/// <summary>
/// Creates an analysis naming view model
/// </summary>
/// <param name="configuration"></param>
public AnalysisNamingViewModel(AnalysisConfig configuration)
{
m_configuration = configuration;
var command = new BrowseFolderCommand(command_FolderSelected);
BrowseCommand = command;
}
/// <summary>
/// Determines if all of the data is valid yet for the analysis.
/// </summary>
/// <returns></returns>
public static bool IsStepValid(AnalysisConfig config, AnalysisSetupStep step, ref string errorMessage)
{
var analysis = config.Analysis;
var isStepValid = true;
switch (step)
{
case AnalysisSetupStep.DatasetSelection:
if (analysis.MetaData.Datasets.Count < 1)
{
errorMessage = "Select datasets before continuing.";
isStepValid = false;
}
break;
case AnalysisSetupStep.BaselineSelection:
isStepValid = ValidateBaseline(analysis, ref errorMessage);
break;
case AnalysisSetupStep.OptionsSelection:
break;
case AnalysisSetupStep.Naming:
isStepValid = ValidateNames(config, ref errorMessage);
break;
case AnalysisSetupStep.Started:
if (analysis.AnalysisType != AnalysisType.Full)
{
isStepValid = false;
}
break;
}
return isStepValid;
}
/// <summary>
/// Initializes a new instance of the <see cref="MainViewModel"/> class.
/// </summary>
public MainViewModel()
{
m_config = new AnalysisConfig();
Analysis = new MultiAlignAnalysis();
m_config.AnalysisName = "Analysis.db3";
m_config.Analysis = Analysis;
this.WindowTitle = "MultiAlign Rogue";
DataSelectionViewModel = new AnalysisDatasetSelectionViewModel(Analysis);
SelectFilesCommand = new RelayCommand(SelectFiles, () => !string.IsNullOrWhiteSpace(this.ProjectPath));
SelectDirectoryCommand = new RelayCommand(SelectDirectory, () => !string.IsNullOrWhiteSpace(this.ProjectPath));
AddFolderCommand = new RelayCommand(AddFolderDelegate, () => !string.IsNullOrWhiteSpace(this.InputFilePath) && Directory.Exists(this.InputFilePath) && !string.IsNullOrWhiteSpace(this.ProjectPath));
SearchDmsCommand = new RelayCommand(SearchDms, () => this.ShowOpenFromDms && !string.IsNullOrWhiteSpace(this.ProjectPath));
CreateNewProjectCommand = new RelayCommand(this.CreateNewProject);
SaveProjectCommand = new RelayCommand(SaveProject, () => !string.IsNullOrWhiteSpace(this.ProjectPath));
LoadProjectCommand = new RelayCommand(LoadProject);
SaveAsProjectCommand = new RelayCommand(this.SaveProjectAs, () => !string.IsNullOrWhiteSpace(this.ProjectPath));
featureCache = new FeatureLoader { Providers = Analysis.DataProviders };
this.SelectedDatasets = new List<DatasetInformationViewModel>();
Datasets = new ObservableCollection<DatasetInformationViewModel>();
featureCache.Providers = Analysis.DataProviders;
this.FeatureFindingSettingsViewModel = new FeatureFindingSettingsViewModel(Analysis, featureCache);
this.AlignmentSettingsViewModel = new AlignmentSettingsViewModel(Analysis, featureCache);
this.ClusterSettingsViewModel = new ClusterSettingsViewModel(Analysis);
}
/// <summary>
/// Load the data from the dataset information objects to the cache at the analysis Path
/// </summary>
private void PerformDataLoadAndAlignment(AnalysisConfig config)
{
UmcLoaderFactory.Status += UMCLoaderFactory_Status;
UpdateStatus("Loading data.");
var analysisOptions = config.Analysis.Options;
var datasets = config.Analysis.MetaData.Datasets.ToList();
var lcmsFilterOptions = analysisOptions.LcmsFilteringOptions;
var msFilterOptions = analysisOptions.MsFilteringOptions;
var baselineDataset = config.Analysis.MetaData.BaselineDataset;
var baselineFeatures = LoadBaselineData(baselineDataset,
msFilterOptions,
analysisOptions.LcmsFindingOptions,
lcmsFilterOptions,
config.Analysis.DataProviders,
config.Analysis.MassTagDatabase,
config.Analysis.Options.AlignmentOptions.IsAlignmentBaselineAMasstagDB);
var alignmentData = new AlignmentDAOHibernate();
alignmentData.ClearAll();
var providers = config.Analysis.DataProviders;
var featureCache = new FeatureLoader
{
Providers = providers
};
RegisterProgressNotifier(featureCache);
MassTagDatabase database = null;
if (config.Analysis.MassTagDatabase != null)
database = new MassTagDatabase(config.Analysis.MassTagDatabase,
config.Analysis.Options.AlignmentOptions.MassTagObservationCount);
SingletonDataProviders.Providers = config.Analysis.DataProviders;
foreach (var dataset in datasets)
{
if (dataset.IsBaseline)
continue;
var features = featureCache.LoadDataset(dataset,
analysisOptions.MsFilteringOptions,
analysisOptions.LcmsFindingOptions,
analysisOptions.LcmsFilteringOptions);
features = AlignDataset(features,
baselineFeatures,
database,
dataset,
baselineDataset);
featureCache.CacheFeatures(features);
}
UmcLoaderFactory.Status -= UMCLoaderFactory_Status;
}
private void LoadMtdb(AnalysisConfig config)
{
UpdateStatus("Loading the database from the SQLite result database.");
var provider = new MassTagDatabaseLoaderCache {Provider = m_config.Analysis.DataProviders.MassTags};
RegisterProgressNotifier(provider);
var database = provider.LoadDatabase();
config.Analysis.MassTagDatabase = database;
if (MassTagsLoaded != null)
{
MassTagsLoaded(this, new MassTagsLoadedEventArgs(database.MassTags, database));
}
DeRegisterProgressNotifier(provider);
}
/// <summary>
/// Creates an entry in the DB if a new database should be created.
/// </summary>
/// <param name="config"></param>
private void CreateMtdb(AnalysisConfig config)
{
MassTagDatabase database;
// Load the mass tag database if we are aligning, or if we are
// peak matching (but aligning to a reference dataset.
if (m_config.Analysis.Options.AlignmentOptions.IsAlignmentBaselineAMasstagDB)
{
UpdateStatus("Loading Mass Tag database from database: " +
m_config.Analysis.MetaData.Database.DatabaseName);
database = MtdbLoaderFactory.LoadMassTagDatabase(m_config.Analysis.MetaData.Database,
m_config.Analysis.Options.MassTagDatabaseOptions);
}
else if (m_config.Analysis.MetaData.Database != null &&
m_config.Analysis.MetaData.Database.DatabaseFormat != MassTagDatabaseFormat.None)
{
UpdateStatus("Loading Mass Tag database from database: " +
m_config.Analysis.MetaData.Database.DatabaseName);
database = MtdbLoaderFactory.LoadMassTagDatabase(m_config.Analysis.MetaData.Database,
m_config.Analysis.Options.MassTagDatabaseOptions);
}
else
{
config.Analysis.MassTagDatabase = null;
config.ShouldPeakMatch = false;
return;
}
if (database != null)
{
config.ShouldPeakMatch = true;
var totalMassTags = database.MassTags.Count;
UpdateStatus("Loaded " + totalMassTags + " mass tags.");
}
config.Analysis.MassTagDatabase = database;
if (database == null)
return;
config.Analysis.DataProviders.MassTags.AddAll(database.MassTags);
var proteinCache = new ProteinDAO();
proteinCache.AddAll(database.AllProteins);
var map = (from massTagId in database.Proteins.Keys
from p in database.Proteins[massTagId]
select new MassTagToProteinMap
{
ProteinId = p.ProteinId,
MassTagId = massTagId,
RefId = p.RefId
}).ToList();
var tempCache = new GenericDAOHibernate<MassTagToProteinMap>();
tempCache.AddAll(map);
if (MassTagsLoaded != null)
MassTagsLoaded(this, new MassTagsLoadedEventArgs(database.MassTags, database));
}
/// <summary>
/// Processes the MA analysis data.
/// </summary>
public int StartMultiAlign(AnalysisConfig config, IAnalysisReportGenerator reporter)
{
m_reportCreator = reporter;
m_config = config;
// Builds the list of algorithm providers.
var builder = new AlgorithmBuilder();
// Use this to signal when the analysis is done.
config.triggerEvent = new ManualResetEvent(false);
config.errorEvent = new ManualResetEvent(false);
m_config.stopEvent = new ManualResetEvent(false);
config.errorException = null;
// Print Help
// See if the user wants help
if (config.showHelp)
{
PrintHelp();
config.errorEvent.Dispose();
config.triggerEvent.Dispose();
return 0;
}
// Validate the command line
var validated = AnalysisValidator.ValidateSetup(m_config);
if (validated == AnalysisType.InvalidParameters)
{
PrintHelp();
return 0;
}
// Setup log path, analysis path, and print version to log file.
SetupAnalysisEssentials();
// Determine if we have specified a valid database to extract
// data from or to re-start an analysis.
var databasePath = Path.Combine(config.AnalysisPath, config.AnalysisName);
var databaseExists = File.Exists(databasePath);
var createDatabase = ShouldCreateDatabase(validated, databaseExists);
// make sure that we were not told to skip to a new part of the analysis.
if (config.InitialStep >= AnalysisStep.Alignment)
{
createDatabase = false;
}
var result = 0;
switch (validated)
{
case AnalysisType.Full:
result = PerformAnalysis(config, builder, validated, createDatabase);
break;
}
return result;
}
private static bool ValidateNames(AnalysisConfig config, ref string errorMessage)
{
var isStepValid = true;
if (config.AnalysisPath == null)
{
errorMessage = "An output folder location needs to be supplied.";
isStepValid = false;
}
else
{
var chars = Path.GetInvalidPathChars();
var name = config.AnalysisPath;
foreach (var c in chars)
{
if (name.Contains(c))
{
errorMessage = "The path you provided has invalid characters.";
return false;
}
}
//if (!System.IO.Directory.Exists(config.AnalysisPath))
//{
// errorMessage = "The root folder you specified does not exist or is invalid.";
// isStepValid = false;
//}
if (config.AnalysisName == null)
{
errorMessage = "An analysis name needs to be supplied.";
isStepValid = false;
}
}
return isStepValid;
}
public AnalysisController()
{
m_config = null;
m_reportCreator = null;
m_chargeMap = new Dictionary<int, int>();
}
public AnalysisStatusArgs(AnalysisConfig configuration)
{
Configuration = configuration;
}
/// <summary>
/// Shows the new analysis setup
/// </summary>
private void ShowNewAnalysisSetup()
{
string message;
var canStart = StateModerator.CanPerformNewAnalysis(out message);
Status = message;
if (!canStart)
{
return;
}
ApplicationStatusMediator.SetStatus("Creating new analysis.");
StateModerator.CurrentViewState = ViewState.SetupAnalysisView;
StateModerator.CurrentAnalysisState = AnalysisState.Setup;
var config = new AnalysisConfig
{
Analysis = new MultiAlignAnalysis(),
AnalysisPath = MainDataDirectory,
AnalysisName = MainDataName
};
config.Analysis.AnalysisType = AnalysisType.Full;
config.Analysis.Options.AlignmentOptions.IsAlignmentBaselineAMasstagDB = false;
AnalysisSetupViewModel = new AnalysisSetupViewModel(config);
AnalysisSetupViewModel.AnalysisQuit += AnalysisSetupViewModel_AnalysisQuit;
AnalysisSetupViewModel.AnalysisStart += AnalysisSetupViewModel_AnalysisStart;
AnalysisSetupViewModel.CurrentStep = AnalysisSetupStep.DatasetSelection;
}
public void Start(AnalysisConfig config)
{
// Set the messages
Messages.Clear();
GalleryImages.Clear();
IsAnalysisRunning = true;
Reporter.Config = config;
m_configuration = config;
Controller = new AnalysisController();
Controller.AnalysisComplete += Controller_AnalysisComplete;
Controller.AnalysisError += Controller_AnalysisError;
Controller.AnalysisCancelled += Controller_AnalysisCancelled;
Controller.AnalysisStarted += ControllerOnAnalysisStarted;
// Start the analysis.
Controller.StartMultiAlignGui(config, this);
}
/// <summary>
/// Validates the input options to make sure everything is set.
/// </summary>
/// <returns></returns>
public static AnalysisType ValidateSetup(AnalysisConfig config)
{
var analysisType = AnalysisType.Full;
var isExporting = (config.ExporterNames.CrossTabPath != null);
isExporting = (isExporting || config.ExporterNames.ClusterScanPath != null);
isExporting = (isExporting || config.ExporterNames.ClusterMSMSPath != null);
isExporting = (isExporting || config.ExporterNames.CrossTabAbundance != null);
// --------------------------------------------------------------------------------
// Make sure that the analysis name and path are provided first.
// --------------------------------------------------------------------------------
if (config.AnalysisName == null)
{
Logger.PrintMessage("No analysis database name provided.");
analysisType = AnalysisType.InvalidParameters;
return analysisType;
}
if (config.AnalysisPath == null)
{
Logger.PrintMessage("No analysis path provided.");
analysisType = AnalysisType.InvalidParameters;
return analysisType;
}
// --------------------------------------------------------------------------------
// If no input is provided. then they are using the database.
// --------------------------------------------------------------------------------
if (config.InputPaths == null)
{
Logger.PrintMessage("No input file provided.");
analysisType = AnalysisType.ExportDataOnly;
}
if (config.ParameterFile == null)
{
Logger.PrintMessage("No parameter file specified.");
analysisType = AnalysisType.ExportDataOnly;
}
// --------------------------------------------------------------------------------
// Determine if they are exporting data only or not.
// --------------------------------------------------------------------------------
if (analysisType == AnalysisType.ExportDataOnly)
{
// --------------------------------------------------------------------------------
// Imports the factors into the database.
// --------------------------------------------------------------------------------
if (config.ShouldUseFactors)
{
Logger.PrintMessage("Importing factors only");
analysisType = AnalysisType.FactorImporting;
}
else if (!isExporting)
{
Logger.PrintMessage("No export file names provided.");
analysisType = AnalysisType.InvalidParameters;
return analysisType;
}
}
return analysisType;
}
/// <summary>
/// Performs the analysis.
/// </summary>
private void PerformAnalysisGui(AnalysisConfig config, AlgorithmBuilder builder, AnalysisType validated,
bool createDatabase, WorkerObject worker)
{
Logger.PrintMessage("Performing analysis.");
MultiAlignAnalysisProcessor processor = null;
try
{
// Creates or connects to the underlying analysis database.
var providers = SetupDataProviders(createDatabase);
// Create the clustering, analysis, and plotting paths.
builder.BuildClusterer(config.Analysis.Options.LcmsClusteringOptions.LcmsFeatureClusteringAlgorithm);
config.Analysis.DataProviders = providers;
config.Analysis.AnalysisType = validated;
ConstructPlotPath();
ExportParameterFile();
Logger.PrintSpacer();
PrintParameters(config.Analysis, createDatabase);
Logger.PrintSpacer();
// Setup the processor.
processor = ConstructAnalysisProcessor(builder, providers);
// Tell the processor whether to load data or not.
processor.ShouldLoadData = createDatabase;
// Construct the dataset information for export.// Create dataset information.
Logger.PrintMessage("Storing dataset information into the database.");
var information = Enumerable.ToList(config.Analysis.MetaData.Datasets);
m_config.Analysis.DataProviders.DatasetCache.AddAll(information);
Logger.PrintMessage("Creating exporter options.");
if (config.ExporterNames.CrossTabPath == null)
{
config.ExporterNames.CrossTabPath = config.AnalysisName.Replace(".db3", "");
}
if (config.ExporterNames.CrossTabAbundance == null)
{
config.ExporterNames.CrossTabAbundance = config.AnalysisName.Replace(".db3", "");
}
ConstructExporting();
Logger.PrintMessage("Cleaning up old analysis branches.");
CleanupOldAnalysisBranches(config);
Logger.PrintMessage("Analysis Started.");
processor.StartAnalysis(config);
var handleId =
WaitHandle.WaitAny(new WaitHandle[] { config.triggerEvent, config.errorEvent, config.stopEvent });
if (handleId == 1)
{
Logger.PrintMessageWorker("There was an error during processing.", 1, false);
config.triggerEvent.Dispose();
config.errorEvent.Dispose();
processor.Dispose();
if (AnalysisError != null)
{
AnalysisError(this, null);
}
return;
}
if (handleId == 2)
{
Logger.PrintMessageWorker("Stopping the analysis.", 1, false);
processor.StopAnalysis();
worker.SynchEvent.Set();
Thread.Sleep(50);
config.triggerEvent.Dispose();
config.errorEvent.Dispose();
processor.Dispose();
if (AnalysisCancelled != null)
{
AnalysisCancelled(this, null);
}
return;
}
}
catch (Exception ex)
{
Logger.PrintMessage(
"There was an error Performing analysis");
Logger.PrintMessage(ex.Message);
Logger.PrintMessage(ex.StackTrace);
return;
}
try
{
m_reportCreator.CreatePlotReport();
}
catch (Exception ex)
{
Logger.PrintMessage(
"There was an error when trying to create the final analysis plots, however, the data analysis is complete.");
Logger.PrintMessage(ex.Message);
Logger.PrintMessage(ex.StackTrace);
}
config.triggerEvent.Dispose();
config.errorEvent.Dispose();
processor.Dispose();
CleanupDataProviders();
Logger.PrintMessage("Indexing Database Clusters for Faster Retrieval");
var databasePath = Path.Combine(m_config.AnalysisPath, m_config.AnalysisName);
DatabaseIndexer.IndexClusters(databasePath);
Logger.PrintMessage("Indexing Database Features");
DatabaseIndexer.IndexFeatures(databasePath);
Logger.PrintMessage("Analysis Complete");
if (AnalysisComplete != null)
{
AnalysisComplete(this, null);
}
}
/// <summary>
/// Performs the analysis.
/// </summary>
private int PerformAnalysis(AnalysisConfig config, AlgorithmBuilder builder, AnalysisType validated,
bool createDatabase)
{
InputAnalysisInfo analysisSetupInformation;
Logger.PrintMessage("Performing analysis.");
// Read the input files.
bool useMtdb;
var isInputFileOk = ReadInputDefinitionFile(out analysisSetupInformation, out useMtdb);
if (!isInputFileOk)
return 1;
// Figure out if the factors are defined.
if (config.options.ContainsKey("-factors"))
{
Logger.PrintMessage("Factor file specified.");
var factorFile = config.options["-factors"][0];
analysisSetupInformation.FactorFile = factorFile;
}
// Creates or connects to the underlying analysis database.
var providers = SetupDataProviders(createDatabase);
// Create the clustering, analysis, and plotting paths.
ConstructClustering(builder);
config.Analysis = ConstructAnalysisObject(analysisSetupInformation);
config.Analysis.DataProviders = providers;
config.Analysis.AnalysisType = validated;
ConstructPlotPath();
// Read the parameter files.
ReadParameterFile();
// Construct Dataset information
// Construct the dataset information for export.
ConstructDatasetInformation(analysisSetupInformation, config.Analysis, createDatabase);
if (config.ShouldUseFactors)
{
ConstructFactorInformation(analysisSetupInformation, config.Analysis.MetaData.Datasets,
config.Analysis.DataProviders);
}
var isBaselineSpecified = ConstructBaselines(analysisSetupInformation, config.Analysis.MetaData, useMtdb);
if (!isBaselineSpecified)
{
return 1;
}
ExportParameterFile();
Logger.PrintSpacer();
PrintParameters(config.Analysis, createDatabase);
Logger.PrintSpacer();
// Setup the processor.
var processor = ConstructAnalysisProcessor(builder, providers);
// Tell the processor whether to load data or not.
processor.ShouldLoadData = createDatabase;
Logger.PrintMessage("Creating exporter options.");
if (config.ExporterNames.CrossTabPath == null)
{
config.ExporterNames.CrossTabPath = config.AnalysisName.Replace(".db3", "");
}
if (config.ExporterNames.CrossTabAbundance == null)
{
config.ExporterNames.CrossTabAbundance = config.AnalysisName.Replace(".db3", "");
}
ConstructExporting();
Logger.PrintMessage("Cleaning up old analysis branches.");
CleanupOldAnalysisBranches(config);
// Start the analysis
Logger.PrintMessage("Analysis Started.");
processor.StartAnalysis(config);
var handleId = WaitHandle.WaitAny(new WaitHandle[] { config.triggerEvent, config.errorEvent });
var wasError = false;
if (handleId != 1)
{
try
{
m_reportCreator.CreatePlotReport();
}
catch (Exception ex)
{
wasError = true;
Logger.PrintMessage(
"There was an error when trying to create the final analysis plots, however, the data analysis is complete.");
Logger.PrintMessage(ex.Message);
Logger.PrintMessage(ex.StackTrace);
}
config.Analysis.Dispose();
config.triggerEvent.Dispose();
config.errorEvent.Dispose();
processor.Dispose();
CleanupDataProviders();
if (!wasError)
{
Logger.PrintMessage("Indexing Database Features");
DatabaseIndexer.IndexFeatures(config.AnalysisPath);
DatabaseIndexer.IndexClusters(config.AnalysisPath);
}
Logger.PrintMessage("Analysis Complete.");
return 0;
}
// Finalize the analysis plots etc.
Logger.PrintMessage("There was an error during processing.");
return 1;
}
private void ImportFactors(AnalysisConfig config, bool databaseExists)
{
Logger.PrintMessage("Updating factors");
if (!databaseExists)
{
Logger.PrintMessage("The database you specified to extract data from does not exist.");
return;
}
// Create access to data.
var providers = SetupDataProviders(false);
if (providers == null)
{
Logger.PrintMessage("Could not create connection to database.");
return;
}
// Find all the datasets
var datasetsFactors = providers.DatasetCache.FindAll();
if (datasetsFactors == null || datasetsFactors.Count == 0)
{
Logger.PrintMessage("There are no datasets present in the current database.");
CleanupDataProviders();
return;
}
var info = new InputAnalysisInfo();
if (config.options.ContainsKey("-factors"))
{
Logger.PrintMessage("Factor file specified.");
var factorFile = config.options["-factors"][0];
info.FactorFile = factorFile;
}
ConstructFactorInformation(info, datasetsFactors.ToObservableCollection(), providers);
CleanupDataProviders();
}
/// <summary>
/// Performs peak matching with loaded clusters.
/// </summary>
private void PerformPeakMatching(AnalysisConfig config)
{
if (!config.ShouldPeakMatch)
return;
if (m_config.Analysis.MassTagDatabase == null)
{
UpdateStatus("Could not peak match. The database was not set.");
}
else
{
var clusters = m_config.Analysis.DataProviders.ClusterCache.FindAll();
var peakMatcher = m_algorithms.PeakMatcher;
UpdateStatus("Performing Peak Matching");
var adapter = peakMatcher as STACAdapter<UMCClusterLight>;
if (adapter != null)
{
UpdateStatus(adapter.Options.UseDriftTime ? "Using drift time." : "Ignoring drift time.");
}
var matchResults = new PeakMatchingResults<UMCClusterLight, MassTagLight>();
clusters.ForEach(x => x.Net = x.Net);
matchResults.Matches = peakMatcher.PerformPeakMatching(clusters, m_config.Analysis.MassTagDatabase);
if (adapter != null)
{
matchResults.FdrTable = adapter.Matcher.StacFdrTable;
}
m_config.Analysis.MatchResults = matchResults;
if (FeaturesPeakMatched != null)
{
FeaturesPeakMatched(this, new FeaturesPeakMatchedEventArgs(clusters, matchResults.Matches));
}
UpdateStatus("Updating database with peak matched results.");
var writer = new PeakMatchResultsWriter();
int matchedMassTags;
int matchedProteins;
writer.WritePeakMatchResults(matchResults,
m_config.Analysis.MassTagDatabase,
out matchedMassTags,
out matchedProteins);
UpdateStatus(string.Format("Found {0} mass tag matches. Matching to {1} potential proteins.",
matchedMassTags,
matchedProteins));
}
}
/// <summary>
/// Default constructor.
/// </summary>
static Program()
{
m_config = new AnalysisConfig();
m_reportCreator = new AnalysisReportGenerator();
m_reportCreator.Config = m_config;
}
public AnalysisSetupViewModel(AnalysisConfig configuration)
{
SetupViewModels(configuration);
}
public void BuildAnalysisGraph(AnalysisConfig config)
{
var graph = new AnalysisGraph();
// Create a feature database
if (config.ShouldCreateFeatureDatabaseOnly)
{
graph.AddNode(CreateNode(AnalysisStep.FindFeatures, "Feature Creation",
"Creates or loads features from deisotoped data."));
}
else
{
if (config.ShouldLoadMTDB)
{
var node = new AnalysisGraphNode
{
Name = "Load MTDB",
Description = "Loads an AMT Tag Database for alignment or peptide identification",
CurrentStep = AnalysisStep.LoadMtdb,
Method =
config.InitialStep == AnalysisStep.FindFeatures
? CreateMtdb
: new DelegateAnalysisMethod(LoadMtdb)
};
graph.AddNode(node);
}
switch (config.InitialStep)
{
case AnalysisStep.LoadMtdb:
case AnalysisStep.FindFeatures:
graph.AddNode(CreateNode(AnalysisStep.FindFeatures, "Feature Creation And Alignment",
"Creates or loads features from deisotoped data and aligns them to a baseline."));
graph.AddNode(CreateNode(AnalysisStep.Clustering, "Cluster Features",
"Clusters features across datasets."));
graph.AddNode(CreateNode(AnalysisStep.PeakMatching, "Feature Identification",
"Matches features to an AMT Tag database."));
break;
case AnalysisStep.Alignment:
graph.AddNode(CreateNode(AnalysisStep.Alignment, "Feature Alignment",
"Aligns features to a reference to correct for systematic errors."));
graph.AddNode(CreateNode(AnalysisStep.Clustering, "Cluster Features",
"Clusters features across datasets."));
graph.AddNode(CreateNode(AnalysisStep.PeakMatching, "Feature Identification",
"Matches features to an AMT Tag database."));
break;
case AnalysisStep.Clustering:
graph.AddNode(CreateNode(AnalysisStep.Clustering, "Cluster Features",
"Clusters features across datasets."));
graph.AddNode(CreateNode(AnalysisStep.PeakMatching, "Feature Identification",
"Matches features to an AMT Tag database."));
break;
case AnalysisStep.PeakMatching:
graph.AddNode(CreateNode(AnalysisStep.PeakMatching, "Feature Identification",
"Matches features to an AMT Tag database."));
break;
}
}
config.AnalysisGraph = graph;
}
/// <summary>
/// This is horrible. A common ground of feature / functionality should be made here.
/// </summary>
/// <param name="config"></param>
/// <param name="reporter"></param>
/// <returns></returns>
public void StartMultiAlignGui(AnalysisConfig config, IAnalysisReportGenerator reporter)
{
m_worker = new BackgroundWorker();
m_worker.DoWork += m_worker_DoWork;
m_workerManager = new WorkerObject(m_worker);
m_reportCreator = reporter;
m_config = config;
m_worker.WorkerSupportsCancellation = true;
m_worker.RunWorkerAsync();
}
private void SetupViewModels(AnalysisConfig configuration)
{
m_config = configuration;
CurrentStep = AnalysisSetupStep.DatasetSelection;
CancelCommand = new AnalysisCancelCommand(this);
BackCommand = new AnalysisBackCommand(this);
NextCommand = new AnalysisNextCommand(this);
DatasetSelectionViewModel = new AnalysisDatasetSelectionViewModel(configuration.Analysis);
BaselineSelectionViewModel = new AnalysisBaselineSelectionViewModel(configuration.Analysis);
AnalysisNamingViewModel = new AnalysisNamingViewModel(configuration);
AnalysisOptionsViewModel = new AnalysisOptionsViewModel(configuration.Analysis.Options);
}
/// <summary>
/// Aligns all of the datasets.
/// </summary>
public void PerformAlignment(AnalysisConfig config)
{
UpdateStatus("Performing Alignment");
// Connect to database of features.
var featureCache = config.Analysis.DataProviders.FeatureCache;
var options = config.Analysis.Options;
// Load the baseline data.
var baselineInfo = config.Analysis.MetaData.BaselineDataset;
var baselineFeatures = LoadBaselineData(baselineInfo,
options.MsFilteringOptions,
options.LcmsFindingOptions,
options.LcmsFilteringOptions,
config.Analysis.DataProviders,
config.Analysis.MassTagDatabase,
config.Analysis.Options.AlignmentOptions.IsAlignmentBaselineAMasstagDB);
// Create the alignment cache and clear it.
var alignmentCache = new AlignmentDAOHibernate();
alignmentCache.ClearAll();
//config.Analysis.Options.AlignmentOptions
foreach (var datasetInfo in config.Analysis.MetaData.Datasets)
{
if (!datasetInfo.IsBaseline)
{
UpdateStatus("Retrieving data from " + datasetInfo.DatasetName + " for alignment.");
var features = featureCache.FindByDatasetId(datasetInfo.DatasetId) as IList<UMCLight>;
features = AlignDataset(features,
baselineFeatures,
config.Analysis.MassTagDatabase,
datasetInfo,
baselineInfo);
featureCache.UpdateAll(features);
// This dataset is done!
if (FeaturesLoaded != null)
FeaturesLoaded(this, new FeaturesLoadedEventArgs(datasetInfo, features));
}
else
{
config.Analysis.AlignmentData.Add(null);
}
}
}
/// <summary>
/// Processes the command line arguments.
/// </summary>
/// <param name="args"></param>
public static void ProcessCommandLineArguments(string[] args, AnalysisConfig config)
{
var jobID = -1;
var worked = false;
config.options = CommandLineParser.ProcessArgs(args, 0);
foreach (var option in config.options.Keys)
{
try
{
var values = config.options[option];
switch (option)
{
case "-job":
worked = int.TryParse(values[0], out jobID);
if (worked)
{
config.JobID = jobID;
}
else
{
Logger.PrintMessage(string.Format("The job Id {0} was not understood", values[0]));
return;
}
break;
case "-charge":
config.ChargeState = Convert.ToInt32(values[0]);
config.ShouldClusterOnlyCharge = true;
break;
//--------------------------------------------------------------------
// Path and name
//--------------------------------------------------------------------
case "-path":
config.AnalysisPath = values[0];
break;
case "-name":
config.AnalysisName = values[0];
break;
//--------------------------------------------------------------------
// Files and parameters
//--------------------------------------------------------------------
case "-files":
config.InputPaths = values[0];
break;
case "-params":
config.ParameterFile = values[0];
break;
case "-usefactors":
config.ShouldUseFactors = true;
break;
//--------------------------------------------------------------------
// Log, HTML names
//--------------------------------------------------------------------
case "-log":
config.logPath = values[0];
break;
case "-html":
config.HtmlPathName = values[0];
break;
//--------------------------------------------------------------------
// Print helps
//--------------------------------------------------------------------
case "-h":
config.showHelp = true;
break;
case "-help":
config.showHelp = true;
break;
//--------------------------------------------------------------------
// Feature databases
//--------------------------------------------------------------------
case "-useexistingdatabase":
config.ShouldUseExistingDatabase = true;
break;
case "-buildfeaturedatabase":
config.ShouldCreateFeatureDatabaseOnly = true;
break;
//--------------------------------------------------------------------
// Data exporting
//--------------------------------------------------------------------
case "-exportmsms":
config.ExporterNames.ClusterMSMSPath = values[0];
config.ShouldExportMSMS = true;
break;
case "-exportsics":
config.ShouldExportSICs = true;
break;
case "-exportcrosstab":
config.ExporterNames.CrossTabPath = values[0];
break;
case "-exportabundances":
config.ExporterNames.CrossTabAbundance = values[0];
break;
//--------------------------------------------------------------------
// Exporting
//--------------------------------------------------------------------
case "-export":
config.ExporterNames.ClusterScanPath = values[0];
break;
case "-noplots":
config.ShouldCreateChargeStatePlots = false;
config.ShouldCreatePlots = false;
break;
default:
Logger.PrintMessage("One option was not understood: " + option);
break;
}
}
catch (ArgumentOutOfRangeException)
{
Logger.PrintMessage(string.Format("You did not provide enough information for the option {0}",
option));
return;
}
}
}
/// <summary>
/// Performs clustering of LCMS Features
/// </summary>
public void PerformLcmsFeatureClustering(AnalysisConfig config)
{
var analysis = config.Analysis;
var clusterer = m_algorithms.Clusterer;
RegisterProgressNotifier(clusterer);
UpdateStatus("Using Cluster Algorithm: " + clusterer);
clusterer.Parameters = LcmsClusteringOptions.ConvertToOmics(analysis.Options.LcmsClusteringOptions);
// This just tells us whether we are using mammoth memory partitions or not.
var featureCache = config.Analysis.DataProviders.FeatureCache;
var clusterCount = 0;
var providers = config.Analysis.DataProviders;
// Here we see if we need to separate the charge...
// IMS is said to require charge separation
if (!analysis.Options.LcmsClusteringOptions.ShouldSeparateCharge)
{
UpdateStatus("Clustering features from all charge states.");
UpdateStatus("Retrieving features for clustering from cache.");
var features = featureCache.FindAll();
UpdateStatus(string.Format("Clustering {0} features. ", features.Count));
var clusters = new List<UMCClusterLight>();
clusters = clusterer.Cluster(features, clusters);
foreach (var cluster in clusters)
{
cluster.Id = clusterCount++;
cluster.UmcList.ForEach(x => x.ClusterId = cluster.Id);
// Updates the cluster with statistics
foreach (var feature in cluster.UmcList)
{
cluster.MsMsCount += feature.MsMsCount;
cluster.IdentifiedSpectraCount += feature.IdentifiedSpectraCount;
}
}
providers.ClusterCache.AddAll(clusters);
providers.FeatureCache.UpdateAll(features);
config.Analysis.Clusters = clusters;
UpdateStatus(string.Format("Found {0} clusters.", clusters.Count));
if (FeaturesClustered != null)
{
FeaturesClustered(this, new FeaturesClusteredEventArgs(clusters));
}
}
else
{
var maxChargeState = featureCache.FindMaxCharge();
/*
* Here we cluster all charge states separately. Probably IMS Data.
*/
UpdateStatus("Clustering charge states individually.");
for (var chargeState = 1; chargeState <= maxChargeState; chargeState++)
{
var features = featureCache.FindByCharge(chargeState);
if (features.Count < 1)
{
UpdateStatus(string.Format("No features found for charge state {0}. Stopping clustering",
chargeState));
break;
}
UpdateStatus(
string.Format("Retrieved and is clustering {0} features from charge state {1}.",
features.Count, chargeState));
var clusters = clusterer.Cluster(features);
foreach (var cluster in clusters)
{
cluster.Id = clusterCount++;
cluster.UmcList.ForEach(x => x.ClusterId = cluster.Id);
// Updates the cluster with statistics
foreach (var feature in cluster.Features)
{
cluster.MsMsCount += feature.MsMsCount;
cluster.IdentifiedSpectraCount += feature.IdentifiedSpectraCount;
}
}
config.Analysis.DataProviders.ClusterCache.AddAll(clusters);
config.Analysis.DataProviders.FeatureCache.UpdateAll(features);
UpdateStatus(string.Format("Found {0} clusters.", clusters.Count));
if (FeaturesClustered != null)
{
FeaturesClustered(this, new FeaturesClusteredEventArgs(clusters, chargeState));
}
}
config.Analysis.Clusters = config.Analysis.DataProviders.ClusterCache.FindAll();
}
DeRegisterProgressNotifier(clusterer);
UpdateStatus(string.Format("Finished clustering. Found {0} total clusters.", clusterCount));
}
/// <summary>
/// Starts a multi-Align analysis job.
/// </summary>
public void StartAnalysis(AnalysisConfig config)
{
m_config = config;
if (m_algorithms == null)
{
throw new NullReferenceException("The algorithms have not been set for this analysis.");
}
if (config.Analysis == null)
{
throw new NullReferenceException("The analysis data storage cannot be null.");
}
if (config.Analysis.DataProviders == null)
{
throw new NullReferenceException("The data cache providers have not been set for this analysis.");
}
Logger.LogPath = AnalysisPathUtils.BuildLogPath(config.AnalysisPath, config.AnalysisName);
// Make sure we start with a fresh analysis.
AbortAnalysisThread(m_analysisThread);
var threadStart = new ThreadStart(PerformAnalysis);
m_analysisThread = new Thread(threadStart);
m_analysisThread.Start();
}
public void CleanupOldAnalysisBranches(AnalysisConfig config)
{
switch (config.InitialStep)
{
case AnalysisStep.None:
break;
case AnalysisStep.LoadMtdb:
break;
case AnalysisStep.FindFeatures:
break;
case AnalysisStep.Alignment:
config.Analysis.DataProviders.FeatureCache.ClearAlignmentData();
config.Analysis.DataProviders.ClusterCache.ClearAllClusters();
config.Analysis.DataProviders.MassTagMatches.ClearAllMatches();
break;
case AnalysisStep.Clustering:
config.Analysis.DataProviders.ClusterCache.ClearAllClusters();
config.Analysis.DataProviders.MassTagMatches.ClearAllMatches();
break;
case AnalysisStep.PeakMatching:
config.Analysis.DataProviders.MassTagMatches.ClearAllMatches();
break;
}
}