public override void ImportPeaks(List <DeconTools.Backend.DTO.MSPeakResult> peakList)
{
this.m_peakIndex = 0;
var oldPeakResults = new DeconToolsV2.Results.clsTransformResults();
Engine.Results.LcmsPeak[] importedPeaks = null;
try
{
oldPeakResults.ReadResults(this.m_filename);
oldPeakResults.GetRawData(out importedPeaks);
}
catch (Exception ex)
{
throw ex;
}
foreach (var p in importedPeaks)
{
var peak = ConvertDecon2LSPeakToPeakResult(p);
m_peakIndex++;
peakList.Add(peak);
}
}
private void mmnuOpenResults_Click(object sender, System.EventArgs e)
{
try
{
var openFileDialog1 = new OpenFileDialog();
openFileDialog1.Filter = "Raw Peak Files (*.dat)|*.dat";
openFileDialog1.FilterIndex = 1;
openFileDialog1.RestoreDirectory = true;
openFileDialog1.InitialDirectory = mobj_config.OpenDir;
if (openFileDialog1.ShowDialog() == DialogResult.OK)
{
var file_name = openFileDialog1.FileName;
var index = file_name.LastIndexOf("\\");
var path_dir = "";
if (index > 0)
{
path_dir = file_name.Substring(0, index);
mobj_config.OpenDir = path_dir;
}
var transformResults = new DeconToolsV2.Results.clsTransformResults();
transformResults.ReadResults(file_name);
var frmTwoD = new frm2DPeakProcessing(transformResults);
frmTwoD.HornTransformParameters = mobjTransformParameters;
frmTwoD.PeakProcessorParameters = mobjPeakParameters;
frmTwoD.FTICRPreProcessOptions = mobjFTICRRawPreProcessParameters;
mMediator.RequestFormOpen(frmTwoD);
}
}
catch (Exception ex)
{
MessageBox.Show(ex.ToString());
}
}
public frm2DPeakProcessing(DeconToolsV2.Results.clsTransformResults results)
{
//
// Required for Windows Form Designer support
//
InitializeComponent();
//
// TODO: Add any constructor code after InitializeComponent call
//
Init();
SetData(results);
}
public void WriteFile(string file_name, DeconToolsV2.Results.clsTransformResults results,
Peaks.clsPeakProcessorParameters peak_parameters,
HornTransform.clsHornTransformParameters transform_parameters)
{
using (var file = new StreamWriter(new FileStream(file_name, FileMode.Create, FileAccess.Write)))
{
// Write out descriptors. Some information is unavailable for now.
// i.e. what is the start position of the peaks data block and
// the transform data block. Fill in place holders for now.
// Once the data is actually written out, we can return to the stream and
// write it.
float version_num = 1;
file.Write("<Version>" + version_num + "</version>");
WritePeakParameters(file, peak_parameters);
WriteTransformParameters(file, transform_parameters);
WritePeaks(file, results);
}
}
private void WritePeaks(StreamWriter file, DeconToolsV2.Results.clsTransformResults results)
{
var num_peaks = results.GetNumPeaks();
file.Write("<PeakResults><NumPeaks>" + num_peaks + "</NumPeaks>");
file.Write("<Peaks>");
//const int PK_SIZE = sizeof (Engine.Results.LCMSPeak);
//char[] peaks = new char[num_peaks * PK_SIZE];
//for (int pk_num = 0; pk_num < num_peaks; pk_num++)
//{
// *((Engine.Results.LCMSPeak*) &peaks[pk_num]) = results.mobj_lcms_results.GetPeak(pk_num);
//}
//file.Write(peaks);
file.Flush();
using (var bWriter = new BinaryWriter(file.BaseStream, Encoding.ASCII, true))
{
for (var pk_num = 0; pk_num < num_peaks; pk_num++)
{
results.mobj_lcms_results.GetPeak(pk_num).WriteToBinaryStream(bWriter);
}
}
file.Write("</Peaks>");
}
private void frmDecon2LS_DragDrop(object sender, System.Windows.Forms.DragEventArgs e)
{
foreach (var fileName in (string[])e.Data.GetData(DataFormats.FileDrop))
{
var index = fileName.LastIndexOf("\\");
var path_dir = "";
if (index > 0)
{
path_dir = fileName.Substring(0, index);
mobj_config.OpenDir = path_dir;
}
if (fileName.EndsWith("_scans.csv"))
{
index++;
var file_name_without_path = "";
if (index > 0)
{
file_name_without_path = fileName.Substring(index, fileName.Length - index);
}
var frmTIC = new frmTICViewer();
frmTIC.mFileName = fileName;
frmTIC.mFileNameForHeader = file_name_without_path;
frmTIC.LoadScansTICFile();
mMediator.RequestFormOpen(frmTIC);
}
else if (fileName.EndsWith(".dat"))
{
var transformResults = new DeconToolsV2.Results.clsTransformResults();
transformResults.ReadResults(fileName);
var frmTwoD = new frm2DPeakProcessing(transformResults);
frmTwoD.HornTransformParameters = mobjTransformParameters;
frmTwoD.PeakProcessorParameters = mobjPeakParameters;
frmTwoD.FTICRPreProcessOptions = mobjFTICRRawPreProcessParameters;
mMediator.RequestFormOpen(frmTwoD);
}
else if (fileName.EndsWith(".tic"))
{
index++;
var file_name_without_path = "";
if (index > 0)
{
file_name_without_path = fileName.Substring(index, fileName.Length - index);
}
var frmTIC = new frmTICViewer();
frmTIC.mFileName = fileName;
frmTIC.mFileNameForHeader = file_name_without_path;
frmTIC.LoadIcr2lsTICFile();
mMediator.RequestFormOpen(frmTIC);
}
else
{
Console.WriteLine("File cannot be dragged and dropped");
}
}
}
public void SetData(DeconToolsV2.Results.clsTransformResults results)
{
try
{
mobj_results = results;
marr_peaks = new Engine.Results.LcmsPeak[1];
var min_intensity = float.MaxValue;
var max_intensity = float.MinValue;
mobj_results.GetRawData(out marr_peaks);
if (marr_peaks.Length == 0)
{
return;
}
var myComparer = new clsRawDataComparer();
Array.Sort(marr_peaks, myComparer);
min_intensity = (float)marr_peaks[0].Intensity;
max_intensity = (float)marr_peaks[marr_peaks.Length - 1].Intensity;
var startIndex = 0;
if (min_intensity < mfltMinIntensity)
{
while (startIndex < marr_peaks.Length && marr_peaks[startIndex].Intensity < mfltMinIntensity)
{
startIndex++;
}
}
if (startIndex == marr_peaks.Length)
{
return;
}
if (max_intensity < 0)
{
max_intensity = 1f;
}
marr_scans = new float [marr_peaks.Length - startIndex];
marr_mzs = new float [marr_peaks.Length - startIndex];
marr_intensities = new float [marr_peaks.Length - startIndex];
for (var i = startIndex; i < marr_peaks.Length; i++)
{
marr_scans[i - startIndex] = Convert.ToSingle(marr_peaks[i].ScanNum);
marr_mzs[i - startIndex] = (float)marr_peaks[i].Mz;
marr_intensities[i - startIndex] = (float)marr_peaks[i].Intensity;
}
mctl_rawdata.SetData(marr_scans, marr_mzs, marr_intensities, min_intensity, max_intensity);
var mono_masses = results.MonoMasses;
var charges = results.Charges;
var scans = results.Scans;
mctl_rawdata.SetDeisotopedData(scans, mono_masses, charges);
this.Text = mobj_results.FileName;
var slashIndex = mobj_results.FileName.LastIndexOf("\\") + 1;
this.CategorizedText = mobj_results.FileName.Substring(slashIndex, mobj_results.FileName.Length - slashIndex);
}
catch (Exception ex)
{
MessageBox.Show(this, ex.Message + ex.StackTrace);
}
}
public void ReadFile(string file_name, DeconToolsV2.Results.clsTransformResults results,
Peaks.clsPeakProcessorParameters peak_parameters,
HornTransform.clsHornTransformParameters transform_parameters)
{
}
