public IdentificationCollectionTreeViewModel(IEnumerable <UMCClusterLightMatched> clusters,
IEnumerable <Peptide> peptides,
TreeItemViewModel parent)
{
var tags = new GenericCollectionTreeViewModel();
tags.Name = "AMT Tags";
foreach (var cluster in clusters)
{
foreach (var match in cluster.ClusterMatches)
{
tags.Items.Add(new MassTagToClusterMatch(match.MassTag));
}
}
var peptideItems = new GenericCollectionTreeViewModel();
peptideItems.Name = "Database Searches";
var peptideModels = (from peptide in peptides
select new PeptideTreeViewModel(peptide)).ToList();
foreach (var item in peptideModels)
{
peptideItems.Items.Add(item);
}
}
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);
}
public override void LoadChildren()
{
if (m_loaded)
{
return;
}
var peptides = m_parentCluster.FindPeptides();
if (peptides.Count < 1)
{
return;
}
// Tally up the unique peptides
var uniqueCounts = new Dictionary <string, List <Peptide> >();
foreach (var peptide in peptides)
{
if (!uniqueCounts.ContainsKey(peptide.Sequence))
{
uniqueCounts.Add(peptide.Sequence, new List <Peptide>());
}
uniqueCounts[peptide.Sequence].Add(peptide);
}
// Show that to the user
AddStatistic("Unique Identifications", uniqueCounts.Count);
AddStatistic("Total Identifications", peptides.Count);
foreach (var sequence in uniqueCounts.Keys)
{
// Create a collection for each unique sequence
var model = new GenericCollectionTreeViewModel();
model.Name = sequence;
model.AddStatistic("Total Members", uniqueCounts[sequence].Count);
foreach (var p in uniqueCounts[sequence])
{
var peptideModel = new PeptideTreeViewModel(p);
peptideModel.FeatureSelected += peptideModel_FeatureSelected;
model.Items.Add(peptideModel);
}
m_items.Add(model);
}
m_loaded = true;
}
public override void LoadChildren()
{
if (m_loaded)
return;
var peptides = m_parentCluster.FindPeptides();
if (peptides.Count < 1)
return;
// Tally up the unique peptides
var uniqueCounts = new Dictionary<string, List<Peptide>>();
foreach (var peptide in peptides)
{
if (!uniqueCounts.ContainsKey(peptide.Sequence))
{
uniqueCounts.Add(peptide.Sequence, new List<Peptide>());
}
uniqueCounts[peptide.Sequence].Add(peptide);
}
// Show that to the user
AddStatistic("Unique Identifications", uniqueCounts.Count);
AddStatistic("Total Identifications", peptides.Count);
foreach (var sequence in uniqueCounts.Keys)
{
// Create a collection for each unique sequence
var model = new GenericCollectionTreeViewModel();
model.Name = sequence;
model.AddStatistic("Total Members", uniqueCounts[sequence].Count);
foreach (var p in uniqueCounts[sequence])
{
var peptideModel = new PeptideTreeViewModel(p);
peptideModel.FeatureSelected += peptideModel_FeatureSelected;
model.Items.Add(peptideModel);
}
m_items.Add(model);
}
m_loaded = true;
}
public IdentificationCollectionTreeViewModel(IEnumerable<UMCClusterLightMatched> clusters,
IEnumerable<Peptide> peptides,
TreeItemViewModel parent)
{
var tags = new GenericCollectionTreeViewModel();
tags.Name = "AMT Tags";
foreach (var cluster in clusters)
{
foreach (var match in cluster.ClusterMatches)
{
tags.Items.Add(new MassTagToClusterMatch(match.MassTag));
}
}
var peptideItems = new GenericCollectionTreeViewModel();
peptideItems.Name = "Database Searches";
var peptideModels = (from peptide in peptides
select new PeptideTreeViewModel(peptide)).ToList();
foreach (var item in peptideModels)
{
peptideItems.Items.Add(item);
}
}
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);
}
