public static binStack[] genIndex(DataView _quiXMLv,
string rawPath,
int scansbyframe,
BinStackOptions options)
{
int numMatches = _quiXMLv.Count;
int numFrames = countFrames(_quiXMLv, scansbyframe);
int numRawFiles;
//LookupCollection RawFilesColl = countRawFiles(fileXml, out numRawFiles);
LookupCollection RawFilesColl = countRawFiles(_quiXMLv, out numRawFiles);
//create index
binStack[] stackIndex = new binStack[numRawFiles];
//fill rawfilenames in the index
ArrayList rawFilesKeys = (ArrayList)RawFilesColl.Keys;
ArrayList rawFilesValues = (ArrayList)RawFilesColl.Values;
for (int i = 0; i < numRawFiles; i++)
{
stackIndex[i] = new binStack((int)rawFilesValues[i]);
stackIndex[i].rawFileName = rawFilesKeys[i].ToString();
}
fillScans(stackIndex, _quiXMLv, options);
//share out the spectra amongst the frames
int currFrame = 1;
int currScanofFrame = 1;
for (int i = 0; i < numRawFiles; i++)
{
for (int j = 0; j <= stackIndex[i].scan.GetUpperBound(0); j++)
{
stackIndex[i].scan[j].frame = currFrame;
currScanofFrame++;
if (currScanofFrame > scansbyframe)
{
currFrame++;
currScanofFrame = 1;
}
}
}
//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).
return(stackIndex);
}
private static void fillScans(binStack[] stackIndex,
DataView dv,
BinStackOptions options)
{
double protonMass = 1.007276466812; // source: http://physics.nist.gov/cgi-bin/cuu/Value?mpu
//associate the dataset to a dataview
string filter = "";
scanIndexStrt newScan = new scanIndexStrt();
int spectrumIndex = 0;
for (int i = 0; i <= stackIndex.GetUpperBound(0); i++)
{
filter = "RAWFileName = '" + stackIndex[i].rawFileName.Trim() + "'";
dv.RowFilter = filter;
for (int j = 0; j < dv.Count; j++)
{
int firstScan = int.Parse(dv[j]["FirstScan"].ToString());
newScan.scanNumbers[0] = firstScan;
newScan.FirstScan = firstScan;
newScan.spectrumIndex = spectrumIndex;
dv[j]["spectrumIndex"] = spectrumIndex;
if (!(options.averagingMethod == averagingMethod.mostIntense ||
options.averagingMethod == averagingMethod.none))
{
newScan.peakStart = int.Parse(dv[j]["PeakStart"].ToString());
newScan.peakEnd = int.Parse(dv[j]["PeakEnd"].ToString());
}
spectrumIndex++;
if (options.useParentalMass)
{
try
{
int charge = int.Parse(dv[j]["Charge"].ToString());
newScan.parentMass = double.Parse(dv[j]["PrecursorMass"].ToString());
newScan.parentMass = (newScan.parentMass + (charge - 1) * protonMass) / charge;
}
catch { }
}
stackIndex[i].insert(newScan);
}
}
}
private void createBinStackBtn_Click(object sender, EventArgs e)
{
options = new BinStackOptions();
if (quiXMLtxt.Text.Trim() == "")
{
MessageBox.Show("No QuiXML selected", "Error");
return;
}
if (schemaTxt.Text.Trim() == "")
{
MessageBox.Show("No QuiXML schema selected", "Error");
return;
}
if (specFolderTxt.Text.Trim() == "")
{
MessageBox.Show("No spectra folder selected", "Error");
return;
}
//if (specTypeBox.Text.Trim() == "")
//{
// MessageBox.Show("No spectrum type selected", "Error");
// return;
//}
//if (posBox.Text == "")
//{
// MessageBox.Show("No spectrum position selected", "Error");
// return;
//}
if (parentalMassChb.Checked && parentalMassTxt.Text == "")
{
MessageBox.Show("No parental mass selected", "Error");
return;
}
options.mode = adquisitionMode.position;
//foreach (spectrumPositions sp in specPositionsChoose)
//{
// if (posBox.Text == sp.ToString())
// {
// options.spectrumPos = sp;
// break;
// }
//}
options.spectrumPos = spectrumPositions.same;
//foreach (spectrumTypes spt in spectrumTypesChoose)
//{
// if (specTypeBox.Text == spt.ToString())
// {
// options.spectrumType = spt;
// break;
// }
//}
options.spectrumType = spectrumTypes.ZoomScan;
if (parentalMassChb.Checked)
{
options.useParentalMass = true;
foreach (massUnits mu in massUnitsChoose)
{
if (massUnitsCmb.Text == mu.ToString())
{
options.parentalMassUnits = mu;
break;
}
}
try
{
options.parentalMass = float.Parse(parentalMassTxt.Text.Trim(), CultureInfo.InvariantCulture.NumberFormat);
}
catch
{
MessageBox.Show("Parental mass is not valid (not a number)", "Error");
return;
}
}
int scannumber = 0;
bool tryScanNumber = int.TryParse(scanNumberResTxt.Text, out scannumber);
if (!tryScanNumber)
{
MessageBox.Show("Scan number is not an integer!", "Error");
return;
}
options.individualRow = false;
options.split_chars = (char[])split_chars.Clone();
options.scanField = scanField;
genStack(specFolderTxt.Text.Trim(), options);
}
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!!");
}
public static binFrame genFrame(binStack[] stackIndex, int frame, int scansbyframe, string rawPath, BinStackOptions options)
{
binFrame currFrame = new binFrame(scansbyframe);
currFrame.frame = frame;
int currScanofFrame = 0;
for (int j = 0; j <= stackIndex.GetUpperBound(0); j++)
{
for (int k = 0; k <= stackIndex[j].scan.GetUpperBound(0); k++)
{
if (currFrame.frame == stackIndex[j].scan[k].frame)
{
currFrame.scan[currScanofFrame].rawFileName = stackIndex[j].rawFileName;
currFrame.scan[currScanofFrame].scanNumber = stackIndex[j].scan[k].FirstScan;
currFrame.scan[currScanofFrame].parentMass = stackIndex[j].scan[k].parentMass;
currFrame.scan[currScanofFrame].spectrumIndex = stackIndex[j].scan[k].spectrumIndex;
currScanofFrame++;
}
}
}
int nRawsinFrame;
LookupCollection rawsinFrame = RawFilesinFrame(currFrame, out nRawsinFrame);
DA_raws[] tRawList = new DA_raws[nRawsinFrame];
ArrayList rawFilesKeys = (ArrayList)rawsinFrame.Keys;
ArrayList rawFilesValues = (ArrayList)rawsinFrame.Values;
for (int i = 0; i < nRawsinFrame; i++)
{
tRawList[i] = new DA_raws((int)rawFilesValues[i]);
tRawList[i].rawFile = rawFilesKeys[i].ToString();
for (int j = tRawList[i].scan.GetLowerBound(0); j <= tRawList[i].scan.GetUpperBound(0); j++)
{
tRawList[i].scan[j].rawFileName = rawFilesKeys[i].ToString();
}
}
for (int i = 0; i <= currFrame.scan.GetUpperBound(0); i++)
{
for (int j = tRawList.GetLowerBound(0); j <= tRawList.GetUpperBound(0); j++)
{
if (currFrame.scan[i].rawFileName != null)
{
if (currFrame.scan[i].rawFileName.Trim() == tRawList[j].rawFile.Trim())
{
for (int k = tRawList[j].scan.GetLowerBound(0); k <= tRawList[j].scan.GetUpperBound(0); k++)
{
if (tRawList[j].scan[k].scanNumber == 0)
{
tRawList[j].scan[k].scanNumber = currFrame.scan[i].scanNumber;
tRawList[j].scan[k].parentMass = currFrame.scan[i].parentMass;
tRawList[j].scan[k].spectrumIndex = currFrame.scan[i].spectrumIndex;
break;
}
}
}
}
}
}
for (int i = 0; i < nRawsinFrame; i++)
{
int[] scansRawList = new int[tRawList[i].scan.GetLength(0)];
double[] parentMassList;
if (options.useParentalMass)
{
parentMassList = new double[tRawList[i].scan.GetLength(0)];
}
else
{
parentMassList = null;
}
for (int j = 0; j <= scansRawList.GetUpperBound(0); j++)
{
scansRawList[j] = tRawList[i].scan[j].scanNumber; //These are the MSMS identified spectra
if (options.useParentalMass)
{
parentMassList[j] = tRawList[i].scan[j].parentMass;
}
}
int t = tRawList[i].size();
string rawFileName = tRawList[i].rawFile;
DA_raw daRaw1 = new DA_raw();
Comb.mzI[][] scansRaw = daRaw1.ReadScanRaw(rawPath, rawFileName, scansRawList, parentMassList, options);
daRaw1 = null;
for (int j = 0; j <= scansRawList.GetUpperBound(0); j++)
{
if (scansRaw[j] != null)
{
tRawList[i].scan[j].spectrum = (Comb.mzI[])scansRaw[j];
tRawList[i].scan[j].rawFileName = tRawList[i].rawFile;
}
}
}
for (int i = currFrame.scan.GetLowerBound(0); i <= currFrame.scan.GetUpperBound(0); i++)
{
for (int j = tRawList.GetLowerBound(0); j <= tRawList.GetUpperBound(0); j++)
{
if (currFrame.scan[i].rawFileName != null)
{
if (currFrame.scan[i].rawFileName.Trim() == tRawList[j].rawFile.Trim())
{
for (int k = tRawList[j].scan.GetLowerBound(0); k <= tRawList[j].scan.GetUpperBound(0); k++)
{
if (currFrame.scan[i].spectrumIndex == tRawList[j].scan[k].spectrumIndex)
{
currFrame.scan[i].spectrum = tRawList[j].scan[k].spectrum;
break;
}
}
break;
}
}
}
}
//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 = currFrame.scan.GetLowerBound(0); i <= currFrame.scan.GetUpperBound(0); i++)
{
int scanNumber_t = currFrame.scan[i].scanNumber;
currFrame.scan[i].scanNumber = currFrame.scan[i].spectrumIndex;
//this is not necessary, but I want to maintain the scanNumber elsewhere...
currFrame.scan[i].spectrumIndex = scanNumber_t;
}
return(currFrame);
}
private static void fillScans(binStack[] stackIndex, string fileXml, string schemaFile, BinStackOptions options)
{
DataSet ds = new DataSet();
ds.ReadXmlSchema(schemaFile);
ds.ReadXml(fileXml);
DataView dv = new DataView(ds.Tables["peptide_match"]);
scanIndexStrt newScan = new scanIndexStrt();
int spectrumIndex = 1;
for (int i = 0; i <= stackIndex.GetUpperBound(0); i++)
{
for (int j = 0; j < dv.Count; j++)
{
String RAWfilename = dv[j]["RAWFileName"].ToString().Trim();
if (RAWfilename == stackIndex[i].rawFileName.Trim())
{
int firstscan = int.Parse(dv[j]["FirstScan"].ToString(), CultureInfo.InvariantCulture.NumberFormat);
newScan.FirstScan = firstscan;
newScan.spectrumIndex = spectrumIndex;
dv[j]["spectrumIndex"] = spectrumIndex;
if (options.useParentalMass)
{
try
{
int charge = int.Parse(dv[j]["Charge"].ToString(), CultureInfo.InvariantCulture.NumberFormat);
newScan.parentMass = (double)dv[j]["PrecursorMass"];
newScan.parentMass = (newScan.parentMass + charge) / charge;
}
catch { }
}
stackIndex[i].insert(newScan);
spectrumIndex++;
}
}
}
//Save the QuiXML with the new index (spectrumIndex)
DataSet dsSave = new DataSet();
dsSave = ds.Copy();
try
{
dsSave.WriteXml(fileXml);
}
catch
{
FileInfo f = new FileInfo(fileXml);
string quiXMLfilenew = f.DirectoryName + "\\" + f.Name + "_binStackProcessed" + f.Extension;
dsSave.WriteXml(quiXMLfilenew);
}
}
public static binStack[] genIndex(string fileXml, string schemaFile, string rawPath, int scansbyframe, BinStackOptions options)
{
int numMatches = countMatches(fileXml);
int numFrames = countFrames(fileXml, scansbyframe);
int numRawFiles;
LookupCollection RawFilesColl = countRawFiles(fileXml, out numRawFiles);
//create index
binStack[] stackIndex = new binStack[numRawFiles];
//fill rawfilenames in the index
ArrayList rawFilesKeys = (ArrayList)RawFilesColl.Keys;
ArrayList rawFilesValues = (ArrayList)RawFilesColl.Values;
for (int i = 0; i < numRawFiles; i++)
{
stackIndex[i] = new binStack((int)rawFilesValues[i]);
stackIndex[i].rawFileName = rawFilesKeys[i].ToString();
}
fillScans(stackIndex, fileXml, schemaFile, options);
//share out the spectra amongst the frames
int currFrame = 1;
int currScanofFrame = 1;
for (int i = 0; i < numRawFiles; i++)
{
for (int j = 0; j <= stackIndex[i].scan.GetUpperBound(0); j++)
{
stackIndex[i].scan[j].frame = currFrame;
currScanofFrame++;
if (currScanofFrame > scansbyframe)
{
currFrame++;
currScanofFrame = 1;
}
}
}
return(stackIndex);
}
public static binFrame genFrame(binStack[] stackIndex,
int frame,
int scansbyframe,
string rawPath,
BinStackOptions options,
Label _status,
ref object _parObject,
int currNumFrame,
int totNumFrames)
{
binFrame currFrame = new binFrame(scansbyframe);
currFrame.frame = frame;
int currScanofFrame = 0;
for (int j = 0; j <= stackIndex.GetUpperBound(0); j++)
{
for (int k = 0; k <= stackIndex[j].scan.GetUpperBound(0); k++)
{
if (currFrame.frame == stackIndex[j].scan[k].frame)
{
currFrame.scan[currScanofFrame].rawFileName = stackIndex[j].rawFileName;
currFrame.scan[currScanofFrame].scanNumber = stackIndex[j].scan[k].FirstScan;
currFrame.scan[currScanofFrame].parentMass = stackIndex[j].scan[k].parentMass;
currFrame.scan[currScanofFrame].spectrumIndex = stackIndex[j].scan[k].spectrumIndex;
currFrame.scan[currScanofFrame].peakStart = stackIndex[j].scan[k].peakStart;
currFrame.scan[currScanofFrame].peakEnd = stackIndex[j].scan[k].peakEnd;
currScanofFrame++;
}
}
}
int nRawsinFrame;
LookupCollection rawsinFrame = RawFilesinFrame(currFrame, out nRawsinFrame);
DA_raws[] tRawList = new DA_raws[nRawsinFrame];
ArrayList rawFilesKeys = (ArrayList)rawsinFrame.Keys;
ArrayList rawFilesValues = (ArrayList)rawsinFrame.Values;
for (int i = 0; i < nRawsinFrame; i++)
{
tRawList[i] = new DA_raws((int)rawFilesValues[i]);
tRawList[i].rawFile = rawFilesKeys[i].ToString();
for (int j = tRawList[i].scan.GetLowerBound(0); j <= tRawList[i].scan.GetUpperBound(0); j++)
{
tRawList[i].scan[j].rawFileName = rawFilesKeys[i].ToString();
}
}
for (int i = 0; i <= currFrame.scan.GetUpperBound(0); i++)
{
for (int j = tRawList.GetLowerBound(0); j <= tRawList.GetUpperBound(0); j++)
{
if (currFrame.scan[i].rawFileName != null)
{
if (currFrame.scan[i].rawFileName.Trim() == tRawList[j].rawFile.Trim())
{
for (int k = tRawList[j].scan.GetLowerBound(0); k <= tRawList[j].scan.GetUpperBound(0); k++)
{
if (tRawList[j].scan[k].scanNumber == 0)
{
tRawList[j].scan[k].rawFileName = currFrame.scan[i].rawFileName;
tRawList[j].scan[k].scanNumber = currFrame.scan[i].scanNumber;
tRawList[j].scan[k].parentMass = currFrame.scan[i].parentMass;
tRawList[j].scan[k].spectrumIndex = currFrame.scan[i].spectrumIndex;
tRawList[j].scan[k].peakStart = currFrame.scan[i].peakStart;
tRawList[j].scan[k].peakEnd = currFrame.scan[i].peakEnd;
break;
}
}
}
}
}
}
// gets spectra (added to tRawList)
for (int i = 0; i < nRawsinFrame; i++)
{
int[] firstScans = new int[tRawList[i].scan.GetLength(0)];
int[] peakStarts = new int[tRawList[i].scan.GetLength(0)];
int[] peakEnds = new int[tRawList[i].scan.GetLength(0)];
double[] parentMassList;
if (options.useParentalMass)
{
parentMassList = new double[tRawList[i].scan.GetLength(0)];
}
else
{
parentMassList = null;
}
for (int j = 0; j <= firstScans.GetUpperBound(0); j++)
{
firstScans[j] = tRawList[i].scan[j].scanNumber; //These are the MSMS identified spectra
if (!(options.averagingMethod == averagingMethod.mostIntense ||
options.averagingMethod == averagingMethod.none))
{
peakStarts[j] = tRawList[i].scan[j].peakStart;
peakEnds[j] = tRawList[i].scan[j].peakEnd;
}
if (options.useParentalMass)
{
parentMassList[j] = tRawList[i].scan[j].parentMass;
}
}
int t = tRawList[i].size();
string rawFileName = tRawList[i].rawFile;
DA_raw daRaw1 = new DA_raw();
// reads raws, and saves spectra to scansRaw
Comb.mzI[][] scansRaw = daRaw1.ReadScanRaw(rawPath,
rawFileName,
firstScans,
peakStarts,
peakEnds,
parentMassList,
options,
_status,
ref _parObject,
currNumFrame,
totNumFrames);
//Comb.mzI[][] scansRaw = null;
if (scansRaw == null)
{
return(null);
}
daRaw1 = null;
for (int j = 0; j <= firstScans.GetUpperBound(0); j++)
{
if (scansRaw[j] != null)
{ // transfers spectra from scansRaw to tRawList
tRawList[i].scan[j].spectrum = (Comb.mzI[])scansRaw[j];
tRawList[i].scan[j].rawFileName = tRawList[i].rawFile;
}
}
}
// adds spectra to currFrame
for (int i = currFrame.scan.GetLowerBound(0); i <= currFrame.scan.GetUpperBound(0); i++)
{
for (int j = tRawList.GetLowerBound(0); j <= tRawList.GetUpperBound(0); j++)
{
if (currFrame.scan[i].rawFileName != null)
{
if (currFrame.scan[i].rawFileName.Trim() == tRawList[j].rawFile.Trim())
{
for (int k = tRawList[j].scan.GetLowerBound(0); k <= tRawList[j].scan.GetUpperBound(0); k++)
{
if (currFrame.scan[i].spectrumIndex == tRawList[j].scan[k].spectrumIndex) //Bug corrected: currFrame.scan[i].scanNumber == tRawList[j].scan[k].scanNumber
{
currFrame.scan[i].spectrum = tRawList[j].scan[k].spectrum;
break;
}
}
break;
}
}
}
}
//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 = currFrame.scan.GetLowerBound(0); i <= currFrame.scan.GetUpperBound(0); i++)
{
int scanNumber_t = currFrame.scan[i].scanNumber;
currFrame.scan[i].scanNumber = currFrame.scan[i].spectrumIndex;
//this is not necessary, but I want to maintain the scanNumber elsewhere...
currFrame.scan[i].spectrumIndex = scanNumber_t;
}
return(currFrame);
}
