protected void Page_Load(object sender, EventArgs e)
{
SpectrumData = new ArrayList();
GuestSpectrumData = new ArrayList();
SessionID = Request.QueryString["SessionID"];
TaskID = Request.QueryString["TaskID"];
if (Request.QueryString["file"] != null)
{
string file_path = Request.QueryString["file"];
if (Request.QueryString["mode"] != null)
{
if (Request.QueryString["mode"] == "ZoomOut")
{
//get the param how to show the spectrum
string displayMin = Request.QueryString["xmin"];
string displayMax = Request.QueryString["xmax"];
string displayYMax = Request.QueryString["ymax"];
try
{
if (displayMin == null)
DisplayMinX = -1;
else
{
DisplayMinX = int.Parse(displayMin);
if (DisplayMinX < 0)
DisplayMinX = -1;
}
if (displayMax == null)
DisplayMaxX = -1;
else
{
DisplayMaxX = int.Parse(displayMax);
if (DisplayMaxX < 0 || DisplayMaxX <= DisplayMinX)
DisplayMaxX = -1;
}
}
catch
{
DisplayMaxX = -1;
DisplayMinX = -1;
}
//use the params to decide the seg distance will show on the axial
if (DisplayMaxX != -1 && DisplayMinX != -1)
{
int Length = DisplayMaxX - DisplayMinX;
if (Length > 1000)
XBIGSEG = 100;
else if (Length > 500)
XBIGSEG = 50;
else if (Length > 200)
XBIGSEG = 25;
else if (Length > 100)
XBIGSEG = 15;
else if (Length > 50)
XBIGSEG = 10;
else if (Length > 20)
XBIGSEG = 5;
else if (Length > 10)
XBIGSEG = 2;
else
XBIGSEG = 1;
}
try
{
if (displayYMax == null)
DisplayMaxY = 100;
else
{
DisplayMaxY = int.Parse(displayYMax);
if (DisplayMaxY < 75 && DisplayMaxY > 30)
{
YBIGSEG = 10;
}
else if (DisplayMaxY <= 30 && DisplayMaxY > 20)
{
YBIGSEG = 5;
}
else if (DisplayMaxY >= 0 && DisplayMaxY <= 20)
{
YBIGSEG = 2;
}
else if (DisplayMaxY <= 100 && DisplayMaxY >= 75)
{
YBIGSEG = 25;
}
else
{
DisplayMaxY = 100;
YBIGSEG = 25;
}
}
}
catch (Exception ex)
{
DisplayMaxY = 100; ;
}
bZoomOut = true;
}
else
{
bZoomOut = false;
}
}
if (Request.QueryString["Printable"] != null)
{
if (Request.QueryString["Printable"] == "True")
WIDTH = 580;
else
WIDTH = 800;
}
if (Request.QueryString["ShowTheory"] != null)
{
if (Request.QueryString["ShowTheory"] == "True")
{
bShowTheory = true;
}
else
bShowTheory = false;
}
if (Request.QueryString["Noise"] != null)
{
if (Request.QueryString["Noise"] == "True")
bShowNoise = true;
else
bShowNoise = false;
}
if (Request.QueryString["Label"] != null)
{
if (Request.QueryString["Label"] == "True")
bShowLabel = true;
else
bShowLabel = false;
}
AdditionalSequence = Request.QueryString["SEQ"];
ChargeState = Request.QueryString["CS"];
SearchType = Request.QueryString["ST"];
PrecursorMZ = float.Parse(Request.QueryString["pmz"]);
mzTolerance = float.Parse(WebConfigurationManager.ConnectionStrings["mzTolerance"].ConnectionString);
// get the library spectrum data
if (true)//File.Exists(file_path))
{
//multiuser-fridendly streamreader
//FileInfo fiLibSpectra = new FileInfo(file_path);
//if (!fiLibSpectra.Exists)
// return;
//FileStream fs = File.Open(file_path, FileMode.Open, FileAccess.Read, FileShare.ReadWrite);
//StreamReader sr = new StreamReader(fs);
string lines = "";
String strSQL = string.Format("select spectrum,ptm_sequence from spectrum_tbl where spectrum_seq={0}", file_path);
DataSet result = DBInterface.QuerySQL2(strSQL);
if (result != null)
{
if (result.Tables[0].Rows.Count > 0)
{
lines = result.Tables[0].Rows[0].ItemArray[0].ToString();
PeptideSequence = result.Tables[0].Rows[0].ItemArray[1].ToString();
}
}
String[] dtaLines = lines.Split(new string[] { "\r\n" }, StringSplitOptions.RemoveEmptyEntries);
if (bZoomOut && DisplayMaxX != -1 && DisplayMinX != -1)
{
MinX = DisplayMinX;
MaxX = DisplayMaxX;
}
foreach (String line in dtaLines)
{
if (char.IsDigit(line, 0))
{
string[] tokens = line.Split (new string[]{" ","\t"},StringSplitOptions.RemoveEmptyEntries );
string mz = tokens[0];
string intensity = tokens [1];
MZintensitiy mzi = new MZintensitiy();
try
{
mzi.mz = float.Parse(mz);
if (bZoomOut && DisplayMaxX != -1 && DisplayMinX != -1)
{
if (mzi.mz < DisplayMaxX && mzi.mz > DisplayMinX)
{
//if (mzi.mz < MinX)
// MinX = mzi.mz;
//if (mzi.mz > MaxX)
// MaxX = mzi.mz;
mzi.intensity = float.Parse(intensity);
if (mzi.intensity > MaxIntensitiy)
MaxIntensitiy = mzi.intensity;
SpectrumData.Add(mzi);
}
}
else
{
if (mzi.mz < MinX)
MinX = mzi.mz;
if (mzi.mz > MaxX)
MaxX = mzi.mz;
mzi.intensity = float.Parse(intensity);
if (mzi.intensity > MaxIntensitiy)
MaxIntensitiy = mzi.intensity;
SpectrumData.Add(mzi);
}
}
catch
{ }
}
}
//sr.Close();
if (SearchType == "DTA")
{
////get the guest spectrum data
//if (GuestSpectrums == "")
// GuestSpectrums = (string)(Session[SessionID]);
//string[] lines = GuestSpectrums.Split(new string[] { "\r\n" }, StringSplitOptions.RemoveEmptyEntries);
//foreach (string pair in lines)
//{
// if (char.IsDigit(pair, 0))
// {
// int sperator = pair.IndexOf(" ");
// string mz = pair.Substring(0, sperator);
// string intensity = pair.Substring(sperator);
// MZintensitiy mzi = new MZintensitiy();
// try
// {
// mzi.mz = float.Parse(mz);
// if (bZoomOut && DisplayMaxX != -1 && DisplayMinX != -1)
// {
// // if mz in the zoom view
// if (mzi.mz < DisplayMaxX && mzi.mz > DisplayMinX)
// {
// if (mzi.mz < GuestMinX)
// GuestMinX = mzi.mz;
// if (mzi.mz > GuestMaxX)
// GuestMaxX = mzi.mz;
// mzi.intensity = float.Parse(intensity);
// if (mzi.intensity > GuestMaxIntensitiy)
// GuestMaxIntensitiy = mzi.intensity;
// GuestSpectrumData.Add(mzi);
// }
// }
// else
// {
// if (mzi.mz < GuestMinX)
// GuestMinX = mzi.mz;
// if (mzi.mz > GuestMaxX)
// GuestMaxX = mzi.mz;
// mzi.intensity = float.Parse(intensity);
// if (mzi.intensity > GuestMaxIntensitiy)
// GuestMaxIntensitiy = mzi.intensity;
// GuestSpectrumData.Add(mzi);
// }
// }
// catch (Exception ex)
// { }
// }
//}
}
else
{
string msFile = Request.QueryString["MSFile"];
string dtaFilePath = WebConfigurationManager.ConnectionStrings["UploadPath"].ConnectionString + TaskID + string.Format ("\\{0}_dta\\",msFile ) + SessionID + ".dta";
FileInfo fiDta = new FileInfo(dtaFilePath);
if (!fiDta.Exists)
return;
// get from the generated dta file
FileStream gfs = File.Open(dtaFilePath, FileMode.Open, FileAccess.Read, FileShare.ReadWrite );
StreamReader gsr = new StreamReader(gfs);
if (bZoomOut && DisplayMaxX != -1 && DisplayMinX != -1)
{
GuestMinX = DisplayMinX;
GuestMaxX = DisplayMaxX;
}
string line;
while ((line = gsr.ReadLine()) != null)
{
if (char.IsDigit(line, 0))
{
int sperator = line.IndexOf(" ");
string mz = line.Substring(0, sperator);
string intensity = line.Substring(sperator);
MZintensitiy mzi = new MZintensitiy();
try
{
mzi.mz = float.Parse(mz);
if (bZoomOut && DisplayMaxX != -1 && DisplayMinX != -1)
{
if (mzi.mz < DisplayMaxX && mzi.mz > DisplayMinX)
{
//if (mzi.mz < GuestMinX)
// GuestMinX = mzi.mz;
//if (mzi.mz > GuestMaxX)
// GuestMaxX = mzi.mz;
mzi.intensity = float.Parse(intensity);
if (mzi.intensity > GuestMaxIntensitiy)
GuestMaxIntensitiy = mzi.intensity;
GuestSpectrumData.Add(mzi);
}
}
else
{
if (mzi.mz < GuestMinX)
GuestMinX = mzi.mz;
if (mzi.mz > GuestMaxX)
GuestMaxX = mzi.mz;
mzi.intensity = float.Parse(intensity);
if (mzi.intensity > GuestMaxIntensitiy)
GuestMaxIntensitiy = mzi.intensity;
GuestSpectrumData.Add(mzi);
}
}
catch
{ }
}
}
gsr.Close();
}
DrawSpectrum();
}
}
}
//string PeptideSequence = "";
//string ChargeState = "";
//float mzTolerance = 1F;
//float PrecursorMZ = 0.0F;
protected void Page_Load(object sender, EventArgs e)
{
SpectrumData = new ArrayList();
if (Request.QueryString["file"] != null)
{
string file_path = Request.QueryString["file"];
//PeptideSequence = Request.QueryString["SEQ"];
//ChargeState = Request.QueryString["CS"];
//PrecursorMZ = float.Parse(Request.QueryString["pmz"]);
//mzTolerance = float.Parse(WebConfigurationManager.ConnectionStrings["mzTolerance"].ConnectionString);
if (true)//File.Exists(file_path))
{
//multiuser-fridendly streamreader
//FileStream fs = File.Open(file_path, FileMode.Open, FileAccess.Read, FileShare.ReadWrite );
//StreamReader sr = new StreamReader(fs);
string lines = "";
string strSQL;
if (file_path.Length < 10)
{
strSQL = string.Format("select spectrum from spectrum_tbl where spectrum_seq={0}", file_path);
}
else
{
strSQL = string.Format("select spectrum from spectrum_tbl where spectrum_seq={0}", "159268");
}
DataSet result = DBInterface.QuerySQL2(strSQL);
if (result != null)
{
if (result.Tables[0].Rows.Count > 0)
{
lines = result.Tables[0].Rows[0].ItemArray[0].ToString();
}
}
String[] dtaLines = lines.Split(new string[] { "\r\n" }, StringSplitOptions.RemoveEmptyEntries);
foreach (String line in dtaLines)
{
if (char.IsDigit(line, 0))
{
int sperator = line.IndexOf(" ");
string mz = line.Substring(0, sperator);
string intensity = line.Substring(sperator);
MZintensitiy mzi = new MZintensitiy();
try
{
mzi.mz = float.Parse(mz);
if (bZoomOut && DisplayMaxX != -1 && DisplayMinX != -1)
{
if (mzi.mz < DisplayMaxX && mzi.mz > DisplayMinX)
{
if (mzi.mz < MinX)
{
MinX = mzi.mz;
}
if (mzi.mz > MaxX)
{
MaxX = mzi.mz;
}
mzi.intensity = float.Parse(intensity);
if (mzi.intensity > MaxIntensitiy)
{
MaxIntensitiy = mzi.intensity;
}
SpectrumData.Add(mzi);
}
}
else
{
if (mzi.mz < MinX)
{
MinX = mzi.mz;
}
if (mzi.mz > MaxX)
{
MaxX = mzi.mz;
}
mzi.intensity = float.Parse(intensity);
if (mzi.intensity > MaxIntensitiy)
{
MaxIntensitiy = mzi.intensity;
}
SpectrumData.Add(mzi);
}
}
catch
{ }
}
}
DrawSpectrum();
}
}
}
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!");
}
}
protected void Page_Load(object sender, EventArgs e)
{
SpectrumData = new ArrayList() ;
if (Request.QueryString["file"] != null)
{
string file_path = Request.QueryString["file"];
if (Request.QueryString["mode"] != null)
{
if (Request.QueryString["mode"] == "ZoomOut")
{
string displayMin = Request.QueryString["xmin"];
string displayMax = Request.QueryString["xmax"];
string displayYMax = Request.QueryString["ymax"];
try
{
if (displayMin == null)
DisplayMinX = -1;
else
{
DisplayMinX = int.Parse(displayMin);
if (DisplayMinX < 0)
DisplayMinX = -1;
}
if (displayMax == null)
DisplayMaxX = -1;
else
{
DisplayMaxX = int.Parse(displayMax);
if (DisplayMaxX < 0 || DisplayMaxX <= DisplayMinX)
DisplayMaxX = -1;
}
}
catch
{
DisplayMaxX = -1;
DisplayMinX = -1;
}
if (DisplayMaxX != -1 && DisplayMinX != -1)
{
int Length = DisplayMaxX - DisplayMinX;
if (Length > 1000)
XBIGSEG = 250;
else if (Length > 500)
XBIGSEG = 100;
else if (Length > 200)
XBIGSEG = 50;
else if (Length > 100)
XBIGSEG = 25;
else if (Length > 50)
XBIGSEG = 10;
else if (Length > 20)
XBIGSEG = 5;
else
XBIGSEG = 2;
}
try
{
if (displayYMax == null)
DisplayMaxY = 100;
else
{
DisplayMaxY = int.Parse(displayYMax);
if (DisplayMaxY < 75 && DisplayMaxY > 30)
{
YBIGSEG = 10;
}
else if (DisplayMaxY <= 30 && DisplayMaxY > 20)
{
YBIGSEG = 5;
}
else if (DisplayMaxY >= 0 && DisplayMaxY <= 20)
{
YBIGSEG = 2;
}
else if (DisplayMaxY <= 100 && DisplayMaxY >= 75)
{
YBIGSEG = 25;
}
else
{
DisplayMaxY = 100;
YBIGSEG = 25;
}
}
}
catch (Exception ex)
{
DisplayMaxY = 100; ;
}
bZoomOut = true;
}
else
{
bZoomOut = false;
}
}
if (Request.QueryString["Printable"] != null)
{
if (Request.QueryString["Printable"] == "True")
{
bShowLabel = true;
//HEIGHT = 250;
}
else
bShowLabel = false;
}
if (Request.QueryString["ShowTheory"] != null)
{
if (Request.QueryString["ShowTheory"] == "True")
{
bShowTheory = true;
}
else
bShowTheory = false;
}
PeptideSequence = Request.QueryString["SEQ"];
ChargeState = Request.QueryString["CS"];
PrecursorMZ = float.Parse (Request.QueryString["pmz"]);
mzTolerance = float.Parse(WebConfigurationManager.ConnectionStrings["mzTolerance"].ConnectionString);
if (true)//File.Exists(file_path))
{
//multiuser-fridendly streamreader
//FileStream fs = File.Open(file_path, FileMode.Open, FileAccess.Read, FileShare.ReadWrite );
//StreamReader sr = new StreamReader(fs);
string lines="";
string strSQL;
if (file_path.Length < 10)
{
strSQL = string.Format("select spectrum from spectrum_tbl where spectrum_seq={0}", file_path);
}
else
{
strSQL = string.Format("select spectrum from spectrum_tbl where spectrum_seq={0}", "159268");
}
DataSet result = DBInterface.QuerySQL2(strSQL);
if (result != null)
{
if (result.Tables[0].Rows.Count > 0)
{
lines = result.Tables[0].Rows[0].ItemArray[0].ToString();
}
}
String[] dtaLines = lines.Split(new string[] { "\r\n" }, StringSplitOptions.RemoveEmptyEntries);
foreach (String line in dtaLines )
{
if (char.IsDigit(line, 0))
{
string[] tokens = line.Split(new string[]{" ","\t"},StringSplitOptions.RemoveEmptyEntries );
string mz = tokens[0];
string intensity = tokens[1];
MZintensitiy mzi = new MZintensitiy();
try
{
mzi.mz = float.Parse(mz);
if (bZoomOut && DisplayMaxX != -1 && DisplayMinX != -1)
{
if (mzi.mz < DisplayMaxX && mzi.mz > DisplayMinX)
{
if (mzi.mz < MinX)
MinX = mzi.mz;
if (mzi.mz > MaxX)
MaxX = mzi.mz;
mzi.intensity = float.Parse(intensity);
if (mzi.intensity > MaxIntensitiy)
MaxIntensitiy = mzi.intensity;
SpectrumData.Add(mzi);
}
}
else
{
if (mzi.mz < MinX)
MinX = mzi.mz;
if (mzi.mz > MaxX)
MaxX = mzi.mz;
mzi.intensity = float.Parse(intensity);
if (mzi.intensity > MaxIntensitiy)
MaxIntensitiy = mzi.intensity;
SpectrumData.Add(mzi);
}
}
catch
{ }
}
}
DrawSpectrum();
}
}
}
//string PeptideSequence = "";
//string ChargeState = "";
//float mzTolerance = 1F;
//float PrecursorMZ = 0.0F;
protected void Page_Load(object sender, EventArgs e)
{
SpectrumData = new ArrayList();
if (Request.QueryString["file"] != null)
{
string file_path = Request.QueryString["file"];
//PeptideSequence = Request.QueryString["SEQ"];
//ChargeState = Request.QueryString["CS"];
//PrecursorMZ = float.Parse(Request.QueryString["pmz"]);
//mzTolerance = float.Parse(WebConfigurationManager.ConnectionStrings["mzTolerance"].ConnectionString);
if (true)//File.Exists(file_path))
{
//multiuser-fridendly streamreader
//FileStream fs = File.Open(file_path, FileMode.Open, FileAccess.Read, FileShare.ReadWrite );
//StreamReader sr = new StreamReader(fs);
string lines = "";
string strSQL;
if (file_path.Length < 10)
{
strSQL = string.Format("select spectrum from spectrum_tbl where spectrum_seq={0}", file_path);
}
else
{
strSQL = string.Format("select spectrum from spectrum_tbl where spectrum_seq={0}", "159268");
}
DataSet result = DBInterface.QuerySQL2(strSQL);
if (result != null)
{
if (result.Tables[0].Rows.Count > 0)
{
lines = result.Tables[0].Rows[0].ItemArray[0].ToString();
}
}
String[] dtaLines = lines.Split(new string[] { "\r\n" }, StringSplitOptions.RemoveEmptyEntries);
foreach (String line in dtaLines)
{
if (char.IsDigit(line, 0))
{
int sperator = line.IndexOf(" ");
string mz = line.Substring(0, sperator);
string intensity = line.Substring(sperator);
MZintensitiy mzi = new MZintensitiy();
try
{
mzi.mz = float.Parse(mz);
if (bZoomOut && DisplayMaxX != -1 && DisplayMinX != -1)
{
if (mzi.mz < DisplayMaxX && mzi.mz > DisplayMinX)
{
if (mzi.mz < MinX)
MinX = mzi.mz;
if (mzi.mz > MaxX)
MaxX = mzi.mz;
mzi.intensity = float.Parse(intensity);
if (mzi.intensity > MaxIntensitiy)
MaxIntensitiy = mzi.intensity;
SpectrumData.Add(mzi);
}
}
else
{
if (mzi.mz < MinX)
MinX = mzi.mz;
if (mzi.mz > MaxX)
MaxX = mzi.mz;
mzi.intensity = float.Parse(intensity);
if (mzi.intensity > MaxIntensitiy)
MaxIntensitiy = mzi.intensity;
SpectrumData.Add(mzi);
}
}
catch
{ }
}
}
DrawSpectrum();
}
}
}
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!");
}
protected void Page_Load(object sender, EventArgs e)
{
SpectrumData = new ArrayList();
if (Request.QueryString["file"] != null)
{
string file_path = Request.QueryString["file"];
if (Request.QueryString["mode"] != null)
{
if (Request.QueryString["mode"] == "ZoomOut")
{
string displayMin = Request.QueryString["xmin"];
string displayMax = Request.QueryString["xmax"];
string displayYMax = Request.QueryString["ymax"];
try
{
if (displayMin == null)
{
DisplayMinX = -1;
}
else
{
DisplayMinX = int.Parse(displayMin);
if (DisplayMinX < 0)
{
DisplayMinX = -1;
}
}
if (displayMax == null)
{
DisplayMaxX = -1;
}
else
{
DisplayMaxX = int.Parse(displayMax);
if (DisplayMaxX < 0 || DisplayMaxX <= DisplayMinX)
{
DisplayMaxX = -1;
}
}
}
catch
{
DisplayMaxX = -1;
DisplayMinX = -1;
}
if (DisplayMaxX != -1 && DisplayMinX != -1)
{
int Length = DisplayMaxX - DisplayMinX;
if (Length > 1000)
{
XBIGSEG = 250;
}
else if (Length > 500)
{
XBIGSEG = 100;
}
else if (Length > 200)
{
XBIGSEG = 50;
}
else if (Length > 100)
{
XBIGSEG = 25;
}
else if (Length > 50)
{
XBIGSEG = 10;
}
else if (Length > 20)
{
XBIGSEG = 5;
}
else
{
XBIGSEG = 2;
}
}
try
{
if (displayYMax == null)
{
DisplayMaxY = 100;
}
else
{
DisplayMaxY = int.Parse(displayYMax);
if (DisplayMaxY < 75 && DisplayMaxY > 30)
{
YBIGSEG = 10;
}
else if (DisplayMaxY <= 30 && DisplayMaxY > 20)
{
YBIGSEG = 5;
}
else if (DisplayMaxY >= 0 && DisplayMaxY <= 20)
{
YBIGSEG = 2;
}
else if (DisplayMaxY <= 100 && DisplayMaxY >= 75)
{
YBIGSEG = 25;
}
else
{
DisplayMaxY = 100;
YBIGSEG = 25;
}
}
}
catch (Exception ex)
{
DisplayMaxY = 100;;
}
bZoomOut = true;
}
else
{
bZoomOut = false;
}
}
if (Request.QueryString["Printable"] != null)
{
if (Request.QueryString["Printable"] == "True")
{
bShowLabel = true;
//HEIGHT = 250;
}
else
{
bShowLabel = false;
}
}
if (Request.QueryString["ShowTheory"] != null)
{
if (Request.QueryString["ShowTheory"] == "True")
{
bShowTheory = true;
}
else
{
bShowTheory = false;
}
}
PeptideSequence = Request.QueryString["SEQ"];
ChargeState = Request.QueryString["CS"];
PrecursorMZ = float.Parse(Request.QueryString["pmz"]);
mzTolerance = float.Parse(WebConfigurationManager.ConnectionStrings["mzTolerance"].ConnectionString);
if (true)//File.Exists(file_path))
{
//multiuser-fridendly streamreader
//FileStream fs = File.Open(file_path, FileMode.Open, FileAccess.Read, FileShare.ReadWrite );
//StreamReader sr = new StreamReader(fs);
string lines = "";
string strSQL;
if (file_path.Length < 10)
{
strSQL = string.Format("select spectrum from spectrum_tbl where spectrum_seq={0}", file_path);
}
else
{
strSQL = string.Format("select spectrum from spectrum_tbl where spectrum_seq={0}", "159268");
}
DataSet result = DBInterface.QuerySQL2(strSQL);
if (result != null)
{
if (result.Tables[0].Rows.Count > 0)
{
lines = result.Tables[0].Rows[0].ItemArray[0].ToString();
}
}
String[] dtaLines = lines.Split(new string[] { "\r\n" }, StringSplitOptions.RemoveEmptyEntries);
foreach (String line in dtaLines)
{
if (char.IsDigit(line, 0))
{
string[] tokens = line.Split(new string[] { " ", "\t" }, StringSplitOptions.RemoveEmptyEntries);
string mz = tokens[0];
string intensity = tokens[1];
MZintensitiy mzi = new MZintensitiy();
try
{
mzi.mz = float.Parse(mz);
if (bZoomOut && DisplayMaxX != -1 && DisplayMinX != -1)
{
if (mzi.mz < DisplayMaxX && mzi.mz > DisplayMinX)
{
if (mzi.mz < MinX)
{
MinX = mzi.mz;
}
if (mzi.mz > MaxX)
{
MaxX = mzi.mz;
}
mzi.intensity = float.Parse(intensity);
if (mzi.intensity > MaxIntensitiy)
{
MaxIntensitiy = mzi.intensity;
}
SpectrumData.Add(mzi);
}
}
else
{
if (mzi.mz < MinX)
{
MinX = mzi.mz;
}
if (mzi.mz > MaxX)
{
MaxX = mzi.mz;
}
mzi.intensity = float.Parse(intensity);
if (mzi.intensity > MaxIntensitiy)
{
MaxIntensitiy = mzi.intensity;
}
SpectrumData.Add(mzi);
}
}
catch
{ }
}
}
DrawSpectrum();
}
}
}
