public PeptideTreeViewModel(Peptide peptide, TreeItemViewModel parent)
{
m_parent = parent;
m_peptide = peptide;
var information = SingletonDataProviders.GetDatasetInformation(m_peptide.GroupId);
if (information != null)
{
Name = information.DatasetName;
}
else
{
Name = string.Format("Dataset {0}", m_peptide.GroupId);
}
AddStatistic("Id", m_peptide.Id);
AddStatistic("Dataset Id", m_peptide.GroupId);
AddStatistic("Precursor m/z", m_peptide.Spectrum.PrecursorMz);
if (m_peptide.Spectrum.ParentFeature != null)
{
AddStatistic("Charge", m_peptide.Spectrum.ParentFeature.ChargeState);
}
else
{
AddStatistic("Charge", m_peptide.Spectrum.PrecursorChargeState);
}
AddString("Sequence", peptide.Sequence);
AddStatistic("Score", peptide.Score);
AddStatistic("Scan", peptide.Scan);
}
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 MsMsTreeViewModel(MSSpectra feature, TreeItemViewModel parent)
{
m_feature = feature;
m_parent = parent;
var information = SingletonDataProviders.GetDatasetInformation(m_feature.GroupId);
AddStatistic("Id", m_feature.Id);
AddStatistic("Dataset Id", m_feature.GroupId);
AddStatistic("Precursor m/z", m_feature.PrecursorMz);
if (feature.ParentFeature != null)
{
AddStatistic("Charge", m_feature.ParentFeature.ChargeState);
}
else
{
AddStatistic("Charge", m_feature.PrecursorChargeState);
}
AddStatistic("Scan", m_feature.Scan);
Peptides = new ObservableCollection<Peptide>();
Peptide maxPeptide = null;
foreach (var p in m_feature.Peptides)
{
Peptides.Add(p);
if (maxPeptide == null)
{
maxPeptide = p;
}
else if (p.Score < maxPeptide.Score)
{
maxPeptide = p;
}
}
if (maxPeptide != null)
{
Name = maxPeptide.Sequence;
AddStatistic("Score", maxPeptide.Score);
AddStatistic("Scan", maxPeptide.Scan);
}
else
{
Name = string.Format("Unknown - Scan: {0} m/z: {1:.00} ", m_feature.Scan, m_feature.PrecursorMz);
}
}
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 PeptideCollectionTreeViewModel(UMCClusterLight parentCluster, TreeItemViewModel parent)
{
m_parent = parent;
m_parentCluster = parentCluster;
}
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 MassTagCollectionMatchTreeViewModel(List<ClusterToMassTagMap> matches, TreeItemViewModel parent)
{
m_parent = parent;
m_massTags = new ObservableCollection<MassTagMatchTreeViewModel>();
}
public UMCCollectionTreeViewModel(UMCClusterLight parentCluster, TreeItemViewModel parent)
{
m_parent = parent;
m_parentCluster = parentCluster;
m_features = new ObservableCollection <UMCTreeViewModel>();
}
public PeptideCollectionTreeViewModel(UMCClusterLight parentCluster, TreeItemViewModel parent)
{
m_parent = parent;
m_parentCluster = parentCluster;
}
public MassTagCollectionMatchTreeViewModel(List <ClusterToMassTagMap> matches, TreeItemViewModel parent)
{
m_parent = parent;
m_massTags = new ObservableCollection <MassTagMatchTreeViewModel>();
}
public UMCCollectionTreeViewModel(UMCClusterLight parentCluster, TreeItemViewModel parent)
{
m_parent = parent;
m_parentCluster = parentCluster;
m_features = new ObservableCollection<UMCTreeViewModel>();
}