public bool LoadSettings(string FileLocation)
{
XmlSerializer mySerializer = null;
FileStream myFileStream = null;
bool fileExisits = false;
try
{
mySerializer = new XmlSerializer(typeof(SearchingParameters));
FileInfo fi = new FileInfo(FileLocation);
if (fi.Exists)
{
myFileStream = fi.OpenRead();
SearchingParameters mySetting = (SearchingParameters)mySerializer.Deserialize(myFileStream);
this._bOnlyTop1 = mySetting.OnlyTop1;
this._DefaultPossibility = mySetting.ConfidenceLevel;
this._DistinctPeptide = mySetting.DistinctPeptide;
this._LibraryModule = mySetting.LibraryModule;
this._PeptideTolerance = mySetting.Peptidetolerance;
this._PTMShift = mySetting.PTMShift;
this._ScoreCriteria = mySetting.ScoreCriteria;
this._SlideSize = mySetting.SlideSize;
this._UseNoiseLibrary = mySetting.UseNoiseLibrary;
this._UseStatisticalMode = mySetting.UseStatisticalMode;
this._PeptideToleranceHR = mySetting.PeptideToleranceHR;
this._IsotopePeaks = mySetting.IsotopePeaks;
this._HighResolution = mySetting.HighResolution;
this._UniquePeptide = mySetting.UniquePeptide;
this._bUsePTMModule = mySetting.UsePTMModule;
this._PTMType = mySetting.PTMType;
this._bCustomizedLibraryFDR = mySetting.CustomizedLibraryFDR;
this._LibraryFDR = mySetting.LibraryFDR;
this.SettingChanged = false;
fileExisits = true;
}
}
catch (Exception ex)
{ }
finally
{
if (myFileStream != null)
{
myFileStream.Close();
}
}
return(fileExisits);
}
void LoadSearchingCondition(string TaskID)
{
string scLocation = WebConfigurationManager.ConnectionStrings["UploadPath"].ConnectionString + TaskID + "\\searchcondition.xml";
this.con1.Text = scLocation;
FileInfo fi = new FileInfo(scLocation);
if (fi.Exists)
{
this.con3.Text = "enter";
SearchingParameters mySP = new SearchingParameters(scLocation);
if (mySP.HighResolution)
this.lbPeptideTolerance.Text = string.Format("{0}ppm consider {1} isotope peaks", mySP.PeptideToleranceHR, mySP.IsotopePeaks);
else
this.lbPeptideTolerance.Text = mySP.Peptidetolerance.ToString() + " Th (Da/e)";
this.lbSlideSize.Text = mySP.SlideSize.ToString();
if (mySP.UseNoiseLibrary)
this.lbIsUsingNoiseDecoy.Text = "True";
else
this.lbIsUsingNoiseDecoy.Text = "False";
if (mySP.BonusDetaMz)
this.lbBonusms.Text = "True";
else
this.lbBonusms.Text = "False";
if (mySP.UseStatisticalMode)
{
this.lbThreshold.Text = string.Format("{0}%", mySP.ConfidenceLevel * 100);
}
else
{
this.lbThreshold.Text = mySP.ScoreCriteria;
}
this.lbPeptideNumber.Text = mySP.DistinctPeptide.ToString();
}
else
{
this.con3.Text = "fail";
}
}
protected void btUpload_Click(object sender, EventArgs e)
{
//if (this.tbUserID.Text == "")
//{
// this.lbEmailMessage1.Text = "Required field.";
// return;
//}
//else
// this.lbEmailMessage1.Text = "*";
if (!this.RegularExpressionValidator2.IsValid || !this.RegularExpressionValidator1.IsValid)
{
return;
//validation group for mzMl or raw file
}
if (!cbUseURL.Checked && !this.InputFile1.HasFile)
return;
if (cbUseURL.Checked && this.tbURL.Text == "")
{
this.lbMessage.Text = "You need to upload a local file or provide the URL of a file in the web.";
return;
}
string FileName = "";
string SingleFileName = "";
if (cbUseURL.Checked)
{
FileName = this.tbURL.Text;
SingleFileName = FileName.Substring(FileName.LastIndexOf("/") + 1);
}
else
{
FileName = this.InputFile1.FileName;
SingleFileName = FileName;
}
string strSQL = "insert into search_task (task_user,upload_filename,search_model,report_filename) values ('{0}','{1}','{2}','{3}')";
string strReportName = SingleFileName.Substring(0, SingleFileName.LastIndexOf(".")) + ".txt";
strSQL = string.Format(strSQL, DBInterface.SQLValidString(this.tbUserID.Text), DBInterface.SQLValidString(FileName), this.ddlModels.Text, DBInterface.SQLValidString(strReportName));
//DBInterface.ConnectDB();
string taskID = "";
if (DBInterface.UpdateSQL(strSQL) > 0)
{
strSQL = "select task_seq from search_task where task_user='******' and upload_filename = '{1}' order by task_seq desc";
strSQL = string.Format(strSQL, DBInterface.SQLValidString(this.tbUserID.Text), DBInterface.SQLValidString(FileName));
IDataReader result = DBInterface.QuerySQL(strSQL);
if (result != null)
{
result.Read();
taskID = result.GetValue(0).ToString();
}
DBInterface.CloseDB();
string UploadPath = WebConfigurationManager.ConnectionStrings["UploadPath"].ConnectionString + taskID + "\\";
DirectoryInfo newpath = new DirectoryInfo(UploadPath);
if (!newpath.Exists)
{
newpath.Create();
}
if (!cbUseURL.Checked)
{
string TargeFile = UploadPath + FileName;
this.InputFile1.MoveTo(TargeFile, Brettle.Web.NeatUpload.MoveToOptions.Overwrite);
}
//***save the searching conditions in files***
SearchingParameters mySP = new SearchingParameters();
if (cbUseDefault.Checked)
{
mySP.ConfidenceLevel = 0.95F;
mySP.DistinctPeptide = 1;
mySP.LibraryModule = this.ddlModels.Text;
mySP.OnlyTop1 = true;
mySP.Peptidetolerance = 2;
mySP.PTMShift = 0;
mySP.SlideSize = 1;
mySP.ScoreCriteria = "|0;-1";
mySP.UseNoiseLibrary = true;
mySP.UseStatisticalMode = true;
mySP.HighResolution = false;
mySP.PeptideToleranceHR = 20;
mySP.IsotopePeaks = 2;
mySP.BonusDetaMz = false;
mySP.CustomizedLibraryFDR = false;
mySP.UniquePeptide = 0;
mySP.UsePTMModule = false;
}
else
{
try
{
mySP.ConfidenceLevel = float.Parse(this.ddl_Threshold.Text.Substring(0, this.ddl_Threshold.Text.Length - 1)) / 100;
if (mySP.ConfidenceLevel >= 1 || mySP.ConfidenceLevel <= 0)
{
lbMessage.Text = "The peptide confidence should be set in the range 0%-100%.";
return;
}
}
catch
{
lbMessage.Text = "The peptide confidence setting is out of range.";
return;
}
mySP.DistinctPeptide = int.Parse(this.ddl_DistinctPepties.Text);// sc.DistinctPeptide;
mySP.UniquePeptide = int.Parse(this.ddl_UniquePeptides.Text);
mySP.LibraryModule = this.ddlModels.Text;// GetModuleName(sc.searchModule);
mySP.OnlyTop1 = true;// sc.bOnlyTop1;
mySP.Peptidetolerance = float.Parse(this.ddl_PrecursorTolerance.Text);//sc.fPrecursorWindow;
mySP.PTMShift = float.Parse(this.ddl_PTMshift.Text);// sc.fPTMShift;
string Criterias = "|0;-1";
//foreach (SearchingThreadPair stp in sc.NormalSearchCondition)
//{
// Criterias += string.Format("|{0};{1}", stp.MatchScore, stp.DetaDecoyScore);
//}
mySP.ScoreCriteria = Criterias;
mySP.SlideSize = int.Parse(this.ddl_SlideSize.Text);// sc.iSlideSize;
mySP.UseNoiseLibrary = this.cbUseNDP.Checked;// sc.bUseNoiseLibrary;
mySP.UseStatisticalMode = true;// sc.bStatisticSearching;
mySP.HighResolution = this.cbHighResolution.Checked;
mySP.PeptideToleranceHR = float.Parse(this.ddlHRPrecursorTolerance.Text);
mySP.IsotopePeaks = int.Parse(this.ddlIsotopePeaks.Text);
mySP.BonusDetaMz = this.cbBonusMS.Checked;
mySP.CustomizedLibraryFDR = false;
mySP.UsePTMModule = false;
}
string sclocation = UploadPath + "searchcondition.xml";
mySP.SaveSettings(sclocation);
//*****************************************
strSQL = "update search_task set task_status=1 where task_seq=" + taskID;
if (DBInterface.UpdateSQL(strSQL) > 0)
{
if (cbUseURL.Checked)
{
informationShow.Text = @"<div id='helpNote' class='collapse'>";
informationBtn.Text = @"<button type='button' class='close button collapsed' data-toggle='collapse' data-target='#helpNote'>×</button>";
lbMessage.Text = "You URL resource has been submitted. The task ID is <a href=\"SearchReport.aspx?QType=" + this.tbUserID.Text + "&QValue=" + taskID + "\" style=\"font-size: large; color: #FF0000\" >" + taskID + "</a>.";
//this.cbUseURL.Checked = false;
}
else
{
lbMessage.Text = "You mzML file has been successfully uploaded. The task ID is <a href=\"SearchReport.aspx?QType=" + this.tbUserID.Text + "&QValue=" + taskID + "\" style=\"font-size: large; color: #FF0000\" >" + taskID + "</a>.";
}
}
}
}
void UpdateSearchingCondition(string TaskID, float confidence, int distinctPeptides, int UniquePeptides)
{
string scLocation = WebConfigurationManager.ConnectionStrings["UploadPath"].ConnectionString + TaskID + "\\searchcondition.xml";
FileInfo fi = new FileInfo(scLocation);
if (fi.Exists)
{
SearchingParameters mySP = new SearchingParameters(scLocation);
mySP.ConfidenceLevel = confidence;
mySP.DistinctPeptide = distinctPeptides;
mySP.UniquePeptide = UniquePeptides;
mySP.SaveSettings();
}
COPaWS.COPaWS copaws = new COPaWS.COPaWS();
if (copaws.ChangeCreteria(TaskID, this.lbmzML.Text.Replace("<br/>", "\r\n")))
Response.Redirect(string.Format("Report.aspx?TaskID={0}", TaskID));
}
int UpdateSearchConditionFile(string TaskID, float newPossibility)
{
string scLocation = WebConfigurationManager.ConnectionStrings["UploadPath"].ConnectionString + TaskID + "\\searchcondition.xml";
FileInfo fi = new FileInfo(scLocation);
if (fi.Exists)
{
SearchingParameters mySP = new SearchingParameters(scLocation);
mySP.ConfidenceLevel = newPossibility / 100;
mySP.SaveSettings(scLocation);
return mySP.DistinctPeptide;
}
return 1;
}
