internal void ClusterFeatures(IProgress <ProgressData> workflowProgress = null) { var taskBarProgress = TaskBarProgress.GetInstance(); taskBarProgress.ShowProgress(this, true); workflowProgress = workflowProgress ?? new Progress <ProgressData>(); IProgress <ProgressData> internalProgress = new Progress <ProgressData>(pd => { this.progress.Report((int)pd.Percent); this.ProgressPercent = pd.Percent; taskBarProgress.SetProgress(this, pd.Percent); workflowProgress.Report(pd); }); this.algorithms = this.builder.GetAlgorithmProvider(this.options); var clusterer = this.algorithms.Clusterer; clusterer.Parameters = LcmsClusteringOptions.ConvertToOmics(this.options.LcmsClusteringOptions); this.featureCache = this.analysis.DataProviders.FeatureCache; if (clusterer is PromexClusterer) { var promexClusterer = clusterer as PromexClusterer; promexClusterer.Readers = this.analysis.DataProviders.ScanSummaryProviderCache; } foreach (var dataset in this.Datasets) { if (dataset.FeaturesFound) { dataset.DatasetState = DatasetInformationViewModel.DatasetStates.Clustering; } } ThreadSafeDispatcher.Invoke(this.ClusterFeaturesCommand.RaiseCanExecuteChanged); ThreadSafeDispatcher.Invoke(this.DisplayClustersCommand.RaiseCanExecuteChanged); this.ShouldShowProgress = true; var progData = new ProgressData(internalProgress); var clusterProgress = new Progress <ProgressData>(pd => progData.Report(pd.Percent)); this.analysis.DataProviders.DatabaseLock.EnterWriteLock(); DatabaseIndexer.IndexClustersDrop(NHibernateUtil.Path); this.analysis.DataProviders.ClusterCache.ClearAllClusters(); this.analysis.DataProviders.DatabaseLock.ExitWriteLock(); // The id for a cluster - keep track here to avoid duplicates when separating by charge. var clusterCount = 0; // Here we see if we need to separate the charge... // IMS is said to require charge separation if (!this.analysis.Options.LcmsClusteringOptions.ShouldSeparateCharge) { progData.StepRange(45); var features = new List <UMCLight>(); var i = 0; var datasets = this.Datasets.Where(ds => ds.FeaturesFound).ToList(); foreach (var dataset in datasets) { this.analysis.DataProviders.DatabaseLock.EnterReadLock(); features.AddRange(this.featureCache.FindByDatasetId(dataset.DatasetId)); this.analysis.DataProviders.DatabaseLock.ExitReadLock(); progData.Report(++i, datasets.Count); } progData.StepRange(100); ClusterGroupOfFeatures(clusterer, features, ref clusterCount, clusterProgress); } else { var maxChargeState = this.featureCache.FindMaxCharge(); // Here we cluster all charge states separately. Probably IMS Data. for (var chargeState = 1; chargeState <= maxChargeState; chargeState++) { var maxPercent = ((100.0 * chargeState) / maxChargeState); // TODO: Add restriction by selected dataset ids? var features = this.featureCache.FindByCharge(chargeState); if (features.Count < 1) { continue; } progData.StepRange(maxPercent); ClusterGroupOfFeatures(clusterer, features, ref clusterCount, clusterProgress); } this.analysis.Clusters = this.analysis.DataProviders.ClusterCache.FindAll(); } this.analysis.DataProviders.DatabaseLock.EnterWriteLock(); DatabaseIndexer.IndexClusters(NHibernateUtil.Path); this.analysis.DataProviders.DatabaseLock.ExitWriteLock(); foreach (var dataset in this.Datasets) { if (dataset.DatasetState == DatasetInformationViewModel.DatasetStates.PersistingClusters) { dataset.DatasetState = DatasetInformationViewModel.DatasetStates.Clustered; } } try { // Write to file this.WriteClusterData(string.Format("{0}_crosstab.tsv", this.analysis.AnalysisName), this.analysis.Clusters); } catch (Exception ex) { var errMsg = "Error writing results to text file: " + ex.Message; Logger.PrintMessage(errMsg); // Todo: Add this: if (!GlobalSettings.AutomatedAnalysisMode) MessageBox.Show(errMsg); } ThreadSafeDispatcher.Invoke(this.ClusterFeaturesCommand.RaiseCanExecuteChanged); ThreadSafeDispatcher.Invoke(this.DisplayClustersCommand.RaiseCanExecuteChanged); taskBarProgress.ShowProgress(this, false); this.ShouldShowProgress = false; }
/// <summary> /// Perform alignment. /// </summary> /// <param name="workFlowDatasets">Datasets to run on when being called externally form this view model.</param> /// <param name="workflowProgress">The progress reporter for when this method is called externally from this view model.</param> internal void AlignToBaseline(List <DatasetInformationViewModel> workFlowDatasets = null, IProgress <ProgressData> workflowProgress = null) { // Use Promiscuous points when aligning to an AMT tag database // Do not use Promiscuous points when aligning to a baseline dataset this.analysis.Options.AlignmentOptions.UsePromiscuousPoints = !this.ShouldAlignToBaseline; // Flag whether we are aligning to an AMT tag database this.analysis.Options.AlignmentOptions.LCMSWarpOptions.AlignToMassTagDatabase = !this.ShouldAlignToBaseline; // Show the progress bar this.ShowAlignmentProgress = true; var taskBarProgress = TaskBarProgress.GetInstance(); taskBarProgress.ShowProgress(this, true); // Update algorithms and providers var featureCache = new FeatureLoader { Providers = this.analysis.DataProviders }; this.algorithms = this.builder.GetAlgorithmProvider(this.analysis.Options); ////this.algorithms.DatabaseAligner.Progress += aligner_Progress; ////this.algorithms.DatasetAligner.Progress += aligner_Progress; this.aligner.m_algorithms = this.algorithms; var baselineFeatures = new List <UMCLight>(); if (this.ShouldAlignToBaseline) { baselineFeatures = featureCache.Providers.FeatureCache.FindByDatasetId(this.selectedBaseline.DatasetId); this.SelectedBaseline.DatasetState = DatasetInformationViewModel.DatasetStates.Baseline; var priorAlignment = (from x in this.alignmentInformation where x.DatasetID == this.selectedBaseline.DatasetId select x).ToList(); if (priorAlignment.Any()) { this.alignmentInformation.Remove(priorAlignment.Single()); } } var alignmentData = new AlignmentDAOHibernate(); alignmentData.ClearAll(); var selectedFiles = workFlowDatasets ?? this.Datasets.Where(file => file.IsSelected && !file.DoingWork && (this.ShouldAlignToAMT || !file.IsBaseline)).ToList(); foreach (var file in selectedFiles) { file.DatasetState = DatasetInformationViewModel.DatasetStates.Aligning; } workflowProgress = workflowProgress ?? new Progress <ProgressData>(); IProgress <ProgressData> totalProgress = new Progress <ProgressData>(pd => { this.AlignmentProgress = pd.Percent; workflowProgress.Report(pd); taskBarProgress.SetProgress(this, pd.Percent); }); var totalProgressData = new ProgressData(totalProgress); DatabaseIndexer.IndexClustersDrop(NHibernateUtil.Path); DatabaseIndexer.IndexFeaturesDrop(NHibernateUtil.Path); var i = 1; foreach (var file in selectedFiles) { ThreadSafeDispatcher.Invoke(() => this.AlignCommand.RaiseCanExecuteChanged()); ThreadSafeDispatcher.Invoke(() => this.DisplayAlignmentCommand.RaiseCanExecuteChanged()); ThreadSafeDispatcher.Invoke(() => this.SaveAlignmentPlotsCommand.RaiseCanExecuteChanged()); if ((file.Dataset.IsBaseline || !file.FeaturesFound) && this.ShouldAlignToBaseline) { file.DatasetState = DatasetInformationViewModel.DatasetStates.Aligned; continue; } this.analysis.DataProviders.DatabaseLock.EnterReadLock(); IList <UMCLight> features = featureCache.Providers.FeatureCache.FindByDatasetId(file.DatasetId); this.analysis.DataProviders.DatabaseLock.ExitReadLock(); AlignmentData alignment; totalProgressData.StepRange((100.0 * i++) / selectedFiles.Count); var fileInstance = file; var datasetProgress = new Progress <ProgressData>( pd => { fileInstance.Progress = pd.Percent; totalProgressData.Report(pd.Percent); }); if (this.ShouldAlignToBaseline) { // Aligning to a baseline dataset alignment = this.aligner.AlignToDataset(ref features, file.Dataset, baselineFeatures, datasetProgress); alignment.BaselineIsAmtDB = false; } else { // Aligning to a database alignment = this.aligner.AlignToDatabase(ref features, file.Dataset, this.analysis.MassTagDatabase, datasetProgress); alignment.BaselineIsAmtDB = true; } // Check if there is information from a previous alignment for this dataset. If so, replace it. If not, just add the new one. var priorAlignment = this.alignmentInformation.Where(x => x.DatasetID == alignment.DatasetID).ToList(); if (priorAlignment.Any()) { this.alignmentInformation.Remove(priorAlignment.Single()); this.alignmentInformation.Add(alignment); } else { this.alignmentInformation.Add(alignment); } file.Dataset.AlignmentData = alignment; this.analysis.DataProviders.DatabaseLock.EnterWriteLock(); featureCache.CacheFeatures(features); this.analysis.DataProviders.DatabaseLock.ExitWriteLock(); file.DatasetState = DatasetInformationViewModel.DatasetStates.Aligned; ThreadSafeDispatcher.Invoke(() => this.AlignCommand.RaiseCanExecuteChanged()); ThreadSafeDispatcher.Invoke(() => this.DisplayAlignmentCommand.RaiseCanExecuteChanged()); ThreadSafeDispatcher.Invoke(() => this.SaveAlignmentPlotsCommand.RaiseCanExecuteChanged()); file.Progress = 0; } if (this.ShouldAlignToBaseline) { this.SelectedBaseline.DatasetState = DatasetInformationViewModel.DatasetStates.Aligned; } DatabaseIndexer.IndexFeatures(NHibernateUtil.Path); taskBarProgress.ShowProgress(this, false); this.ShowAlignmentProgress = false; this.AlignmentProgress = 0; }