/// <summary>
/// Writes the peak matching results to the local peak matching database.
/// </summary>
public void WritePeakMatchResults(PeakMatchingResults <UMCClusterLight, MassTagLight> results,
MassTagDatabase database,
out int matchedMassTags,
out int matchedProteins)
{
var clusterToMassTagMapDaoHibernate = new ClusterToMassTagMapDAOHibernate();
var stacFdrdaoHibernate = new STACDAOHibernate();
var massTagList = new List <MassTagLight>();
var proteinList = new Dictionary <int, Protein>();
var clusterToMassTagMapList = new List <ClusterToMassTagMap>();
clusterToMassTagMapDaoHibernate.ClearAll();
stacFdrdaoHibernate.ClearAll();
foreach (var match in results.Matches)
{
var tag = match.Target;
var feature = match.Observed;
var clusterToMassTagMap = new ClusterToMassTagMap(feature.Id, tag.Id);
clusterToMassTagMap.ConformerId = tag.ConformationId;
if (!clusterToMassTagMapList.Contains(clusterToMassTagMap))
{
clusterToMassTagMapList.Add(clusterToMassTagMap);
clusterToMassTagMap.StacScore = match.Confidence;
clusterToMassTagMap.StacUP = match.Uniqueness;
}
if (!massTagList.Contains(tag))
{
massTagList.Add(tag);
}
var databaseContainsProtein = database.Proteins.ContainsKey(tag.Id);
if (databaseContainsProtein)
{
var proteins = database.Proteins[tag.Id];
foreach (var protein in proteins.Where(protein => !proteinList.ContainsKey(protein.ProteinId)))
{
proteinList.Add(protein.ProteinId, protein);
}
}
}
var uniqueProteins = new List <Protein>();
foreach (var protein in proteinList.Values)
{
uniqueProteins.Add(protein);
}
matchedMassTags = massTagList.Count;
matchedProteins = uniqueProteins.Count;
clusterToMassTagMapDaoHibernate.AddAll(clusterToMassTagMapList);
stacFdrdaoHibernate.AddAll(results.FdrTable);
}
/// <summary>
/// Writes the peak matching results to the local peak matching database.
/// </summary>
public void WritePeakMatchResults(PeakMatchingResults<UMCClusterLight, MassTagLight> results,
MassTagDatabase database,
out int matchedMassTags,
out int matchedProteins)
{
var clusterToMassTagMapDaoHibernate = new ClusterToMassTagMapDAOHibernate();
var stacFdrdaoHibernate = new STACDAOHibernate();
var massTagList = new List<MassTagLight>();
var proteinList = new Dictionary<int, Protein>();
var clusterToMassTagMapList = new List<ClusterToMassTagMap>();
clusterToMassTagMapDaoHibernate.ClearAll();
stacFdrdaoHibernate.ClearAll();
foreach (var match in results.Matches)
{
var tag = match.Target;
var feature = match.Observed;
var clusterToMassTagMap = new ClusterToMassTagMap(feature.Id, tag.Id);
clusterToMassTagMap.ConformerId = tag.ConformationId;
if (!clusterToMassTagMapList.Contains(clusterToMassTagMap))
{
clusterToMassTagMapList.Add(clusterToMassTagMap);
clusterToMassTagMap.StacScore = match.Confidence;
clusterToMassTagMap.StacUP = match.Uniqueness;
}
if (!massTagList.Contains(tag))
{
massTagList.Add(tag);
}
var databaseContainsProtein = database.Proteins.ContainsKey(tag.Id);
if (databaseContainsProtein)
{
var proteins = database.Proteins[tag.Id];
foreach (var protein in proteins.Where(protein => !proteinList.ContainsKey(protein.ProteinId)))
{
proteinList.Add(protein.ProteinId, protein);
}
}
}
var uniqueProteins = new List<Protein>();
foreach (var protein in proteinList.Values)
{
uniqueProteins.Add(protein);
}
matchedMassTags = massTagList.Count;
matchedProteins = uniqueProteins.Count;
clusterToMassTagMapDaoHibernate.AddAll(clusterToMassTagMapList);
stacFdrdaoHibernate.AddAll(results.FdrTable);
}
/// <summary>
/// Performs peak matching with loaded clusters.
/// </summary>
private void PerformPeakMatching(AnalysisConfig config)
{
if (!config.ShouldPeakMatch)
{
return;
}
if (m_config.Analysis.MassTagDatabase == null)
{
UpdateStatus("Could not peak match. The database was not set.");
}
else
{
var clusters = m_config.Analysis.DataProviders.ClusterCache.FindAll();
var peakMatcher = m_algorithms.PeakMatcher;
UpdateStatus("Performing Peak Matching");
var adapter = peakMatcher as STACAdapter <UMCClusterLight>;
if (adapter != null)
{
UpdateStatus(adapter.Options.UseDriftTime ? "Using drift time." : "Ignoring drift time.");
}
var matchResults = new PeakMatchingResults <UMCClusterLight, MassTagLight>();
clusters.ForEach(x => x.Net = x.Net);
matchResults.Matches = peakMatcher.PerformPeakMatching(clusters, m_config.Analysis.MassTagDatabase);
if (adapter != null)
{
matchResults.FdrTable = adapter.Matcher.StacFdrTable;
}
m_config.Analysis.MatchResults = matchResults;
if (FeaturesPeakMatched != null)
{
FeaturesPeakMatched(this, new FeaturesPeakMatchedEventArgs(clusters, matchResults.Matches));
}
UpdateStatus("Updating database with peak matched results.");
var writer = new PeakMatchResultsWriter();
int matchedMassTags;
int matchedProteins;
writer.WritePeakMatchResults(matchResults,
m_config.Analysis.MassTagDatabase,
out matchedMassTags,
out matchedProteins);
UpdateStatus(string.Format("Found {0} mass tag matches. Matching to {1} potential proteins.",
matchedMassTags,
matchedProteins));
}
}
/// <summary>
/// Performs peak matching with loaded clusters.
/// </summary>
private void PerformPeakMatching(AnalysisConfig config)
{
if (!config.ShouldPeakMatch)
return;
if (m_config.Analysis.MassTagDatabase == null)
{
UpdateStatus("Could not peak match. The database was not set.");
}
else
{
var clusters = m_config.Analysis.DataProviders.ClusterCache.FindAll();
var peakMatcher = m_algorithms.PeakMatcher;
UpdateStatus("Performing Peak Matching");
var adapter = peakMatcher as STACAdapter<UMCClusterLight>;
if (adapter != null)
{
UpdateStatus(adapter.Options.UseDriftTime ? "Using drift time." : "Ignoring drift time.");
}
var matchResults = new PeakMatchingResults<UMCClusterLight, MassTagLight>();
clusters.ForEach(x => x.Net = x.Net);
matchResults.Matches = peakMatcher.PerformPeakMatching(clusters, m_config.Analysis.MassTagDatabase);
if (adapter != null)
{
matchResults.FdrTable = adapter.Matcher.StacFdrTable;
}
m_config.Analysis.MatchResults = matchResults;
if (FeaturesPeakMatched != null)
{
FeaturesPeakMatched(this, new FeaturesPeakMatchedEventArgs(clusters, matchResults.Matches));
}
UpdateStatus("Updating database with peak matched results.");
var writer = new PeakMatchResultsWriter();
int matchedMassTags;
int matchedProteins;
writer.WritePeakMatchResults(matchResults,
m_config.Analysis.MassTagDatabase,
out matchedMassTags,
out matchedProteins);
UpdateStatus(string.Format("Found {0} mass tag matches. Matching to {1} potential proteins.",
matchedMassTags,
matchedProteins));
}
}