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>();
}
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);
}
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);
}