public UMCClusterTreeViewModel(UMCClusterLightMatched matchedCluster, TreeItemViewModel parent)
{
m_items = new ObservableCollection<TreeItemViewModel>();
m_parent = parent;
m_cluster = matchedCluster;
var features = new UMCCollectionTreeViewModel(matchedCluster.Cluster);
features.FeatureSelected += feature_FeatureSelected;
features.Name = "Features";
// Cluster level statistics
var cluster = matchedCluster.Cluster;
AddStatistics("Mass", cluster.MassMonoisotopic);
var item = new StringTreeViewItem(
cluster.Net.ToString("F3",
CultureInfo.InvariantCulture),
"NET");
m_items.Add(item);
if (cluster.DriftTime > 0)
{
AddStatistics("Drift Time", cluster.DriftTime);
}
AddStatistics("Datasets", cluster.DatasetMemberCount);
AddStatistics("Total", cluster.MemberCount);
AddStatistics("Total MS/MS", cluster.MsMsCount);
AddStatistics("Total Identifications", cluster.IdentifiedSpectraCount);
var allIdentifications = new GenericCollectionTreeViewModel();
allIdentifications.Name = "Identifications";
// Items to display the base childen.
var identifications = new PeptideCollectionTreeViewModel(cluster);
identifications.Name = "Search Results";
identifications.FeatureSelected += feature_FeatureSelected;
var spectra = new MsMsCollectionTreeViewModel(cluster);
spectra.Name = "MS/MS";
m_spectra = spectra;
spectra.SpectrumSelected += spectra_SpectrumSelected;
spectra.FeatureSelected += feature_FeatureSelected;
var matches = new MassTagCollectionMatchTreeViewModel(matchedCluster.ClusterMatches);
matches.Name = "AMT Tags";
allIdentifications.Items.Add(identifications);
allIdentifications.Items.Add(spectra);
allIdentifications.Items.Add(matches);
m_allIdentifications = allIdentifications;
m_items.Add(features);
m_items.Add(allIdentifications);
}
private void LoadCluster(UMCClusterLightMatched cluster)
{
m_selectedCluster = cluster;
MassTagResults.Clear();
DatabaseResults.Clear();
var peptides = cluster.Cluster.FindPeptides();
peptides.ForEach(x => DatabaseResults.Add(new PeptideViewModel(x)));
cluster.ClusterMatches.ForEach(x => MassTagResults.Add(new MassTagMatchedViewModel(x)));
}
public UMCClusterTreeViewModel(UMCClusterLightMatched cluster)
: this(cluster, null)
{
}
private void LoadCluster(UMCClusterLightMatched cluster)
{
Spectra.Clear();
if (cluster == null)
return;
//TODO: Make this a task!!!
var spectra = cluster.Cluster.GetLoadedSpectra();
m_maxMz = 0.0;
m_maxIntensity = 0.0;
foreach (var spectrum in spectra)
{
spectrum.Peaks = SpectraLoader.LoadSpectrum(spectrum);
if (spectrum.Peaks.Count > 0)
{
m_maxMz = Math.Max(m_maxMz, spectrum.Peaks.Max(x => x.X));
m_maxIntensity = Math.Max(m_maxIntensity, spectrum.Peaks.Max(x => x.Y));
}
var msSpectrum = new MsSpectraViewModel(spectrum);
Spectra.Add(msSpectrum);
}
foreach (var model in Spectra)
{
model.SetMax(m_maxMz, m_maxIntensity);
model.SelectedSpectrumPlotModel.PlotSpectra(model.Spectrum);
}
if (spectra.Count > 0)
{
SelectedSpectra = Spectra[0];
}
}
/// <summary>
/// Reconstructs the mass tags and clusters joining tabled data.
/// </summary>
/// <param name="clusters"></param>
/// <param name="matches"></param>
/// <param name="database"></param>
/// <returns></returns>
public static Tuple<List<UMCClusterLightMatched>, List<MassTagToCluster>> MapMassTagsToClusters(
this List<UMCClusterLight> clusters,
List<ClusterToMassTagMap> matches,
MassTagDatabase database)
{
var matchedClusters = new List<UMCClusterLightMatched>();
var matchedTags = new List<MassTagToCluster>();
// Maps a cluster ID to a cluster that was matched (or not in which case it will have zero matches).
var clusterMap = new Dictionary<int, UMCClusterLightMatched>();
// Maps the mass tags to clusters, the second dictionary is for the conformations.
var massTagMap =
new Dictionary<int, Dictionary<int, MassTagToCluster>>();
// Index the clusters.
foreach (var cluster in clusters)
{
if (!clusterMap.ContainsKey(cluster.Id))
{
var matchedCluster = new UMCClusterLightMatched();
matchedCluster.Cluster = cluster;
clusterMap.Add(cluster.Id, matchedCluster);
}
}
if (database != null)
{
// Index the mass tags.
foreach (var tag in database.MassTags)
{
if (!massTagMap.ContainsKey(tag.Id))
{
massTagMap.Add(tag.Id, new Dictionary<int, MassTagToCluster>());
}
if (!massTagMap[tag.Id].ContainsKey(tag.ConformationId))
{
var matchedTag = new MassTagToCluster();
matchedTag.MassTag = tag;
massTagMap[tag.Id].Add(tag.ConformationId, matchedTag);
}
}
// Keeps track of all the proteins that we have mapped so far.
var proteinList = new Dictionary<int, ProteinToMassTags>();
// Link up the protein data
foreach (var massTagId in massTagMap.Keys)
{
foreach (var conformationID in massTagMap[massTagId].Keys)
{
var clusterTag = massTagMap[massTagId][conformationID];
// Here we make sure we link up the protein data too
if (database.Proteins.ContainsKey(massTagId))
{
// Get a list of the proteins this tag mapped to.
var proteins = database.Proteins[massTagId];
// Then for each protein, wrap it with a proteintomasstag map, then
// mapping the tag to the protein
// and mapping the protein to the tags.
foreach (var p in proteins)
{
if (!proteinList.ContainsKey(p.ProteinId))
{
var tempProtein = new ProteinToMassTags();
tempProtein.Protein = p;
proteinList.Add(p.ProteinId, tempProtein);
}
var protein = proteinList[p.ProteinId];
// Double link the data so we can go back and forth
protein.MassTags.Add(clusterTag);
clusterTag.MatchingProteins.Add(protein);
}
}
}
}
}
// Index and align matches
foreach (var match in matches)
{
// Find the cluster map
if (clusterMap.ContainsKey(match.ClusterId))
{
var cluster = clusterMap[match.ClusterId];
cluster.ClusterMatches.Add(match);
MassTagToCluster tag = null;
if (massTagMap.ContainsKey(match.MassTagId))
{
tag = massTagMap[match.MassTagId][match.ConformerId];
tag.Matches.Add(cluster);
match.MassTag = tag;
}
}
}
foreach (var clusterId in clusterMap.Keys)
{
matchedClusters.Add(clusterMap[clusterId]);
}
foreach (var tagId in massTagMap.Keys)
{
foreach (var conformerId in massTagMap[tagId].Keys)
{
matchedTags.Add(massTagMap[tagId][conformerId]);
}
}
var tuple =
new Tuple<List<UMCClusterLightMatched>, List<MassTagToCluster>>(matchedClusters, matchedTags);
return tuple;
}
/// <summary>
/// Updates the plots with data stored in the cache.
/// </summary>
private void UpdatePlotsWithClusterData(UMCClusterLightMatched matchedCluster)
{
//TODO: Make this select mass!
ClusterMassPlot = ScatterPlotFactory.CreateFeatureMassScatterPlot(matchedCluster.Cluster.Features);
//TODO: Make this select drift time!
ClusterDriftPlot = ScatterPlotFactory.CreateFeatureDriftTimeScatterPlot(matchedCluster.Cluster.Features);
var cluster = matchedCluster.Cluster;
// Then we find all the nearby clusters
var massPpm = ClusterTolerances.Mass;
var net = ClusterTolerances.Net;
//TODO: Add other clusters back
// var minMass = FeatureLight.ComputeDaDifferenceFromPPM(cluster.MassMonoisotopic, massPpm);
//var maxMass = FeatureLight.ComputeDaDifferenceFromPPM(cluster.MassMonoisotopic, -massPpm);
//var minNet = cluster.Net - net;
//var maxNet = cluster.Net + net;
//var otherClusters
// = SingletonDataProviders.Providers.ClusterCache.FindNearby(minMass, maxMass, minNet, maxNet);
//// Remove self from the list
//var index = otherClusters.FindIndex(x => x.Id == cluster.Id);
//if (index > -1)
//{
// otherClusters.RemoveAt(index);
//}
//// Then find the matching clusters and map them back to previously matched (to mass tag data)
//var otherClusterMatches = new List<UMCClusterLightMatched>();
//otherClusters.ForEach(x => otherClusterMatches.Add(FeatureCacheManager<UMCClusterLightMatched>.FindById(x.Id)));
//foreach (var matchedOtherCluster in otherClusterMatches)
//{
// matchedOtherCluster.Cluster.Features.Clear();
// matchedOtherCluster.Cluster.ReconstructUMCCluster(SingletonDataProviders.Providers, false, false);
//}
// Map out the MS/MS spectra.
var msmsFeatures = new List<MSFeatureMsMs>();
foreach (var feature in cluster.Features)
{
foreach (var msFeature in feature.MsFeatures)
{
msmsFeatures.AddRange(msFeature.MSnSpectra.Select(spectrum => new MSFeatureMsMs
{
FeatureID = msFeature.Id,
FeatureGroupID = msFeature.GroupId,
Mz = msFeature.Mz,
PrecursorMZ = spectrum.PrecursorMz,
FeatureScan = msFeature.Scan,
MsMsScan = spectrum.Scan,
MassMonoisotopicAligned = msFeature.MassMonoisotopicAligned,
ChargeState = msFeature.ChargeState,
Sequence = "",
PeptideSequence = ""
}));
}
}
var features = new List<UMCLight>();
features.AddRange(matchedCluster.Cluster.Features);
Features.Clear();
features.ForEach(x => Features.Add(new UMCTreeViewModel(x)));
SelectedFeature = Features[0];
}
/// <summary>
/// Grabs the data from the provider cache and shoves into UI where needed. This is done
/// here like this to prevent holding large amounts of data in memory.
/// </summary>
private void SetCluster(UMCClusterLightMatched cluster)
{
// Grab the data from the cache
UpdatePlotsWithClusterData(cluster);
ChargeHistogramModel = new UmcClusterChargeHistogram(cluster.Cluster, "Charge State Histogram");
}