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 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>
/// 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);
}
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 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);
}
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;
}
/// <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();
//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);
}