private List <MatchedData> GetMatchedData(XmlReader xmlReader)
{
List <MassPoint> lstMassPoint = new List <MassPoint>();
List <MatchedData> lstMatchedData = new List <MatchedData>();
List <MatchedData> lstTemp = null;
MassScan scanMS = new MassScan();
PeptideModResBLL peModResBLL = new PeptideModResBLL(DBName);
ParameterModel model = this.SaveControlToModel();
peModResBLL.ParameterModel = model;
bool bSingle = false;
int iScanCount = 0;
int currentCnt = 0;
int allCnt = (int)99998;
int avgCnt = 0;
int surplusCnt = 0;
if (allCnt >= 90)
{
avgCnt = allCnt / 90;
}
else
{
avgCnt = (int)Math.Round(90.0 / allCnt, MidpointRounding.AwayFromZero);
surplusCnt = (int)Math.Round((avgCnt - 90.0 / allCnt) * allCnt);
}
while (xmlReader.Read())
{
if (xmlReader.Name == "sha1")
{
break;
}
if (xmlReader.NodeType != XmlNodeType.Element)
{
continue;
}
if (xmlReader.Name == "msRun")
{
xmlReader.MoveToAttribute("scanCount");
iScanCount = int.Parse(xmlReader.Value);
if (allCnt > iScanCount)
{
allCnt = iScanCount;
if (allCnt >= 90)
{
avgCnt = allCnt / 90;
}
else
{
avgCnt = (int)Math.Round(90.0 / allCnt, MidpointRounding.AwayFromZero);
surplusCnt = (int)Math.Round((avgCnt - 90.0 / allCnt) * allCnt);
}
}
if (iScanCount == 1)
{
bSingle = true;
}
}
if (xmlReader.Name == "scan")
{
if (!xmlReader.HasAttributes)
{
continue;
}
//判断 是MS 还是MS2
xmlReader.MoveToAttribute("msLevel");
if ("1".Equals(xmlReader.Value))
{
xmlReader.MoveToAttribute("num");
scanMS.Index = UInt32.Parse(xmlReader.Value);
xmlReader.MoveToAttribute("msLevel");
scanMS.MsLevel = UInt32.Parse(xmlReader.Value);
xmlReader.MoveToAttribute("peaksCount");
scanMS.PeaksCount = UInt32.Parse(xmlReader.Value);
xmlReader.MoveToAttribute("polarity");
scanMS.Polarity = xmlReader.Value == "+" ? true : false;
xmlReader.MoveToAttribute("basePeakIntensity");
scanMS.BasePeakIntensity = double.Parse(xmlReader.Value);
while (xmlReader.Read())
{
if (xmlReader.Name == "peaks")
{
scanMS.IsPeaks = true;
scanMS.Peaks = xmlReader.ReadInnerXml();
lstMassPoint = Base64Convert.CalcMz(scanMS.Peaks, scanMS.PeaksCount);
break;
}
}
}
else if ("2".Equals(xmlReader.Value))
{
//读取属性
MassScan scanMS2 = new MassScan();
xmlReader.MoveToAttribute("num");
scanMS2.Index = UInt32.Parse(xmlReader.Value);
xmlReader.MoveToAttribute("msLevel");
scanMS2.MsLevel = UInt32.Parse(xmlReader.Value);
xmlReader.MoveToAttribute("peaksCount");
scanMS2.PeaksCount = UInt32.Parse(xmlReader.Value);
xmlReader.MoveToAttribute("polarity");
scanMS2.Polarity = xmlReader.Value == "+" ? true : false;
xmlReader.MoveToAttribute("basePeakIntensity");
scanMS2.BasePeakIntensity = double.Parse(xmlReader.Value);
while (xmlReader.Read())
{
if (xmlReader.NodeType != XmlNodeType.Element)
{
continue;
}
if (xmlReader.Name == "precursorMz")
{
xmlReader.MoveToAttribute("activationMethod");
scanMS2.ScanType = xmlReader.Value;
xmlReader.MoveToElement();
scanMS2.PrecursorMz = float.Parse(xmlReader.ReadInnerXml());
}
if (xmlReader.Name == "peaks")
{
scanMS2.Peaks = xmlReader.ReadInnerXml();
break;
}
}
if (bSingle == true)
{
if (scanMS2 == null)
{
return(null);
}
lstTemp = peModResBLL.getMSMatchs(scanMS2);
if (lstTemp != null && lstTemp.Count != 0)
{
lstMatchedData.AddRange(lstTemp);
}
return(lstMatchedData);
}
if (scanMS.IsPeaks == true)
{
if (scanMS2.Index >= 1 && scanMS2.Index <= 99999)
{
lstTemp = peModResBLL.getMSMatchs(scanMS, scanMS2);
if (lstTemp != null && lstTemp.Count != 0)
{
lstMatchedData.AddRange(lstTemp);
}
if (allCnt <= 0)
{
}
else if (allCnt >= 90)
{
currentCnt++;
}
else
{
currentCnt++;
}
}
}
}
else
{
continue;
}
}
}
return(lstMatchedData);
}
private void ConvertMatchData()
{
//sMZXMLFileName XML 文件
FileProcess filePro = new FileProcess();
XmlReader xmlReader = XmlReader.Create(sMZXMLFileName);
PeptideBLL peptideBLL = new PeptideBLL(DBName);
PeptideModResBLL peModResBLL = new PeptideModResBLL(DBName);
try
{
List <MatchedData> lstMatchedData = this.GetMatchedData(xmlReader);
if (lstMatchedData == null || lstMatchedData.Count == 0)
{
this.OutputFile(lstMatchedData);
}
DataTable dtFlat_Txt = peptideBLL.GetPeptideData();
for (int idx = 0; idx < dtFlat_Txt.Rows.Count; idx++)
{
DataRow drArr = dtFlat_Txt.Rows[idx];
string sAC = drArr["AC"].ToString().Split(';')[0];
string sDE = drArr["DE"].ToString();
sDE = sDE.Replace("RecName: Full=", "");
sDE = sDE.Remove(sDE.Length - 1);
string sCC = drArr["CC"].ToString();
int iIndex = sCC.IndexOf("-!-", 5);
sCC = iIndex == -1 ? sCC.Substring(4) : sCC.Substring(4, iIndex - 4);
string sID = drArr["ID"].ToString();
string sSQ = drArr["SQ"].ToString();
string sModResSingle = drArr["ModResSingle"].ToString();
lstMatchedData.Where(ms => ms.ID == sID).ToList().ForEach(ms =>
{
ms.Database = DBName;
ms.DatasetFile = sMZXMLFileName;
ms.Repository = FileName;
ms.AccessionNumber = sAC;
ms.Function = sCC;
ms.ID = sID;
ms.ProteinName = sDE;
ms.Length = ms.Sequence.Length;
ms.Actualpmfs = (double.Parse(ms.NMFS) / (2 * (sSQ.Length - 1)) * 100).ToString();
});
}
lstMatchedData = lstMatchedData.Where(ms => string.IsNullOrEmpty(ms.Actualpmfs) == false &&
decimal.Parse(ms.Actualpmfs) >= 5).ToList();
for (int idx = 0; idx < lstMatchedData.Count; idx++)
{
string[] modResArray = lstMatchedData[idx].MOD_RES.Split(new char[] { ';' }, StringSplitOptions.RemoveEmptyEntries);
int iCnt;
int iTotalCnt = 0;
int iStart;
int iEnd;
string sKey;
DataRow[] drArr = dtFlat_Txt.Select("ID = '" + lstMatchedData[0].ID + "'");
string sModResSingle = drArr[0]["ModResSingle"].ToString();
if (sModResSingle == null || sModResSingle == string.Empty || sModResSingle.Length == 0)
{
continue;
}
string[] modResDB = sModResSingle.Split('@');
for (int iModRes = 0; iModRes < modResArray.Length; iModRes++)
{
iCnt = 0;
List <string> lstStart = (from p in modResDB
where p.EndsWith(string.Format(",{0};", modResArray[iModRes].Split(',')[1]))
orderby int.Parse(p.Split(',')[0].Substring(1))
select p).ToList();
lstStart = this.PTM_Score_Filter(lstStart, modResArray[iModRes], "asc");
List <string> lstEnd = (from p in modResDB
where p.EndsWith(string.Format(",{0};", modResArray[iModRes].Split(',')[1]))
orderby int.Parse(p.Split(',')[0].Substring(1)) descending
select p).ToList();
lstEnd = this.PTM_Score_Filter(lstEnd, modResArray[iModRes], "desc");
sKey = modResArray[iModRes].Split(',')[0].Substring(0, 1);
if ((lstStart == null || lstStart.Count == 0) && (lstEnd == null || lstEnd.Count == 0))
{
lstMatchedData[idx].DataBase_PTM_SCORE += string.Format("{0},{1};", sKey, iCnt.ToString());
continue;
}
if (lstStart != null && lstStart.Count != 0)
{
if (lstStart.Count == 1)
{
iStart = int.Parse(lstStart[0].Split(',')[0].Substring(1));
iEnd = lstMatchedData[idx].Sequence.Length;
}
else
{
iStart = int.Parse(lstStart[0].Split(',')[0].Substring(1));
iEnd = int.Parse(lstStart[1].Split(',')[0].Substring(1));
}
for (int i = iStart; i < iEnd; i++)
{
string strC = string.Format("C{0}", i.ToString());
string strB = string.Format("B{0}", i.ToString());
if (lstMatchedData[idx].MatchedMs2.Exists(ms2 => ms2.ID == strC || ms2.ID == strB))
{
iCnt++;
iTotalCnt++;
}
}
}
if (lstEnd != null && lstEnd.Count != 0)
{
if (lstEnd.Count == 1)
{
iStart = int.Parse(lstEnd[0].Split(',')[0].Substring(1));
iEnd = 0;
}
else
{
iStart = int.Parse(lstEnd[0].Split(',')[0].Substring(1));
iEnd = int.Parse(lstEnd[1].Split(',')[0].Substring(1));
}
for (int i = lstMatchedData[idx].Length - iStart + 1; i < lstMatchedData[idx].Length - iEnd + 1; i++)
{
string strZ = string.Format("Z{0}", i.ToString());
string strY = string.Format("Y{0}", i.ToString());
if (lstMatchedData[idx].MatchedMs2.Exists(ms2 => ms2.ID == strZ || ms2.ID == strY))
{
iCnt++;
iTotalCnt++;
}
}
}
sKey = modResArray[iModRes].Split(',')[0].Substring(0, 1);
lstMatchedData[idx].DataBase_PTM_SCORE += string.Format("{0},{1};", sKey, iCnt.ToString());
}
lstMatchedData[idx].Total_PTM_Score = iTotalCnt.ToString();
}
lstMatchedData = lstMatchedData.Where(ms =>
{
if (ms.MOD_RES == string.Empty)
{
return(true);
}
var temp = ms.DataBase_PTM_SCORE.Split(new char[] { ';' }, StringSplitOptions.RemoveEmptyEntries);
for (int i = 0; i < temp.Length; i++)
{
if (decimal.Parse(temp[i].Split(',')[1]) < 1)
{
return(false);
}
}
return(true);
}).ToList();
if (lstMatchedData == null || lstMatchedData.Count == 0)
{
this.OutputFile(lstMatchedData);
return;
}
this.OutputFile(lstMatchedData);
string sSaveResultPath = "MetaData";
if (Directory.Exists(sSaveResultPath) == false)
{
System.IO.Directory.CreateDirectory(sSaveResultPath);
}
sSaveResultPath = string.Format(@"{0}\{1}.bin", sSaveResultPath, FileName);
filePro.Serializer <List <MatchedData> >(lstMatchedData, sSaveResultPath);
//if (sSaveResultPath != string.Empty)
//{
// this.Invoke(new InvokeDialog(OpenView), new object[] { sSaveResultPath, lstMatchedData });
//}
}
catch (Exception ex)
{
throw ex;
}
finally
{
xmlReader.Close();
xmlReader = null;
}
}
