private void LoadResultsV1Data(string dataFileName)
{
_saveStructsInMemory = true;
_dataInMemoryIsIncomplete = false;
ClearPeaksAndIso();
using (
var fin = new BinaryReader(new FileStream(dataFileName, FileMode.Open, FileAccess.Read, FileShare.Read))
)
{
_fileName = fin.ReadString();
var versionStr = fin.ReadString();
// how many peaks do we need to read ?
_numPeaksStored = fin.ReadInt32();
//var numRead = 0;
var totalRead = 0;
while (totalRead < _numPeaksStored)
{
var peak = LcmsPeak.ReadFromBinaryStream(fin);
if (_peaksList.Count + 1 > _peaksList.Capacity && _peaksList.Capacity > int.MaxValue / 2)
{
_peaksList.Capacity = int.MaxValue - 150;
}
_peaksList.Add(peak);
totalRead++;
}
var readTransforms = true;
if (readTransforms)
{
_numIsoStored = fin.ReadInt32();
while (_transforms.Count < _numIsoStored)
{
var record = new clsHornTransformResults(IsotopeFitRecord.ReadFromBinaryStream(fin));
if (_transforms.Count + 1 > _transforms.Capacity &&
_transforms.Capacity > int.MaxValue / 2)
{
_transforms.Capacity = int.MaxValue - 150;
}
_transforms.Add(record);
}
}
if (_numPeaksStored != 0)
{
_minScan = _peaksList[0].ScanNum;
_maxScan = _peaksList[_peaksList.Count - 1].ScanNum;
_lastScanAdded = _maxScan;
}
else
{
_minScan = _maxScan = _lastScanAdded = -1;
}
}
CreateIndexesOnData();
}
private void SaveResultsV1Iso(string isoFileName)
{
using (
var fout =
new StreamWriter(new FileStream(isoFileName, FileMode.Create, FileAccess.ReadWrite, FileShare.None))
)
{
//Preserve column headers for VIPER to load it in
fout.WriteLine("{0},{1},{2},{3},{4},{5},{6},{7},{8},{9},{10},{11}", "scan_num", "charge", "abundance",
"mz", "fit", "average_mw", "monoisotopic_mw", "mostabundant_mw", "fwhm", "signal_noise",
"mono_abundance", "mono_plus2_abundance");
if (_saveStructsInMemory && !_dataInMemoryIsIncomplete)
{
// write from stored data in _transforms
foreach (var record in _transforms)
{
fout.WriteLine("{0},{1},{2:F0},{3:F4},{4:F4},{5:F4},{6:F4},{7:F4},{8:F4},{9:F2},{10},{11}",
record.ScanNum, record.ChargeState, record.Abundance, record.Mz, record.Fit,
record.AverageMw, record.MonoMw, record.MostIntenseMw, record.FWHM, record.SignalToNoise,
record.MonoIntensity, record.MonoPlus2Intensity);
}
}
else
{
// Read in from stored file, little at a time and write it out;
_isoFile.Seek(0, SeekOrigin.Begin);
_isoFile.Flush();
if (!_isoFile.CanRead || _isoFile.Position != 0)
{
_isoFile.Close();
_isoFile = new FileStream(_tempIsoFilePath, FileMode.Create, FileAccess.ReadWrite,
FileShare.None);
}
_isoFile.Flush();
using (var bReader = new BinaryReader(_isoFile, Encoding.ASCII, true))
{
while (_isoFile.Position < _isoFile.Length)
{
var record = IsotopeFitRecord.ReadFromBinaryStream(bReader);
fout.WriteLine("{0},{1},{2},{3:F4},{4:F4},{5:F4},{6:F4},{7:F4},{8:F4},{9:F2},{10},{11}",
record.ScanNum, record.ChargeState, record.AbundanceInt, record.Mz, record.Fit,
record.AverageMw, record.MonoMw, record.MostIntenseMw, record.FWHM, record.SignalToNoise,
record.MonoIntensity, record.MonoPlus2Intensity);
}
}
_isoFile.Close();
}
}
}
internal clsHornTransformResults(IsotopeFitRecord fitRecord)
{
PeakIndex = fitRecord.PeakIndex;
ScanNum = fitRecord.ScanNum;
ChargeState = fitRecord.ChargeState;
//AbundanceInt = fitRecord.AbundanceInt;
Abundance = fitRecord.Abundance;
Mz = fitRecord.Mz;
Fit = fitRecord.Fit;
FitCountBasis = fitRecord.FitCountBasis;
AverageMw = fitRecord.AverageMw;
MonoMw = fitRecord.MonoMw;
MostIntenseMw = fitRecord.MostIntenseMw;
FWHM = fitRecord.FWHM;
SignalToNoise = fitRecord.SignalToNoise;
MonoIntensity = fitRecord.MonoIntensity;
MonoPlus2Intensity = fitRecord.MonoPlus2Intensity;
DeltaMz = fitRecord.DeltaMz;
for (var i = 0; i < fitRecord.NumIsotopesObserved; i++)
{
IsotopePeakIndices.Add(fitRecord.IsotopePeakIndices[i]);
}
}
