public MassTagDatabase LoadDatabase()
{
var database = new MassTagDatabase();
var massTags = new List<MassTagLight>();
var masstagMap = new Dictionary<int, List<Protein>>();
//TODO: Put into base table file reader
var lines = File.ReadAllLines(DatabasePath);
var delimiters = new[] {"\t"};
for (var i = 1; i < lines.Length; i++)
{
var data = lines[i].Split(delimiters, StringSplitOptions.RemoveEmptyEntries);
var tag = new MassTagLight();
if (data.Length > 4)
{
tag.Id = Convert.ToInt32(data[0]);
tag.PeptideSequence = data[1];
tag.MassMonoisotopic = Convert.ToDouble(data[2]);
tag.Net = Convert.ToDouble(data[3]);
tag.DriftTime = Convert.ToDouble(data[4]);
}
massTags.Add(tag);
}
database.AddMassTagsAndProteins(massTags, masstagMap);
return database;
}
/// <summary>
/// Aligns a dataset to a mass tag database
/// </summary>
/// <param name="massTagDatabase"></param>
/// <param name="features"></param>
/// <param name="progress"></param>
/// <returns></returns>
public AlignmentData Align(MassTagDatabase massTagDatabase,
IEnumerable <UMCLight> features,
IProgress <ProgressData> progress = null)
{
var alignmentProcessor = new LcmsWarpAlignmentProcessor(_options);
alignmentProcessor.Progress += AlignmentProcessor_Progress;
var umcLights = features as IList <UMCLight> ?? features.ToList();
var featureTest = umcLights.ToList().Find(x => x.DriftTime > 0);
if (featureTest != null && !massTagDatabase.DoesContainDriftTime)
{
OnStatus("Warning! Data contains drift time information and the database does not.");
}
OnStatus("Configuring features as mass tags.");
OnStatus("Setting reference features using mass tags.");
alignmentProcessor.SetReferenceDatasetFeatures(massTagDatabase.MassTags);
var data = AlignFeatures(alignmentProcessor,
umcLights,
_options,
progress);
return(data);
}
public MassTagDatabase LoadDatabase()
{
var database = new MassTagDatabase();
var massTags = new List <MassTagLight>();
var masstagMap = new Dictionary <int, List <Protein> >();
//TODO: Put into base table file reader
var lines = File.ReadAllLines(DatabasePath);
var delimiters = new[] { "\t" };
for (var i = 1; i < lines.Length; i++)
{
var data = lines[i].Split(delimiters, StringSplitOptions.RemoveEmptyEntries);
var tag = new MassTagLight();
if (data.Length > 4)
{
tag.Id = Convert.ToInt32(data[0]);
tag.PeptideSequence = data[1];
tag.MassMonoisotopic = Convert.ToDouble(data[2]);
tag.Net = Convert.ToDouble(data[3]);
tag.DriftTime = Convert.ToDouble(data[4]);
}
massTags.Add(tag);
}
database.AddMassTagsAndProteins(massTags, masstagMap);
return(database);
}
public AnalysisControl()
{
InitializeComponent();
m_processor = new MTDBProcessor();
m_processor.DatabaseCreated += new EventHandler <DatabaseCreatedEventArgs>(processor_DatabaseCreated);
m_processor.Status += new EventHandler <StatusEventArgs>(processor_Status);
m_processor.Error += new EventHandler <StatusEventArgs>(processor_Error);
m_processor.AnalysisCompleted += new EventHandler <AnalysisCompletedEventArgs>(processor_AnalysisCompleted);
m_processor.ProcessingAnalysis += new EventHandler <AnalysisCompletedEventArgs>(processor_ProcessingAnalysis);
m_processor.AnalysisFailed += new EventHandler <DatabaseCreatedEventArgs>(m_processor_AnalysisFailed);
m_displayCache = new Dictionary <Analysis, clsSeries>();
m_manager = new AnalysisManager();
radioButtonPredictedNET.Checked = true;
radioButtonAverageNET.Enabled = false;
m_database = null;
listViewDatasets.SmallImageList = imageList1;
// Create a save MTDB Dialog window for selecting where to output the data
m_saveMTDBDialog = new SaveFileDialog();
m_saveMTDBDialog.FileName = CONST_DEFAULT_DATABASE_NAME;
mobjTransformPlotter = new ChartPostRenderingProcessor(this.DrawNetRegressionLine);
ctlChartScanVsNET.AddPostProcessor(mobjTransformPlotter, PostProcessPriority.Mid);
listViewDatasets.DoubleClick += new EventHandler(listViewDatasets_DoubleClick);
}
/// <summary>
/// Aligns to a mass tag database. The baseline provider should be able to convert a mass tag sequence into a theoretical spectrum.
/// </summary>
/// <param name="baseline"></param>
/// <param name="alignee"></param>
/// <returns></returns>
public IEnumerable <SpectralAnchorPointMatch> Align(MassTagDatabase baseline,
IEnumerable <UMCLight> alignee, IProgress <ProgressData> progress = null)
{
OnProgress("Finding anchor point matches");
var finder = new SpectralAnchorPointFinder();
var matches = finder.FindAnchorPoints(BaselineSpectraProvider as ISpectraProvider,
AligneeSpectraProvider as ISpectraProvider,
SpectralComparer,
Filter,
Options);
OnProgress("Creating Alignment Functions");
var aligner = new SpectralAnchorPointAligner();
var spectralAnchorPointMatches = matches as SpectralAnchorPointMatch[] ?? matches.ToArray();
//TODO: Brian modified to test alignment using LCMSWarp regression code.
aligner.CreateAlignmentFunctions(spectralAnchorPointMatches);
OnProgress("Transforming sub-features");
foreach (var feature in alignee)
{
feature.NetAligned = feature.Net; // aligner.AlignNet(feature.Net);
}
return(spectralAnchorPointMatches);
}
/// <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);
}
private IList <UMCLight> AlignDataset(
IList <UMCLight> features,
IEnumerable <UMCLight> baselineFeatures,
MassTagDatabase database,
DatasetInformation datasetInfo,
DatasetInformation baselineInfo)
{
AlignmentData alignmentData;
if (baselineInfo == null && database == null)
{
throw new NullReferenceException("No reference was set for LC-MS alignment.");
}
// align the data.
if (baselineFeatures != null && baselineInfo != null && baselineInfo.IsBaseline)
{
// Align pairwise and cache results intermediately.
var aligner = m_algorithms.DatasetAligner;
RegisterProgressNotifier(aligner);
UpdateStatus("Aligning " + datasetInfo.DatasetName + " to baseline.");
alignmentData = aligner.Align(baselineFeatures, features);
DeRegisterProgressNotifier(aligner);
}
else
{
// Align pairwise and cache results intermediately.
var aligner = m_algorithms.DatabaseAligner;
RegisterProgressNotifier(aligner);
UpdateStatus("Aligning " + datasetInfo.DatasetName + " to mass tag database.");
alignmentData = aligner.Align(database, features);
DeRegisterProgressNotifier(aligner);
}
if (alignmentData != null)
{
alignmentData.AligneeDataset = datasetInfo.DatasetName;
alignmentData.DatasetID = datasetInfo.DatasetId;
}
var args = new FeaturesAlignedEventArgs(datasetInfo,
baselineFeatures,
features,
alignmentData);
if (FeaturesAligned != null)
{
FeaturesAligned(this, args);
}
UpdateStatus("Updating cache with aligned features.");
return(features);
}
/// <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>
/// Loads the mass tag database from the underlying database system.
/// </summary>
/// <returns></returns>
public virtual MassTagDatabase LoadDatabase()
{
var database = new MassTagDatabase();
var tags = LoadMassTags();
var proteinMap = LoadProteins();
database.AddMassTagsAndProteins(tags, proteinMap);
return(database);
}
/// <summary>
/// Loads the mass tag database from the underlying database system.
/// </summary>
/// <returns></returns>
public virtual MassTagDatabase LoadDatabase()
{
var database = new MassTagDatabase();
var tags = LoadMassTags();
var proteinMap = LoadProteins();
database.AddMassTagsAndProteins(tags, proteinMap);
return database;
}
/// <summary>
/// Default constructor for a MultiAlign analysis object.
/// </summary>
public MultiAlignAnalysis()
{
// Meta Data Information about the analysis and datasets.
MetaData = new AnalysisMetaData {AnalysisName = string.Empty};
Options = new MultiAlignAnalysisOptions();
MassTagDatabase = new MassTagDatabase();
// Alignment options and data.
AlignmentData = new List<classAlignmentData>();
MatchResults = null;
}
public new AlignmentData Align(MassTagDatabase database, IEnumerable <UMCLight> alignee, IProgress <ProgressData> progress = null)
{
var matches = base.Align(database, alignee);
var data = new AlignmentData {
Matches = matches
};
Matches = matches;
return(data);
}
/// <summary>
/// Default constructor for a MultiAlign analysis object.
/// </summary>
public MultiAlignAnalysis()
{
// Meta Data Information about the analysis and datasets.
MetaData = new AnalysisMetaData {
AnalysisName = string.Empty
};
Options = new MultiAlignAnalysisOptions();
MassTagDatabase = new MassTagDatabase();
// Alignment options and data.
AlignmentData = new List <AlignmentData>();
MatchResults = null;
}
/// <summary>
/// Saves the database to file.
/// </summary>
/// <param name="database"></param>
/// <param name="path"></param>
private void SaveDatabase(MassTagDatabase database, string path)
{
IMassTagDatabaseWriter writer = MassTagDatabaseWriterFactory.CreateWriter(MtdbWriterType.Sqlite);
OnStatus("Filtering Database For Export Based on Options.");
// Here we make sure that we filter the database...
//MassTagDatabase filteredDatabase = new MassTagDatabase(database, m_options);
OnStatus("Saving Database.");
writer.WriteDatabase(database, path);
OnStatus("Database Saved.");
mbutton_showDatabase.Visible = true;
}
private static MassTagDatabase ReadDatabase(string databasePath)
{
MassTagDatabase database = null;
//Perform the reading from the binary file, saving data into database
var fileBytes = File.ReadAllBytes(databasePath);
var sb = new StringBuilder();
foreach (var b in fileBytes)
{
sb.Append(Convert.ToString(b, 2).PadLeft(8, '0'));
}
//Now it's a string of data
var data = sb.ToString();
return(database);
}
public MassTagDatabase LoadDatabase()
{
var database = new MassTagDatabase();
var sink = new MAGEMetaSampleDatabaseSink();
var reader = new DelimitedFileReader();
reader.Delimiter = ",";
reader.FilePath = Path;
var pipeline = ProcessingPipeline.Assemble("MetaSample", reader, sink);
pipeline.RunRoot(null);
var tags =
sink.MassTags.FindAll(
delegate(MassTagLight x) { return x.ObservationCount >= m_options.MinimumObservationCountFilter; });
database.AddMassTagsAndProteins(tags, new Dictionary<int, List<Protein>>());
// Fill in logic to read new type of mass tag database.
return database;
}
public AlignmentData AlignToDatabase(
ref IList <UMCLight> features,
DatasetInformation datasetInfo,
MassTagDatabase mtdb,
IProgress <ProgressData> progress = null)
{
progress = progress ?? new Progress <ProgressData>();
var aligner = this.m_algorithms.DatabaseAligner;
var alignmentData = aligner.Align(mtdb, features, progress);
aligner.Progress += aligner_Progress;
if (alignmentData != null)
{
alignmentData.AligneeDataset = datasetInfo.DatasetName;
alignmentData.DatasetID = datasetInfo.DatasetId;
}
aligner.Progress -= aligner_Progress;
return(alignmentData);
}
void processor_DatabaseCreated(object sender, DatabaseCreatedEventArgs e)
{
// This is a thread safe thing here. We can never access the GUI elements except from the
// thread that created it...STA.
if (InvokeRequired)
{
Invoke(new EventHandler <DatabaseCreatedEventArgs>(processor_DatabaseCreated), sender, e);
return;
}
mprogress_analysis.Visible = false;
m_database = e.Database;
mbutton_saveDatabase.Visible = true;
radioButtonAverageNET.Enabled = true;
databaseControl1.UpdateDatabaseView(m_database);
OnStatus("Database Created.");
if (DatabaseCreated != null)
{
DatabaseCreated(sender, new DatabaseCreatedEventArgs(e.Database));
}
m_database.ConsensusTargets.ForEach(x => x.Targets.Clear());
}
public MassTagDatabase LoadDatabase()
{
var database = new MassTagDatabase();
var sink = new MAGEMetaSampleDatabaseSink();
var reader = new DelimitedFileReader();
reader.Delimiter = ",";
reader.FilePath = Path;
var pipeline = ProcessingPipeline.Assemble("MetaSample", reader, sink);
pipeline.RunRoot(null);
var tags = sink.MassTags.Where(x => x.ObservationCount >= m_options.MinimumObservationCountFilter);
database.AddMassTagsAndProteins(tags.ToList(), new Dictionary <int, List <Protein> >());
// Fill in logic to read new type of mass tag database.
return(database);
}
/// <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;
}
public MassTagDatabase LoadDatabase()
{
var database = new MassTagDatabase();
//Implement the loading / reading of the MTDB Framework objects.
var reader = new SqLiteTargetDatabaseReader();
var mtdbDatabase = reader.ReadDb(m_path);
var massTags = new List <MassTagLight>();
// Mapping objects to create unique proteins and for the mass tag database to load only those proteins for
// the given consensus targets/mass tags.
var proteinMap = new Dictionary <int, Protein>();
var massTagProteinMap = new Dictionary <int, List <Protein> >();
if (mtdbDatabase == null)
{
return(database);
}
foreach (var target in mtdbDatabase.ConsensusTargets)
{
// Copy the consensus data into a mass tag light.
var tag = new MassTagLight
{
Id = target.Id,
MassMonoisotopic = target.TheoreticalMonoIsotopicMass,
NetAverage = target.AverageNet,
NetPredicted = target.PredictedNet,
PeptideSequence = target.Sequence,
NetStandardDeviation = target.StdevNet
};
// Here we create unique proteins for the mass tag copying information from the consensus target proteins.
var proteinsForMassTag = new List <Protein>();
foreach (var targetProtein in target.Proteins)
{
if (!proteinMap.ContainsKey(targetProtein.Id))
{
var newProtein = new Protein
{
Id = targetProtein.Id,
Name = targetProtein.ProteinName,
ResidueStartPosition = targetProtein.ResidueStart,
ResidueEndPosition = targetProtein.ResidueEnd
};
//TODO: Do something about the cleavage state and terminus state of a protein loaded from MTDBCreator database.
//protein.CleavageState = ??
//protein.TerminusState = ??
proteinMap.Add(newProtein.Id, newProtein);
}
var protein = proteinMap[targetProtein.Id];
proteinsForMassTag.Add(protein);
}
massTagProteinMap.Add(tag.Id, proteinsForMassTag);
massTags.Add(tag);
}
database.AddMassTagsAndProteins(massTags, massTagProteinMap);
return(database);
}
public MassTagDatabase LoadDatabase()
{
var database = new MassTagDatabase {Name = ""};
UpdateStatus("Loading all of the mass tags.");
// Get all of the mass tags
var massTags = Provider.FindAll();
UpdateStatus("Loading all of the tag to protein references.");
// Then get all of the mass tag to protein maps
IGenericDAO<MassTagToProteinMap> tagToProteinMapCache = new GenericDAOHibernate<MassTagToProteinMap>();
var maps = tagToProteinMapCache.FindAll();
// Then get all of the proteins
UpdateStatus("Loading all of the protein data.");
IProteinDAO proteinCache = new ProteinDAO();
var proteins = proteinCache.FindAll();
UpdateStatus("Indexing the protein data for faster assembly.");
var proteinMap = new Dictionary<int, Protein>();
foreach (var p in proteins)
{
if (!proteinMap.ContainsKey(p.ProteinId))
{
proteinMap.Add(p.ProteinId, p);
}
}
var matchedMaps = new Dictionary<int, List<MassTagToProteinMap>>();
foreach (var singleMap in maps)
{
if (!matchedMaps.ContainsKey(singleMap.MassTagId))
{
matchedMaps.Add(singleMap.MassTagId, new List<MassTagToProteinMap>());
}
matchedMaps[singleMap.MassTagId].Add(singleMap);
}
UpdateStatus("Re-mapping the proteins to the mass tags.");
var massTagProteinMap = new Dictionary<int, List<Protein>>();
// Then map them.
foreach (var tag in massTags)
{
var id = tag.Id;
if (!massTagProteinMap.ContainsKey(id))
{
massTagProteinMap.Add(id, new List<Protein>());
}
var matches = new List<MassTagToProteinMap>();
if (matchedMaps.ContainsKey(id))
{
matches = matchedMaps[id];
}
var newProteins = new List<Protein>();
foreach (var mtMap in matches)
{
if (proteinMap.ContainsKey(mtMap.ProteinId))
{
newProteins.Add(proteinMap[mtMap.ProteinId]);
}
}
massTagProteinMap[id].AddRange(newProteins);
}
UpdateStatus("Building the in memory mass tag database.");
database.AddMassTagsAndProteins(massTags, massTagProteinMap);
database.AllProteins = proteins;
var totalMassTags = database.MassTags.Count;
UpdateStatus("Loaded " + totalMassTags + " mass tags.");
return database;
}
public BaselineFeaturesLoadedEventArgs(DatasetInformation info, List <UMCLight> features,
MassTagDatabase database) :
base(info, features)
{
Database = database;
}
/// <summary>
/// Arguments that hold dataset information when features are loaded.
/// </summary>
public MassTagsLoadedEventArgs(List <MassTagLight> tags, MassTagDatabase database)
{
MassTags = tags;
Database = database;
}
public AlignmentData Align(MassTagDatabase database,
IEnumerable <UMCLight> features, IProgress <ProgressData> progress = null)
{
return(null);
}
/// <summary>
/// Loads baseline data for alignment.
/// </summary>
private IList<UMCLight> LoadBaselineData(DatasetInformation baselineInfo,
MsFeatureFilteringOptions msFilterOptions,
LcmsFeatureFindingOptions lcmsFindingOptions,
LcmsFeatureFilteringOptions lcmsFilterOptions,
FeatureDataAccessProviders dataProviders,
MassTagDatabase database,
bool shouldUseMassTagDbAsBaseline)
{
IList<UMCLight> baselineFeatures = null;
UpdateStatus("Loading baseline features.");
if (!shouldUseMassTagDbAsBaseline)
{
if (baselineInfo == null)
{
throw new Exception("The baseline dataset was never set.");
}
var cache = new FeatureLoader
{
Providers = dataProviders
};
RegisterProgressNotifier(cache);
UpdateStatus("Loading baseline features from " + baselineInfo.DatasetName + " for alignment.");
baselineFeatures = cache.LoadDataset(baselineInfo,
msFilterOptions,
lcmsFindingOptions,
lcmsFilterOptions);
cache.CacheFeatures(baselineFeatures);
if (BaselineFeaturesLoaded != null)
{
BaselineFeaturesLoaded(this,
new BaselineFeaturesLoadedEventArgs(baselineInfo, baselineFeatures.ToList()));
}
DeRegisterProgressNotifier(cache);
}
else
{
if (database == null)
throw new NullReferenceException(
"The mass tag database has to have data in it if it's being used for drift time alignment.");
UpdateStatus("Setting baseline features for post drift time alignment from mass tag database.");
var tags = FeatureDataConverters.ConvertToUMC(database.MassTags);
if (BaselineFeaturesLoaded == null)
return tags;
if (tags != null)
BaselineFeaturesLoaded(this, new BaselineFeaturesLoadedEventArgs(null, tags.ToList(), database));
}
return baselineFeatures;
}
/// <summary>
/// Loads baseline data for alignment.
/// </summary>
private IList <UMCLight> LoadBaselineData(DatasetInformation baselineInfo,
MsFeatureFilteringOptions msFilterOptions,
LcmsFeatureFindingOptions lcmsFindingOptions,
LcmsFeatureFilteringOptions lcmsFilterOptions,
DataLoadingOptions dataLoadOptions,
FeatureDataAccessProviders dataProviders,
MassTagDatabase database,
bool shouldUseMassTagDbAsBaseline)
{
IList <UMCLight> baselineFeatures = null;
UpdateStatus("Loading baseline features.");
if (!shouldUseMassTagDbAsBaseline)
{
if (baselineInfo == null)
{
throw new Exception("The baseline dataset was never set.");
}
var cache = new FeatureLoader
{
Providers = dataProviders
};
RegisterProgressNotifier(cache);
UpdateStatus("Loading baseline features from " + baselineInfo.DatasetName + " for alignment.");
baselineFeatures = cache.LoadDataset(baselineInfo,
msFilterOptions,
lcmsFindingOptions,
lcmsFilterOptions,
dataLoadOptions,
m_scanSummaryProviderCache,
this.m_identificationsProvider);
cache.CacheFeatures(baselineFeatures);
if (BaselineFeaturesLoaded != null)
{
BaselineFeaturesLoaded(this,
new BaselineFeaturesLoadedEventArgs(baselineInfo, baselineFeatures.ToList()));
}
DeRegisterProgressNotifier(cache);
}
else
{
if (database == null)
{
throw new NullReferenceException(
"The mass tag database has to have data in it if it's being used for drift time alignment.");
}
UpdateStatus("Setting baseline features for post drift time alignment from mass tag database.");
var tags = FeatureDataConverters.ConvertToUMC(database.MassTags);
if (BaselineFeaturesLoaded == null)
{
return(tags);
}
if (tags != null)
{
BaselineFeaturesLoaded(this, new BaselineFeaturesLoadedEventArgs(null, tags.ToList(), database));
}
}
return(baselineFeatures);
}
public BaselineFeaturesLoadedEventArgs(DatasetInformation info, List<UMCLight> features,
MassTagDatabase database)
: base(info, features)
{
Database = database;
}
/// <summary>
/// Load a Liquid lipd MS/MS search results file as a MultiAlign
/// <see cref="MassTagDatabase" />.
/// </summary>
/// <returns>The resulting mass tag database.</returns>
/// <exception cref="FormatException">
/// Throws a format exception when there are missing headers, or
/// a non-numeric value was found in a column that was expected to be numeric.
/// </exception>
public MassTagDatabase LoadDatabase()
{
var headers = new Dictionary <string, int>();
var massTags = new List <MassTagLight>();
// Mapping between protein (actually lipid) name, to protein object (currently represents lipids).
var commonNameToProtein = new Dictionary <string, Protein>();
int lipidId = 0;
// Parse lines of file into mass tags.
int lineCount = 0;
foreach (var line in File.ReadLines(this.filePath))
{
var parts = line.Split('\t');
if (lineCount++ == 0)
{ // Header line, store header indices
for (int i = 0; i < parts.Length; i++)
{
headers.Add(parts[i], i);
}
// Make sure all of the headers we are expecting are actually in the file.
this.DetectMissingHeaders(headers);
continue;
}
var net = Convert.ToDouble(parts[headers["NET"]]);
var mz = Convert.ToDouble(parts[headers["Exact m/z"]]);
var mass = mz - Constants.Proton;
var name = parts[headers["Common Name"]];
var formula = parts[headers["Formula"]];
// Add lipid to mapping if it isn't already there
if (!commonNameToProtein.ContainsKey(name))
{
commonNameToProtein.Add(
name,
new Protein
{
Id = lipidId++,
ChargeState = 1,
ChemicalFormula = formula,
MassMonoisotopic = mass,
Mz = mz,
Name = name,
Sequence = formula,
});
}
// Data line, create mass tag
massTags.Add(
new MassTagLight
{ // TODO: We have lipid data now, we're not doing just proteomics anymore. We should have omic-independent names for this stuff.
Id = lineCount - 2, // Subtract 2 because i will be incremented once when it sees the headers, and once before it gets to this line
ProteinName = name,
PeptideSequence = formula,
Net = net,
NetAligned = net,
NetAverage = net,
NetPredicted = net,
MassMonoisotopic = mass,
MassMonoisotopicAligned = mass,
Mz = mz,
});
}
// Mapping from masstags to proteins (actually lipids)
var massTagToProtein = new Dictionary <int, List <Protein> >();
// Create mappings.
foreach (var massTag in massTags)
{
var protein = commonNameToProtein[massTag.ProteinName];
massTagToProtein.Add(massTag.Id, new List <Protein>());
massTagToProtein[massTag.Id].Add(protein);
}
// Finally, create the mass tag database.
var massTagDatabase = new MassTagDatabase();
massTagDatabase.AddMassTagsAndProteins(massTags, massTagToProtein);
return(massTagDatabase);
}
public MassTagDatabase LoadDatabase()
{
var database = new MassTagDatabase {
Name = ""
};
UpdateStatus("Loading all of the mass tags.");
// Get all of the mass tags
var massTags = Provider.FindAll();
UpdateStatus("Loading all of the tag to protein references.");
// Then get all of the mass tag to protein maps
IGenericDAO <MassTagToProteinMap> tagToProteinMapCache = new GenericDAOHibernate <MassTagToProteinMap>();
var maps = tagToProteinMapCache.FindAll();
// Then get all of the proteins
UpdateStatus("Loading all of the protein data.");
IProteinDAO proteinCache = new ProteinDAO();
var proteins = proteinCache.FindAll();
UpdateStatus("Indexing the protein data for faster assembly.");
var proteinMap = new Dictionary <int, Protein>();
foreach (var p in proteins)
{
if (!proteinMap.ContainsKey(p.ProteinId))
{
proteinMap.Add(p.ProteinId, p);
}
}
var matchedMaps = new Dictionary <int, List <MassTagToProteinMap> >();
foreach (var singleMap in maps)
{
if (!matchedMaps.ContainsKey(singleMap.MassTagId))
{
matchedMaps.Add(singleMap.MassTagId, new List <MassTagToProteinMap>());
}
matchedMaps[singleMap.MassTagId].Add(singleMap);
}
UpdateStatus("Re-mapping the proteins to the mass tags.");
var massTagProteinMap = new Dictionary <int, List <Protein> >();
// Then map them.
foreach (var tag in massTags)
{
var id = tag.Id;
if (!massTagProteinMap.ContainsKey(id))
{
massTagProteinMap.Add(id, new List <Protein>());
}
var matches = new List <MassTagToProteinMap>();
if (matchedMaps.ContainsKey(id))
{
matches = matchedMaps[id];
}
var newProteins = new List <Protein>();
foreach (var mtMap in matches)
{
if (proteinMap.ContainsKey(mtMap.ProteinId))
{
newProteins.Add(proteinMap[mtMap.ProteinId]);
}
}
massTagProteinMap[id].AddRange(newProteins);
}
UpdateStatus("Building the in memory mass tag database.");
database.AddMassTagsAndProteins(massTags, massTagProteinMap);
database.AllProteins = proteins;
var totalMassTags = database.MassTags.Count;
UpdateStatus("Loaded " + totalMassTags + " mass tags.");
return(database);
}
/// <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>
/// Arguments that hold dataset information when features are loaded.
/// </summary>
public MassTagsLoadedEventArgs(List<MassTagLight> tags, MassTagDatabase database)
{
MassTags = tags;
Database = database;
}
public MassTagDatabase LoadDatabase()
{
var database = new MassTagDatabase();
//Implement the loading / reading of the MTDB Framework objects.
var reader = new SqLiteTargetDatabaseReader();
var mtdbDatabase = reader.ReadDb(m_path);
var massTags = new List<MassTagLight>();
// Mapping objects to create unique proteins and for the mass tag database to load only those proteins for
// the given consensus targets/mass tags.
var proteinMap = new Dictionary<int, Protein>();
var massTagProteinMap = new Dictionary<int, List<Protein>>();
if (mtdbDatabase == null)
return database;
foreach (var target in mtdbDatabase.ConsensusTargets)
{
// Copy the consensus data into a mass tag light.
var tag = new MassTagLight
{
Id = target.Id,
MassMonoisotopic = target.TheoreticalMonoIsotopicMass,
NetAverage = target.AverageNet,
NetPredicted = target.PredictedNet,
PeptideSequence = target.Sequence,
NetStandardDeviation = target.StdevNet
};
// Here we create unique proteins for the mass tag copying information from the consensus target proteins.
var proteinsForMassTag = new List<Protein>();
foreach (var targetProtein in target.Proteins)
{
if (!proteinMap.ContainsKey(targetProtein.Id))
{
var newProtein = new Protein
{
Id = targetProtein.Id,
Name = targetProtein.ProteinName,
ResidueStartPosition = targetProtein.ResidueStart,
ResidueEndPosition = targetProtein.ResidueEnd
};
//TODO: Do something about the cleavage state and terminus state of a protein loaded from MTDBCreator database.
//protein.CleavageState = ??
//protein.TerminusState = ??
proteinMap.Add(newProtein.Id, newProtein);
}
var protein = proteinMap[targetProtein.Id];
proteinsForMassTag.Add(protein);
}
massTagProteinMap.Add(tag.Id, proteinsForMassTag);
massTags.Add(tag);
}
database.AddMassTagsAndProteins(massTags, massTagProteinMap);
return database;
}
private IList<UMCLight> AlignDataset(
IList<UMCLight> features,
IEnumerable<UMCLight> baselineFeatures,
MassTagDatabase database,
DatasetInformation datasetInfo,
DatasetInformation baselineInfo)
{
classAlignmentData alignmentData;
if (baselineInfo == null && database == null)
{
throw new NullReferenceException("No reference was set for LC-MS alignment.");
}
// align the data.
if (baselineFeatures != null && baselineInfo != null && baselineInfo.IsBaseline)
{
// Align pairwise and cache results intermediately.
var aligner = m_algorithms.DatasetAligner;
RegisterProgressNotifier(aligner);
UpdateStatus("Aligning " + datasetInfo.DatasetName + " to baseline.");
alignmentData = aligner.Align(baselineFeatures, features);
DeRegisterProgressNotifier(aligner);
}
else
{
// Align pairwise and cache results intermediately.
var aligner = m_algorithms.DatabaseAligner;
RegisterProgressNotifier(aligner);
UpdateStatus("Aligning " + datasetInfo.DatasetName + " to mass tag database.");
alignmentData = aligner.Align(database, features);
DeRegisterProgressNotifier(aligner);
}
if (alignmentData != null)
{
alignmentData.aligneeDataset = datasetInfo.DatasetName;
alignmentData.DatasetID = datasetInfo.DatasetId;
}
var args = new FeaturesAlignedEventArgs(datasetInfo,
baselineFeatures,
features,
alignmentData);
if (FeaturesAligned != null)
FeaturesAligned(this, args);
UpdateStatus("Updating cache with aligned features.");
return features;
}
public LcmsWarpAlignmentData Align(MassTagDatabase baseline, IEnumerable <UMCLight> alignee)
{
throw new NotImplementedException();
}
/// <summary>
/// Performs STAC against the mass tag database.
/// </summary>
public List <MultiAlignCore.Data.MassTags.FeatureMatchLight <T, MassTagLight> > PerformPeakMatching(List <T> clusters, MassTagDatabase database)
{
var clusterMap = new Dictionary <int, T>();
var tagMap = new Dictionary <int, Dictionary <int, MassTagLight> >();
var massTags = new List <MassTagLight>();
var i = 0;
foreach (var tag in database.MassTags)
{
var mt = new MassTagLight
{
Abundance = Convert.ToInt32(tag.Abundance),
ChargeState = tag.ChargeState,
CleavageState = tag.CleavageState,
ConformationId = tag.ConformationId,
ConformationObservationCount = tag.ConformationObservationCount,
DiscriminantMax = tag.DiscriminantMax,
DriftTime = Convert.ToSingle(tag.DriftTime),
DriftTimePredicted = tag.DriftTimePredicted,
Id = tag.Id,
MassMonoisotopic = tag.MassMonoisotopic,
ModificationCount = tag.ModificationCount,
Modifications = tag.Modifications,
Molecule = tag.Molecule,
MsgfSpecProbMax = tag.MsgfSpecProbMax,
Net = tag.NetAverage,
NetAverage = tag.NetAverage,
NetPredicted = tag.NetPredicted,
NetStandardDeviation = tag.NetStandardDeviation,
ObservationCount = tag.ObservationCount,
PeptideSequence = tag.PeptideSequence,
PeptideSequenceEx = tag.PeptideSequenceEx,
PriorProbability = tag.PriorProbability,
QualityScore = tag.QualityScore,
XCorr = tag.XCorr
};
mt.Index = i++;
massTags.Add(mt);
if (!tagMap.ContainsKey(tag.Id))
{
tagMap.Add(tag.Id, new Dictionary <int, MassTagLight>());
}
tagMap[tag.Id].Add(tag.ConformationId, tag);
}
// convert data needed by the algorithm.
var features = new List <UMCClusterLight>();
foreach (var cluster in clusters)
{
var feature = new UMCClusterLight
{
Id = cluster.Id,
MassMonoisotopicAligned = cluster.MassMonoisotopic,
MassMonoisotopic = cluster.MassMonoisotopic
};
feature.Net = cluster.Net;
feature.NetAligned = cluster.Net;
feature.ChargeState = cluster.ChargeState;
feature.DriftTime = Convert.ToSingle(cluster.DriftTime);
feature.DriftTimeAligned = Convert.ToDouble(cluster.DriftTime);
features.Add(feature);
clusterMap.Add(cluster.Id, cluster);
}
// create a stac manager and run.
var matcher = new FeatureMatcher <UMCClusterLight, MassTagLight>(features, massTags, Options);
matcher.MessageEvent += StatusHandler;
matcher.ProcessingCompleteEvent += StatusHandler;
matcher.MatchFeatures();
Matcher = matcher;
Matcher.PopulateStacfdrTable(matcher.MatchList);
var matches = new List <MultiAlignCore.Data.MassTags.FeatureMatchLight <T, MassTagLight> >();
foreach (var match in matcher.MatchList)
{
var matched = new MultiAlignCore.Data.MassTags.FeatureMatchLight <T, MassTagLight>
{
Observed = clusterMap[match.ObservedFeature.Id],
Target = tagMap[match.TargetFeature.Id][match.TargetFeature.ConformationId],
Confidence = match.STACScore,
Uniqueness = match.STACSpecificity
};
matches.Add(matched);
}
matcher.MessageEvent -= StatusHandler;
matcher.ProcessingCompleteEvent -= StatusHandler;
return(matches);
}
/// <summary>
/// Load the data from the dataset information objects to the cache at the analysis Path
/// </summary>
private void PerformDataLoadAndAlignment(AnalysisConfig config)
{
UmcLoaderFactory.Status += UMCLoaderFactory_Status;
UpdateStatus("Loading data.");
var analysisOptions = config.Analysis.Options;
var datasets = config.Analysis.MetaData.Datasets.ToList();
var lcmsFilterOptions = analysisOptions.LcmsFilteringOptions;
var msFilterOptions = analysisOptions.MsFilteringOptions;
var baselineDataset = config.Analysis.MetaData.BaselineDataset;
var baselineFeatures = LoadBaselineData(baselineDataset,
msFilterOptions,
analysisOptions.LcmsFindingOptions,
lcmsFilterOptions,
config.Analysis.DataProviders,
config.Analysis.MassTagDatabase,
config.Analysis.Options.AlignmentOptions.IsAlignmentBaselineAMasstagDB);
var alignmentData = new AlignmentDAOHibernate();
alignmentData.ClearAll();
var providers = config.Analysis.DataProviders;
var featureCache = new FeatureLoader
{
Providers = providers
};
RegisterProgressNotifier(featureCache);
MassTagDatabase database = null;
if (config.Analysis.MassTagDatabase != null)
database = new MassTagDatabase(config.Analysis.MassTagDatabase,
config.Analysis.Options.AlignmentOptions.MassTagObservationCount);
SingletonDataProviders.Providers = config.Analysis.DataProviders;
foreach (var dataset in datasets)
{
if (dataset.IsBaseline)
continue;
var features = featureCache.LoadDataset(dataset,
analysisOptions.MsFilteringOptions,
analysisOptions.LcmsFindingOptions,
analysisOptions.LcmsFilteringOptions);
features = AlignDataset(features,
baselineFeatures,
database,
dataset,
baselineDataset);
featureCache.CacheFeatures(features);
}
UmcLoaderFactory.Status -= UMCLoaderFactory_Status;
}
/// <summary>
/// Load the data from the dataset information objects to the cache at the analysis Path
/// </summary>
private void PerformDataLoadAndAlignment(AnalysisConfig config)
{
UmcLoaderFactory.Status += UMCLoaderFactory_Status;
UpdateStatus("Loading data.");
var analysisOptions = config.Analysis.Options;
var datasets = config.Analysis.MetaData.Datasets.ToList();
var lcmsFilterOptions = analysisOptions.LcmsFilteringOptions;
var msFilterOptions = analysisOptions.MsFilteringOptions;
var dataLoadOptions = analysisOptions.DataLoadOptions;
var baselineDataset = config.Analysis.MetaData.BaselineDataset;
var baselineFeatures = LoadBaselineData(baselineDataset,
msFilterOptions,
analysisOptions.LcmsFindingOptions,
lcmsFilterOptions,
dataLoadOptions,
config.Analysis.DataProviders,
config.Analysis.MassTagDatabase,
config.Analysis.Options.AlignmentOptions.IsAlignmentBaselineAMasstagDB);
var alignmentData = new AlignmentDAOHibernate();
alignmentData.ClearAll();
var providers = config.Analysis.DataProviders;
var featureCache = new FeatureLoader
{
Providers = providers
};
RegisterProgressNotifier(featureCache);
MassTagDatabase database = null;
if (config.Analysis.MassTagDatabase != null)
{
database = new MassTagDatabase(config.Analysis.MassTagDatabase,
config.Analysis.Options.AlignmentOptions.MassTagObservationCount);
}
SingletonDataProviders.Providers = config.Analysis.DataProviders;
foreach (var dataset in datasets)
{
if (dataset.IsBaseline)
{
continue;
}
var features = featureCache.LoadDataset(dataset,
analysisOptions.MsFilteringOptions,
analysisOptions.LcmsFindingOptions,
analysisOptions.LcmsFilteringOptions,
analysisOptions.DataLoadOptions,
m_scanSummaryProviderCache,
m_identificationsProvider);
features = AlignDataset(features,
baselineFeatures,
database,
dataset,
baselineDataset);
featureCache.CacheFeatures(features);
}
UmcLoaderFactory.Status -= UMCLoaderFactory_Status;
}
public void UpdateDatabaseView(MassTagDatabase database)
{
mtree_proteins.Nodes.Clear();
if (database == null)
{
return;
}
List <ConsensusTarget> targets = database.ConsensusTargets;
TreeNode rootNode = new TreeNode(string.Format("Mass Tags ({0})", targets.Count));
rootNode.ImageIndex = CONST_DATABASE;
targets.Sort(delegate(ConsensusTarget p, ConsensusTarget p2)
{
return(p.Sequence.CompareTo(p2.Sequence));
});
long count = 0;
foreach (ConsensusTarget target in targets)
{
if (count++ > 100)
{
count = 0;
Application.DoEvents(); // I hate doing this but we should "draw" every N nodes (100 in this case)
}
// Only for predicted targets
bool skip = false;
foreach (Target t in target.Targets)
{
if (!t.IsPredicted)
{
skip = true;
}
}
if (skip)
{
continue;
}
TreeNode targetNode = new TreeNode(
string.Format("{0} ({1})",
target.CleanSequence,
target.Targets.Count
));
targetNode.ImageIndex = CONST_MASS_TAG_RED;
targetNode.Nodes.Add(string.Format("Avg NET: {0:F2}", target.GaNetAverage));
targetNode.Nodes.Add(string.Format("Stdev. NET: {0:F2}", target.GaNetStdev));
targetNode.Nodes.Add(string.Format("Min NET: {0:F2}", target.GaNetMinium));
targetNode.Nodes.Add(string.Format("MaxNET: {0:F2}", target.GaNetMax));
// Cheating...
targetNode.Nodes[0].ImageIndex = CONST_PROPERTY;
targetNode.Nodes[1].ImageIndex = CONST_PROPERTY;
targetNode.Nodes[2].ImageIndex = CONST_PROPERTY;
targetNode.Nodes[3].ImageIndex = CONST_PROPERTY;
TreeNode targetSubNode = new TreeNode("Peptides");
targetSubNode.ImageIndex = CONST_FLAME;
targetNode.Nodes.Add(targetSubNode);
foreach (Target t in target.Targets)
{
TreeNode node = new TreeNode(t.Sequence);
node.ImageIndex = CONST_FLAME;
targetSubNode.Nodes.Add(node);
node.Nodes.Add(string.Format("Mass: {0:F2}", t.MonoisotopicMass));
node.Nodes.Add(string.Format("Scan: {0}", t.Scan));
node.Nodes.Add(string.Format("NET Pred: {0:F2}", t.NetPredicted));
node.Nodes.Add(string.Format("NET Align: {0:F2}", t.NetAligned));
node.Nodes[0].ImageIndex = CONST_PROPERTY;
node.Nodes[1].ImageIndex = CONST_PROPERTY;
node.Nodes[2].ImageIndex = CONST_PROPERTY;
node.Nodes[3].ImageIndex = CONST_PROPERTY;
}
TreeNode proteinSubNode = new TreeNode("Proteins");
proteinSubNode.ImageIndex = CONST_PROTEIN;
targetNode.Nodes.Add(proteinSubNode);
foreach (Protein p in target.GetProteins())
{
int matchedTargets = p.GetMappedTargets().Count;
TreeNode proteinNode = new TreeNode(
string.Format("{0} ({1})",
p.Reference,
matchedTargets));
proteinNode.ImageIndex = CONST_PROTEIN;
proteinNode.Nodes.Add(string.Format("Matching Mass Tags: {0}", matchedTargets));
proteinNode.Nodes[0].ImageIndex = CONST_PROTEIN;
proteinSubNode.Nodes.Add(proteinNode);
}
rootNode.Nodes.Add(targetNode);
}
mtree_proteins.Nodes.Add(rootNode);
SetNodeSelectImage(rootNode);
rootNode.Expand();
}
/// <summary>
/// Writes the database to the path provided.
/// </summary>
/// <param name="database"></param>
/// <param name="path"></param>
public void WriteDatabase(MassTagDatabase database, string path)
{
// Remove the path if it already exists.
if (File.Exists(path))
{
File.Delete(path);
}
string connectionString = string.Format("Data Source = {0}", path);
using (SQLiteConnection connection = new SQLiteConnection(connectionString))
{
connection.Open();
using (SQLiteCommand command = connection.CreateCommand())
{
command.CommandText = string.Format("CREATE TABLE {0} ({1})", CONST_MASS_TAG_TABLE, CONST_MASS_TAG_COLUMNS);
command.ExecuteNonQuery();
command.CommandText = string.Format("CREATE TABLE {0} ({1})", CONST_PROTEIN_TABLE, CONST_PROTEIN_COLUMNS);
command.ExecuteNonQuery();
command.CommandText = string.Format("CREATE TABLE {0} ({1})", CONST_META_DATA_TABLE, CONST_META_DATA_COLUMNS);
command.ExecuteNonQuery();
}
string massTagValueFormatString = "{0},{1},{2},{3},{4},{5},{6},{7},{8},{9},{10},{11},{12},{13},{14},{15}";
string metaDataValueFormatString = "'{0}','{1}','{2}','{3}'";
using (SQLiteTransaction transaction = connection.BeginTransaction())
{
using (SQLiteCommand command = connection.CreateCommand())
{
foreach (Analysis analysis in database.MetaData)
{
string values = string.Format(metaDataValueFormatString, analysis.Name, analysis.FilePath, analysis.CreationDate, analysis.NumberOfUniqueMassTags);
command.CommandText = BuildTableInsertCommand(CONST_META_DATA_TABLE,
values);
command.ExecuteNonQuery();
}
}
// Write the mass tags
foreach (ConsensusTarget averageTarget in database.ConsensusTargets)
{
using (SQLiteCommand command = connection.CreateCommand())
{
string values = string.Format(massTagValueFormatString,
averageTarget.Id, // 0
string.Format("'{0}'", averageTarget.Sequence), // 1
averageTarget.GaNetAverage, // 2
averageTarget.HighNormalizedScore, // 3
0,
averageTarget.GaNetStdev, // 4
averageTarget.MonoisotopicMass, // 5
averageTarget.MinimumSpecProbability, // 6
averageTarget.Targets.Count, // 7
averageTarget.ModificationCount, // 8
string.Format("'{0}'", averageTarget.ModificationDescription), // 9
averageTarget.HighPeptideProphetProbability, // 10
0, // 11
averageTarget.DriftTime, // 12
averageTarget.ConformerCharge, // 13
averageTarget.ConformerId); // 14
string commandText = BuildTableInsertCommand(CONST_MASS_TAG_TABLE,
values);
command.CommandText = commandText;
command.ExecuteNonQuery();
}
}
// Write the proteins - each protein may by mapped by multiple mass tags - or consensus targets
foreach (Protein protein in database.Proteins)
{
List <ConsensusTarget> targets = protein.GetMappedTargets();
foreach (ConsensusTarget target in targets)
{
using (SQLiteCommand command = connection.CreateCommand())
{
string values = string.Format("{0}, {1}, '{2}', {3}", target.Id,
protein.Id,
protein.Reference,
protein.Id);
string commandText = BuildTableInsertCommand(CONST_PROTEIN_TABLE,
values);
command.CommandText = commandText;
command.ExecuteNonQuery();
}
}
}
transaction.Commit();
}
connection.Close();
}
foreach (ConsensusTarget target in database.ConsensusTargets)
{
target.Targets.Clear();
}
}