public void CreateMsnTest()
{
var msnFeatures = new MSnFeatureToMSFeatureDAOHibernate();
var map = new MSFeatureToMSnFeatureMap();
map.LCMSFeatureID = 0;
map.MSDatasetID = 0;
map.MSFeatureID = 0;
map.MSMSFeatureID = 0;
map.RawDatasetID = 0;
msnFeatures.Add(map);
}
public void CacheFeatures(IList<UMCLight> features)
{
// SpectraTracker - Makes sure that we only record a MS spectra once, before we cache
// this keeps us from trying to put duplicate entries into the MS/MS data
// table/container.
var spectraTracker = new Dictionary<int, MSSpectra>();
var msmsFeatures = new List<MSSpectra>();
var mappedPeptides = new List<DatabaseSearchSequence>();
var sequenceMaps = new List<SequenceToMsnFeature>();
// This dictionary makes sure that the peptide was not seen already, since a peptide can be mapped multiple times...?
var matches = new List<MSFeatureToMSnFeatureMap>();
var msFeatures = new List<MSFeatureLight>();
var peptideId = 0;
// Next we may want to map our MSn features to our parents. This would allow us to do traceback...
foreach (var feature in features)
{
var totalMsMs = 0;
var totalIdentified = 0;
var datasetId = feature.GroupId;
msFeatures.AddRange(feature.MsFeatures);
// For Each MS Feature
foreach (var msFeature in feature.MsFeatures)
{
totalMsMs += msFeature.MSnSpectra.Count;
// For each MS / MS
foreach (var spectrum in msFeature.MSnSpectra)
{
var match = new MSFeatureToMSnFeatureMap
{
RawDatasetID = datasetId,
MSDatasetID = datasetId,
MSFeatureID = msFeature.Id,
MSMSFeatureID = spectrum.Id,
LCMSFeatureID = feature.Id
};
spectrum.GroupId = datasetId;
matches.Add(match);
if (spectraTracker.ContainsKey(spectrum.Id))
continue;
msmsFeatures.Add(spectrum);
spectraTracker.Add(spectrum.Id, spectrum);
// We are prepping the sequences that we found from peptides that were
// matched only, not all of the results.
// These maps here are made to help establish database search results to msms
// spectra
foreach (var peptide in spectrum.Peptides)
{
peptide.GroupId = datasetId;
var newPeptide = new DatabaseSearchSequence(peptide, feature.Id)
{
GroupId = datasetId,
Id = peptideId++
};
mappedPeptides.Add(newPeptide);
var sequenceMap = new SequenceToMsnFeature
{
UmcFeatureId = feature.Id,
DatasetId = msFeature.GroupId,
MsnFeatureId = spectrum.Id,
SequenceId = peptide.Id
};
sequenceMaps.Add(sequenceMap);
}
totalIdentified += spectrum.Peptides.Count;
}
}
feature.MsMsCount = totalMsMs;
feature.IdentifiedSpectraCount = totalIdentified;
}
var count = 0;
//TODO: Fix!!! make sure sequence maps are unique
sequenceMaps.ForEach(x => x.Id = count++);
if (msmsFeatures.Count > 0)
Providers.MSnFeatureCache.AddAll(msmsFeatures);
if (matches.Count > 0)
Providers.MSFeatureToMSnFeatureCache.AddAll(matches);
if (sequenceMaps.Count > 0)
Providers.SequenceMsnMapCache.AddAll(sequenceMaps);
if (mappedPeptides.Count > 0)
Providers.DatabaseSequenceCache.AddAll(mappedPeptides);
if (msFeatures.Count > 0)
Providers.MSFeatureCache.AddAll(msFeatures);
Providers.FeatureCache.AddAll(features);
}