/// <summary>
/// Loads a mass tag database.
/// </summary>
/// <param name="databaseDefinition"></param>
/// <param name="options">Loading options.</param>
/// <returns>The mass tag database.</returns>
public static IMtdbLoader Create(InputDatabase databaseDefinition, MassTagDatabaseOptions options)
{
IMtdbLoader loader = null;
switch (databaseDefinition.DatabaseFormat)
{
case MassTagDatabaseFormat.SkipAlignment:
loader = new DriftTimeTextFileDatabaseLoader(databaseDefinition.LocalPath);
break;
case MassTagDatabaseFormat.MassTagSystemSql:
loader = new MtsMassTagDatabaseLoader(databaseDefinition.DatabaseName,
databaseDefinition.DatabaseServer, options);
break;
case MassTagDatabaseFormat.Sqlite:
loader = new SQLiteMassTagDatabaseLoader(databaseDefinition.LocalPath, options);
break;
case MassTagDatabaseFormat.MtdbCreator:
loader = new MtdbCreatorDatabaseLoader(databaseDefinition.LocalPath);
break;
case MassTagDatabaseFormat.DelimitedTextFile:
loader = new MetaSampleDatbaseLoader(databaseDefinition.LocalPath, options);
break;
}
return loader;
}
public void OnlyLoadWithDriftTime(string server, string databaseName)
{
var analysis = new MultiAlignAnalysis();
analysis.Options.MassTagDatabaseOptions.OnlyLoadTagsWithDriftTime = true;
analysis.MetaData.Database = new InputDatabase(MassTagDatabaseFormat.MassTagSystemSql)
{
DatabaseServer = server,
DatabaseName = databaseName
};
var loader = new MtsMassTagDatabaseLoader(databaseName, server, analysis.Options.MassTagDatabaseOptions);
var database = loader.LoadDatabase();
foreach (var tag in database.MassTags)
{
Assert.IsTrue(tag.DriftTime > 0);
}
}
public void LoadWithoutDriftTime(string server, string databaseName)
{
var analysis = new MultiAlignAnalysis();
analysis.Options.MassTagDatabaseOptions.OnlyLoadTagsWithDriftTime = false;
analysis.MetaData.Database = new InputDatabase(MassTagDatabaseFormat.MassTagSystemSql)
{
DatabaseServer = server,
DatabaseName = databaseName
};
MassTagDatabaseLoader loader = new MtsMassTagDatabaseLoader(databaseName, server,
analysis.Options.MassTagDatabaseOptions);
var database = loader.LoadDatabase();
MassTagDatabaseLoader loader2 = new MtsMassTagDatabaseLoader(databaseName, server,
analysis.Options.MassTagDatabaseOptions);
loader2.Options.OnlyLoadTagsWithDriftTime = true;
var database2 = loader.LoadDatabase();
Assert.Greater(database.MassTags.Count, database2.MassTags.Count);
}
/// <summary>
/// Loads a mass tag database.
/// </summary>
/// <param name="databaseDefinition"></param>
/// <param name="options">Loading options.</param>
/// <returns>The mass tag database.</returns>
public static IMtdbLoader Create(InputDatabase databaseDefinition, MassTagDatabaseOptions options)
{
IMtdbLoader loader = null;
switch (databaseDefinition.DatabaseFormat)
{
case MassTagDatabaseFormat.SkipAlignment:
loader = new DriftTimeTextFileDatabaseLoader(databaseDefinition.LocalPath);
break;
case MassTagDatabaseFormat.MassTagSystemSql:
loader = new MtsMassTagDatabaseLoader(databaseDefinition.DatabaseName,
databaseDefinition.DatabaseServer, options);
break;
case MassTagDatabaseFormat.Sqlite:
loader = new SQLiteMassTagDatabaseLoader(databaseDefinition.LocalPath, options);
break;
case MassTagDatabaseFormat.MtdbCreator:
loader = new MtdbCreatorDatabaseLoader(databaseDefinition.LocalPath);
break;
case MassTagDatabaseFormat.DelimitedTextFile:
loader = new MetaSampleDatbaseLoader(databaseDefinition.LocalPath, options);
break;
case MassTagDatabaseFormat.LiquidResultsFile:
loader = new LiquidResultsFileLoader(databaseDefinition.LocalPath);
break;
case MassTagDatabaseFormat.GenericTsvFile:
loader = new MtdbFromGenericTsvReader(databaseDefinition.LocalPath);
break;
}
return(loader);
}
