private void genStack(string rawPath,
BinStackOptions options)
{
Application.DoEvents();
string schemaFile = schemaTxt.Text.Trim();
try
{
this.statusLabel.Text = "Generating binaries stack... Creating index...";
this.statusLabel.Visible = true;
string idFileXml = this.quiXMLtxt.Text.Trim();
string stackIndexFolder = idFileXml.Substring(0, idFileXml.LastIndexOf(@"\")) + "\\binStack\\";
string stackIndexFile = stackIndexFolder + "index.idx";
if (!Directory.Exists(stackIndexFolder))
{
Directory.CreateDirectory(stackIndexFolder);
}
//scans by frame
int scbyframe = 100;
//calculate number of frames
int inumFrames = binStack.countFrames(idFileXml, scbyframe);
//MessageBox.Show(inumFrames.ToString());
//generate index
binStack[] stackIndex = binStack.genIndex(idFileXml, schemaFile, rawPath, scbyframe, options);
//Dangerous thing: we swap the values of FirstScan and spectrumIndex at the binStack
//generate and save frames
for (int i = 1; i <= inumFrames; i++)
{
Application.DoEvents();
this.statusLabel.Text = "Generating binaries stack... generating frame " + i.ToString() + "/" + inumFrames.ToString();
binFrame currFrame = binStack.genFrame(stackIndex, i, scbyframe, rawPath, options);
string frameFile = stackIndexFolder + currFrame.frame.ToString() + ".bfr";
FileStream qFr = new FileStream(frameFile, FileMode.Create, FileAccess.Write);
BinaryFormatter bFr = new BinaryFormatter();
bFr.Serialize(qFr, currFrame);
qFr.Close();
}
//Save index
//WARNING: very dangerous change, but necessary to maintain old binstacks: in currFrame
// we swap the values of scanNumber by spectrumIndex (once we have obtained the desired
// spectrum, we use the unique index (spectrumIndex).
for (int i = stackIndex.GetLowerBound(0); i <= stackIndex.GetUpperBound(0); i++)
{
for (int j = stackIndex[i].scan.GetLowerBound(0); j <= stackIndex[i].scan.GetUpperBound(0); j++)
{
int scanNumber_t = stackIndex[i].scan[j].FirstScan;
stackIndex[i].scan[j].FirstScan = stackIndex[i].scan[j].spectrumIndex;
//this is not necessary, but I want to maintain the scanNumber elsewhere...
stackIndex[i].scan[j].spectrumIndex = scanNumber_t;
}
}
FileStream q = new FileStream(stackIndexFile, FileMode.Create, FileAccess.Write);
BinaryFormatter b = new BinaryFormatter();
b.Serialize(q, stackIndex);
q.Close();
}
catch
{
MessageBox.Show("Unable to generate binaries stack");
this.statusLabel.Text = "";
this.statusLabel.Visible = false;
return;
}
this.statusLabel.Text = "";
this.statusLabel.Visible = false;
MessageBox.Show("BinStack successfully created!!");
}
private void genStack(string rawPath,
BinStackOptions options)
{
Application.DoEvents();
try
{
this.lblStatus.Text = "Generating binaries stack... Creating index...";
this.lblStatus.Visible = true;
string idFileXml = this.tbxQuiXML.Text.Trim();
string idSchema = this.tbxSchema.Text.Trim();
string stackIndexFolder = idFileXml.Substring(0, idFileXml.LastIndexOf(@"\")) + "\\binStack\\";
string stackIndexFile = stackIndexFolder + "index.idx";
if (!Directory.Exists(stackIndexFolder))
{
Directory.CreateDirectory(stackIndexFolder);
}
//scans by frame
int scbyframe = 100;
//load the XML file to a DataSet object
DataSet quiXML = new DataSet();
quiXML.ReadXmlSchema(idSchema);
quiXML.ReadXml(idFileXml, XmlReadMode.Auto);
DataView quiXMLv = new DataView(quiXML.Tables["peptide_match"]);
if (!(options.averagingMethod == averagingMethod.mostIntense ||
options.averagingMethod == averagingMethod.none))
{
if (!quiXMLv.Table.Columns.Contains("PeakStart") ||
!quiXMLv.Table.Columns.Contains("PeakEnd"))
{
MessageBox.Show("This QuiXML file does not seem" +
"to contain PeakStart / PeakEnd columns,\n" +
"did you forget to use QuiXtoQuiX to get the inflection points?");
lblStatus.Text = "Error: no inflection points in QuiXML.";
return;
}
}
//calculate number of frames
//int inumFrames = binStack.countFrames(idFileXml, scbyframe);
int inumFrames = binStack.countFrames(quiXMLv, scbyframe);
//generate index
object parObject = "";
binStack[] stackIndex = binStack.genIndex(quiXMLv,
rawPath,
scbyframe,
options);
//generate and save frames
for (int i = 1; i <= inumFrames; i++)
{
Application.DoEvents();
this.lblStatus.Text = "Generating binaries stack... generating frame " + i.ToString() + "/" + inumFrames.ToString();
binFrame currFrame = binStack.genFrame(stackIndex,
i, scbyframe, rawPath, options, this.lblStatus, ref parObject, i, inumFrames);
if (currFrame == null)
{
return;
}
string frameFile = stackIndexFolder + currFrame.frame.ToString() + ".bfr";
FileStream qFr = new FileStream(frameFile, FileMode.Create, FileAccess.Write);
BinaryFormatter bFr = new BinaryFormatter();
bFr.Serialize(qFr, currFrame);
qFr.Close();
}
//save index
//WARNING: very dangerous change, but necessary to maintain old binstacks: in currFrame
// we swap the values of scanNumber by spectrumIndex (once we have obtained the desired
// spectrum, we use the unique index (spectrumIndex).
for (int i = stackIndex.GetLowerBound(0); i <= stackIndex.GetUpperBound(0); i++)
{
for (int j = stackIndex[i].scan.GetLowerBound(0); j <= stackIndex[i].scan.GetUpperBound(0); j++)
{
int scanNumber_t = stackIndex[i].scan[j].FirstScan;
stackIndex[i].scan[j].FirstScan = stackIndex[i].scan[j].spectrumIndex;
//this is not necessary, but I want to maintain the scanNumber elsewhere...
stackIndex[i].scan[j].spectrumIndex = scanNumber_t;
}
}
FileStream q = new FileStream(stackIndexFile, FileMode.Create, FileAccess.Write);
BinaryFormatter b = new BinaryFormatter();
b.Serialize(q, stackIndex);
q.Close();
string bsXml = Path.GetDirectoryName(idFileXml) + "\\" +
Path.GetFileNameWithoutExtension(idFileXml) + "_bs.xml";
//Save the quiXML changes (spectrumIndex is now written)
quiXML.WriteXml(bsXml);
MessageBox.Show("In order to preserve the old QuiXML, " +
"the new QuiXML containing the spectrumIndex has been saved to:\n\n" +
bsXml + "\n\n" + "Please, remember to use this new QuiXML or its derivations in further analysis.");
}
catch (System.Data.DataException e)
{
MessageBox.Show("Unable to generate binaries stack. System Data Exception thrown : " + e.Message);
}
catch
{
MessageBox.Show("Unable to generate binaries stack");
}
this.lblStatus.Text = "";
this.lblStatus.Visible = false;
}
