public DatasetInformationViewModel(DatasetInformation information)
{
m_information = information;
var data = information.PlotData;
PlotData = new ObservableCollection<PlotViewModel>();
RequestRemovalCommand = new BaseCommand(
() =>
{
if (RemovalRequested != null)
{
RemovalRequested(this, EventArgs.Empty);
}
}, s => !this.DoingWork);
if (data != null)
{
PlotData.Add(new PlotViewModel(data.Alignment,
"Alignment",
new PictureDisplayCommand(data.Alignment, "Alignment" + information.DatasetName)));
PlotData.Add(new PlotViewModel(data.Features,
"Features",
new FeatureDisplayCommand(information)));
PlotData.Add(new PlotViewModel(data.MassErrorHistogram, "Mass Error Histogram"));
PlotData.Add(new PlotViewModel(data.NetErrorHistogram, "NET Error Histogram"));
PlotData.Add(new PlotViewModel(data.MassScanResidual, "Mass vs Scan Residuals"));
PlotData.Add(new PlotViewModel(data.MassMzResidual, "Mass vs m/z Residuals"));
PlotData.Add(new PlotViewModel(data.NetResiduals, "NET Residuals"));
}
ModifyDatasetCommand = new ShowDatasetDetailCommand();
}
public UmcClusterSpectraViewModel()
{
Spectra = new ObservableCollection<MsSpectraViewModel>();
SortTypes = new ObservableCollection<SpectraSortOptions>();
CreateSortOptions();
ExpandIdentifications = new BaseCommand(delegate
{
foreach (var spectrum in Spectra)
{
spectrum.IdentificationsExpanded = true;
}
}
);
CollapseIdentifications = new BaseCommand(delegate
{
foreach (var spectrum in Spectra)
{
spectrum.IdentificationsExpanded = false;
}
}
);
}
public AnalysisBaselineSelectionViewModel(MultiAlignAnalysis analysis)
{
var filter =
"Mass Tag Database (.db3)|*.db3|Direct Infusion IMS Database (.dims)|*.dims|All Files (*.*)|*.*";
m_analysis = analysis;
IsDatabaseDms = false;
IsDatabaseLocal = false;
IsBaselineDataset = true;
SetDatabaseToDms = new BaseCommand(SetDatabaseToDmsDelegate, BaseCommand.AlwaysPass);
SetDatabaseToLocal = new BaseCommand(SetDatabaseToLocalDelegate, BaseCommand.AlwaysPass);
SetBaselineToDatabase = new BaseCommand(SetBaselineToDatabaseDelegate, BaseCommand.AlwaysPass);
SetBaselineToDataset = new BaseCommand(SetBaselineToDatasetDelegate, BaseCommand.AlwaysPass);
FindLocalDatabase = new BrowseOpenFileCommand(x =>
{
DatabaseFilePath = x;
IsDatabaseLocal = true;
OnPropertyChanged("RequiresDatabaseSelection");
}, filter);
FindDmsDatabase = new BaseCommand(FindDmsDatabaseDelegate, BaseCommand.AlwaysPass);
ClearDatabase = new BaseCommand(ClearDatabaseDelegate, BaseCommand.AlwaysPass);
Datasets = new ObservableCollection<DatasetInformationViewModel>();
UpdateDatasets();
StacOptionsViewModel = new StacOptionsViewModel(analysis.Options.StacOptions);
MassTagDatabaseOptionsViewModel =
new MassTagDatabaseOptionsViewModel(analysis.Options.MassTagDatabaseOptions);
}
public MainViewModel()
{
// Create the state moderation (between views)
BuildStateModerator();
MainDataDirectory = Environment.GetFolderPath(Environment.SpecialFolder.MyDocuments);
MainDataName = "analysis";
// Titles and Status
var version = ApplicationUtility.GetEntryAssemblyData();
Title = version;
// Command Setup
ShowAnalysisCommand = new BaseCommand(ShowAnalysis, BaseCommand.AlwaysPass);
ShowStartCommand = new BaseCommand(ShowStart, BaseCommand.AlwaysPass);
// View Models
var workSpacePath = ApplicationUtility.GetApplicationDataFolderPath("MultiAlign");
workSpacePath = Path.Combine(workSpacePath, Settings.Default.WorkspaceFile);
GettingStartedViewModel = new GettingStartedViewModel(workSpacePath, StateModerator);
GettingStartedViewModel.NewAnalysisStarted += GettingStartedViewModel_NewAnalysisStarted;
GettingStartedViewModel.ExistingAnalysisSelected += GettingStartedViewModel_ExistingAnalysisSelected;
AnalysisRunningViewModel = new AnalysisRunningViewModel();
AnalysisRunningViewModel.AnalysisCancelled += AnalysisRunningViewModel_AnalysisCancelled;
AnalysisRunningViewModel.AnalysisComplete += AnalysisRunningViewModel_AnalysisComplete;
LoadingAnalysisViewModel = new AnalysisLoadingViewModel();
LoadingAnalysisViewModel.AnalysisLoaded += LoadingAnalysisViewModel_AnalysisLoaded;
ApplicationStatusMediator.SetStatus("Ready.");
}
public DatasetResolveCollectionViewModel(IEnumerable<DatasetResolveMatchViewModel> matches)
{
Datasets = new ObservableCollection<DatasetResolveMatchViewModel>(matches);
CheckAllCommand = new BaseCommand(CheckAll, BaseCommand.AlwaysPass);
UncheckAllCommand = new BaseCommand(UncheckAll, BaseCommand.AlwaysPass);
}
public AnalysisDatasetSelectionViewModel(MultiAlignAnalysis analysis)
{
m_inputFileFilter = "Input Files (*.txt)| *.txt| All Files (*.*)|*.*";
m_featureFileFilter = DatasetFilterFactory.BuildFileFilters(InputFileType.Features);
m_openFileDialog = new OpenFileDialog {Filter = m_inputFileFilter};
m_analysis = analysis;
ShouldSearchSubDirectories = SearchOption.TopDirectoryOnly;
// Create The Dataset View Model for Binding
Datasets = new ObservableCollection<DatasetInformationViewModel>();
foreach (var information in analysis.MetaData.Datasets)
{
var info = new DatasetInformationViewModel(information);
info.Selected += info_Selected;
Datasets.Add(info);
}
// Route the events here...
AddFolderCommand = new BaseCommand(AddFolderDelegate, BaseCommand.AlwaysPass);
AddInputFileCommand = new BaseCommand(AddInputFileDelegate, BaseCommand.AlwaysPass);
AddSingleFileCommand = new BaseCommand(AddSingleFileDelegate, BaseCommand.AlwaysPass);
BrowseSingleFileCommand = new BaseCommand(BrowseSingleFile, BaseCommand.AlwaysPass);
BrowseInputFileCommand = new BaseCommand(BrowseInput, BaseCommand.AlwaysPass);
BrowseDataFolderCommand = new BrowseFolderCommand(x => { DataFolderPath = x; });
RemoveSelectedCommand = new BaseCommand(RemoveSelected, BaseCommand.AlwaysPass);
SelectAllCommand = new BaseCommand(SelectAllDelegate, BaseCommand.AlwaysPass);
SelectNoneCommand = new BaseCommand(SelectNoneDelegate, BaseCommand.AlwaysPass);
SelectedDatasets = new ObservableCollection<DatasetInformationViewModel>();
}
public AnalysisRunningViewModel()
{
Messages = new ObservableCollection<StatusEventArgs>();
GalleryImages = new ObservableCollection<UserControl>();
Reporter = new AnalysisReportGenerator();
AnalysisNodes = new ObservableCollection<AnalysisGraphNodeViewModel>();
CancelAnalysis = new BaseCommand(CancelAnalysisDelegate, BaseCommand.AlwaysPass);
RouteMessages();
}
public UmcClusterCollectionTreeViewModel(List<UMCClusterLightMatched> clusters, UMCClusterTreeViewModel parent)
{
m_clusters = clusters;
m_filteredClusters = new ObservableCollection<UMCClusterTreeViewModel>(
(from cluster in clusters
select new UMCClusterTreeViewModel(cluster)).ToList());
m_exportCommand = new BaseCommand(ShowFilterWindow);
m_filterViewModel = new UMCClusterFilterViewModel(Clusters);
FilterCommand = new BaseCommand(FilterWindow, BaseCommand.AlwaysPass);
RegisterEvents();
}
public ClusterExportViewModel(IEnumerable<UMCClusterLightMatched> allClusters,
ObservableCollection<UMCClusterTreeViewModel> filteredClusters)
{
m_allClusters = allClusters;
m_filteredClusters = filteredClusters;
m_datasets = SingletonDataProviders.GetAllInformation();
Exporters = new ObservableCollection<IFeatureClusterWriter>();
var filters = "";
m_writerExtensionMap = new Dictionary<string, IFeatureClusterWriter>();
foreach (var exporter in UmcClusterExporterFactory.Create())
{
exporter.ShouldLoadClusterData = true;
if (filters.Length > 1)
filters += "| ";
filters += string.Format(" {0} (*{1}) | *{1}", exporter.Name,
exporter.Extension
);
m_writerExtensionMap.Add(exporter.Extension, exporter);
Exporters.Add(exporter);
}
filters += string.Format("| All Files (*.*) | (*.*)");
BrowseSave = new BrowseSaveFileCommand((string x) => { OutputPath = x; },
BaseCommand.AlwaysPass, filters);
// Action for saving all clusters
Action saveAction = delegate
{
SelectedExporter.Path = OutputPath;
var clusters = new List<UMCClusterLight>();
if (IsFilteredClusters)
{
foreach (var x in m_filteredClusters)
clusters.Add(x.Cluster.Cluster);
}
else
{
foreach (var x in m_allClusters)
clusters.Add(x.Cluster);
}
try
{
SelectedExporter.WriteClusters(clusters, m_datasets.ToList());
Status = "The file was saved: " + SelectedExporter.Path;
}
catch (Exception ex)
{
Status = "Could not save the file: " + ex.Message;
}
};
SaveData = new BaseCommand(saveAction, CanSave);
}
public AnalysisOptionsViewModel(MultiAlignAnalysisOptions options)
{
m_options = options;
ClusteringAlgorithms = new ObservableCollection<LcmsFeatureClusteringAlgorithmType>();
AlignmentAlgorithms = new ObservableCollection<FeatureAlignmentType>();
FeatureFindingAlgorithms = new ObservableCollection<FeatureFinderType>();
UpdateOptions();
InstrumentPresets = new ObservableCollection<InstrumentPresetViewModel>();
ExperimentPresets = new ObservableCollection<ExperimentPresetViewModel>();
TimeOptions = new ObservableCollection<string>();
var presets = new Dictionary<string, bool>();
foreach (var preset in ExperimentPresetFactory.Create())
{
ExperimentPresets.Add(preset);
if (!presets.ContainsKey(preset.InstrumentPreset.Name))
{
presets.Add(preset.InstrumentPreset.Name, false);
InstrumentPresets.Add(preset.InstrumentPreset);
}
}
foreach (var preset in InstrumentPresetFactory.Create())
{
if (!presets.ContainsKey(preset.Name))
{
InstrumentPresets.Add(preset);
}
}
TimeOptions.Add("Minutes");
TimeOptions.Add("Scans");
SelectedPreset = InstrumentPresets[0];
SelectedExperimentPreset = ExperimentPresets[0];
TreatAsTimeOrScan = TimeOptions[0];
m_saveDialog = new SaveFileDialog();
m_dialog = new OpenFileDialog
{
Filter = Resources.MultiAlignParameterFileFilter
};
m_saveDialog.Filter = Resources.MultiAlignParameterFileFilter;
ShowAdvancedWindowCommand = new BaseCommand(ShowAdvancedWindow);
SaveOptionsCommand = new BaseCommand(SaveCurrentParameters);
LoadExistingCommand = new BaseCommand(LoadExistingParameters);
Enum.GetValues(typeof (LcmsFeatureClusteringAlgorithmType))
.Cast<LcmsFeatureClusteringAlgorithmType>()
.ToList()
.ForEach(x => ClusteringAlgorithms.Add(x));
Enum.GetValues(typeof (FeatureAlignmentType))
.Cast<FeatureAlignmentType>()
.ToList()
.ForEach(x => AlignmentAlgorithms.Add(x));
Enum.GetValues(typeof (FeatureFinderType))
.Cast<FeatureFinderType>()
.ToList()
.ForEach(x => FeatureFindingAlgorithms.Add(x));
}
public AnalysisViewModel(MultiAlignAnalysis analysis)
{
m_showDriftTime = false;
LoadDatasets(analysis);
// Create matching clusters and AMT Matches.
var matches = analysis.DataProviders.MassTagMatches.FindAll();
var clusters =
analysis.Clusters.MapMassTagsToClusters(matches, analysis.MassTagDatabase);
// Cache the clusters so that they can be readily accessible later on.
// This will help speed up performance, so that we dont have to hit the database
// when we want to find matching mass tags, and dont have to map clusters to tags multiple times.
FeatureCacheManager<UMCClusterLightMatched>.SetFeatures(clusters.Item1);
FeatureCacheManager<MassTagToCluster>.SetFeatures(clusters.Item2);
SingletonDataProviders.Providers = analysis.DataProviders;
// Create sub-view models
MassTags = new ObservableCollection<MassTagToCluster>(clusters.Item2);
ClusterTree = new UmcClusterCollectionTreeViewModel(clusters.Item1);
ClusterSpectraViewModel = new UmcClusterSpectraViewModel();
ClusterIdentificationViewModel = new UMCClusterIdentificationViewModel();
AnalysisOptionsViewModel = new AnalysisOptionsViewModel(analysis.Options);
ClusterViewModel = new ClusterDetailViewModel();
var charges = SingletonDataProviders.Providers.FeatureCache.RetrieveChargeStates();
GlobalStatisticsViewModel = new GlobalStatisticsViewModel(clusters.Item1, charges);
HasIdentifications = (MassTags.Count > 0);
SelectedClusterName = "Cluster Details:";
LoadClusters(clusters.Item1);
ApplyViewAsFilter = new BaseCommand(FilterFromView);
}
private void CreateCommands()
{
Action removeRecentList = delegate
{
RecentAnalyses.Clear();
SaveWorkSpace();
};
ClearRecentList = new BaseCommand(removeRecentList);
var command = new LoadExistingAnalysisCommand();
command.ExistingAnalysisSelected += command_ExistingAnalysisSelected;
LoadExistingAnalysis = command;
var startNew = new BaseCommand(startNew_StartNewAnalysis, BaseCommand.AlwaysPass);
StartNewAnalysis = startNew;
}