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 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 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 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);
}