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) { }