/// <summary>
/// Default constructor for a MultiAlign analysis object.
/// </summary>
public MultiAlignAnalysis()
{
// Meta Data Information about the analysis and datasets.
MetaData = new AnalysisMetaData {AnalysisName = string.Empty};
Options = new MultiAlignAnalysisOptions();
MassTagDatabase = new MassTagDatabase();
// Alignment options and data.
AlignmentData = new List<classAlignmentData>();
MatchResults = null;
}
/// <summary>
/// Constructs the baseline databases.
/// </summary>
private bool ConstructBaselines(InputAnalysisInfo analysisSetupInformation, AnalysisMetaData analysisMetaData,
bool useMtdb)
{
Logger.PrintMessage("Confirming baseline selections.");
if (useMtdb)
{
switch (analysisSetupInformation.Database.DatabaseFormat)
{
case MassTagDatabaseFormat.MassTagSystemSql:
Logger.PrintMessage("Using Mass Tag Database:");
Logger.PrintMessage(string.Format("\tServer: {0}",
analysisSetupInformation.Database.DatabaseServer));
Logger.PrintMessage(string.Format("\tDatabase Name: {0}",
analysisSetupInformation.Database.DatabaseName));
m_config.Analysis.MetaData.Database = analysisSetupInformation.Database;
break;
case MassTagDatabaseFormat.Sqlite:
Logger.PrintMessage("Using local Sqlite Mass Tag Database at location: ");
Logger.PrintMessage(string.Format("\tFull Path: {0}",
analysisSetupInformation.Database.LocalPath));
Logger.PrintMessage(string.Format("\tDatabase Name: {0}",
Path.GetFileName(analysisSetupInformation.Database.LocalPath)));
m_config.Analysis.MetaData.Database = analysisSetupInformation.Database;
break;
case MassTagDatabaseFormat.DelimitedTextFile:
Logger.PrintMessage("Using local MetaSample Mass Tag Database at location: ");
Logger.PrintMessage(string.Format("\tFull Path: {0}",
analysisSetupInformation.Database.LocalPath));
Logger.PrintMessage(string.Format("\tDatabase Name: {0}",
Path.GetFileName(analysisSetupInformation.Database.LocalPath)));
m_config.Analysis.MetaData.Database = analysisSetupInformation.Database;
break;
}
// Validate the baseline
if (analysisSetupInformation.BaselineFile == null)
{
m_config.Analysis.Options.AlignmentOptions.IsAlignmentBaselineAMasstagDB = true;
Logger.PrintMessage(string.Format("Using mass tag database {0} as the alignment baseline.",
analysisSetupInformation.Database.DatabaseName));
}
else
{
m_config.Analysis.Options.AlignmentOptions.IsAlignmentBaselineAMasstagDB = false;
m_config.Analysis.MetaData.BaselineDataset = null;
foreach (var info in analysisMetaData.Datasets)
{
if (info.Features.Path == analysisSetupInformation.BaselineFile.Path)
{
m_config.Analysis.MetaData.BaselineDataset = info;
info.IsBaseline = true;
m_config.Analysis.DataProviders.DatasetCache.Update(info);
}
}
Logger.PrintMessage(string.Format("Using dataset {0} as the alignment baseline.",
m_config.Analysis.MetaData.BaselineDataset));
}
}
else
{
m_config.Analysis.MetaData.Database = analysisSetupInformation.Database;
m_config.Analysis.Options.AlignmentOptions.IsAlignmentBaselineAMasstagDB = false;
if (analysisSetupInformation.BaselineFile == null)
{
Logger.PrintMessage("No baseline dataset or database was selected.");
return false;
}
m_config.Analysis.MetaData.BaselineDataset = null;
foreach (var info in analysisMetaData.Datasets)
{
if (info.Features.Path == analysisSetupInformation.BaselineFile.Path)
{
info.IsBaseline = true;
m_config.Analysis.MetaData.BaselineDataset = info;
m_config.Analysis.DataProviders.DatasetCache.Update(info);
}
}
Logger.PrintMessage(string.Format("Using dataset {0} as the alignment baseline.",
m_config.Analysis.MetaData.BaselineDataset));
}
return true;
}
