/// <summary>
/// Constructor.
/// </summary>
/// <param name="featureCache">LCMS Features</param>
/// <param name="clusterCache">LCMS Feature clusters</param>
/// <param name="msFeatureCache">MS Features</param>
/// <param name="msnFeatureCache">MS/MS Features</param>
/// <param name="msFeatureMap">MS To LCMS Feature map</param>
/// <param name="msnFeatureMap">MS to MSn Feature map</param>
public FeatureDataAccessProviders(IUmcDAO featureCache,
IUmcClusterDAO clusterCache,
IMSFeatureDAO msFeatureCache,
IMSnFeatureDAO msnFeatureCache,
IMsnFeatureToMSFeatureDAO msnFeatureMap,
IDatasetDAO datasetCache,
IMassTagMatchDAO massTagMatches,
IMassTagDAO massTags,
IFactorDao factorCache,
IDatasetToFactorMapDAO factorAssignmentCache,
IMSMSClusterMapDAO msmsClusterCache,
IDatabaseSearchSequenceDAO sequenceCache,
ISequenceToMsnFeatureDAO sequenceMapCache) :
this()
{
ClusterCache = clusterCache;
FeatureCache = featureCache;
MSFeatureCache = msFeatureCache;
MSnFeatureCache = msnFeatureCache;
MSFeatureToMSnFeatureCache = msnFeatureMap;
DatasetCache = datasetCache;
MassTagMatches = massTagMatches;
MassTags = massTags;
FactorAssignmentCache = factorAssignmentCache;
FactorCache = factorCache;
MSMSClusterCache = msmsClusterCache;
DatabaseSequenceCache = sequenceCache;
SequenceMsnMapCache = sequenceMapCache;
}
public void LoadSequenceData(string path,
int datasetID,
IDatabaseSearchSequenceDAO databaseSequenceCache)
{
IMageSink sink = null;
if (path.ToLower().EndsWith("fht.txt"))
{
UpdateStatus("First Hit File MAGE Sink created. ");
var sequest = new SequestFirstHitSink(databaseSequenceCache);
sequest.DatasetID = datasetID;
sink = sequest;
}
else
{
UpdateStatus("File type is not supported for this kind of sequence data. ");
return;
}
var reader = new DelimitedFileReader();
reader.Delimiter = "\t";
reader.FilePath = path;
var pipeline = ProcessingPipeline.Assemble("PlainFactors", reader, sink);
pipeline.RunRoot(null);
sink.CommitChanges();
}
/// <summary>
/// Constructor.
/// </summary>
/// <param name="featureCache">LCMS Features</param>
/// <param name="clusterCache">LCMS Feature clusters</param>
/// <param name="msFeatureCache">MS Features</param>
/// <param name="msnFeatureCache">MS/MS Features</param>
/// <param name="msFeatureMap">MS To LCMS Feature map</param>
/// <param name="msnFeatureMap">MS to MSn Feature map</param>
public FeatureDataAccessProviders(IUmcDAO featureCache,
IUmcClusterDAO clusterCache,
IMSFeatureDAO msFeatureCache,
IMSnFeatureDAO msnFeatureCache,
IMsnFeatureToMSFeatureDAO msnFeatureMap,
IDatasetDAO datasetCache,
IMassTagMatchDAO massTagMatches,
IMassTagDAO massTags,
IFactorDao factorCache,
IDatasetToFactorMapDAO factorAssignmentCache,
IMSMSClusterMapDAO msmsClusterCache,
IDatabaseSearchSequenceDAO sequenceCache,
ISequenceToMsnFeatureDAO sequenceMapCache)
: this()
{
ClusterCache = clusterCache;
FeatureCache = featureCache;
MSFeatureCache = msFeatureCache;
MSnFeatureCache = msnFeatureCache;
MSFeatureToMSnFeatureCache = msnFeatureMap;
DatasetCache = datasetCache;
MassTagMatches = massTagMatches;
MassTags = massTags;
FactorAssignmentCache = factorAssignmentCache;
FactorCache = factorCache;
MSMSClusterCache = msmsClusterCache;
DatabaseSequenceCache = sequenceCache;
SequenceMsnMapCache = sequenceMapCache;
}
public void LoadSequenceData(string path,
int datasetID,
IDatabaseSearchSequenceDAO databaseSequenceCache)
{
IMageSink sink = null;
if (path.ToLower().EndsWith("fht.txt"))
{
UpdateStatus("First Hit File MAGE Sink created. ");
var sequest = new SequestFirstHitSink(databaseSequenceCache);
sequest.DatasetID = datasetID;
sink = sequest;
}
else
{
UpdateStatus("File type is not supported for this kind of sequence data. ");
return;
}
var reader = new DelimitedFileReader();
reader.Delimiter = "\t";
reader.FilePath = path;
var pipeline = ProcessingPipeline.Assemble("PlainFactors", reader, sink);
pipeline.RunRoot(null);
sink.CommitChanges();
}
/// <summary>
/// Constructor.
/// </summary>
/// <param name="datasets">Datasets to store data about.</param>
public SequestFirstHitSink(IDatabaseSearchSequenceDAO databaseInterface)
{
m_sequences = new List <DatabaseSearchSequence>();
m_columnMapping = new Dictionary <string, int>();
m_database = databaseInterface;
}
/// <summary>
/// Constructor.
/// </summary>
/// <param name="datasets">Datasets to store data about.</param>
public SequestFirstHitSink(IDatabaseSearchSequenceDAO databaseInterface)
{
m_sequences = new List<DatabaseSearchSequence>();
m_columnMapping = new Dictionary<string, int>();
m_database = databaseInterface;
}
