/// <summary>
/// Loads mass tags from AMT database into analysis database.
/// </summary>
private void AddMassTags()
{
var loadProgress = new Progress <ProgressData>(pd => this.MassTagLoadProgress = pd.Percent);
this.Analysis.MetaData.Database = this.SelectedDatabase;
this.Analysis.MassTagDatabase = MtdbLoaderFactory.LoadMassTagDatabase(
this.analysis.MetaData.Database,
this.analysis.Options.MassTagDatabaseOptions);
this.Analysis.DataProviders.MassTags.DeleteAll();
this.ShowMassTagProgress = true;
this.Analysis.DataProviders.MassTags.AddAllStateless(this.Analysis.MassTagDatabase.MassTags, loadProgress);
this.ShowMassTagProgress = false;
}
/// <summary>
/// The main entry point for the application.
/// </summary>
static int Main(string[] args)
{
var handle = System.Diagnostics.Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, ENABLE_EXTENDED_FLAGS);
var clusterIdMap = new Dictionary <int, UMCClusterLight>();
try
{
if (args.Length < 2)
{
Console.WriteLine("MultiAlignSTACRunner crosstabDirectory databasePath outputName");
Console.WriteLine("\tThe cross-tab file will be named similar to the database path");
return(1);
}
// Setup the analysis processing
Logger.PrintMessage("Find all datasets", true);
var directoryPath = args[0].Replace("\r", "").Replace("\n", "");
var databasePath = args[1].Replace("\r", "").Replace("\n", "");
var name = args[2].Replace("\r", "").Replace("\n", "");
var files = Directory.GetFiles(directoryPath, "*.csv");
Logger.PrintMessage("Creating Log File");
var loggerPath = AnalysisPathUtils.BuildLogPath(Path.GetDirectoryName(name), Path.GetFileNameWithoutExtension(name));
Logger.LogPath = loggerPath;
Logger.PrintMessage("Saving Log Data to: " + loggerPath);
Logger.PrintMessage(string.Format("Creating STAC"), true);
// Hardcode bad, but per discussions with OHSU
var stac = new STACAdapter <UMCClusterLight>
{
Options = new FeatureMatcherParameters
{
UserTolerances =
{
MassTolerancePPM = 25,
NETTolerance = .035,
DriftTimeTolerance = 3
},
UseDriftTime = true
}
};
var clusterFilteringOptions = new FilteringOptions();
WriteOptionsToLogFile(clusterFilteringOptions);
WriteOptionsToLogFile(stac.Options);
// Read the cluster data
var allClusters = new List <UMCClusterLight>();
var clusterId = 0;
foreach (var file in files)
{
var filename = Path.GetFileName(file);
Logger.PrintMessage(string.Format("Reading {0}", filename));
const string chargeString = "charge";
if (filename == null)
{
continue;
}
if (!filename.Contains(chargeString))
{
continue;
}
// Read each file.
var start = DateTime.Now;
var xname = filename.Replace("_", "");
// ReSharper disable once StringIndexOfIsCultureSpecific.1
var indexOfChargeString = xname.IndexOf(chargeString);
var charge = Convert.ToInt32(xname.Substring(indexOfChargeString + chargeString.Length, 1));
var clusters = ReadClusters(file, clusterFilteringOptions);
var end = DateTime.Now;
Logger.PrintMessage(string.Format("\tReading Took {0:.00} seconds", end.Subtract(start).TotalSeconds));
foreach (var cluster in clusters)
{
clusterIdMap.Add(clusterId, cluster);
cluster.Id = clusterId++;
cluster.ChargeState = charge;
}
allClusters.AddRange(clusters);
}
// Load the database
Logger.PrintMessage(string.Format("Loading Mass Tag Database: {0}", Path.GetFileNameWithoutExtension(databasePath)));
var options = new MassTagDatabaseOptions();
var databaseDefinition = new InputDatabase
{
DatabaseFormat = MassTagDatabaseFormat.Sqlite,
LocalPath = databasePath
};
var database = MtdbLoaderFactory.LoadMassTagDatabase(databaseDefinition, options);
// Run stac
try
{
Logger.PrintMessage("Matching clusters to peptides in mass tag database.");
var matches = stac.PerformPeakMatching(allClusters, database);
Logger.PrintMessage(string.Format("Writing Results To {0}", name));
var duplicateMatches = new Dictionary <int, Dictionary <int, FeatureMatchLight <UMCClusterLight, MassTagLight> > >();
foreach (var match in matches)
{
if (!duplicateMatches.ContainsKey(match.Observed.Id))
{
duplicateMatches.Add(match.Observed.Id, new Dictionary <int, FeatureMatchLight <UMCClusterLight, MassTagLight> >());
}
if (!duplicateMatches[match.Observed.Id].ContainsKey(match.Target.Id))
{
duplicateMatches[match.Observed.Id].Add(match.Target.Id, match);
}
}
WriteClusterData(name, duplicateMatches, clusterIdMap);
Logger.PrintMessage("ANALYSIS SUCCESS");
return(0);
}
catch (Exception ex)
{
Logger.PrintMessage("Unhandled Error: " + ex.Message);
var innerEx = ex.InnerException;
while (innerEx != null)
{
Logger.PrintMessage("Inner Exception: " + innerEx.Message);
innerEx = innerEx.InnerException;
}
Logger.PrintMessage("Stack: " + ex.StackTrace);
Logger.PrintMessage("");
Logger.PrintMessage("ANALYSIS FAILED");
return(1);
}
}
catch (Exception ex)
{
Logger.PrintMessage("Unhandled Error: " + ex.Message, true);
var innerEx = ex.InnerException;
while (innerEx != null)
{
Logger.PrintMessage("Inner Exception: " + innerEx.Message);
innerEx = innerEx.InnerException;
}
Logger.PrintMessage("Stack: " + ex.StackTrace, true);
Logger.PrintMessage("");
Logger.PrintMessage("ANALYSIS FAILED");
return(1);
}
}
/// <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));
}
}
