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 SaveMSFeatures()
{
var lights = new List<MSFeatureLight>();
for (var i = 0; i < 100; i++)
{
lights.Add(new MSFeatureLight());
lights[i].Id = i;
}
IMSFeatureDAO cache = new MSFeatureDAOHibernate();
cache.AddAll(lights);
}
/// <summary>
///
/// </summary>
/// <param name="args"></param>
static void Main(string[] args)
{
//MassTagDOATest massTagTest = new MassTagDOATest();
SetupDataProviders(@"m:\data\proteomics\matest-gui\guitest.db3");
MSFeatureDAOHibernate dao = new MSFeatureDAOHibernate();
System.DateTime start = DateTime.Now;
List <MSFeatureLight> features = dao.FindByDatasetId(0);
System.DateTime end = DateTime.Now;
//msFeatureTest.LoadMSFeaturesFromCache(@"m:\data\proteomics\matest-gui\guitest.db3");
TimeSpan span = end.Subtract(start);
System.Console.WriteLine("{0} total ms", span.TotalMilliseconds);
MSFeatureDOATest msFeatureTest = new MSFeatureDOATest();
start = System.DateTime.Now;
msFeatureTest.LoadMSFeaturesFromCache(@"m:\data\proteomics\matest-gui\guitest.db3");
end = System.DateTime.Now;
span = end.Subtract(start);
System.Console.WriteLine("{0} total ms", span.TotalMilliseconds);
//UMCFeatureFinding finding = new UMCFeatureFinding();
//finding.Test();
//return;
//try
//{
// string data = "-2147483648";
// long abu = Int64.Parse(data);
// UMCReaderFailure failTest = new UMCReaderFailure();
// failTest.Test();
//}
//catch (Exception ex)
//{
// throw ex;
//}
// SetupDataProviders();
//MassTagDOATest massTagTest = new MassTagDOATest();
//MSFeatureDOATest msFeatureTest = new MSFeatureDOATest();
//msFeatureTest.LoadMSFeaturesFromCache(@"m:\data\proteomics\matest-gui\guitest.db3");
//massTagTest.SaveMassTags();
//msFeatureTest.SaveMSFeatures();
//NHibernateUtil.CloseSession();
}
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 SaveMSFeatures()
{
var lights = new List <MSFeatureLight>();
for (var i = 0; i < 100; i++)
{
lights.Add(new MSFeatureLight());
lights[i].Id = i;
}
IMSFeatureDAO cache = new MSFeatureDAOHibernate();
cache.AddAll(lights);
}
/// <summary>
///
/// </summary>
/// <param name="args"></param>
static void Main(string[] args)
{
//MassTagDOATest massTagTest = new MassTagDOATest();
SetupDataProviders(@"m:\data\proteomics\matest-gui\guitest.db3");
MSFeatureDAOHibernate dao = new MSFeatureDAOHibernate();
System.DateTime start = DateTime.Now;
List<MSFeatureLight> features = dao.FindByDatasetId(0);
System.DateTime end = DateTime.Now;
//msFeatureTest.LoadMSFeaturesFromCache(@"m:\data\proteomics\matest-gui\guitest.db3");
TimeSpan span = end.Subtract(start);
System.Console.WriteLine("{0} total ms", span.TotalMilliseconds);
MSFeatureDOATest msFeatureTest = new MSFeatureDOATest();
start = System.DateTime.Now;
msFeatureTest.LoadMSFeaturesFromCache(@"m:\data\proteomics\matest-gui\guitest.db3");
end = System.DateTime.Now;
span = end.Subtract(start);
System.Console.WriteLine("{0} total ms", span.TotalMilliseconds);
//UMCFeatureFinding finding = new UMCFeatureFinding();
//finding.Test();
//return;
//try
//{
// string data = "-2147483648";
// long abu = Int64.Parse(data);
// UMCReaderFailure failTest = new UMCReaderFailure();
// failTest.Test();
//}
//catch (Exception ex)
//{
// throw ex;
//}
// SetupDataProviders();
//MassTagDOATest massTagTest = new MassTagDOATest();
//MSFeatureDOATest msFeatureTest = new MSFeatureDOATest();
//msFeatureTest.LoadMSFeaturesFromCache(@"m:\data\proteomics\matest-gui\guitest.db3");
//massTagTest.SaveMassTags();
//msFeatureTest.SaveMSFeatures();
//NHibernateUtil.CloseSession();
}
public void TestLoad(string path)
{
SetupDataProviders(path);
var dao = new MSFeatureDAOHibernate();
var start = DateTime.Now;
dao.FindByDatasetId(0);
var end = DateTime.Now;
var span = end.Subtract(start);
Console.WriteLine("{0} total ms", span.TotalMilliseconds);
var msFeatureTest = new MSFeatureDOATest();
start = DateTime.Now;
msFeatureTest.LoadMSFeaturesFromCache(path);
end = DateTime.Now;
span = end.Subtract(start);
Console.WriteLine("{0} total ms", span.TotalMilliseconds);
}
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 TestLoad(string path)
{
SetupDataProviders(path);
var dao = new MSFeatureDAOHibernate();
var start = DateTime.Now;
dao.FindByDatasetId(0);
var end = DateTime.Now;
var span = end.Subtract(start);
Console.WriteLine("{0} total ms", span.TotalMilliseconds);
var msFeatureTest = new MSFeatureDOATest();
start = DateTime.Now;
msFeatureTest.LoadMSFeaturesFromCache(path);
end = DateTime.Now;
span = end.Subtract(start);
Console.WriteLine("{0} total ms", span.TotalMilliseconds);
}
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());
}
