public void TestDatabaseInsertion(string relativePath, string databasePathRelative, int expectedFeatureCount)
{
// Get the absolute path
var path = GetPath(relativePath);
var databasePath = GetPath(databasePathRelative);
var features = TestUmcFeatures(path, expectedFeatureCount);
if (File.Exists(databasePath))
{
File.Delete(databasePath);
}
try
{
NHibernateUtil.ConnectToDatabase(databasePath, true);
var cache = new MSFeatureDAOHibernate();
var msFeatures = new List <MSFeatureLight>();
foreach (var feature in features)
{
msFeatures.AddRange(feature.MsFeatures);
}
cache.AddAll(msFeatures);
var umcCache = new UmcDAOHibernate();
umcCache.AddAll(features.ToList());
}
catch (Exception ex)
{
Console.WriteLine("Exception caching features: " + ex.Message);
Console.WriteLine(ex.StackTrace);
throw;
}
}
public void SaveUMCFeatures()
{
var lights = new List<UMCLight>();
for (var i = 0; i < 100; i++)
{
lights.Add(new UMCLight());
lights[i].Id = i;
}
IUmcDAO cache = new UmcDAOHibernate();
cache.AddAll(lights);
}
public static FeatureDataAccessProviders CreateDataAccessProviders(string path, bool deleteIfExists)
{
if (deleteIfExists)
{
var exists = File.Exists(path);
if (exists)
{
File.Delete(path);
}
}
try
{
NHibernateUtil.ConnectToDatabase(path, true);
}
catch (Exception ex)
{
throw ex;
}
IUmcDAO featureCache = new UmcDAOHibernate();
IUmcClusterDAO clusterCache = new UmcClusterDAOHibernate();
IMSFeatureDAO msFeatureCache = new MSFeatureDAOHibernate();
IMSnFeatureDAO msnFeatureCache = new MSnFeatureDAOHibernate();
IMsnFeatureToMSFeatureDAO msnMSCache = new MSnFeatureToMSFeatureDAOHibernate();
IDatasetDAO datasetCache = new DatasetDAOHibernate();
IMassTagDAO massTagCache = new MassTagDAOHibernate();
IMassTagMatchDAO massTagMatchCache = new MassTagMatchDAO();
ISequenceToMsnFeatureDAO sequenceMap = new SequenceToMsnDAOHibernate();
var providers =
new FeatureDataAccessProviders(featureCache,
clusterCache,
msFeatureCache,
msnFeatureCache,
msnMSCache,
datasetCache,
massTagMatchCache,
massTagCache,
new FactorDAOHibernate(),
new DatasetToFactorDAOHibernate(),
new MSMSClusterMapClusterDAOHibernate(),
new DatabaseSearchSequenceDAOHibernate(),
sequenceMap)
{
ScanSummaryDao = new ScanSummaryDAOHibernate(),
ScanSummaryProviderCache = new ScanSummaryProviderCache(),
OptionsDao = new OptionsDAOHibernate(),
};
return(providers);
}
public void SaveUMCFeatures()
{
var lights = new List <UMCLight>();
for (var i = 0; i < 100; i++)
{
lights.Add(new UMCLight());
lights[i].Id = i;
}
IUmcDAO cache = new UmcDAOHibernate();
cache.AddAll(lights);
}
public void CreateCrossTab(string databasePath, string crossPath, int charge, int minimumClusterSize)
{
NHibernateUtil.ConnectToDatabase(databasePath, false);
IDatasetDAO datasetCache = new DatasetDAOHibernate();
IUmcClusterDAO clusterCache = new UmcClusterDAOHibernate();
IUmcDAO featureCache = new UmcDAOHibernate();
Console.WriteLine("Find all datasets");
var datasets = datasetCache.FindAll();
Console.WriteLine("Find all clusters");
var clusters = clusterCache.FindByCharge(charge);
WriteClusters(datasets, clusters, minimumClusterSize, charge, crossPath, databasePath, 50000);
}
public void TestClusterWriting(string databasePath, string crossPath, int charge, int minimumClusterSize)
{
NHibernateUtil.ConnectToDatabase(databasePath, false);
IDatasetDAO datasetCache = new DatasetDAOHibernate();
IUmcClusterDAO clusterCache = new UmcClusterDAOHibernate();
IUmcDAO featureCache = new UmcDAOHibernate();
Console.WriteLine("Find all datasets");
var datasets = datasetCache.FindAll();
Console.WriteLine("Find all clusters");
var clusters = clusterCache.FindByCharge(charge);
WriteClusters(datasets, clusters, minimumClusterSize, charge, crossPath, databasePath, 300000);
}
public static FeatureDataAccessProviders CreateDataAccessProviders(string path, bool deleteIfExists)
{
if (deleteIfExists)
{
var exists = File.Exists(path);
if (exists)
{
File.Delete(path);
}
}
try
{
NHibernateUtil.ConnectToDatabase(path, true);
}
catch (Exception ex)
{
throw ex;
}
IUmcDAO featureCache = new UmcDAOHibernate();
IUmcClusterDAO clusterCache = new UmcClusterDAOHibernate();
IMSFeatureDAO msFeatureCache = new MSFeatureDAOHibernate();
IMSnFeatureDAO msnFeatureCache = new MSnFeatureDAOHibernate();
IMsnFeatureToMSFeatureDAO msnMSCache = new MSnFeatureToMSFeatureDAOHibernate();
IDatasetDAO datasetCache = new DatasetDAOHibernate();
IMassTagDAO massTagCache = new MassTagDAOHibernate();
IMassTagMatchDAO massTagMatchCache = new MassTagMatchDAO();
ISequenceToMsnFeatureDAO sequenceMap = new SequenceToMsnDAOHibernate();
var providers =
new FeatureDataAccessProviders(featureCache,
clusterCache,
msFeatureCache,
msnFeatureCache,
msnMSCache,
datasetCache,
massTagMatchCache,
massTagCache,
new FactorDAOHibernate(),
new DatasetToFactorDAOHibernate(),
new MSMSClusterMapClusterDAOHibernate(),
new DatabaseSearchSequenceDAOHiberate(),
sequenceMap);
return providers;
}
public void CreateDatasetMap(string databasePath, string crossPath, int charge, int minimumClusterSize)
{
NHibernateUtil.ConnectToDatabase(databasePath, false);
IDatasetDAO datasetCache = new DatasetDAOHibernate();
IUmcClusterDAO clusterCache = new UmcClusterDAOHibernate();
IUmcDAO featureCache = new UmcDAOHibernate();
Console.WriteLine("Find all datasets");
var datasets = datasetCache.FindAll();
using (TextWriter writer = File.CreateText(crossPath + ".csv"))
{
writer.WriteLine("Dataset, Dataset Id");
foreach (var info in datasets)
{
writer.WriteLine("{0},{1}", info.DatasetName, info.DatasetId);
}
}
}
public void CreateDatasetMap(string databasePath, string crossPath, int charge, int minimumClusterSize)
{
NHibernateUtil.ConnectToDatabase(databasePath, false);
IDatasetDAO datasetCache = new DatasetDAOHibernate();
IUmcClusterDAO clusterCache = new UmcClusterDAOHibernate();
IUmcDAO featureCache = new UmcDAOHibernate();
Console.WriteLine("Find all datasets");
var datasets = datasetCache.FindAll();
using (TextWriter writer = File.CreateText(crossPath + ".csv"))
{
writer.WriteLine("Dataset, Dataset Id");
foreach (var info in datasets)
{
writer.WriteLine("{0},{1}", info.DatasetName, info.DatasetId);
}
}
}
public void TestDatabaseInsertion(string path, string databasePath)
{
var features = TestUmcFeatures(path);
if (File.Exists(databasePath))
{
File.Delete(databasePath);
}
NHibernateUtil.ConnectToDatabase(databasePath, true);
var cache = new MSFeatureDAOHibernate();
var msFeatures = new List <MSFeatureLight>();
foreach (var feature in features)
{
msFeatures.AddRange(feature.MsFeatures);
}
cache.AddAll(msFeatures);
var umcCache = new UmcDAOHibernate();
umcCache.AddAll(features.ToList());
}
public void TestDatabaseInsertion(string path, string databasePath)
{
var features = TestUmcFeatures(path);
if (File.Exists(databasePath))
File.Delete(databasePath);
NHibernateUtil.ConnectToDatabase(databasePath, true);
var cache = new MSFeatureDAOHibernate();
var msFeatures = new List<MSFeatureLight>();
foreach (var feature in features)
msFeatures.AddRange(feature.MsFeatures);
cache.AddAll(msFeatures);
var umcCache = new UmcDAOHibernate();
umcCache.AddAll(features.ToList());
}
public void TestClusterGeneration(string databasePath,
string crossPath,
int charge,
int minimumClusterSize)
{
File.Delete(databasePath);
NHibernateUtil.ConnectToDatabase(databasePath, true);
IDatasetDAO datasetCache = new DatasetDAOHibernate();
IUmcClusterDAO clusterCache = new UmcClusterDAOHibernate();
IUmcDAO featureCache = new UmcDAOHibernate();
// Creating a dataset
Console.WriteLine("Creating dummy datasets");
var datasets = new List<DatasetInformation>();
var total = 10;
for (var i = 0; i < total; i++)
{
var dataset = new DatasetInformation();
dataset.DatasetId = i;
dataset.DatasetName = "test" + i;
datasets.Add(dataset);
}
datasetCache.AddAll(datasets);
datasets.Clear();
datasets = datasetCache.FindAll();
// Create features
Console.WriteLine("Creating features");
var features = new List<UMCLight>();
var clusters = new List<UMCClusterLight>();
var x = new Random();
var featureId = 0;
for (var i = 0; i < 100; i++)
{
var cluster = new UMCClusterLight();
cluster.Id = i;
cluster.AmbiguityScore = i;
cluster.Tightness = i;
var N = x.Next(1, total);
cluster.Id = i;
cluster.ChargeState = charge;
var hash = new HashSet<int>();
for (var j = 0; j < N; j++)
{
var did = -1;
do
{
did = x.Next(0, total);
if (!hash.Contains(did))
{
hash.Add(did);
break;
}
} while (true);
var feature = new UMCLight();
feature.GroupId = did;
feature.Id = featureId++;
feature.ChargeState = charge;
feature.MassMonoisotopic = x.NextDouble();
feature.Net = x.NextDouble();
feature.AbundanceSum = x.Next(100, 200);
feature.Abundance = feature.Abundance;
feature.ClusterId = cluster.Id;
cluster.AddChildFeature(feature);
features.Add(feature);
}
cluster.CalculateStatistics(ClusterCentroidRepresentation.Mean);
clusters.Add(cluster);
}
featureCache.AddAll(features);
clusterCache.AddAll(clusters);
clusters = clusterCache.FindAll();
Console.WriteLine("Find all clusters");
clusters = clusterCache.FindByCharge(charge);
WriteClusters(datasets,
clusters,
minimumClusterSize,
charge,
crossPath,
databasePath,
300000);
}
public void TestCreateDummyDatabase(string databasePath, int totalDatasets, int totalClusters)
{
File.Delete(databasePath);
NHibernateUtil.ConnectToDatabase(databasePath, true);
IDatasetDAO datasetCache = new DatasetDAOHibernate();
IUmcClusterDAO clusterCache = new UmcClusterDAOHibernate();
IUmcDAO featureCache = new UmcDAOHibernate();
// Creating a dataset
Console.WriteLine("Creating dummy datasets");
var datasets = new List<DatasetInformation>();
var total = totalDatasets;
for (var i = 0; i < total; i++)
{
var dataset = new DatasetInformation();
dataset.DatasetId = i;
dataset.DatasetName = "test" + i;
datasets.Add(dataset);
}
datasetCache.AddAll(datasets);
datasets.Clear();
datasets = datasetCache.FindAll();
// Create features
Console.WriteLine("Creating features");
var features = new List<UMCLight>();
var clusters = new List<UMCClusterLight>();
var x = new Random();
var featureId = 0;
for (var i = 0; i < totalClusters; i++)
{
var N = x.Next(1, total);
var charge = x.Next(1, 10);
var hash = new HashSet<int>();
var net = x.NextDouble();
var mass = 400 + (1600*x.NextDouble());
var dt = 60*x.NextDouble();
for (var j = 0; j < N; j++)
{
var did = -1;
do
{
did = x.Next(0, total);
if (!hash.Contains(did))
{
hash.Add(did);
break;
}
} while (true);
var feature = new UMCLight
{
GroupId = did,
Id = featureId++,
ChargeState = charge,
MassMonoisotopic = FeatureLight.ComputeDaDifferenceFromPPM(mass, 3)
};
feature.MassMonoisotopicAligned = feature.MassMonoisotopic;
feature.Net = net + 0.03 * x.NextDouble();
feature.NetAligned = feature.Net;
feature.Net = feature.Net;
feature.DriftTime = dt;
feature.AbundanceSum = x.Next(100, 200);
feature.Abundance = feature.Abundance;
feature.ClusterId = -1;
features.Add(feature);
}
}
featureCache.AddAll(features);
}
public void TestCreateDummyDatabase(string databasePath, int totalDatasets, int totalClusters)
{
File.Delete(databasePath);
NHibernateUtil.ConnectToDatabase(databasePath, true);
IDatasetDAO datasetCache = new DatasetDAOHibernate();
IUmcClusterDAO clusterCache = new UmcClusterDAOHibernate();
IUmcDAO featureCache = new UmcDAOHibernate();
// Creating a dataset
Console.WriteLine("Creating dummy datasets");
var datasets = new List <DatasetInformation>();
var total = totalDatasets;
for (var i = 0; i < total; i++)
{
var dataset = new DatasetInformation();
dataset.DatasetId = i;
dataset.DatasetName = "test" + i;
datasets.Add(dataset);
}
datasetCache.AddAll(datasets);
datasets.Clear();
datasets = datasetCache.FindAll();
// Create features
Console.WriteLine("Creating features");
var features = new List <UMCLight>();
var clusters = new List <UMCClusterLight>();
var x = new Random();
var featureId = 0;
for (var i = 0; i < totalClusters; i++)
{
var N = x.Next(1, total);
var charge = x.Next(1, 10);
var hash = new HashSet <int>();
var net = x.NextDouble();
var mass = 400 + (1600 * x.NextDouble());
var dt = 60 * x.NextDouble();
for (var j = 0; j < N; j++)
{
var did = -1;
do
{
did = x.Next(0, total);
if (!hash.Contains(did))
{
hash.Add(did);
break;
}
} while (true);
var feature = new UMCLight();
feature.GroupId = did;
feature.Id = featureId++;
feature.ChargeState = charge;
feature.MassMonoisotopic = FeatureLight.ComputeDaDifferenceFromPPM(mass, 3);
feature.MassMonoisotopicAligned = feature.MassMonoisotopic;
feature.Net = net + .03 * x.NextDouble();
feature.NetAligned = feature.Net;
feature.Net = feature.Net;
feature.DriftTime = dt;
feature.AbundanceSum = x.Next(100, 200);
feature.Abundance = feature.Abundance;
feature.ClusterId = -1;
features.Add(feature);
}
}
featureCache.AddAll(features);
}
public void TestClusterGeneration(string databasePath,
string crossPath,
int charge,
int minimumClusterSize)
{
File.Delete(databasePath);
NHibernateUtil.ConnectToDatabase(databasePath, true);
IDatasetDAO datasetCache = new DatasetDAOHibernate();
IUmcClusterDAO clusterCache = new UmcClusterDAOHibernate();
IUmcDAO featureCache = new UmcDAOHibernate();
// Creating a dataset
Console.WriteLine("Creating dummy datasets");
var datasets = new List <DatasetInformation>();
var total = 10;
for (var i = 0; i < total; i++)
{
var dataset = new DatasetInformation();
dataset.DatasetId = i;
dataset.DatasetName = "test" + i;
datasets.Add(dataset);
}
datasetCache.AddAll(datasets);
datasets.Clear();
datasets = datasetCache.FindAll();
// Create features
Console.WriteLine("Creating features");
var features = new List <UMCLight>();
var clusters = new List <UMCClusterLight>();
var x = new Random();
var featureId = 0;
for (var i = 0; i < 100; i++)
{
var cluster = new UMCClusterLight();
cluster.Id = i;
cluster.AmbiguityScore = i;
cluster.Tightness = i;
var N = x.Next(1, total);
cluster.Id = i;
cluster.ChargeState = charge;
var hash = new HashSet <int>();
for (var j = 0; j < N; j++)
{
var did = -1;
do
{
did = x.Next(0, total);
if (!hash.Contains(did))
{
hash.Add(did);
break;
}
} while (true);
var feature = new UMCLight();
feature.GroupId = did;
feature.Id = featureId++;
feature.ChargeState = charge;
feature.MassMonoisotopic = x.NextDouble();
feature.Net = x.NextDouble();
feature.AbundanceSum = x.Next(100, 200);
feature.Abundance = feature.Abundance;
feature.ClusterId = cluster.Id;
cluster.AddChildFeature(feature);
features.Add(feature);
}
cluster.CalculateStatistics(ClusterCentroidRepresentation.Mean);
clusters.Add(cluster);
}
featureCache.AddAll(features);
clusterCache.AddAll(clusters);
clusters = clusterCache.FindAll();
Console.WriteLine("Find all clusters");
clusters = clusterCache.FindByCharge(charge);
WriteClusters(datasets,
clusters,
minimumClusterSize,
charge,
crossPath,
databasePath,
300000);
}
