Пример #1
0
        public SeemsPointList(ManagedScan scan)
        {
            fullPointList          = new ZedGraph.PointPairList();
            fullPointList.Capacity = scan.getTotalPeakCount();
            Map <double, double> sortedFullPointList = new Map <double, double>();

            for (int i = 0; i < scan.getTotalPeakCount(); ++i)
            {
                sortedFullPointList[scan.getPeakMz(i)] = scan.getPeakIntensity(i);
            }
            foreach (Map <double, double> .MapPair itr in sortedFullPointList)
            {
                fullPointList.Add(new ZedGraph.PointPair(itr.Key, itr.Value));
            }
            scaledPointList    = new ZedGraph.PointPairList();
            scaledMaxIndexList = new List <int>();
        }
Пример #2
0
        public bool SetInputFile(string filepath)
        {
            ManagedInstrumentInterface tempInterface = new ManagedInstrumentInterface();

            try
            {
                if (!tempInterface.initInterface())
                {
                    throw new Exception("failed to initialize temporary data interface.");
                }

                if (!File.Exists(filepath))
                {
                    throw new ArgumentException("file does not exist");
                }
                sourceFilepath = filepath;

                OnStatusReport("Initializing interface for source file...");

                if (!tempInterface.setInputFile(sourceFilepath))
                {
                    throw new Exception("LibMSR could not open the file");
                }
                tempInterface.setCentroiding(false, false);
            } catch (Exception ex)
            {
                string message = "SeeMS encountered an error opening \"" + filepath + "\" (" + ex.Message + ")";
                if (ex.InnerException != null)
                {
                    message += "\n\nAdditional information: " + ex.InnerException.Message;
                }
                MessageBox.Show(message,
                                "Error opening source file",
                                MessageBoxButtons.OK, MessageBoxIcon.Error, MessageBoxDefaultButton.Button1,
                                0, false);
                return(false);
            }

            try
            {
                OnStatusReport("Loading metadata from source file...");
                OnProgressReport(0);

                int totalScanCount = tempInterface.getTotalScanCount();
                int curScanCount   = 0;

                if (totalScanCount > 1)
                {
                    ManagedScan chromatogram = tempInterface.getChromatogram();
                    if (chromatogram == null)
                    {
                        throw new Exception("failed to generate chromatogram");
                    }
                    else
                    {
                        sourceScanHeaders.Add(new SeemsScan(chromatogram, "Chromatogram"));
                    }
                }

                ParentToFragmentMap transitionMap = new ParentToFragmentMap();

                // get all scans by sequential access
                ManagedScan curScan = tempInterface.getScanHeader(instrumentInterface.getFirstScanNumber());
                while (curScan != null)
                {
                    ++curScanCount;
                    if ((curScanCount % 100) == 0 || curScanCount == totalScanCount)
                    {
                        OnStatusReport(String.Format("Loading metadata from source file ({0} of {1})...",
                                                     curScanCount, totalScanCount));
                        OnProgressReport(curScanCount * 100 / totalScanCount);
                    }

                    if (curScan.ScanType == ScanTypeEnum.SRM || curScan.ScanType == ScanTypeEnum.MRM)
                    {
                        ManagedScan curScanWithPeakData = tempInterface.getScan(curScan.ScanNumber);
                        if (curScanWithPeakData.getTotalPeakCount() > 0)
                        {
                            if (curScan.getPrecursorScanCount() > 0)
                            {
                                FragmentToChromatogramMap fragmentMap = transitionMap[curScan.getPrecursorScanInfo(0).Mz];
                                for (int i = 0; i < curScanWithPeakData.getTotalPeakCount(); ++i)
                                {
                                    fragmentMap[curScanWithPeakData.getPeakMz(i)].Add(curScan.RetentionTime, curScanWithPeakData.getPeakIntensity(i));
                                }
                            }
                        }
                    }
                    else
                    {
                        sourceScanHeaders.Add(new SeemsScan(curScan));
                    }
                    curScan = tempInterface.getScanHeader();
                }
                OnProgressReport(100);

                if (transitionMap.Count > 0)
                {
                    OnStatusReport("Generating chromatograms for SRM/MRM data...");
                    OnProgressReport(0);
                    Map <double, RefPair <ManagedScan, Map <double, ManagedScan> > > transitionChromatograms = new Map <double, RefPair <ManagedScan, Map <double, ManagedScan> > >();
                    foreach (ParentToFragmentMap.MapPair pfPair in transitionMap)
                    {
                        Map <double, List <double> > parentPeaks = new Map <double, List <double> >();
                        foreach (FragmentToChromatogramMap.MapPair fcPair in pfPair.Value)
                        {
                            ManagedScan fragmentChromatogram = transitionChromatograms[pfPair.Key].second[fcPair.Key] = new ManagedScan();
                            foreach (Chromatogram.MapPair tiPair in fcPair.Value)
                            {
                                fragmentChromatogram.addPeak(tiPair.Key, tiPair.Value);
                                parentPeaks[tiPair.Key].Add(tiPair.Value);
                            }
                        }

                        ManagedScan parentChromatogram  = transitionChromatograms[pfPair.Key].first = new ManagedScan();
                        ManagedScan productChromatogram = transitionChromatograms[pfPair.Key].second[pfPair.Key] = new ManagedScan();
                        foreach (Map <double, List <double> > .MapPair itr in parentPeaks)
                        {
                            double totalIntensity = 0, productIntensity = 1;
                            foreach (double intensity in itr.Value)
                            {
                                totalIntensity   += intensity;
                                productIntensity *= intensity;
                            }
                            parentChromatogram.addPeak(itr.Key, totalIntensity);
                            productChromatogram.addPeak(itr.Key, productIntensity);
                        }

                        OnProgressReport(transitionChromatograms.Count * 100 / transitionMap.Count);
                    }

                    foreach (Map <double, RefPair <ManagedScan, Map <double, ManagedScan> > > .MapPair kvp1 in transitionChromatograms)
                    {
                        sourceScanHeaders.Add(new SeemsScan(kvp1.Value.first, String.Format("{0} (Sum)", Math.Round(kvp1.Key, 2))));
                        sourceScanHeaders.Add(new SeemsScan(kvp1.Value.second[kvp1.Key], String.Format("{0} (Product)", Math.Round(kvp1.Key, 2))));
                        foreach (Map <double, ManagedScan> .MapPair kvp2 in kvp1.Value.second)
                        {
                            if (kvp1.Key != kvp2.Key)
                            {
                                sourceScanHeaders.Add(new SeemsScan(kvp2.Value, String.Format("{0} -> {1}", Math.Round(kvp1.Key, 2), Math.Round(kvp2.Key, 2))));
                            }
                        }
                    }

                    OnStatusReport("Finished loading source metadata.");
                    OnProgressReport(100);
                }
            } catch (Exception ex)
            {
                string message = "SeeMS encountered an error reading metadata from \"" + filepath + "\" (" + ex.Message + ")";
                if (ex.InnerException != null)
                {
                    message += "\n\nAdditional information: " + ex.InnerException.Message;
                }
                MessageBox.Show(message,
                                "Error reading source metadata",
                                MessageBoxButtons.OK, MessageBoxIcon.Error, MessageBoxDefaultButton.Button1,
                                0, false);
                OnStatusReport("Failed to read source metadata.");
                return(false);
            }

            return(true);
        }
Пример #3
0
        public bool readScanMetadata(string sourceFilepath)
        {
            try
            {
                if (!File.Exists(sourceFilepath))
                {
                    return(false);
                }
                CurrentSourceFilepath = sourceFilepath;

                SeemsMdiParent.setFileControls(false);
                SeemsMdiParent.setScanControls(false);

                SeemsMdiParent.StatusLabel.Text = "Loading source metadata...";
                SeemsMdiParent.StatusProgressBar.MarqueeAnimationSpeed = 100;
                Application.DoEvents();
                if (!instrumentInterface.setInputFile(CurrentSourceFilepath))
                {
                    throw new Exception("failed to open file \"" + CurrentSourceFilepath + "\"");
                }
                instrumentInterface.setCentroiding(false, false);
                SeemsMdiParent.StatusProgressBar.MarqueeAnimationSpeed = 0;
            } catch (Exception ex)
            {
                string message = "SeeMS encountered an error opening the source file you specified (" + ex.Message + ")";
                if (ex.InnerException != null)
                {
                    message += "\n\nAdditional information: " + ex.InnerException.Message;
                }
                MessageBox.Show(message,
                                "Error opening source file",
                                MessageBoxButtons.OK, MessageBoxIcon.Error, MessageBoxDefaultButton.Button1,
                                0, false);
                SeemsMdiParent.setFileControls(true);
                return(false);
            }

            try
            {
                scanNumberComboBox.Items.Clear();
                SeemsMdiParent.StatusProgressBar.Visible = true;
                SeemsMdiParent.StatusProgressBar.Value   = 0;
                SeemsMdiParent.StatusProgressBar.Minimum = 0;
                SeemsMdiParent.StatusProgressBar.Maximum = instrumentInterface.getTotalScanCount();
                SeemsMdiParent.StatusProgressBar.Step    = 1;
                Application.DoEvents();

                scanNumberComboBox.BeginUpdate();

                ManagedScan chromatogram = instrumentInterface.getChromatogram();
                if (chromatogram == null)
                {
                    throw new Exception("failed to generate chromatogram");
                }
                else
                {
                    scanNumberComboBox.Items.Add(new SeemsScan(chromatogram, "Chromatogram"));
                }

                ParentToFragmentMap transitionMap = new ParentToFragmentMap();
                //Dictionary<double, int> transitionMap = new Dictionary<double,int>();

                //long beforeScanHeaders = Environment.WorkingSet;
                // get all scans by sequential access
                ManagedScan curScan = instrumentInterface.getScanHeader(instrumentInterface.getFirstScanNumber());
                while (curScan != null)
                {
                    SeemsMdiParent.StatusProgressBar.PerformStep();
                    Application.DoEvents();
                    if (curScan.ScanType == ScanTypeEnum.SRM || curScan.ScanType == ScanTypeEnum.MRM)
                    {
                        ManagedScan curScanWithPeakData = instrumentInterface.getScan(curScan.ScanNumber);
                        if (curScanWithPeakData.getTotalPeakCount() > 0)
                        {
                            if (curScan.getPrecursorScanCount() > 0)
                            {
                                FragmentToChromatogramMap fragmentMap = transitionMap[curScan.getPrecursorScanInfo(0).Mz];
                                for (int i = 0; i < curScanWithPeakData.getTotalPeakCount(); ++i)
                                {
                                    fragmentMap[curScanWithPeakData.getPeakMz(i)].Add(curScan.RetentionTime, curScanWithPeakData.getPeakIntensity(i));
                                }
                            }
                        }
                        //if( curScan.getPrecursorScanCount() > 0 )
                        //	transitionMap[curScan.getPrecursorScanInfo( 0 ).Mz] = 0;
                    }
                    else
                    {
                        scanNumberComboBox.Items.Add(new SeemsScan(curScan));
                    }
                    curScan = instrumentInterface.getScanHeader();
                }

                if (transitionMap.Count > 0)
                {
                    SeemsMdiParent.StatusLabel.Text          = "Generating chromatograms for SRM/MRM data...";
                    SeemsMdiParent.StatusProgressBar.Value   = 0;
                    SeemsMdiParent.StatusProgressBar.Minimum = 0;
                    SeemsMdiParent.StatusProgressBar.Maximum = transitionMap.Count;
                    SeemsMdiParent.StatusProgressBar.Step    = 1;
                    Application.DoEvents();
                    Map <double, RefPair <ManagedScan, Map <double, ManagedScan> > > transitionChromatograms = new Map <double, RefPair <ManagedScan, Map <double, ManagedScan> > >();
                    foreach (ParentToFragmentMap.MapPair pfPair in transitionMap)
                    {
                        Map <double, double> parentPeaks = new Map <double, double>();
                        foreach (FragmentToChromatogramMap.MapPair fcPair in pfPair.Value)
                        {
                            ManagedScan fragmentChromatogram = transitionChromatograms[pfPair.Key].second[fcPair.Key] = new ManagedScan();
                            foreach (Chromatogram.MapPair tiPair in fcPair.Value)
                            {
                                fragmentChromatogram.addPeak(tiPair.Key, tiPair.Value);
                                parentPeaks[tiPair.Key] += tiPair.Value;
                            }
                        }

                        ManagedScan parentChromatogram = transitionChromatograms[pfPair.Key].first = new ManagedScan();
                        foreach (Map <double, double> .MapPair peak in parentPeaks)
                        {
                            parentChromatogram.addPeak(peak.Key, peak.Value);
                        }

                        SeemsMdiParent.StatusProgressBar.PerformStep();
                        Application.DoEvents();
                    }

                    foreach (Map <double, RefPair <ManagedScan, Map <double, ManagedScan> > > .MapPair kvp1 in transitionChromatograms)
                    {
                        scanNumberComboBox.Items.Add(new SeemsScan(kvp1.Value.first, kvp1.Key.ToString()));
                        foreach (Map <double, ManagedScan> .MapPair kvp2 in kvp1.Value.second)
                        {
                            scanNumberComboBox.Items.Add(new SeemsScan(kvp2.Value, String.Format("{0} -> {1}", Math.Round(kvp1.Key, 2), Math.Round(kvp2.Key, 2))));
                        }
                    }
                }

                scanNumberComboBox.EndUpdate();
                SeemsMdiParent.StatusProgressBar.Visible = false;
                Application.DoEvents();
                //long afterScanHeaders = Environment.WorkingSet;
                //MessageBox.Show( "Before adding headers: " + beforeScanHeaders + "   After adding headers: " + afterScanHeaders );


                SeemsMdiParent.setFileControls(true);

                if (scanNumberComboBox.Items.Count > 0)
                {
                    SeemsMdiParent.setScanControls(true);
                    scanNumberComboBox.SelectedIndex = 0;                     // triggers initial graph generation
                }
                else
                {
                    SeemsMdiParent.setScanControls(false);
                    return(false);
                }
            } catch (Exception ex)
            {
                string message = "SeeMS encountered an error reading metadata from the source file you specified (" + ex.Message + ")";
                if (ex.InnerException != null)
                {
                    message += "\n\nAdditional information: " + ex.InnerException.Message;
                }
                MessageBox.Show(message,
                                "Error reading source metadata",
                                MessageBoxButtons.OK, MessageBoxIcon.Error, MessageBoxDefaultButton.Button1,
                                0, false);
                SeemsMdiParent.setFileControls(true);
                return(false);
            }
            return(true);
        }