private void DoSearchInWS()
{
double[] NormalizedSpectrum = new double[4096];
string[] lines = this.tbDTA.Text.Split(new string[] { "\r\n" }, StringSplitOptions.RemoveEmptyEntries);
if (lines.Length == 0)
{
lbMessage.Text = "Please input spectrum data.";
return;
}
SessionID = DateTime.Now.ToString("yyyy_MM_dd");
IndexID = DateTime.Now.ToString("fffffff");
// string UploadPath = WebConfigurationManager.ConnectionStrings["UploadPath"].ConnectionString + string.Format ("WebDta\\{0}\\",SessionID );
// DirectoryInfo newpath = new DirectoryInfo(UploadPath);
// if (!newpath.Exists)
// {
// newpath.Create();
// }
//string dtaFilename = UploadPath + IndexID + ".dta";
//try
//{
// using (StreamWriter sw = new StreamWriter(dtaFilename, true))
// {
foreach (string line in lines)
{
//sw.WriteLine(line);
if (char.IsDigit(line, 0))
{
String [] sperator = line.Split(new string [] { " ", "\t" }, StringSplitOptions.RemoveEmptyEntries);
string mz = sperator[0];
string intensity = sperator[1];
MZintensitiy mzi = new MZintensitiy();
try
{
mzi.mz = float.Parse(mz);
mzi.intensity = float.Parse(intensity);
if (mzi.mz > NoiseCutoff)
{
double dintensity = (double)mzi.intensity;
NormalizedSpectrum[(int)mzi.mz] += dintensity;
}
//SpectrumData.Add(mzi);
}
catch (Exception ex)
{ }
}
}
// sw.Close();
// }
//}
// catch (Exception ex)
//{
// this.lbMessage.Text = string.Format ("Write dta file to server with error:{0} ",ex.ToString ());
// }
//double TotalNormal = 0;
//foreach (double mz in NormalizedSpectrum)
//{
// TotalNormal += mz * mz;
//}
//TotalNormal = Math.Sqrt(TotalNormal);
//for (int i = 0; i < 4096; i++)
//{
// NormalizedSpectrum[i] = NormalizedSpectrum[i] / TotalNormal;
//}
int slideSize = int.Parse(this.ddlChargeState.Text);
float PrecursorMZ = float.Parse(this.tbPrecursorMZ.Text);
float mzTolerance = float.Parse(this.tbTolerance.Text);
COPaWS.COPaWS webserv = new COPaWS.COPaWS();
NetworkCredential objCredential = new NetworkCredential(ConfigurationSettings.AppSettings["COPaWSUser"], ConfigurationSettings.AppSettings["COPaWSPassword"]);
webserv.Credentials = objCredential;
COPaWS.SearchingCondition sc = new COPaWS.SearchingCondition();
sc.bUseNoiseLibrary = true;
sc.bStatisticSearching = false;
sc.bHighResolution = false;
sc.fPrecursorWindow = mzTolerance;
sc.iSlideSize = slideSize;
COPaWS.SearchingThreadPair tp = new COPaWS.SearchingThreadPair();
tp.DetaDecoyScore = float.Parse(this.tbCutoff.Text);
tp.MatchScore = 0.0F;
sc.NormalSearchCondition = new COPaWS.SearchingThreadPair[] { tp };
COPaWS.Module lib_mod = COPaWS.Module.human_heart_mitochondria;
if (this.ddlModules.Text != null)
{
try
{
lib_mod = (COPaWS.Module)(int.Parse(this.ddlModules.Text.Substring(0, this.ddlModules.Text.IndexOf("."))) - 1);
}
catch (Exception ex)
{
lbMessage.Text = "Could not recognize the library module!";
return;
}
}
COPaWS.Module[] Modules = new COPaWS.Module[] { lib_mod };
COPaWS.MSPepetideInfo[] results = webserv.SearchDTA2("WebDta", SessionID, IndexID, NormalizedSpectrum, PrecursorMZ, Modules, sc, 2);
if (results != null)
{
string PepIDURL = "<a href='PeptideInfo.aspx?QType=Peptide+ID&QValue={0}' Target='_blank'>{1}</a>";
string SpectrumURL = "<a href='MatchSpectrum.aspx?QValue={0}&SessionID={1}&ST=RUN&TaskID={2}&File={3}' Target='_blank'><img src='_image/mirror_spectrum.gif' /></a>";
foreach (COPaWS.MSPepetideInfo mspep in results)
{
TableRow trResult = new TableRow();
TableCell tcPepID = new TableCell();
string strPepID = mspep.COPaPeptideID;
tcPepID.Text = string.Format(PepIDURL, strPepID, strPepID);
tcPepID.HorizontalAlign = HorizontalAlign.Left;
trResult.Cells.Add(tcPepID);
TableCell tcPepSeq = new TableCell();
string PeptideSeq = mspep.PeptideSequence;
//string ModifiedType = mspep.ModifiedType;
tcPepSeq.Text = PeptideSeq;
tcPepSeq.HorizontalAlign = HorizontalAlign.Left;
trResult.Cells.Add(tcPepSeq);
TableCell tcModifiedType = new TableCell();
tcModifiedType.Text = "";// ModifiedType;
tcModifiedType.HorizontalAlign = HorizontalAlign.Left;
trResult.Cells.Add(tcModifiedType);
//TableCell tcDotProduct = new TableCell();
//double dp = double.Parse(foundRows[i].ItemArray[1].ToString());
//tcDotProduct.Text = string.Format("{0:F3}", dp);
//tcDotProduct.HorizontalAlign = HorizontalAlign.Right;
//trResult.Cells.Add(tcDotProduct);
//TableCell tcDotBias = new TableCell();
//double db = double.Parse(foundRows[i].ItemArray[2].ToString());
//tcDotBias.Text = string.Format("{0:F3}", db);
//tcDotBias.HorizontalAlign = HorizontalAlign.Right;
//trResult.Cells.Add(tcDotBias);
TableCell tcFscore = new TableCell();
double finalScore = double.Parse(mspep.DecoyScore);// double.Parse(foundRows[i].ItemArray[3].ToString());
tcFscore.Text = string.Format("{0:F3}", finalScore);
tcFscore.HorizontalAlign = HorizontalAlign.Right;
trResult.Cells.Add(tcFscore);
TableCell tcSpectrum = new TableCell();
tcSpectrum.Text = string.Format(SpectrumURL, mspep.LibSpectraSeq, IndexID, "WebDta", SessionID);
tcSpectrum.HorizontalAlign = HorizontalAlign.Center;
trResult.Cells.Add(tcSpectrum);
tbPeptides.Rows.Add(trResult);
}
if (results.Length > 0)
{
lbMessage.Text = string.Format(" {0} spectra matched!", results.Length);
}
else
{
lbMessage.Text = string.Format("no spectrum was matched under your criteria, you could adjust the cutoff and try again!");
}
}
else
{
lbMessage.Text = string.Format("no spectrum was matched under your criteria, you could adjust the cutoff and try again!");
}
}
private void DoSearchInWS()
{
double[] NormalizedSpectrum = new double[4096];
string[] lines = this.tbDTA.Text.Split(new string[] { "\r\n" }, StringSplitOptions.RemoveEmptyEntries);
if (lines.Length == 0)
{
lbMessage.Text = "Please input spectrum data.";
return;
}
SessionID = DateTime.Now.ToString("yyyy_MM_dd") ;
IndexID = DateTime.Now.ToString("fffffff");
// string UploadPath = WebConfigurationManager.ConnectionStrings["UploadPath"].ConnectionString + string.Format ("WebDta\\{0}\\",SessionID );
// DirectoryInfo newpath = new DirectoryInfo(UploadPath);
// if (!newpath.Exists)
// {
// newpath.Create();
// }
//string dtaFilename = UploadPath + IndexID + ".dta";
//try
//{
// using (StreamWriter sw = new StreamWriter(dtaFilename, true))
// {
foreach (string line in lines)
{
//sw.WriteLine(line);
if (char.IsDigit(line, 0))
{
String [] sperator = line.Split (new string []{" ","\t"},StringSplitOptions.RemoveEmptyEntries );
string mz = sperator[0];
string intensity = sperator[1];
MZintensitiy mzi = new MZintensitiy();
try
{
mzi.mz = float.Parse(mz);
mzi.intensity = float.Parse(intensity);
if (mzi.mz > NoiseCutoff)
{
double dintensity = (double)mzi.intensity;
NormalizedSpectrum[(int)mzi.mz] += dintensity;
}
//SpectrumData.Add(mzi);
}
catch (Exception ex)
{ }
}
}
// sw.Close();
// }
//}
// catch (Exception ex)
//{
// this.lbMessage.Text = string.Format ("Write dta file to server with error:{0} ",ex.ToString ());
// }
//double TotalNormal = 0;
//foreach (double mz in NormalizedSpectrum)
//{
// TotalNormal += mz * mz;
//}
//TotalNormal = Math.Sqrt(TotalNormal);
//for (int i = 0; i < 4096; i++)
//{
// NormalizedSpectrum[i] = NormalizedSpectrum[i] / TotalNormal;
//}
int slideSize = int.Parse(this.ddlChargeState.Text);
float PrecursorMZ = float.Parse(this.tbPrecursorMZ.Text);
float mzTolerance = float.Parse(this.tbTolerance.Text);
COPaWS.COPaWS webserv = new COPaWS.COPaWS();
NetworkCredential objCredential = new NetworkCredential(ConfigurationSettings.AppSettings["COPaWSUser"], ConfigurationSettings.AppSettings["COPaWSPassword"]);
webserv.Credentials = objCredential;
COPaWS.SearchingCondition sc = new COPaWS.SearchingCondition ();
sc.bUseNoiseLibrary = true ;
sc.bStatisticSearching = false ;
sc.bHighResolution = false;
sc.fPrecursorWindow = mzTolerance ;
sc.iSlideSize = slideSize ;
COPaWS.SearchingThreadPair tp = new COPaWS.SearchingThreadPair() ;
tp.DetaDecoyScore = float.Parse (this.tbCutoff.Text );
tp.MatchScore = 0.0F;
sc.NormalSearchCondition = new COPaWS.SearchingThreadPair[] {tp} ;
COPaWS.Module lib_mod = COPaWS.Module.human_heart_mitochondria ;
if (this.ddlModules.Text != null)
{
try
{
lib_mod = (COPaWS.Module)(int.Parse(this.ddlModules.Text.Substring(0, this.ddlModules.Text.IndexOf("."))) - 1);
}
catch (Exception ex)
{
lbMessage.Text = "Could not recognize the library module!";
return;
}
}
COPaWS.Module[] Modules = new COPaWS.Module[] { lib_mod };
COPaWS.MSPepetideInfo[] results = webserv.SearchDTA2("WebDta", SessionID, IndexID, NormalizedSpectrum, PrecursorMZ, Modules, sc, 2);
if (results != null)
{
string PepIDURL = "<a href='PeptideInfo.aspx?QType=Peptide+ID&QValue={0}' Target='_blank'>{1}</a>";
string SpectrumURL = "<a href='MatchSpectrum.aspx?QValue={0}&SessionID={1}&ST=RUN&TaskID={2}&File={3}' Target='_blank'><img src='_image/mirror_spectrum.gif' /></a>";
foreach (COPaWS.MSPepetideInfo mspep in results)
{
TableRow trResult = new TableRow();
TableCell tcPepID = new TableCell();
string strPepID = mspep.COPaPeptideID;
tcPepID.Text = string.Format(PepIDURL, strPepID, strPepID);
tcPepID.HorizontalAlign = HorizontalAlign.Left;
trResult.Cells.Add(tcPepID);
TableCell tcPepSeq = new TableCell();
string PeptideSeq = mspep.PeptideSequence;
//string ModifiedType = mspep.ModifiedType;
tcPepSeq.Text = PeptideSeq;
tcPepSeq.HorizontalAlign = HorizontalAlign.Left;
trResult.Cells.Add(tcPepSeq);
TableCell tcModifiedType = new TableCell();
tcModifiedType.Text = "";// ModifiedType;
tcModifiedType.HorizontalAlign = HorizontalAlign.Left;
trResult.Cells.Add(tcModifiedType);
//TableCell tcDotProduct = new TableCell();
//double dp = double.Parse(foundRows[i].ItemArray[1].ToString());
//tcDotProduct.Text = string.Format("{0:F3}", dp);
//tcDotProduct.HorizontalAlign = HorizontalAlign.Right;
//trResult.Cells.Add(tcDotProduct);
//TableCell tcDotBias = new TableCell();
//double db = double.Parse(foundRows[i].ItemArray[2].ToString());
//tcDotBias.Text = string.Format("{0:F3}", db);
//tcDotBias.HorizontalAlign = HorizontalAlign.Right;
//trResult.Cells.Add(tcDotBias);
TableCell tcFscore = new TableCell();
double finalScore = double.Parse(mspep.DecoyScore);// double.Parse(foundRows[i].ItemArray[3].ToString());
tcFscore.Text = string.Format("{0:F3}", finalScore);
tcFscore.HorizontalAlign = HorizontalAlign.Right;
trResult.Cells.Add(tcFscore);
TableCell tcSpectrum = new TableCell();
tcSpectrum.Text = string.Format(SpectrumURL, mspep.LibSpectraSeq, IndexID, "WebDta", SessionID);
tcSpectrum.HorizontalAlign = HorizontalAlign.Center;
trResult.Cells.Add(tcSpectrum);
tbPeptides.Rows.Add(trResult);
}
if (results.Length > 0)
lbMessage.Text = string.Format(" {0} spectra matched!", results.Length);
else
lbMessage.Text = string.Format("no spectrum was matched under your criteria, you could adjust the cutoff and try again!");
}
else
lbMessage.Text = string.Format("no spectrum was matched under your criteria, you could adjust the cutoff and try again!");
}
