private static LookupCollection RawFilesinFrame(binFrame frame, out int nRawfiles)
{
//Need the Rawfile names
LookupCollection rawFilesColl = new LookupCollection();
string rawFileName;
nRawfiles = 0;
for (int i = frame.scan.GetLowerBound(0); i <= frame.scan.GetUpperBound(0); i++)
{
if (frame.scan[i].rawFileName != null)
{
rawFileName = frame.scan[i].rawFileName.Trim();
if (!rawFilesColl.Contains(rawFileName))
{
int initScansNum = 1;
rawFilesColl.Add(rawFileName, initScansNum);
}
else
{
int oneMore = (int)rawFilesColl[rawFileName] + 1;
rawFilesColl[rawFileName] = oneMore;
}
}
}
nRawfiles = rawFilesColl.Count;
return(rawFilesColl);
}
public static binFrame genFrame(binStack[] stackIndex, int frame, int scansbyframe, string rawPath, string spectrumType, string spectrumPosition)
{
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;
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;
break;
}
}
}
}
}
}
for (int i = 0; i < nRawsinFrame; i++)
{
int[] scansRawList = new int[tRawList[i].scan.GetLength(0)];
for (int j = 0; j <= scansRawList.GetUpperBound(0); j++)
{
scansRawList[j] = tRawList[i].scan[j].scanNumber; //These are the MSMS identified spectra
}
int t = tRawList[i].size();
string rawFileName = tRawList[i].rawFile;
DA_raw daRaw1 = new DA_raw();
Comb.mzI[][] scansRaw = daRaw1.ReadScanRaw(rawPath, rawFileName, scansRawList, spectrumType, spectrumPosition);
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].scanNumber == tRawList[j].scan[k].scanNumber)
{
currFrame.scan[i].spectrum = tRawList[j].scan[k].spectrum;
break;
}
}
break;
}
}
}
}
return(currFrame);
}
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);
}
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);
}