].Rows[i]["Relative_Abundance_ALL"].ToString().Split(',').Select(ms => double.Parse(ms)).ToList();
List <MassPoint> lstMassPoint = new List <MassPoint>();
for (int j = 0; j < model.M_Z_ALL.Count; j++)
{
MassPoint mp = new MassPoint();
mp.Mass = Convert.ToDouble(model.M_Z_ALL[j]);
mp.Intensity = Convert.ToDouble(model.M_ALL[j]);
if (Convert.ToDouble(model.M_ALL[j]) * 100 > ipaco)
{
if (Convert.ToDouble(model.M_ALL[j]) == 1.000)
{
model.M = lstMassPoint.Count;
}
lstMassPoint.Add(mp);
}
}
model.Mass_Point = lstMassPoint;
lst.Add(model);
}
return(lst);
}
public List<string[]> getFmFromDB(string ID, string mod_res,string scanTpye,string seq)
{
StringBuilder sb = new StringBuilder();
List<string[]> returnValue = new List<string[]>();
sb.Append("SELECT * FROM " + "Fragment_ions");
sb.Append(" WHERE MOD_RES='" + mod_res + "'");
//sb.Append(" and SEQ='" + seq + "'");
//sb.Append(" WHERE ID ='" + ID+"' and MOD_RES='"+mod_res+"'");
//sb.Append(" WHERE ID ='" + ID + "' and MOD_RES='S1,ac;K20,me2;'");
//sb.Append(" WHERE ID ='" + ID + "' and MOD_RES=''");
DataSet ds = sqlHelper.Query(sb.ToString());
//int count = ds.Tables[0].Rows.Count;
var drrArr = ds.Tables[0].AsEnumerable().Where(query => query["SEQ"].Equals(seq));
DataTable dt = drrArr.CopyToDataTable();
int count = dt.Rows.Count;
List<ModResModel> lst = new List<ModResModel>();
ModResModel model = new ModResModel();
string[] etd_mz = null;
string[] etd_m = null;
string[] etd_max = null;
string useStr = "";
for (int i = 0; i < count; i++)
{
if (scanTpye == "ETD")
{
dt.Rows[i]["ETD_MZ"].ToString();
dt.Rows[i]["ETD_Relative_Abundance"].ToString();
dt.Rows[i]["ETD_MZ_MAX"].ToString();
useStr = dt.Rows[i]["ETD_MZ"].ToString();
useStr = System.Text.RegularExpressions.Regex.Replace(useStr, @"([\r\n])[\s]+", "", RegexOptions.IgnoreCase);
etd_mz = useStr.Split(new string[] { "&" }, StringSplitOptions.RemoveEmptyEntries);
useStr = dt.Rows[i]["ETD_Relative_Abundance"].ToString();
useStr = System.Text.RegularExpressions.Regex.Replace(useStr, @"([\r\n])[\s]+", "", RegexOptions.IgnoreCase);
etd_m = useStr.Split(new string[] { "&" }, StringSplitOptions.RemoveEmptyEntries);
useStr = dt.Rows[i]["ETD_MZ_MAX"].ToString();
useStr = System.Text.RegularExpressions.Regex.Replace(useStr, @"([\r\n])[\s]+", "", RegexOptions.IgnoreCase);
etd_max = useStr.Split(new string[] { "&" }, StringSplitOptions.RemoveEmptyEntries);
}
else
{
dt.Rows[i]["CID_MZ"].ToString();
dt.Rows[i]["CID_Relative_Abundance"].ToString();
dt.Rows[i]["CID_MZ_MAX"].ToString();
useStr = dt.Rows[i]["CID_MZ"].ToString();
useStr = System.Text.RegularExpressions.Regex.Replace(useStr, @"([\r\n])[\s]+", "", RegexOptions.IgnoreCase);
etd_mz = useStr.Split(new string[] { "&" }, StringSplitOptions.RemoveEmptyEntries);
useStr = dt.Rows[i]["CID_Relative_Abundance"].ToString();
useStr = System.Text.RegularExpressions.Regex.Replace(useStr, @"([\r\n])[\s]+", "", RegexOptions.IgnoreCase);
etd_m = useStr.Split(new string[] { "&" }, StringSplitOptions.RemoveEmptyEntries);
useStr = dt.Rows[i]["CID_MZ_MAX"].ToString();
useStr = System.Text.RegularExpressions.Regex.Replace(useStr, @"([\r\n])[\s]+", "", RegexOptions.IgnoreCase);
etd_max = useStr.Split(new string[] { "&" }, StringSplitOptions.RemoveEmptyEntries);
}
returnValue.Add(etd_mz);
returnValue.Add(etd_m);
returnValue.Add(etd_max);
}
return returnValue;
}
public List<ModResModel> getPmFromDB(double ipaco)
{
StringBuilder sb = new StringBuilder();
sb.Append("SELECT max(z) MAXZ,Parent_ions.* FROM Parent_ions group by seq,mod_res");
//sb.Append(" WHERE ABS(MZ - " + pmFromFile.ToString() + ") < " + deviation + "order by FORUMLA");
DataSet ds = sqlHelper.Query(sb.ToString());
int count = ds.Tables[0].Rows.Count;
List<ModResModel> lst = new List<ModResModel>();
ModResModel model = new ModResModel();
for (int i = 0; i < count; i++)
{
//if (model.Forumla == ds.Tables[0].Rows[i]["FORUMLA"].ToString())
//{
//continue;
//}
model = new ModResModel();
model.ID = ds.Tables[0].Rows[i]["ID"].ToString();
model.Mod_Res = ds.Tables[0].Rows[i]["MOD_RES"].ToString();
model.Z = int.Parse(ds.Tables[0].Rows[i]["MAXZ"].ToString());
model.Sequence = ds.Tables[0].Rows[i]["SEQ"].ToString();
model.M_Z = double.Parse(ds.Tables[0].Rows[i]["MZ"].ToString());
model.Forumla = ds.Tables[0].Rows[i]["FORUMLA"].ToString();
model.M_Z_ALL = ds.Tables[0].Rows[i]["MZ_ALL"].ToString().Split(',').Select(ms => double.Parse(ms)).ToList();
model.M_ALL = ds.Tables[0].Rows[i]["Relative_Abundance_ALL"].ToString().Split(',').Select(ms => double.Parse(ms)).ToList();
List<MassPoint> lstMassPoint = new List<MassPoint>();
for (int j = 0; j < model.M_Z_ALL.Count; j++)
{
MassPoint mp = new MassPoint();
mp.Mass = Convert.ToDouble(model.M_Z_ALL[j]);
mp.Intensity = Convert.ToDouble(model.M_ALL[j]);
if (Convert.ToDouble(model.M_ALL[j]) * 100 > ipaco)
{
if (Convert.ToDouble(model.M_ALL[j]) == 1.000)
{
model.M = lstMassPoint.Count;
}
lstMassPoint.Add(mp);
}
}
model.Mass_Point = lstMassPoint;
lst.Add(model);
}
return lst;
}
public List<ModResModel> getPmFromDB(double pmFromFile, double deviation, double ipaco)
{
StringBuilder sb = new StringBuilder();
//sb.AppendFormat("SELECT * FROM {0}", sTableName);
//sb.AppendFormat(" WHERE ABS(MZ - {0}) < {1}", pmFromFile, deviation);
//sb.Append(" ORDER BY FORUMLA");
sb.AppendFormat("SELECT * FROM {0}", sTableName);
sb.AppendFormat(" WHERE MZ < {0} + {1} AND MZ > {2}", pmFromFile, deviation, pmFromFile);
sb.AppendFormat(" OR MZ < {0} AND MZ > {1} - {2}", pmFromFile, pmFromFile, deviation);
sb.Append(" ORDER BY FORUMLA");
DataSet ds = sqlHelper.Query(sb.ToString());
List<ModResModel> lst = new List<ModResModel>();
ModResModel model;
for (int i = 0; i < ds.Tables[0].Rows.Count; i++)
{
model = new ModResModel();
model.ID = ds.Tables[0].Rows[i]["ID"].ToString();
model.Mod_Res = ds.Tables[0].Rows[i]["MOD_RES"].ToString();
model.Z = int.Parse(ds.Tables[0].Rows[i]["Z"].ToString());
model.Sequence = ds.Tables[0].Rows[i]["SEQ"].ToString();
model.M_Z = double.Parse(ds.Tables[0].Rows[i]["MZ"].ToString());
model.Forumla = ds.Tables[0].Rows[i]["FORUMLA"].ToString();
model.M_Z_ALL = ds.Tables[0].Rows[i]["MZ_ALL"].ToString().Split(',').Select(ms => double.Parse(ms)).ToList();
model.M_ALL = ds.Tables[0].Rows[i]["Relative_Abundance_ALL"].ToString().Split(',').Select(ms => double.Parse(ms)).ToList();
List<MassPoint> lstMassPoint = new List<MassPoint>();
for (int j = 0; j < model.M_Z_ALL.Count; j++)
{
MassPoint mp = new MassPoint();
mp.Mass = Convert.ToDouble(model.M_Z_ALL[j]);
mp.Intensity = Convert.ToDouble(model.M_ALL[j]);
if (Convert.ToDouble(model.M_ALL[j]) * 100 > ipaco)
{
if (Convert.ToDouble(model.M_ALL[j]) == 1.000)
{
model.M = lstMassPoint.Count;
}
lstMassPoint.Add(mp);
}
}
model.Mass_Point = lstMassPoint;
lst.Add(model);
}
return lst;
}
public List <string[]> getFmFromDB(string ID, string mod_res, string scanTpye, string seq)
{
StringBuilder sb = new StringBuilder();
List <string[]> returnValue = new List <string[]>();
sb.Append("SELECT * FROM " + "Fragment_ions");
sb.Append(" WHERE MOD_RES='" + mod_res + "'");
//sb.Append(" and SEQ='" + seq + "'");
//sb.Append(" WHERE ID ='" + ID+"' and MOD_RES='"+mod_res+"'");
//sb.Append(" WHERE ID ='" + ID + "' and MOD_RES='S1,ac;K20,me2;'");
//sb.Append(" WHERE ID ='" + ID + "' and MOD_RES=''");
DataSet ds = sqlHelper.Query(sb.ToString());
//int count = ds.Tables[0].Rows.Count;
var drrArr = ds.Tables[0].AsEnumerable().Where(query => query["SEQ"].Equals(seq));
DataTable dt = drrArr.CopyToDataTable();
int count = dt.Rows.Count;
List <ModResModel> lst = new List <ModResModel>();
ModResModel model = new ModResModel();
string[] etd_mz = null;
string[] etd_m = null;
string[] etd_max = null;
string useStr = "";
for (int i = 0; i < count; i++)
{
if (scanTpye == "ETD")
{
dt.Rows[i]["ETD_MZ"].ToString();
dt.Rows[i]["ETD_Relative_Abundance"].ToString();
dt.Rows[i]["ETD_MZ_MAX"].ToString();
useStr = dt.Rows[i]["ETD_MZ"].ToString();
useStr = System.Text.RegularExpressions.Regex.Replace(useStr, @"([\r\n])[\s]+", "", RegexOptions.IgnoreCase);
etd_mz = useStr.Split(new string[] { "&" }, StringSplitOptions.RemoveEmptyEntries);
useStr = dt.Rows[i]["ETD_Relative_Abundance"].ToString();
useStr = System.Text.RegularExpressions.Regex.Replace(useStr, @"([\r\n])[\s]+", "", RegexOptions.IgnoreCase);
etd_m = useStr.Split(new string[] { "&" }, StringSplitOptions.RemoveEmptyEntries);
useStr = dt.Rows[i]["ETD_MZ_MAX"].ToString();
useStr = System.Text.RegularExpressions.Regex.Replace(useStr, @"([\r\n])[\s]+", "", RegexOptions.IgnoreCase);
etd_max = useStr.Split(new string[] { "&" }, StringSplitOptions.RemoveEmptyEntries);
}
else
{
dt.Rows[i]["CID_MZ"].ToString();
dt.Rows[i]["CID_Relative_Abundance"].ToString();
dt.Rows[i]["CID_MZ_MAX"].ToString();
useStr = dt.Rows[i]["CID_MZ"].ToString();
useStr = System.Text.RegularExpressions.Regex.Replace(useStr, @"([\r\n])[\s]+", "", RegexOptions.IgnoreCase);
etd_mz = useStr.Split(new string[] { "&" }, StringSplitOptions.RemoveEmptyEntries);
useStr = dt.Rows[i]["CID_Relative_Abundance"].ToString();
useStr = System.Text.RegularExpressions.Regex.Replace(useStr, @"([\r\n])[\s]+", "", RegexOptions.IgnoreCase);
etd_m = useStr.Split(new string[] { "&" }, StringSplitOptions.RemoveEmptyEntries);
useStr = dt.Rows[i]["CID_MZ_MAX"].ToString();
useStr = System.Text.RegularExpressions.Regex.Replace(useStr, @"([\r\n])[\s]+", "", RegexOptions.IgnoreCase);
etd_max = useStr.Split(new string[] { "&" }, StringSplitOptions.RemoveEmptyEntries);
}
returnValue.Add(etd_mz);
returnValue.Add(etd_m);
returnValue.Add(etd_max);
}
return(returnValue);
}
private List<ModResModel> comparePMFromDB(string pmMZ, string pmM, string pmMAX, List<MassPoint> msFromFile, int Z, double fat)
{
string[] pmMS = pmM.Split(new char[] { ';', '=', ',' });
string[] pmMZS = pmMZ.Split(new char[] { ';', '=', ',' });
string[] pmMAXS = pmMAX.Split('=');
int matchedMZ = 0;
//int matchedIndex = 0;
double mz_N = 0.0;
MassPoint massPoint = null;
List<ModResModel> returnValue = new List<ModResModel>();
List<MassPoint> returnMassPointList = null;
for (int i = 1; i < Z; i++)
{
mz_N = (Convert.ToDouble(Convert.ToDouble(pmMAXS[1])) + (i - 1) * 1.00782) / i;
int j = 0;
if (mz_N < msFromFile[0].Mass || mz_N > msFromFile[msFromFile.Count - 1].Mass)
{
continue;
}
int cutFlag = 0;
for (j = 100; j < msFromFile.Count; j = j + 100)
{
//double deviationInten = msFromFile[j].Mass - msFromFile[j].Mass / (mz_N / 1000000.0 + 1.0);
if (mz_N <= msFromFile[j].Mass)
{
cutFlag = 1;
break;
}
}
if (j <= 100)
j = 100;
if (cutFlag == 0)
j = msFromFile.Count;
int k = 0;
for (k = j - 100; k < j; k++)
{
double deviationInten = msFromFile[k].Mass - msFromFile[k].Mass / (mz_N / 1000000.0 + 1.0);
if ((System.Math.Abs(msFromFile[k].Mass - mz_N)) < deviationInten)
{
matchedMZ = i;
ModResModel modResModel = new ModResModel();
returnMassPointList = new List<MassPoint>();
//for (int l = 2; l < pmMS.Count(); l++)
//{
// massPoint = new MassPoint();
// massPoint.Mass = Convert.ToDouble(pmMZS[l]);
// massPoint.Intensity = Convert.ToDouble(pmMZS[l]);
// returnMassPointList.Add(massPoint);
//}
modResModel.ID = pmMAXS[0];
double MZ_N = 0.0;
modResModel.Z = i;
for (int m = 2; m < pmMS.Count(); m++)
{
if (Convert.ToDouble(pmMS[m]) * 100 > fat)
{
MassPoint Mass_Point = new MassPoint();
MZ_N = (Convert.ToDouble(Convert.ToDouble(pmMZS[m])) + (modResModel.Z - 1) * 1.00782) / modResModel.Z;
Mass_Point.Mass = MZ_N;
Mass_Point.Intensity = Convert.ToDouble(pmMS[m]);
if (Mass_Point.Intensity == 1.00)
{
modResModel.M_Z = returnMassPointList.Count;
}
returnMassPointList.Add(Mass_Point);
}
}
modResModel.Mass_Point = returnMassPointList;
//modResModel.M_Z = k;
modResModel.ID = pmMS[0];
modResModel.M = k;
returnValue.Add(modResModel);
break;
}
}
}
return returnValue;
}
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);
// }
//}
}
private List<ModResModel> getFMPointInfo(double mzs, double deviationInten, List<string[]> fmValue, int Z, double fat)
{
string[] useStr;
string[] maxMZ = fmValue[2];
string[] ETD_MZ = fmValue[0];//.Split(new char[] { ';', '=', ',' });
string[] ETD_M = fmValue[1];//.Split(new char[] { ';', '=', ',' });
string[] ETD_FM_MZ = null;
string[] ETD_FM_M = null;
double MZ_N = 0.0;
double deviationIntenNow = deviationInten;
List<ModResModel> returnValue = new List<ModResModel>();
ModResModel modResModel = new ModResModel();
List<MassPoint> Mass_PointList = new List<MassPoint>();
int flag = -1;
List<int> matchedList = new List<int>();
for (int i = 0; i < maxMZ.Count(); i++)
{
//MZ_N = mzs * j - (j - 1) * 1.00782;
useStr = maxMZ[i].Split('=');
for (int j = 1; j < Z; j++)
{
MZ_N = (Convert.ToDouble(useStr[1]) + (j - 1) * 1.00782) / j;
if (System.Math.Abs(MZ_N - mzs) < deviationIntenNow)
{
deviationIntenNow = System.Math.Abs(MZ_N - mzs);
modResModel = new ModResModel();
modResModel.Z = j;
flag = i;
modResModel.M_Z = MZ_N;
matchedList.Add(i);
returnValue.Add(modResModel);
//i = maxMZ.Count();
// break;
}
}
}
//ETD_FM_MZ = ETD_MZ[i].Split(new char[] { ';', '=', ',' });
//ETD_FM_M = ETD_M[i].Split(new char[]{';','=',','});
if (flag < 0)
{
return null;
}
for (int k = 0; k < matchedList.Count(); k++)
{
ETD_FM_MZ = ETD_MZ[matchedList[k]].Split(new char[] { ';', '=', ',' });
ETD_FM_M = ETD_M[matchedList[k]].Split(new char[] { ';', '=', ',' });
returnValue[k].ID = ETD_FM_MZ[0];
modResModel.ID = ETD_FM_MZ[0];
Mass_PointList = new List<MassPoint>();
for (int i = 2; i < ETD_FM_MZ.Count(); i++)
{
if (Convert.ToDouble(ETD_FM_M[i]) * 100 > fat)
{
MassPoint Mass_Point = new MassPoint();
MZ_N = (Convert.ToDouble(Convert.ToDouble(ETD_FM_MZ[i])) + (returnValue[k].Z - 1) * 1.00782) / returnValue[k].Z;
Mass_Point.Mass = MZ_N;
Mass_Point.Intensity = Convert.ToDouble(ETD_FM_M[i]);
if (Mass_Point.Intensity == 1.00)
{
returnValue[k].M_Z = Mass_PointList.Count;
}
Mass_PointList.Add(Mass_Point);
}
}
returnValue[k].Mass_Point = Mass_PointList;
}
/*
if (flag >= 0)
{
ETD_FM_MZ = ETD_MZ[flag].Split(new char[] { ';', '=', ',' });
ETD_FM_M = ETD_M[flag].Split(new char[] { ';', '=', ',' });
modResModel.ID = ETD_FM_MZ[0];
for (int i = 2; i < ETD_FM_MZ.Count(); i++)
{
if (Convert.ToDouble(ETD_FM_M[i]) * 100 > fat)
{
MassPoint Mass_Point = new MassPoint();
MZ_N = (Convert.ToDouble(Convert.ToDouble(ETD_FM_MZ[i])) + (modResModel.Z - 1) * 1.00782) / modResModel.Z;
Mass_Point.Mass = MZ_N;
Mass_Point.Intensity = Convert.ToDouble(ETD_FM_M[i]);
if (Mass_Point.Intensity == 1.00)
{
modResModel.M_Z = Mass_PointList.Count;
}
Mass_PointList.Add(Mass_Point);
}
}
}
modResModel.Mass_Point = Mass_PointList;
*/
//returnValue.Add(modResModel);
return returnValue;
}
