/*private double curMRMPrecursor;
* private bool MRMFilter( ManagedScan scan )
* {
* if( scan.getPrecursorScanInfo( 0 ).Mz == curMRMPrecursor )
* return true;
* return false;
* }*/
private void InitForm(Form mdiParent)
{
MdiParent = mdiParent;
InitializeComponent();
initPeakAnnotationSettings();
scanNumberComboBox.AccessibleName = "scanNumberComboBox";
scanNumberComboBox.Anchor = ((System.Windows.Forms.AnchorStyles)((System.Windows.Forms.AnchorStyles.Top | System.Windows.Forms.AnchorStyles.Right)));
scanNumberComboBox.Enabled = false;
scanNumberComboBox.IntegralHeight = true;
scanNumberComboBox.ItemHeight = 13;
scanNumberComboBox.ListDisplayMember = "ComboBoxView";
scanNumberComboBox.Location = new System.Drawing.Point(397, 3);
scanNumberComboBox.Name = "scanNumberComboBox";
scanNumberComboBox.SelectedIndex = -1;
scanNumberComboBox.SelectedItem = null;
scanNumberComboBox.SelectedValue = null;
scanNumberComboBox.Size = new System.Drawing.Size(72, 22);
scanNumberComboBox.TabIndex = 8;
scanNumberComboBox.TextDisplayMember = "Id";
scanNumberComboBox.ValueMember = "Id";
scanNumberComboBox.ListBox.SelectedIndexChanged += new EventHandler(scanNumberComboBox_SelectedIndexChanged);
scanNumberComboBox.ListHeaderText = scanNumberHeaderString;
scanNumberComboBoxToolStripHost = new ToolStripControlHost(scanNumberComboBox);
scanNumberComboBoxToolStripHost.Alignment = ToolStripItemAlignment.Right;
if (SeemsMdiParent != null)
{
SeemsMdiParent.ToolStrip1.Items.Insert(SeemsMdiParent.ToolStrip1.Items.IndexOf(SeemsMdiParent.ToolStripScanLabel), scanNumberComboBoxToolStripHost);
}
scanNumberChangedTimer.Tick += new EventHandler(scanNumberChangedTimer_Tick);
scanNumberChangedTimer.Interval = 500;
webBrowserLeftKeyDownTimer.Tick += new EventHandler(webBrowserLeftKeyDownTimer_Tick);
webBrowserLeftKeyDownTimer.Interval = 50;
webBrowserRightKeyDownTimer.Tick += new EventHandler(webBrowserRightKeyDownTimer_Tick);
webBrowserRightKeyDownTimer.Interval = 50;
instrumentInterface = new ManagedInstrumentInterface();
if (!instrumentInterface.initInterface())
{
MessageBox.Show("Fatal error: failed to initialize data interface.");
Process.GetCurrentProcess().Kill();
}
}
public DataSource(string filepath)
{
instrumentInterface = new ManagedInstrumentInterface();
if (!instrumentInterface.initInterface())
{
throw new Exception("failed to initialize data interface.");
}
setInputFileWaitHandle = new EventWaitHandle(false, EventResetMode.ManualReset);
setInputFileDelegate = new ParameterizedThreadStart(startSetInputFile);
Thread setInputFileThread = new Thread(setInputFileDelegate);
//setInputFileThread.IsBackground = true;
setInputFileThread.Start((object)filepath);
if (!instrumentInterface.setInputFile(filepath))
{
throw new Exception("LibMSR could not open the file");
}
}
/*private double curMRMPrecursor;
private bool MRMFilter( ManagedScan scan )
{
if( scan.getPrecursorScanInfo( 0 ).Mz == curMRMPrecursor )
return true;
return false;
}*/
private void InitForm( Form mdiParent )
{
MdiParent = mdiParent;
InitializeComponent();
initPeakAnnotationSettings();
scanNumberComboBox.AccessibleName = "scanNumberComboBox";
scanNumberComboBox.Anchor = ( (System.Windows.Forms.AnchorStyles) ( ( System.Windows.Forms.AnchorStyles.Top | System.Windows.Forms.AnchorStyles.Right ) ) );
scanNumberComboBox.Enabled = false;
scanNumberComboBox.IntegralHeight = true;
scanNumberComboBox.ItemHeight = 13;
scanNumberComboBox.ListDisplayMember = "ComboBoxView";
scanNumberComboBox.Location = new System.Drawing.Point( 397, 3 );
scanNumberComboBox.Name = "scanNumberComboBox";
scanNumberComboBox.SelectedIndex = -1;
scanNumberComboBox.SelectedItem = null;
scanNumberComboBox.SelectedValue = null;
scanNumberComboBox.Size = new System.Drawing.Size( 72, 22 );
scanNumberComboBox.TabIndex = 8;
scanNumberComboBox.TextDisplayMember = "Id";
scanNumberComboBox.ValueMember = "Id";
scanNumberComboBox.ListBox.SelectedIndexChanged += new EventHandler( scanNumberComboBox_SelectedIndexChanged );
scanNumberComboBox.ListHeaderText = scanNumberHeaderString;
scanNumberComboBoxToolStripHost = new ToolStripControlHost( scanNumberComboBox );
scanNumberComboBoxToolStripHost.Alignment = ToolStripItemAlignment.Right;
if( SeemsMdiParent != null )
SeemsMdiParent.ToolStrip1.Items.Insert( SeemsMdiParent.ToolStrip1.Items.IndexOf( SeemsMdiParent.ToolStripScanLabel ), scanNumberComboBoxToolStripHost );
scanNumberChangedTimer.Tick += new EventHandler( scanNumberChangedTimer_Tick );
scanNumberChangedTimer.Interval = 500;
webBrowserLeftKeyDownTimer.Tick += new EventHandler( webBrowserLeftKeyDownTimer_Tick );
webBrowserLeftKeyDownTimer.Interval = 50;
webBrowserRightKeyDownTimer.Tick += new EventHandler( webBrowserRightKeyDownTimer_Tick );
webBrowserRightKeyDownTimer.Interval = 50;
instrumentInterface = new ManagedInstrumentInterface();
if( !instrumentInterface.initInterface() )
{
MessageBox.Show( "Fatal error: failed to initialize data interface." );
Process.GetCurrentProcess().Kill();
}
}
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);
}