private void initializeManagedDataSource( ManagedDataSource managedDataSource, object idOrIndex, IAnnotation annotation, string[] spectrumListFilters )
{
try
{
SpectrumSource source = managedDataSource.Source;
MSData msDataFile = source.MSDataFile;
ChromatogramListForm chromatogramListForm = managedDataSource.ChromatogramListForm;
SpectrumListForm spectrumListForm = managedDataSource.SpectrumListForm;
chromatogramListForm.CellDoubleClick += new ChromatogramListCellDoubleClickHandler( chromatogramListForm_CellDoubleClick );
chromatogramListForm.CellClick += new ChromatogramListCellClickHandler( chromatogramListForm_CellClick );
chromatogramListForm.GotFocus += new EventHandler( form_GotFocus );
spectrumListForm.CellDoubleClick += new SpectrumListCellDoubleClickHandler( spectrumListForm_CellDoubleClick );
spectrumListForm.CellClick += new SpectrumListCellClickHandler( spectrumListForm_CellClick );
spectrumListForm.FilterChanged += new SpectrumListFilterChangedHandler( spectrumListForm_FilterChanged );
spectrumListForm.GotFocus += new EventHandler( form_GotFocus );
bool firstChromatogramLoaded = false;
bool firstSpectrumLoaded = false;
GraphForm firstGraph = null;
ChromatogramList cl = msDataFile.run.chromatogramList;
SpectrumList sl = msDataFile.run.spectrumList;
//sl = new SpectrumList_Filter( sl, new SpectrumList_FilterAcceptSpectrum( acceptSpectrum ) );
if (sl.size()+cl.size() == 0)
throw new Exception("Error loading metadata: no spectra or chromatograms");
Type indexType = typeof(MassSpectrum);
int index = -1;
if( idOrIndex is int )
index = (int) idOrIndex;
else if( idOrIndex is string )
{
int findIndex = sl.find(idOrIndex as string);
if (findIndex != sl.size())
index = findIndex;
if (index == -1)
{
indexType = typeof(Chromatogram);
findIndex = cl.find(idOrIndex as string);
if (findIndex != cl.size())
index = findIndex;
}
}
// conditionally load the spectrum at the specified index first
if( index > -1 )
{
GraphItem item = null;
if (indexType == typeof(MassSpectrum))
{
MassSpectrum spectrum = managedDataSource.GetMassSpectrum(index);
if (spectrumListFilters.Length > 0)
spectrum = managedDataSource.GetMassSpectrum(spectrum, spectrumListFilters);
spectrum.AnnotationSettings = defaultScanAnnotationSettings;
spectrumListForm.Add(spectrum);
source.Spectra.Add(spectrum);
firstSpectrumLoaded = true;
if (ShowSpectrumListForNewSources)
{
spectrumListForm.Show(DockPanel, DockState.DockBottom);
Application.DoEvents();
}
if (annotation != null)
spectrum.AnnotationList.Add(annotation);
item = spectrum;
}
else
{
Chromatogram chromatogram = managedDataSource.GetChromatogram(index);
chromatogram.AnnotationSettings = defaultChromatogramAnnotationSettings;
chromatogramListForm.Add(chromatogram);
source.Chromatograms.Add(chromatogram);
firstChromatogramLoaded = true;
if (ShowChromatogramListForNewSources)
{
chromatogramListForm.Show(DockPanel, DockState.DockBottom);
Application.DoEvents();
}
item = chromatogram;
}
firstGraph = OpenFileUsesCurrentGraphForm && CurrentGraphForm != null ? CurrentGraphForm
: OpenGraph(OpenFileGivesFocus);
showData(firstGraph, item);
return;
}
int ticIndex = cl.find( "TIC" );
if( ticIndex < cl.size() )
{
pwiz.CLI.msdata.Chromatogram tic = cl.chromatogram( ticIndex );
Chromatogram ticChromatogram = managedDataSource.GetChromatogram( ticIndex );
ticChromatogram.AnnotationSettings = defaultChromatogramAnnotationSettings;
chromatogramListForm.Add( ticChromatogram );
source.Chromatograms.Add( ticChromatogram );
if( !firstSpectrumLoaded )
{
firstGraph = OpenGraph( true );
showData( firstGraph, ticChromatogram );
firstChromatogramLoaded = true;
if (ShowChromatogramListForNewSources)
{
chromatogramListForm.Show(DockPanel, DockState.DockBottom);
Application.DoEvents();
}
}
}
// get spectrum type from fileContent if possible, otherwise from first spectrum
CVParam spectrumType = msDataFile.fileDescription.fileContent.cvParamChild( CVID.MS_spectrum_type );
if( spectrumType.cvid == CVID.CVID_Unknown && sl.size() > 0 )
spectrumType = sl.spectrum( 0 ).cvParamChild( CVID.MS_spectrum_type );
// load the rest of the chromatograms
for( int i = 0; i < cl.size(); ++i )
{
if( i == ticIndex )
continue;
Chromatogram chromatogram = managedDataSource.GetChromatogram( i );
if (OnLoadDataSourceProgress(String.Format("Loading chromatograms from {0} ({1} of {2})...",
managedDataSource.Source.Name, (i + 1), cl.size()),
(i + 1) * 100 / cl.size()))
return;
chromatogram.AnnotationSettings = defaultChromatogramAnnotationSettings;
chromatogramListForm.Add( chromatogram );
source.Chromatograms.Add( chromatogram );
if( !firstSpectrumLoaded && !firstChromatogramLoaded )
{
firstChromatogramLoaded = true;
if (ShowChromatogramListForNewSources)
{
chromatogramListForm.Show(DockPanel, DockState.DockBottom);
Application.DoEvents();
}
firstGraph = OpenGraph( true );
showData(firstGraph, chromatogram );
}
Application.DoEvents();
}
// get all scans by sequential access
for( int i = 0; i < sl.size(); ++i )
{
if( i == index ) // skip the preloaded spectrum
continue;
MassSpectrum spectrum = managedDataSource.GetMassSpectrum( i );
if (((i + 1) % 100) == 0 || (i + 1) == sl.size())
{
if (OnLoadDataSourceProgress(String.Format("Loading spectra from {0} ({1} of {2})...",
managedDataSource.Source.Name, (i + 1), sl.size()),
(i + 1) * 100 / sl.size()))
return;
}
spectrum.AnnotationSettings = defaultScanAnnotationSettings;
spectrumListForm.Add( spectrum );
source.Spectra.Add( spectrum );
if( !firstSpectrumLoaded )
{
firstSpectrumLoaded = true;
spectrumListForm.Show( DockPanel, DockState.DockBottom );
Application.DoEvents();
if( firstChromatogramLoaded )
{
GraphForm spectrumGraph = CreateGraph();
spectrumGraph.Show( firstGraph.Pane, DockPaneAlignment.Bottom, 0.5 );
showData(spectrumGraph, spectrum );
} else
{
firstGraph = OpenGraph( true );
showData(firstGraph, spectrum );
}
}
Application.DoEvents();
}
OnLoadDataSourceProgress("Finished loading source metadata.", 100);
} catch( Exception ex )
{
string message = "SeeMS encountered an error reading metadata from \"" + managedDataSource.Source.CurrentFilepath + "\" (" + ex.ToString() + ")";
if( ex.InnerException != null )
message += "\n\nAdditional information: " + ex.InnerException.ToString();
MessageBox.Show( message,
"Error reading source metadata",
MessageBoxButtons.OK, MessageBoxIcon.Error, MessageBoxDefaultButton.Button1,
0, false );
OnLoadDataSourceProgress("Failed to load data: " + ex.Message, 100);
}
}
public void OpenFile( string filepath, object idOrIndex, IAnnotation annotation, string spectrumListFilters )
{
try
{
OnLoadDataSourceProgress("Opening data source: " + Path.GetFileNameWithoutExtension(filepath), 0);
string[] spectrumListFilterList = spectrumListFilters.Split(';');
if (!dataSourceMap.ContainsKey(filepath))
{
var newSource = new ManagedDataSource(new SpectrumSource(filepath));
dataSourceMap.Add(filepath, newSource);
if (spectrumListFilters.Length > 0)
SpectrumListFactory.wrap(newSource.Source.MSDataFile, spectrumListFilterList);
initializeManagedDataSource( newSource, idOrIndex, annotation, spectrumListFilterList );
} else
{
GraphForm graph = OpenFileUsesCurrentGraphForm && CurrentGraphForm != null ? CurrentGraphForm
: OpenGraph(OpenFileGivesFocus);
ManagedDataSource source = dataSourceMap[filepath];
int index = -1;
if( idOrIndex is int )
index = (int) idOrIndex;
else if( idOrIndex is string )
{
SpectrumList sl = source.Source.MSDataFile.run.spectrumList;
int findIndex = sl.find( idOrIndex as string );
if( findIndex != sl.size() )
index = findIndex;
}
// conditionally load the spectrum at the specified index
if( index > -1 )
{
MassSpectrum spectrum = source.GetMassSpectrum( index );
if (spectrumListFilters.Length > 0)
SpectrumListFactory.wrap(source.Source.MSDataFile, spectrumListFilterList);
spectrum.AnnotationSettings = defaultScanAnnotationSettings;
if( annotation != null )
spectrum.AnnotationList.Add( annotation );
if (source.Source.Spectra.Count < source.Source.MSDataFile.run.spectrumList.size() &&
source.SpectrumListForm.IndexOf(spectrum) < 0)
{
source.SpectrumListForm.Add(spectrum);
source.Source.Spectra.Add(spectrum);
}
showData(graph, spectrum);
} else
{
if( source.Source.Chromatograms.Count > 0 )
showData(graph, source.Source.Chromatograms[0]);
else
showData(graph, source.Source.Spectra[0]);
}
}
} catch( Exception ex )
{
string message = 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 );
OnLoadDataSourceProgress("Failed to load data: " + ex.Message, 100);
}
}
private void showDataOverlay( GraphForm hostGraph, ManagedDataSource managedDataSource, GraphItem item )
{
if( item.IsChromatogram )
{
hostGraph.ShowDataOverlay( managedDataSource.Source, managedDataSource.Source.GetChromatogram( item.Index, true ) );
} else
{
SpectrumList sl = managedDataSource.SpectrumProcessingForm.ProcessingListView.ProcessingWrapper( managedDataSource.Source.MSDataFile.run.spectrumList );
hostGraph.ShowDataOverlay( managedDataSource.Source, managedDataSource.Source.GetMassSpectrum( item as MassSpectrum, sl ) );
}
}
private void showDataOverlay( GraphForm hostGraph, ManagedDataSource managedDataSource, DataGridViewRow row )
{
showDataOverlay( hostGraph, managedDataSource, row.Tag as GraphItem );
}
private void initializeManagedDataSource( ManagedDataSource managedDataSource )
{
try
{
DataSource source = managedDataSource.Source;
MSDataFile msDataFile = source.MSDataFile;
ChromatogramListForm chromatogramListForm = managedDataSource.ChromatogramListForm;
SpectrumListForm spectrumListForm = managedDataSource.SpectrumListForm;
chromatogramListForm.Text = source.Name + " chromatograms";
chromatogramListForm.TabText = source.Name + " chromatograms";
chromatogramListForm.ShowIcon = false;
chromatogramListForm.CellDoubleClick += new ChromatogramListCellDoubleClickHandler( chromatogramListForm_CellDoubleClick );
spectrumListForm.Text = source.Name + " spectra";
spectrumListForm.TabText = source.Name + " spectra";
spectrumListForm.ShowIcon = false;
spectrumListForm.CellDoubleClick += new SpectrumListCellDoubleClickHandler( spectrumListForm_CellDoubleClick );
bool firstChromatogramLoaded = false;
bool firstSpectrumLoaded = false;
GraphForm firstGraph = null;
ChromatogramList cl = msDataFile.run.chromatogramList;
SpectrumList sl = msDataFile.run.spectrumList;
if( sl == null )
throw new Exception( "Error loading metadata: no spectrum list" );
int ticIndex = 0;
if( cl != null )
{
ticIndex = cl.findNative( "TIC" );
if( ticIndex < cl.size() )
{
pwiz.CLI.msdata.Chromatogram tic = cl.chromatogram( ticIndex );
Chromatogram ticChromatogram = new Chromatogram( source, tic );
chromatogramListForm.Add( ticChromatogram );
source.Chromatograms.Add( ticChromatogram );
firstGraph = OpenGraph( true );
showData( firstGraph, managedDataSource, ticChromatogram );
firstChromatogramLoaded = true;
chromatogramListForm.Show( mainForm.DockPanel, DockState.DockBottomAutoHide );
Application.DoEvents();
}
}
CVParam spectrumType = msDataFile.fileDescription.fileContent.cvParamChild( CVID.MS_spectrum_type );
if( spectrumType.cvid == CVID.CVID_Unknown && !sl.empty() )
spectrumType = sl.spectrum( 0 ).cvParamChild( CVID.MS_spectrum_type );
if( spectrumType.cvid == CVID.MS_SRM_spectrum )
{
if( cl != null && cl.empty() )
throw new Exception( "Error loading metadata: SRM file contains no chromatograms" );
} else //if( spectrumType.cvid == CVID.MS_MS1_spectrum ||
// spectrumType.cvid == CVID.MS_MSn_spectrum )
{
if( sl.empty() )
throw new Exception( "Error loading metadata: MSn file contains no spectra" );
}// else
// throw new Exception( "Error loading metadata: unable to open files with spectrum type \"" + spectrumType.name + "\"" );
if( cl != null )
{
// load the rest of the chromatograms
for( int i = 0; i < cl.size(); ++i )
{
if( i == ticIndex )
continue;
pwiz.CLI.msdata.Chromatogram c = cl.chromatogram( i );
mainForm.SetStatusLabel( String.Format( "Loading chromatograms from source file ({0} of {1})...",
( i + 1 ), cl.size() ) );
mainForm.SetProgressPercentage( ( i + 1 ) * 100 / cl.size() );
Chromatogram chromatogram = new Chromatogram( source, c );
chromatogramListForm.Add( chromatogram );
source.Chromatograms.Add( chromatogram );
if( !firstChromatogramLoaded )
{
firstChromatogramLoaded = true;
chromatogramListForm.Show( mainForm.DockPanel, DockState.DockBottomAutoHide );
firstGraph = OpenGraph( true );
showData( firstGraph, managedDataSource, chromatogram );
}
Application.DoEvents();
}
}
// get all scans by sequential access
for( int i = 0; i < sl.size(); ++i )
{
pwiz.CLI.msdata.Spectrum s = sl.spectrum( i );
if( ( ( i + 1 ) % 100 ) == 0 || ( i + 1 ) == sl.size() )
{
mainForm.SetStatusLabel( String.Format( "Loading spectra from source file ({0} of {1})...",
( i + 1 ), sl.size() ) );
mainForm.SetProgressPercentage( ( i + 1 ) * 100 / sl.size() );
}
MassSpectrum spectrum = new MassSpectrum( source, s );
spectrumListForm.Add( spectrum );
source.Spectra.Add( spectrum );
if( !firstSpectrumLoaded )
{
firstSpectrumLoaded = true;
spectrumListForm.Show( mainForm.DockPanel, DockState.DockBottomAutoHide );
if( firstChromatogramLoaded )
{
GraphForm spectrumGraph = CreateGraph();
spectrumGraph.Show( firstGraph.Pane, DockPaneAlignment.Bottom, 0.5 );
showData( spectrumGraph, managedDataSource, spectrum );
} else
{
firstGraph = OpenGraph( true );
showData( firstGraph, managedDataSource, spectrum );
}
}
Application.DoEvents();
}
mainForm.SetStatusLabel( "Finished loading source metadata." );
mainForm.SetProgressPercentage( 100 );
} catch( Exception ex )
{
string message = "SeeMS encountered an error reading metadata from \"" + managedDataSource.Source.CurrentFilepath + "\" (" + 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 );
mainForm.SetStatusLabel( "Failed to read source metadata." );
}
}
