public MassTagDatabase LoadDatabase()
{
var database = new MassTagDatabase {Name = ""};
UpdateStatus("Loading all of the mass tags.");
// Get all of the mass tags
var massTags = Provider.FindAll();
UpdateStatus("Loading all of the tag to protein references.");
// Then get all of the mass tag to protein maps
IGenericDAO<MassTagToProteinMap> tagToProteinMapCache = new GenericDAOHibernate<MassTagToProteinMap>();
var maps = tagToProteinMapCache.FindAll();
// Then get all of the proteins
UpdateStatus("Loading all of the protein data.");
IProteinDAO proteinCache = new ProteinDAO();
var proteins = proteinCache.FindAll();
UpdateStatus("Indexing the protein data for faster assembly.");
var proteinMap = new Dictionary<int, Protein>();
foreach (var p in proteins)
{
if (!proteinMap.ContainsKey(p.ProteinId))
{
proteinMap.Add(p.ProteinId, p);
}
}
var matchedMaps = new Dictionary<int, List<MassTagToProteinMap>>();
foreach (var singleMap in maps)
{
if (!matchedMaps.ContainsKey(singleMap.MassTagId))
{
matchedMaps.Add(singleMap.MassTagId, new List<MassTagToProteinMap>());
}
matchedMaps[singleMap.MassTagId].Add(singleMap);
}
UpdateStatus("Re-mapping the proteins to the mass tags.");
var massTagProteinMap = new Dictionary<int, List<Protein>>();
// Then map them.
foreach (var tag in massTags)
{
var id = tag.Id;
if (!massTagProteinMap.ContainsKey(id))
{
massTagProteinMap.Add(id, new List<Protein>());
}
var matches = new List<MassTagToProteinMap>();
if (matchedMaps.ContainsKey(id))
{
matches = matchedMaps[id];
}
var newProteins = new List<Protein>();
foreach (var mtMap in matches)
{
if (proteinMap.ContainsKey(mtMap.ProteinId))
{
newProteins.Add(proteinMap[mtMap.ProteinId]);
}
}
massTagProteinMap[id].AddRange(newProteins);
}
UpdateStatus("Building the in memory mass tag database.");
database.AddMassTagsAndProteins(massTags, massTagProteinMap);
database.AllProteins = proteins;
var totalMassTags = database.MassTags.Count;
UpdateStatus("Loaded " + totalMassTags + " mass tags.");
return database;
}
/// <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>
/// Writes the parameters to the log file and database.
/// </summary>
private void PrintParameters(MultiAlignAnalysis analysis, bool insertIntoDatabase)
{
Logger.PrintMessage("Parameters Loaded");
var options = new Dictionary<string, object>
{
{"Instrument Tolerances", analysis.Options.InstrumentTolerances},
{"Ms Feature Filtering Options", analysis.Options.MsFilteringOptions},
{"Feature Filtering Options", analysis.Options.LcmsFilteringOptions},
{"Mass Tag Database Options", analysis.Options.MassTagDatabaseOptions},
{"Alignment Options", analysis.Options.AlignmentOptions},
{"Clustering Options", analysis.Options.LcmsClusteringOptions},
{"STAC Options", analysis.Options.StacOptions}
};
var allmappings = new List<ParameterHibernateMapping>();
foreach (var key in options.Keys)
{
//var o = options[key];
Logger.PrintMessage(key, true);
//var parameters = ParameterUtility.ConvertParameterObjectToStrings(o);
//foreach (var parameter in parameters)
//{
// Logger.PrintMessage("\t" + parameter, true);
//}
//var mappings = ParameterUtility.ExtractParameterMapObjects(o, key);
//allmappings.AddRange(mappings);
}
var assemblyData = ApplicationUtility.GetAssemblyData();
var assemblyMap = new ParameterHibernateMapping
{
OptionGroup = "Assembly Info",
Parameter = "Version",
Value = assemblyData
};
allmappings.Add(assemblyMap);
var systemData = ApplicationUtility.GetSystemData();
var systemMap = new ParameterHibernateMapping
{
OptionGroup = "Assembly Info",
Parameter = "System Info",
Value = systemData
};
allmappings.Add(systemMap);
if (insertIntoDatabase)
{
Logger.PrintMessage("Writing parameters to the analysis database.");
var parameterCache = new GenericDAOHibernate<ParameterHibernateMapping>();
parameterCache.AddAll(allmappings);
}
}
/// <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));
}
}
public MassTagDatabase LoadDatabase()
{
var database = new MassTagDatabase {
Name = ""
};
UpdateStatus("Loading all of the mass tags.");
// Get all of the mass tags
var massTags = Provider.FindAll();
UpdateStatus("Loading all of the tag to protein references.");
// Then get all of the mass tag to protein maps
IGenericDAO <MassTagToProteinMap> tagToProteinMapCache = new GenericDAOHibernate <MassTagToProteinMap>();
var maps = tagToProteinMapCache.FindAll();
// Then get all of the proteins
UpdateStatus("Loading all of the protein data.");
IProteinDAO proteinCache = new ProteinDAO();
var proteins = proteinCache.FindAll();
UpdateStatus("Indexing the protein data for faster assembly.");
var proteinMap = new Dictionary <int, Protein>();
foreach (var p in proteins)
{
if (!proteinMap.ContainsKey(p.ProteinId))
{
proteinMap.Add(p.ProteinId, p);
}
}
var matchedMaps = new Dictionary <int, List <MassTagToProteinMap> >();
foreach (var singleMap in maps)
{
if (!matchedMaps.ContainsKey(singleMap.MassTagId))
{
matchedMaps.Add(singleMap.MassTagId, new List <MassTagToProteinMap>());
}
matchedMaps[singleMap.MassTagId].Add(singleMap);
}
UpdateStatus("Re-mapping the proteins to the mass tags.");
var massTagProteinMap = new Dictionary <int, List <Protein> >();
// Then map them.
foreach (var tag in massTags)
{
var id = tag.Id;
if (!massTagProteinMap.ContainsKey(id))
{
massTagProteinMap.Add(id, new List <Protein>());
}
var matches = new List <MassTagToProteinMap>();
if (matchedMaps.ContainsKey(id))
{
matches = matchedMaps[id];
}
var newProteins = new List <Protein>();
foreach (var mtMap in matches)
{
if (proteinMap.ContainsKey(mtMap.ProteinId))
{
newProteins.Add(proteinMap[mtMap.ProteinId]);
}
}
massTagProteinMap[id].AddRange(newProteins);
}
UpdateStatus("Building the in memory mass tag database.");
database.AddMassTagsAndProteins(massTags, massTagProteinMap);
database.AllProteins = proteins;
var totalMassTags = database.MassTags.Count;
UpdateStatus("Loaded " + totalMassTags + " mass tags.");
return(database);
}