static NHibernateHelper()
{
if (m_ISessionFactory == null)
{
m_ISessionFactory = GetFactory();
}
}
public static void Init()
{
try
{
NHibernate.Cfg.Configuration config = new NHibernate.Cfg.Configuration();
string path = string.Empty;
string wanted_path = System.IO.Directory.GetCurrentDirectory();
if (string.IsNullOrEmpty(configfilepath))
{
path = wanted_path + "\\hibernate.cfg.xml";
}
else
{
path = configfilepath;
}
config.Configure(path);
config.AddAssembly(Assembly.GetExecutingAssembly());//adds all the embedded resources .hbm.xml
sFactory = config.BuildSessionFactory();
}
catch (Exception ex)
{
throw ex;
//Console.Write(ex.StackTrace);
//logger.Error(ex.Message);
}
}
public void Constructor2Test()
{
Mock <Configuration.IConfigurationResolver> connectionStringDiscovererMock = new Mock <Configuration.IConfigurationResolver>();
connectionStringDiscovererMock.Setup(it => it.GetConfiguration()).Returns("Data Source=:memory:;Version=3;New=True;");
FluentNHibernateSessionFactoryBuilderForSQLite nh1 = (new FluentNHibernateSessionFactoryBuilderForSQLite()
{
InMemory = true,
ConnectionStringDiscoverer = connectionStringDiscovererMock.Object,
TypeNames = new List <string>()
{
this.GetType().AssemblyQualifiedName
},
EnabledDiagnostics = true,
NHibernateRawConfigurationValues = new Dictionary <string, string>()
{
{ "a", "b" }
},
MergeEventListeners = new NHibernate.Event.IMergeEventListener[] { new Mock <NHibernate.Event.IMergeEventListener>().Object }
});
using (NHibernate.ISessionFactory session = nh1.BuildSessionFactory())
{
session.Close();
}
}
public static void Init()
{
string path = System.IO.Path.GetFullPath("~/hibernate.cfg.xml");
SessionFactory.Init();
NHibernate.ISessionFactory session = SessionFactory.sFactory;
}
static void Main()
{
DbConnectionStringBuilder dcsBuilder = new DbConnectionStringBuilder();
dcsBuilder.Add("User ID", "wjzgis");
dcsBuilder.Add("Password", "wjzgis");
dcsBuilder.Add("Service Name", "sunz");
dcsBuilder.Add("Host", "172.16.1.9");
dcsBuilder.Add("Integrated Security", false);
string licPath = Application.StartupPath + "\\DDTek.lic";
//dcsBuilder.Add("License Path", licPath);
//若路径中存在空格，则会在路径名称前加上"\""
string conStr = dcsBuilder.ConnectionString;
conStr = conStr.Replace("\"", "");
Configuration config = new Configuration();
config.AddDirectory(new System.IO.DirectoryInfo(System.IO.Path.Combine(Application.StartupPath, "DataMapping")));
config.Properties["connection.connection_string"] = conStr;
NHibernate.ISessionFactory sFactory = config.BuildSessionFactory();
NHibernate.ISession session = sFactory.OpenSession();
Application.EnableVisualStyles();
Application.SetCompatibleTextRenderingDefault(false);
Application.Run(new Form1());
}
static NHibernateHelper()
{
if (m_ISessionFactory == null)
{
m_ISessionFactory = GetFactory();
}
}
/// <summary>
/// 创建Nhibernate实例
/// 允许指定多个程序集进行
/// </summary>
/// <param name="hibernateConnection"></param>
/// <param name="assemblys"></param>
/// <returns></returns>
public static NhibernateHelper GetNhibernateHelper(string hibernateConnection, List <string> assemblys)
{
if (string.IsNullOrWhiteSpace(hibernateConnection))
{
throw new Exception("NhibernateHelper创建错误：数据库连接为null");
}
if (assemblys == null || assemblys.Count == 0)
{
throw new Exception("NhibernateHelper创建错误：没有指定程序集");
}
Configuration config = new Configuration();
foreach (string strAssembly in assemblys)
{
config.AddAssembly(strAssembly);
}
//config.SetProperty("ConnectionString", @"Provider=Microsoft.Jet.OLEDB.4.0;Data Source=E:\项目\龙岩\Out\Bin\SysWorkspace.mdb;Persist Security Info=False");
config.Properties["connection.connection_string"] = hibernateConnection;
NHibernate.ISessionFactory sFactory = config.BuildSessionFactory();
NHibernate.ISession session = sFactory.OpenSession();
return(new NhibernateHelper(session));
}
public static void Init(IHostingEnvironment env)
{
try
{
NHibernate.Cfg.Configuration config = new NHibernate.Cfg.Configuration();
string path = string.Empty;
if (string.IsNullOrEmpty(configfilepath))
{
// var appEnv = CallContextServiceLocator.Locator.ServiceProvider.GetService(typeof(IHostingEnvironment)) as IHostingEnvironment;
path = System.IO.Path.Combine(env.ContentRootPath, "hibernate.cfg.xml");
//path = @"D:\Suresh\BickBucket\src\Api.Socioboard\hibernate.cfg.xml";
}
else
{
path = configfilepath;
}
config.Configure(path);
config.AddAssembly(Assembly.GetExecutingAssembly());//adds all the embedded resources .hbm.xml
sFactory = config.BuildSessionFactory();
}
catch (Exception ex)
{
throw ex;
//Console.Write(ex.StackTrace);
//logger.Error(ex.Message);
}
}
private static void Init()
{
NHibernate.Cfg.Configuration config = new NHibernate.Cfg.Configuration();
config.AddAssembly(typeof(Product).Assembly);
_factory = config.BuildSessionFactory();
}
public static NHibernate.ISessionFactory BuildSessionFactory()
{
FluentNHibernate.Cfg.Db.MsSqlConfiguration databaseConfiguration = FluentNHibernate.Cfg.Db.MsSqlConfiguration.MsSql2012
.MaxFetchDepth(5)
.IsolationLevel(System.Data.IsolationLevel.ReadCommitted)
.ConnectionString("Data Source=127.0.0.1,1433,db_port;User ID=devweekuser;Password=devweekpwd;Database=DemoDB;Application Name=OragonSamplesTest")
.ShowSql().FormatSql()
.DefaultSchema("dbo");
FluentNHibernate.Cfg.FluentConfiguration configuration = FluentNHibernate.Cfg.Fluently
.Configure()
.Database(databaseConfiguration)
.Cache(it =>
it.UseQueryCache()
.ProviderClass <NHibernate.Cache.HashtableCacheProvider>()
)
.Diagnostics(it =>
it.Enable(true)
.OutputToConsole()
)
.Mappings(it =>
{
it.FluentMappings.AddFromAssemblyOf <Data.Mappings.ClassroomMapper>();
})
.ExposeConfiguration(config =>
{
NHibernate.Tool.hbm2ddl.SchemaUpdate update = new NHibernate.Tool.hbm2ddl.SchemaUpdate(config);
update.Execute(true, true);
});
;
NHibernate.ISessionFactory sessionFactory = configuration.BuildSessionFactory();
return(sessionFactory);
}
public static void Init()
{
try
{
NHibernate.Cfg.Configuration config = new NHibernate.Cfg.Configuration();
string path = string.Empty;
string wanted_path = System.IO.Directory.GetCurrentDirectory();
if (string.IsNullOrEmpty(configfilepath))
{
// var appEnv = CallContextServiceLocator.Locator.ServiceProvider
//.GetService(typeof(IApplicationEnvironment)) as IApplicationEnvironment;
// path = System.IO.Path.Combine(System.Reflection.Assembly.GetExecutingAssembly().Location, "hibernate.cfg.xml");
//path = System.Reflection.Assembly.GetExecutingAssembly().Location;
// path = @"D:\bitbucket\Updated\src\SocioboardDataServices\hibernate.cfg.xml";
path = wanted_path + "\\hibernate.cfg.xml";
}
else
{
path = configfilepath;
}
config.Configure(path);
config.AddAssembly(Assembly.GetExecutingAssembly());//adds all the embedded resources .hbm.xml
sFactory = config.BuildSessionFactory();
}
catch (Exception ex)
{
throw ex;
//Console.Write(ex.StackTrace);
//logger.Error(ex.Message);
}
}
/// <summary>
/// initializes the session for database
/// </summary>
private static void Init()
{
NHibernate.Cfg.Configuration config = new NHibernate.Cfg.Configuration();
config.AddFile("db.cfg.xml");//adds all the embedded resources .hbm.xml
config.AddFile("models.xml");
sFactory = config.BuildSessionFactory();
}
private static void ReadData(NHibernate.ISessionFactory factory)
{
using (var session = factory.OpenSession())
using (var transaction = session.BeginTransaction()) {
var customer = session.Get <Customer>(1);
Console.WriteLine("Name:" + customer.FirstName + " " + customer.LastName);
}
}
/// <summary>
/// initializes the session for database
/// </summary>
private static void Init()
{
NHibernate.Cfg.Configuration config = new NHibernate.Cfg.Configuration();
config.SetProperty(NHibernate.Cfg.Environment.Dialect, "NHibernate.Dialect.PostgreSQL82Dialect");
//NHibernate.Driver.NpgsqlDriver
//config.SetProperty(NHibernate.Cfg.Environment.ConnectionProvider, "NHibernate.Connection.DriverConnectionProvider");
config.SetProperty(NHibernate.Cfg.Environment.ConnectionDriver, "NHibernate.Driver.NpgsqlDriver");
config.SetProperty(NHibernate.Cfg.Environment.ConnectionString, SessionFactory.connectionString);
config.AddXmlFile(".\\AppFiles\\Database\\models.xml");
sFactory = config.BuildSessionFactory();
}
/// <summary>
/// initializes the session for database
/// </summary>
private static void Init()
{
NHibernate.Cfg.Configuration config = new NHibernate.Cfg.Configuration();
config.SetProperty(NHibernate.Cfg.Environment.Dialect, "NHibernate.Dialect.PostgreSQL82Dialect");
//NHibernate.Driver.NpgsqlDriver
//config.SetProperty(NHibernate.Cfg.Environment.ConnectionProvider, "NHibernate.Connection.DriverConnectionProvider");
config.SetProperty(NHibernate.Cfg.Environment.ConnectionDriver, "NHibernate.Driver.NpgsqlDriver");
config.SetProperty(NHibernate.Cfg.Environment.ConnectionString, SessionFactory.connectionString);
config.AddXmlFile(".\\AppFiles\\Database\\models.xml");
sFactory = config.BuildSessionFactory();
}
// This method gets called by the runtime. Use this method to add services to the container.
public void ConfigureServices(IServiceCollection services)
{
string _db_filename = @"c:\tempsq\web-builder.sq3";
services.AddSingleton <FluentConfiguration>((provider) => {
var cfg2 = Fluently.Configure();
cfg2.Database(SQLiteConfiguration.Standard.UsingFile(_db_filename));
cfg2.Mappings(m =>
{
m.FluentMappings.Conventions.Setup(c => c.Add(AutoImport.Never()));
m.FluentMappings.Conventions.AddAssembly(Assembly.GetExecutingAssembly());
m.HbmMappings.AddFromAssembly(Assembly.GetExecutingAssembly());
var assembly = Assembly.Load("web");
m.FluentMappings.Conventions.AddAssembly(assembly);
m.FluentMappings.AddFromAssembly(assembly);
m.HbmMappings.AddFromAssembly(assembly);
});
cfg2.ExposeConfiguration(cfg =>
{
cfg.SetProperty("current_session_context_class", "thread_static");
_cfg = cfg;
});
return(cfg2);
});
services.AddSingleton <NHibernate.ISessionFactory>((provider) => {
var cfg = provider.GetService <FluentConfiguration>();
var fact = cfg.BuildSessionFactory();
return(fact);
});
services.AddScoped <NHibernate.ISession>((provider) =>
{
var cfg = provider.GetService <FluentConfiguration>();
NHibernate.ISessionFactory factory = provider.GetService <NHibernate.ISessionFactory>();
return(factory.OpenSession());
});
services.AddScoped <NHibernate.Cfg.Configuration>((provider) =>
{
return(_cfg);
});
services.AddMvc().SetCompatibilityVersion(CompatibilityVersion.Version_2_1);
}
/// <summary>
/// Static constructor creates a new session factory used by all instances
/// of this class.
/// 构造函数(静态)：创建新的Session
/// </summary>
static Repository()
{
try
{
//加载数据库相关配置信息
NHibernate.Cfg.Configuration config = new NHibernate.Cfg.Configuration().Configure(@"HibernateMapping.cfg.xml");
//创建SessionFactory
_sessionfactory = config.BuildSessionFactory();
//创建存储本地数据的内存槽
_localDataStoreSlot = System.Threading.Thread.AllocateDataSlot();
}
catch (Exception ex)
{
string s = ex.Message;
}
}
static SessionFactoryHelper()
{
var nhConfigs = new Configuration();
nhConfigs.SetProperty(Environment.Dialect, "NHibernate.Dialect.SQLiteDialect");
nhConfigs.SetProperty(Environment.ConnectionDriver, "NHibernate.Driver.SQLite20Driver");
nhConfigs.SetProperty(Environment.ConnectionString, "Data Source=NHibernateExample.db;Version=3;");
nhConfigs.SetProperty(Environment.ProxyFactoryFactoryClass, "NHibernate.ByteCode.Castle.ProxyFactoryFactory, NHibernate.ByteCode.Castle");
nhConfigs.SetProperty(Environment.CommandTimeout, "600");
SessionFactory = Fluently.Configure(nhConfigs)
.Mappings(m => m.FluentMappings
.Add<CatMap>()
.Add<OwnerMap>()
.Add<ToyMap>()
.Conventions.Add<YesNoBoolPropertyConvention>())
.BuildSessionFactory();
}
private static void InsertData(NHibernate.ISessionFactory factory)
{
using (var session = factory.OpenSession())
using (var transaction = session.BeginTransaction())
{
Customer customer1 = new Customer();
//customer1.Id = 1;
customer1.FirstName = "Dipesh";
customer1.LastName = "Kokitkar";
transaction.Begin();
session.Save(customer1);
//session.Save(new Customer {FirstName="Dipesh",LastName="Kokitkar"});
//session.Save(new Customer {FirstName = "Dipali", LastName = "Kokitkar" });
transaction.Commit();
Console.WriteLine("TAble Created");
}
}
private string CreateQueryCountString(ISearchExpression searchExpression, NHibernate.ISessionFactory sessionFactory, Dictionary <string, object> paramNames)
{
if (searchExpression is QueryExpression)
{
string s = (searchExpression as QueryExpression).Query;
int idx;
//// remove joins
//string[] joins = new string[] { "inner join", "left outer join", "right outer join", "full outer join", "left join", "right join", "full join" };
//
//foreach(string join in joins)
//{
// idx = s.IndexOf(join);
// if (idx != -1)
// {
// s = s.Substring(0, idx).Trim();
// }
//}
idx = s.IndexOf("from");
if (idx != -1)
{
s = s.Substring(idx);
}
return("select count(*) " + s);
}
NHibernate.Metadata.IClassMetadata metaData = sessionFactory.GetClassMetadata(typeof(T));
StringBuilder sb = new StringBuilder();
sb.Append("select count(*) ");
sb.Append("from ");
sb.Append(metaData.EntityName);
sb.Append(" ");
if (searchExpression != null)
{
sb.Append("where ");
sb.Append(GetQueryWhere(searchExpression, sessionFactory, paramNames));
}
return(sb.ToString());
}
public void ConnectDB(NHibernate.ISessionFactory session_factory)
{
this.session_factory = session_factory;
using (var db_session = session_factory.OpenSession())
{
using (var tx = db_session.BeginTransaction())
{
var crit = db_session.CreateCriteria <DbObjectMappings.CorpusInfo>();
//.Add(NHibernate.Criterion.Expression.Eq("Status", 1));
var corpora = crit.List <DbObjectMappings.CorpusInfo>();
foreach (var corpus_info in corpora)
{
corpus_infos.Add(corpus_info);
}
}
}
}
public static void Main(string[] args)
{
log4net.Config.XmlConfigurator.Configure();
Log("Starting Up...");
azureStorageAccountName = ConfigurationManager.AppSettings["azure-storage-account-name"];
azureStorageAccountKey = ConfigurationManager.AppSettings["azure-storage-account-key"];
azureStorageBaseURL = "https://" + azureStorageAccountName + ".blob.core.windows.net/" + ConfigurationManager.AppSettings["azure-storage-blob-container"] + "/";
var connectionString = ConfigurationManager.AppSettings["db_fodt"];
var cfg = DatabaseBootstrapper.Bootstrap(connectionString);
sessionFactory = cfg.BuildSessionFactory();
Log("Opening Connection to Old FODT DB");
oldDatabaseConnection = new MySql.Data.MySqlClient.MySqlConnection(ConfigurationManager.AppSettings["db_old_fodt"]);
oldDatabaseConnection.Open();
if (doDatabaseImport)
{
TruncateDatabase();
ImportPhotos();
ImportAwardsList();
ImportPersons();
ImportPersonPhotos();
ImportShows();
ImportShowPhotos();
ImportAwards();
ImportCast();
ImportCrew();
ImportEC();
FixInsertedDateTimeColumns();
}
if (doFixLargePhotoFlag)
{
FixLargePhotoFlag();
}
if (doBlobUpload)
{
ImportPhotoBlobs();
}
}
public int AddOrUpdate(int id, string endereco, object emails, string name, object phones, string empresa)
{
try
{
using (NHibernate.ISessionFactory sessionFactory = SessionFactoryBuilder.BuildSessionFactory())
{
using (NHibernate.ISession session = sessionFactory.OpenSession())
{
using (NHibernate.ITransaction transaction = session.BeginTransaction())
{
ContatoEntitis contatoToBeSave = new ContatoEntitis
{
Id = id,
Endereco = endereco,
Email = JsonConvert.SerializeObject(emails),
Nome = name,
Telefone = JsonConvert.SerializeObject(phones),
Empresa = empresa
};
if (contatoToBeSave.Id > 0)
{
session.Update(contatoToBeSave);
}
else
{
session.Save(contatoToBeSave);
}
transaction.Commit();
return(contatoToBeSave.Id);
}
}
}
}
catch (Exception ex)
{
throw;
}
}
private static NHibernate.ISessionFactory GetFactory()
{
NHibernate.ISessionFactory aISessionFactory = null;
NHibernate.Cfg.Configuration aConfiguration = new NHibernate.Cfg.Configuration();
if (aConfiguration == null)
{
throw new InvalidOperationException("La configurazione di NHibernate non è disponibile.");
}
aConfiguration.Configure();
aISessionFactory = aConfiguration.BuildSessionFactory();
if (aISessionFactory == null)
{
throw new InvalidOperationException("Impossibile creare l'oggetto NHibernate.ISessionFactory.");
}
return(aISessionFactory);
}
public List <ContatoEntitis> List()
{
try
{
List <ContatoEntitis> retorno = new List <ContatoEntitis>();
using (NHibernate.ISessionFactory sessionFactory = SessionFactoryBuilder.BuildSessionFactory())
{
using (NHibernate.ISession session = sessionFactory.OpenSession())
{
retorno = session.Query <ContatoEntitis>().ToList();
session.Flush();
}
}
return(retorno);
}
catch (Exception ex)
{
throw;
}
}
protected void Application_Start()
{
AreaRegistration.RegisterAllAreas();
RegisterGlobalFilters(GlobalFilters.Filters);
RegisterRoutes(RouteTable.Routes);
sessionFactory = Fluently.Configure()
.Database(
MsSqlConfiguration.MsSql2008
.ConnectionString(c => c.Server(@".\MSSQL2008R2")
.Database("objectflow")
.Username("objectflow")
.Password("password"))
.DefaultSchema("dbo")
)
.Mappings(x => x.FluentMappings.AddFromAssemblyOf<MvcApplication>())
//.ExposeConfiguration(cfg => cfg.SetProperty("current_session_context_class", "managed_web"))
.BuildSessionFactory();
//BeginRequest += MvcApplication_BeginRequest;
//EndRequest += MvcApplication_EndRequest;
BootstrapContainer();
}
public ContatoEntitis Get(int id)
{
try
{
ContatoEntitis retorno = new ContatoEntitis();
using (NHibernate.ISessionFactory sessionFactory = SessionFactoryBuilder.BuildSessionFactory())
{
using (NHibernate.ISession session = sessionFactory.OpenSession())
{
retorno = session.Get <ContatoEntitis>(id);
session.Flush();
}
}
return(retorno);
}
catch (Exception exs)
{
throw;
}
}
protected void Application_Start()
{
AreaRegistration.RegisterAllAreas();
RegisterGlobalFilters(GlobalFilters.Filters);
RegisterRoutes(RouteTable.Routes);
sessionFactory = Fluently.Configure()
.Database(
MsSqlConfiguration.MsSql2008
.ConnectionString(c => c.Server(@".\MSSQL2008R2")
.Database("objectflow")
.Username("objectflow")
.Password("password"))
.DefaultSchema("dbo")
)
.Mappings(x => x.FluentMappings.AddFromAssemblyOf <MvcApplication>())
//.ExposeConfiguration(cfg => cfg.SetProperty("current_session_context_class", "managed_web"))
.BuildSessionFactory();
//BeginRequest += MvcApplication_BeginRequest;
//EndRequest += MvcApplication_EndRequest;
BootstrapContainer();
}
/// <summary>
/// Private constructor that initialises the unique instance of this class
/// </summary>
private DataManager()
{
try
{
// Initialise NHibernate Configuration
this.config = new NHibernate.Cfg.Configuration().Configure();
// Add assembly
this.config.AddAssembly( typeof(Person).Assembly );
//this.config.AddAssembly( "Contact.hbm.xml" );
//this.config.AddAssembly( "Person.hbm.xml" );
//this.config.AddAssembly( "Project.hbm.xml" );
//this.config.AddAssembly( "DataModel" );
// Initialise NHibernate factory
sessionFactory = this.config.BuildSessionFactory();
}
catch( Exception ex )
{
throw ex;
}
}
/// <summary> Configures NHibernate to access the data source and map entities to tables. </summary>
public Persister()
{
System.Console.Out.WriteLine("Configuration of NHibernate...\n");
const string connectionString = @"Data Source=(local)\sqlexpress;Initial Catalog=nhibernate;Integrated Security=SSPI";
// Enable the logging of NHibernate operations
log4net.Config.XmlConfigurator.Configure();
// Create the object that will hold the configuration settings
// and fill it with the information to access to the database
NHibernate.Cfg.Configuration configuration = new NHibernate.Cfg.Configuration();
configuration.Properties[NHibernate.Cfg.Environment.ConnectionProvider] = "NHibernate.Connection.DriverConnectionProvider";
System.Console.Out.WriteLine("Use SQL Server database: ConnectionString = <"
+ connectionString + ">\n");
// These are the three lines of code to change in order to use another database
configuration.Properties[NHibernate.Cfg.Environment.Dialect] = "NHibernate.Dialect.MsSql2000Dialect";
configuration.Properties[NHibernate.Cfg.Environment.ConnectionDriver] = "NHibernate.Driver.SqlClientDriver";
configuration.Properties[NHibernate.Cfg.Environment.ConnectionString] = connectionString;
// Use NHibernate.Mapping.Attributes to create mapping information about our entities
System.Console.Out.WriteLine("Generating the mapping information for NHibernate...\n");
NHibernate.Mapping.Attributes.HbmSerializer.Default.Validate = true; // Enable validation (optional)
using (System.IO.MemoryStream stream = NHibernate.Mapping.Attributes.HbmSerializer.Default.Serialize(System.Reflection.Assembly.GetExecutingAssembly()))
{
configuration.AddInputStream(stream); // Send the mapping information to NHibernate configuration
}
// Create the table in the database for the entity Message
System.Console.Out.WriteLine("Creating the table in the database for the entity Message...");
new NHibernate.Tool.hbm2ddl.SchemaExport(configuration).Create(true, true);
// Build the SessionFactory
System.Console.Out.WriteLine("\n\nBuilding the session factory, end of the configuration\n\n");
_sessionFactory = configuration.BuildSessionFactory();
}
public static void Init()
{
try
{
NHibernate.Cfg.Configuration config = new NHibernate.Cfg.Configuration();
string path = string.Empty;
if (string.IsNullOrEmpty(configfilepath))
{
path = HttpContext.Current.Server.MapPath("~/hibernate.cfg.xml");
}
else
{
path = configfilepath;
}
config.Configure(path);
config.AddAssembly("SocioBoardInvitationMailSender");//adds all the embedded resources .hbm.xml
sFactory = config.BuildSessionFactory();
}
catch (Exception ex)
{
Console.WriteLine("Error : " + ex.StackTrace);
}
}
/// <summary>
/// Uses reflection to create a new SoftLimitMRUCache with a specified size and sets session factory query plan cache to it.
/// This is done like this as NHibernate does not currently provide any way to specify the query plan cache size through configuration.
/// </summary>
/// <param name="factory"></param>
/// <param name="size"></param>
/// <returns></returns>
private static bool TrySetQueryPlanCacheSize(NHibernate.ISessionFactory factory, int size)
{
var factoryImpl = factory as NHibernate.Impl.SessionFactoryImpl;
if (factoryImpl != null)
{
var queryPlanCacheFieldInfo = typeof(NHibernate.Impl.SessionFactoryImpl).GetField("queryPlanCache", System.Reflection.BindingFlags.Instance | System.Reflection.BindingFlags.NonPublic);
if (queryPlanCacheFieldInfo != null)
{
var queryPlanCache = (NHibernate.Engine.Query.QueryPlanCache)queryPlanCacheFieldInfo.GetValue(factoryImpl);
var planCacheFieldInfo = typeof(NHibernate.Engine.Query.QueryPlanCache).GetField("planCache", System.Reflection.BindingFlags.Instance | System.Reflection.BindingFlags.NonPublic);
if (planCacheFieldInfo != null)
{
var softLimitMRUCache = new NHibernate.Util.SoftLimitMRUCache(size);
planCacheFieldInfo.SetValue(queryPlanCache, softLimitMRUCache);
return(true);
}
}
}
return(false);
}
public bool Delete(ContatoEntitis contatoToBeDelete)
{
try
{
using (NHibernate.ISessionFactory sessionFactory = SessionFactoryBuilder.BuildSessionFactory())
{
using (NHibernate.ISession session = sessionFactory.OpenSession())
{
using (NHibernate.ITransaction transaction = session.BeginTransaction())
{
session.Delete(contatoToBeDelete);
transaction.Commit();
}
}
}
return(true);
}
catch (Exception ex)
{
throw;
}
}
public static void Init()
{
try
{
NHibernate.Cfg.Configuration config = new NHibernate.Cfg.Configuration();
string path = string.Empty;
if (string.IsNullOrEmpty(configfilepath))
{
path = HttpContext.Current.Server.MapPath("~/hibernate.cfg.xml");
}
else
{
path = configfilepath;
}
config.Configure(path);
config.AddAssembly("SocioBoard");//adds all the embedded resources .hbm.xml
sFactory = config.BuildSessionFactory();
}
catch (Exception ex)
{
Console.WriteLine("Error : " + ex.StackTrace);
}
}
public static void Init()
{
try
{
NHibernate.Cfg.Configuration config = new NHibernate.Cfg.Configuration();
string path = string.Empty;
if (string.IsNullOrEmpty(configfilepath))
{
path = HttpContext.Current.Server.MapPath("~/hibernate.cfg.xml");
}
else
{
path = configfilepath;
}
config.Configure(path);
config.AddAssembly(Assembly.GetExecutingAssembly());//adds all the embedded resources .hbm.xml
sFactory = config.BuildSessionFactory();
}
catch (Exception ex)
{
logger.Error(ex.Message);
}
}
public static void Init()
{
try
{
NHibernate.Cfg.Configuration config = new NHibernate.Cfg.Configuration();
string path = string.Empty;
if (string.IsNullOrEmpty(configfilepath))
{
path = HttpContext.Current.Server.MapPath("~/hibernate.cfg.xml");
}
else
{
path = configfilepath;
}
config.Configure(path);
config.AddAssembly(Assembly.GetExecutingAssembly());//adds all the embedded resources .hbm.xml
sFactory = config.BuildSessionFactory();
}
catch (Exception ex)
{
logger.Error(ex.Message);
}
}
public static NHibernate.ISession OpenSession()
{
if (factory == null)
{
try
{
var config = new Configuration();
//config.Configure(@"D:\workspace\shoperp\DataConvert\bin\Debug\hibernate1.cfg.xml");
string file = EnvironmentDirHelper.PROGRAM_DIR + "\\" + @"hibernate.cfg.xml";
Console.WriteLine("正在使用数据库连接配置文件：" + file);
config.Configure(file);
config.AddAssembly(typeof(NHibernateHelper).Assembly);
config.BuildMappings();
factory = config.BuildSessionFactory();
}
catch (Exception ex)
{
Logger.Log("初始货NHibernate失败", ex);
throw new Exception("初始化数据库连接失败", ex);
}
}
return(factory.OpenSession());
}
public static void PopulateDatabase(object sender, NHibernate.ISessionFactory sessionFactory)
{
using (var session = sessionFactory.OpenSession())
using (var tx = session.BeginTransaction())
{
if (session.Query <Culture>().Any())
{
return;
}
var enCulture = new Culture {
DisplayName = "English", Name = "en-US", FlagFilename = "flag_En.png"
};
var roCulture = new Culture {
DisplayName = "Romana", Name = "ro-RO", FlagFilename = "flag_Ro.png"
};
var deCulture = new Culture {
DisplayName = "Deustch", Name = "de-DE", FlagFilename = "flag_De.png"
};
session.Save(enCulture);
session.Save(roCulture);
session.Save(deCulture);
var USACountry = new Country {
Culture = enCulture, Name = "USA"
};
var RomaniaCountry = new Country {
Culture = roCulture, Name = "Romania"
};
var GermanyCountry = new Country {
Culture = deCulture, Name = "Germany"
};
session.Save(USACountry);
session.Save(RomaniaCountry);
session.Save(GermanyCountry);
tx.Commit();
}
}
public CategoryRepository(NHibernate.ISessionFactory northwind)
{
_northwind = northwind;
}
/// <summary>
/// Initializes the session factory and ensure that the
/// configuration file exists.
/// </summary>
private void InitSessionFactory()
{
//expect the hibernate.cfg.xml file to be in the application folder
NHibernate.Cfg.Configuration temp = new NHibernate.Cfg.Configuration();
cfg = temp.Configure();
cfg.AddAssembly("gooeycms.data");
//build the session factory based upon the configuration
sessionFactory = cfg.BuildSessionFactory();
}
public void TestClusters ()
{
// each protein in the test scenarios is created from simple repeating motifs
var testProteinSequences = new string[]
{
createSimpleProteinSequence("A", 20), // PRO1
createSimpleProteinSequence("B", 20),
createSimpleProteinSequence("C", 20),
createSimpleProteinSequence("D", 20),
createSimpleProteinSequence("E", 20), // PRO5
createSimpleProteinSequence("E", 21),
createSimpleProteinSequence("F", 20),
createSimpleProteinSequence("F", 21),
createSimpleProteinSequence("G", 20),
createSimpleProteinSequence("G", 21), // PRO10
createSimpleProteinSequence("H", 20),
createSimpleProteinSequence("H", 21),
createSimpleProteinSequence("AAAABBBBCCCC", 24),
createSimpleProteinSequence("AAAABBBB", 24),
createSimpleProteinSequence("BBBBCCCC", 24), // PRO15
createSimpleProteinSequence("BBBBBDDDDD", 20),
createSimpleProteinSequence("BBBBDDDD", 24),
createSimpleProteinSequence("ZBBBBDDD", 24),
createSimpleProteinSequence("YBBBDDD", 20),
createSimpleProteinSequence("WBBDD", 21), // PRO20
createSimpleProteinSequence("DDDDDFFFFF", 20),
createSimpleProteinSequence("FFFFFHHHHH", 20),
createSimpleProteinSequence("HHHHHKKKKK", 20),
createSimpleProteinSequence("HHHHHKKKKK", 30),
createSimpleProteinSequence("KKKKKMMMMM", 20), // PRO25
createSimpleProteinSequence("LLLLLNNNNN", 20),
createSimpleProteinSequence("NNNNNQQQQQ", 20),
createSimpleProteinSequence("NNNNNQQQQQ", 30),
createSimpleProteinSequence("MMMMMPPPPP", 20),
createSimpleProteinSequence("PPPPPRRRRR", 20), // PRO30
createSimpleProteinSequence("PPPPPRRRR", 24),
};
string idpDbName = System.Reflection.MethodInfo.GetCurrentMethod().Name + ".idpDB";
File.Delete(idpDbName);
sessionFactory = SessionFactoryFactory.CreateSessionFactory(idpDbName, new SessionFactoryConfig { CreateSchema = true });
var session = sessionFactory.OpenSession();
TestModel.CreateTestProteins(session, testProteinSequences);
const int analysisCount = 2;
const int sourceCount = 1;
const int chargeCount = 2;
for (int analysis = 1; analysis <= analysisCount; ++analysis)
for (int source = 1; source <= sourceCount; ++source)
for (int charge = 1; charge <= chargeCount; ++charge)
{
int scan = 0;
List<SpectrumTuple> testPsmSummary = new List<SpectrumTuple>()
{
// Columns: Group Source Spectrum Analysis Score Q List of Peptide@Charge/ScoreDivider
// 1 protein to 1 peptide to 1 spectrum = 1 additional peptide
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("AAAAAAAAAA@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein to 1 peptide to 2 spectra = 1 additional peptide
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBBBBBBB@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBBBBBBB@{0}/1 CCCCCCCCCC@{0}/8", charge)),
// 1 protein to 2 peptides to 1 spectrum (each)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("CCCCCCCCCC@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("CCCCCCCCC@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein to 2 peptides to 2 spectra (each)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDDDDDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDDDDDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDDDDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDDDDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins to 1 peptide to 1 spectrum (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("EEEEEEEEEE@{0}/1 AAAAAAAAAA@{0}/8", charge)),
// 2 proteins to 1 peptide to 2 spectra (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("FFFFFFFFFF@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("FFFFFFFFFF@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins to 2 peptides to 1 spectrum (each) (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("GGGGGGGGGG@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("GGGGGGGGG@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins to 2 peptides to 2 spectra (each) (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHHHHHHH@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHHHHHHH@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHHHHHH@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHHHHHH@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein to 2 peptides
// 1 protein to 1 of the above peptides (subsumed protein)
// 1 protein to the other above peptide (subsumed protein)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("AAAABBBB@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBCCCC@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein to 5 peptides
// 1 protein to 4 of the above peptides
// 1 protein to 3 of the above peptides and 1 extra peptides
// 1 protein to 2 of the above peptides and 2 extra peptides
// 1 protein to 1 of the above peptides and 3 extra peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBBDDDDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBDDDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBDDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("ZBBBBDDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("YBBBDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("YBBBDDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("WBB@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("WBBD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("WBBDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
// 1 protein to 3 peptides, 1 of which is evidenced by an ambiguous spectrum
// 1 protein to 1 peptide evidenced by the ambiguous spectrum above and 1 extra peptide
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDFFFFF@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDFFFF@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DFFFFF@{0}/1 FFFFFH@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("FFFFFHHHHH@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins to 3 peptides, 1 of which is evidenced by an ambiguous spectrum
// 1 protein to 1 peptide evidenced by the ambiguous spectrum above and 1 extra peptide
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHHKKKKK@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHHKKKK@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HKKKKK@{0}/1 KKKKKM@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("KKKKKMMMMM@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein to 3 peptides, 1 of which is evidenced by an ambiguous spectrum
// 2 proteins to 1 peptide evidenced by the ambiguous spectrum above and 1 extra peptide
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("LLLLLNNNNN@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("LLLLLNNNN@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("LNNNNN@{0}/1 NNNNNQ@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("NNNNNQQQQQ@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein to 3 peptides, 2 of which are evidenced by ambiguous spectra
// 1 protein to 1 peptide evidenced by an ambiguous spectrum above and 1 extra peptide
// 1 protein to 1 peptide evidenced by the other ambiguous spectrum above and 1 extra peptide
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("MMMMMPPPPP@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("MPPPPP@{0}/1 PRRRRR@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("PPPPPRRRRR@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("MPPPP@{0}/1 PRRRRP@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("PPPPRRRRP@{0}/1 AAAAAAAAAA@{0}/8", charge)),
};
TestModel.CreateTestData(session, testPsmSummary);
}
var dataFilter = new DataFilter()
{
MaximumQValue = 1,
MinimumDistinctPeptides = 0,
MinimumSpectra = 0,
MinimumAdditionalPeptides = 0
};
dataFilter.ApplyBasicFilters(session);
// clear session so objects are loaded from database
session.Clear();
// 1 protein to 1 peptide to 1 spectrum
Assert.AreEqual(1, session.UniqueResult<Protein>(o => o.Accession == "PRO1").Cluster);
// 1 protein to 1 peptide to 2 spectra
Assert.AreEqual(6, session.UniqueResult<Protein>(o => o.Accession == "PRO2").Cluster);
// 1 protein to 2 peptides to 1 spectrum (each)
Assert.AreEqual(10, session.UniqueResult<Protein>(o => o.Accession == "PRO3").Cluster);
// 1 protein to 2 peptides to 2 spectra (each)
Assert.AreEqual(12, session.UniqueResult<Protein>(o => o.Accession == "PRO4").Cluster);
// 2 proteins to 1 peptide to 1 spectrum (ambiguous protein group)
Assert.AreEqual(13, session.UniqueResult<Protein>(o => o.Accession == "PRO5").Cluster);
Assert.AreEqual(13, session.UniqueResult<Protein>(o => o.Accession == "PRO6").Cluster);
// 2 proteins to 1 peptide to 2 spectra (ambiguous protein group)
Assert.AreEqual(14, session.UniqueResult<Protein>(o => o.Accession == "PRO7").Cluster);
Assert.AreEqual(14, session.UniqueResult<Protein>(o => o.Accession == "PRO8").Cluster);
// 2 proteins to 2 peptides to 1 spectrum (each) (ambiguous protein group)
Assert.AreEqual(2, session.UniqueResult<Protein>(o => o.Accession == "PRO9").Cluster);
Assert.AreEqual(2, session.UniqueResult<Protein>(o => o.Accession == "PRO10").Cluster);
// 2 proteins to 2 peptides to 2 spectra (each) (ambiguous protein group)
Assert.AreEqual(3, session.UniqueResult<Protein>(o => o.Accession == "PRO11").Cluster);
Assert.AreEqual(3, session.UniqueResult<Protein>(o => o.Accession == "PRO12").Cluster);
// 1 protein to 2 peptides to 1 spectrum (each)
// 1 protein to 1 of the above peptides (subsumed protein)
// 1 protein to the other above peptide (subsumed protein)
Assert.AreEqual(4, session.UniqueResult<Protein>(o => o.Accession == "PRO13").Cluster);
Assert.AreEqual(4, session.UniqueResult<Protein>(o => o.Accession == "PRO14").Cluster);
Assert.AreEqual(4, session.UniqueResult<Protein>(o => o.Accession == "PRO15").Cluster);
// 1 protein to 5 peptides
// 1 protein to 4 of the above peptides
// 1 protein to 3 of the above peptides and 1 extra peptides
// 1 protein to 2 of the above peptides and 2 extra peptides
// 1 protein to 1 of the above peptides and 3 extra peptides
Assert.AreEqual(5, session.UniqueResult<Protein>(o => o.Accession == "PRO16").Cluster);
Assert.AreEqual(5, session.UniqueResult<Protein>(o => o.Accession == "PRO17").Cluster);
Assert.AreEqual(5, session.UniqueResult<Protein>(o => o.Accession == "PRO18").Cluster);
Assert.AreEqual(5, session.UniqueResult<Protein>(o => o.Accession == "PRO19").Cluster);
Assert.AreEqual(5, session.UniqueResult<Protein>(o => o.Accession == "PRO20").Cluster);
// 1 protein to 3 peptides, 1 of which is evidenced by an ambiguous spectrum
// 1 protein to 1 peptide evidenced by the ambiguous spectrum above and 1 extra peptide
Assert.AreEqual(7, session.UniqueResult<Protein>(o => o.Accession == "PRO21").Cluster);
Assert.AreEqual(7, session.UniqueResult<Protein>(o => o.Accession == "PRO22").Cluster);
// 2 proteins to 3 peptides, 1 of which is evidenced by an ambiguous spectrum
// 1 protein to 1 peptide evidenced by the ambiguous spectrum above and 1 extra peptide
Assert.AreEqual(8, session.UniqueResult<Protein>(o => o.Accession == "PRO23").Cluster);
Assert.AreEqual(8, session.UniqueResult<Protein>(o => o.Accession == "PRO24").Cluster);
Assert.AreEqual(8, session.UniqueResult<Protein>(o => o.Accession == "PRO25").Cluster);
// 1 protein to 3 peptides, 1 of which is evidenced by an ambiguous spectrum
// 2 proteins to 1 peptide evidenced by the ambiguous spectrum above and 1 extra peptide
Assert.AreEqual(9, session.UniqueResult<Protein>(o => o.Accession == "PRO26").Cluster);
Assert.AreEqual(9, session.UniqueResult<Protein>(o => o.Accession == "PRO27").Cluster);
Assert.AreEqual(9, session.UniqueResult<Protein>(o => o.Accession == "PRO28").Cluster);
// 1 protein to 3 peptides, 2 of which are evidenced by ambiguous spectra
// 1 protein to 1 peptide evidenced by an ambiguous spectrum above and 1 extra peptide
// 1 protein to 1 peptide evidenced by the other ambiguous spectrum above and 1 extra peptide
Assert.AreEqual(11, session.UniqueResult<Protein>(o => o.Accession == "PRO29").Cluster);
Assert.AreEqual(11, session.UniqueResult<Protein>(o => o.Accession == "PRO30").Cluster);
Assert.AreEqual(11, session.UniqueResult<Protein>(o => o.Accession == "PRO31").Cluster);
session.Close();
}
public ProductRepository(NHibernate.ISessionFactory northwind)
{
_northwind = northwind;
}
public void TestAdditionalPeptides ()
{
// each protein in the test scenarios is created from simple repeating motifs
var testProteinSequences = new string[]
{
createSimpleProteinSequence("A", 20), // PRO1
createSimpleProteinSequence("B", 20),
createSimpleProteinSequence("C", 20),
createSimpleProteinSequence("D", 20),
createSimpleProteinSequence("E", 20), // PRO5
createSimpleProteinSequence("E", 21),
createSimpleProteinSequence("F", 20),
createSimpleProteinSequence("F", 21),
createSimpleProteinSequence("G", 20),
createSimpleProteinSequence("G", 21), // PRO10
createSimpleProteinSequence("H", 20),
createSimpleProteinSequence("H", 21),
createSimpleProteinSequence("AAAABBBBCCCC", 24),
createSimpleProteinSequence("AAAABBBB", 24),
createSimpleProteinSequence("BBBBCCCC", 24), // PRO15
createSimpleProteinSequence("DDDDEEEEFFFF", 24),
createSimpleProteinSequence("DDDDEEEE", 24),
createSimpleProteinSequence("DDDDEEEE", 16),
createSimpleProteinSequence("GGGGHHHHIIII", 24),
createSimpleProteinSequence("GGGGHHHHIIII", 36), // PRO20
createSimpleProteinSequence("GGGGHHHH", 24),
createSimpleProteinSequence("HHHHIIII", 24),
createSimpleProteinSequence("KKKKLLLLMMMM", 24),
createSimpleProteinSequence("KKKKLLLLMMMM", 36),
createSimpleProteinSequence("LLLLMMMM", 24), // PRO25
createSimpleProteinSequence("LLLLMMMM", 16),
createSimpleProteinSequence("NNNNPPPPQQQQ", 24),
createSimpleProteinSequence("PPPPQQQQRRRR", 24),
createSimpleProteinSequence("SSSSTTTTUUUU", 24),
createSimpleProteinSequence("TTTTUUUUVVVV", 24), // PRO30
createSimpleProteinSequence("TTTTUUUUVVVV", 36),
createSimpleProteinSequence("WWWWYYYYZZZZ", 24),
createSimpleProteinSequence("WWWWYYYYZZZZ", 36),
createSimpleProteinSequence("YYYYZZZZFFFF", 24),
createSimpleProteinSequence("AAAACCCCEEEE", 24), // PRO35
createSimpleProteinSequence("AAAACCCCEEEE", 36),
createSimpleProteinSequence("CCCCEEEEGGGG", 24),
createSimpleProteinSequence("CCCCEEEEGGGG", 36),
createSimpleProteinSequence("BBBBBDDDDD", 20),
createSimpleProteinSequence("BBBBDDDD", 24), // PRO40
createSimpleProteinSequence("ZBBBBDDD", 24),
createSimpleProteinSequence("YBBBDDD", 20),
createSimpleProteinSequence("WBBDD", 21),
createSimpleProteinSequence("DDDDDFFFFF", 20),
createSimpleProteinSequence("FFFFFHHHHH", 20), // PRO45
createSimpleProteinSequence("HHHHHKKKKK", 20),
createSimpleProteinSequence("HHHHHKKKKK", 30),
createSimpleProteinSequence("KKKKKMMMMM", 20),
createSimpleProteinSequence("LLLLLNNNNN", 20),
createSimpleProteinSequence("NNNNNQQQQQ", 20), // PRO50
createSimpleProteinSequence("NNNNNQQQQQ", 30),
createSimpleProteinSequence("MMMMMPPPPP", 20),
createSimpleProteinSequence("PPPPPRRRRR", 20),
createSimpleProteinSequence("PPPPPRRRR", 24),
createSimpleProteinSequence("QQQQSSSSUUUU", 24), // PRO55
createSimpleProteinSequence("SSSSUUUUYYYY", 24),
createSimpleProteinSequence("RRRRTTTTWWWWZZZZ", 32),
createSimpleProteinSequence("TTTTWWWWZZZZBBBB", 32),
createSimpleProteinSequence("RRRRTTTTZZZZBBBBTTTTWWWW", 24),
createSimpleProteinSequence("AAAADDDDGGGGKKKK", 32), // PRO60
createSimpleProteinSequence("DDDDGGGGKKKKNNNN", 32),
createSimpleProteinSequence("AAAADDDDKKKKNNNN", 32),
createSimpleProteinSequence("BBBBEEEEHHHH", 24),
createSimpleProteinSequence("EEEEHHHHLLLL", 24),
createSimpleProteinSequence("HHHHLLLLPPPP", 24), // PRO65
createSimpleProteinSequence("CCCCFFFFIIII", 24),
createSimpleProteinSequence("FFFFIIIIMMMM", 24),
createSimpleProteinSequence("IIIIMMMMQQQQ", 24),
createSimpleProteinSequence("NNNNRRRRUUUU", 24),
createSimpleProteinSequence("RRRRUUUUZZZZ", 24), // PRO70
createSimpleProteinSequence("UUUUZZZZCCCC", 24),
};
string idpDbName = System.Reflection.MethodInfo.GetCurrentMethod().Name + ".idpDB";
File.Delete(idpDbName);
sessionFactory = SessionFactoryFactory.CreateSessionFactory(idpDbName, new SessionFactoryConfig { CreateSchema = true });
var session = sessionFactory.OpenSession();
TestModel.CreateTestProteins(session, testProteinSequences);
const int analysisCount = 2;
const int sourceCount = 1;
const int chargeCount = 2;
for (int analysis = 1; analysis <= analysisCount; ++analysis)
for (int source = 1; source <= sourceCount; ++source)
for (int charge = 1; charge <= chargeCount; ++charge)
{
int scan = 0;
List<SpectrumTuple> testPsmSummary = new List<SpectrumTuple>()
{
// Columns: Group Source Spectrum Analysis Score Q List of Peptide@Charge/ScoreDivider
// 1 protein (PRO1) to 1 peptide to 1 spectrum = 1 additional peptide
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("AAAAAAAAAA@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO2) to 1 peptide to 2 spectra = 1 additional peptide
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBBBBBBB@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBBBBBBB@{0}/1 CCCCCCCCCC@{0}/8", charge)),
// 1 protein (PRO3) to 2 peptides to 1 spectrum (each) = 2 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("CCCCCCCCCC@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("CCCCCCCCC@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO4) to 2 peptides to 2 spectra (each) = 2 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDDDDDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDDDDDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDDDDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDDDDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins (PRO5,6) to 1 peptide to 1 spectrum = 1 additional peptide (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("EEEEEEEEEE@{0}/1 AAAAAAAAAA@{0}/8", charge)),
// 2 proteins (PRO7,8) to 1 peptide to 2 spectra = 1 additional peptide (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("FFFFFFFFFF@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("FFFFFFFFFF@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins (PRO9,10) to 2 peptides to 1 spectrum (each) = 2 additional peptides (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("GGGGGGGGGG@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("GGGGGGGGG@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins (PRO11,12) to 2 peptides to 2 spectra (each) = 2 additional peptides (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHHHHHHH@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHHHHHHH@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHHHHHH@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHHHHHH@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO13) to 2 peptides = 2 additional peptide
// 1 protein (PRO14) to 1 of the above peptides = 0 additional peptides (subsumed protein)
// 1 protein (PRO15) to the other above peptide = 0 additional peptides (subsumed protein)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("AAAABBBB@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBCCCC@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO16) to 2 peptides = 2 additional peptide
// 2 proteins (PRO17,18) to 1 of the above peptides = 0 additional peptides (subsumed ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDEEEE@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("EEEEFFFF@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins (PRO19,20) to 2 peptides = 2 additional peptide (ambiguous protein group)
// 1 protein (PRO21) to 1 of the above peptides = 0 additional peptides (subsumed protein)
// 1 protein (PRO22) to the other above peptide = 0 additional peptides (subsumed protein)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("GGGGHHHH@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHIIII@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins (PRO23,24) to 2 peptides = 2 additional peptides (ambiguous protein group)
// 2 proteins (PRO25,26) to 1 of the above peptides = 0 additional peptides (subsumed ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("KKKKLLLL@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("LLLLMMMM@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO27) to 3 peptides = 3 additional peptides
// 1 protein (PRO28) to 1 of the above peptides and 1 extra peptide = 1 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("NNNNPPPP@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("NNNNPPP@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("PPPPQQQQ@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("QQQQRRRR@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO29) to 3 peptides = 3 additional peptides
// 2 proteins (PRO30,31) to 1 of the above peptides and 1 extra peptide = 1 additional peptides (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("SSSSTTTT@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("SSSSTTT@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("TTTTUUUU@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("UUUUVVVV@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins (PRO32,33) to 3 peptides = 3 additional peptides (ambiguous protein group)
// 1 protein (PRO34) to 1 of the above peptides and 1 extra peptide = 1 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("WWWWYYYY@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("WWWWYYY@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("YYYYZZZZ@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("ZZZZFFFF@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins (PRO35,36) to 3 peptides = 3 additional peptides (ambiguous protein group)
// 2 proteins (PRO37,38) to 1 of the above peptides and 1 extra peptide = 1 additional peptides (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("AAAACCCC@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("AAAACCC@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("CCCCEEEE@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("EEEEGGGG@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO39) to 5 peptides = 5 additional peptides
// 1 protein (PRO40) to 4 of the above peptides = 0 additional peptides
// 1 protein (PRO41) to 3 of the above peptides and 1 extra peptides = 1 additional peptides
// 1 protein (PRO42) to 2 of the above peptides and 2 extra peptides = 2 additional peptides
// 1 protein (PRO43) to 1 of the above peptides and 3 extra peptides = 3 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBBDDDDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBDDDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBDDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("ZBBBBDDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("YBBBDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("YBBBDDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("WBB@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("WBBD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("WBBDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
// 1 protein (PRO44) to 3 peptides, 1 of which is evidenced by an ambiguous spectrum = 3 additional peptides
// 1 protein (PRO45) to 1 peptide evidenced by the ambiguous spectrum above and 1 extra peptide = 1 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDFFFFF@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDFFFF@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DFFFFF@{0}/1 FFFFFH@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("FFFFFHHHHH@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins (PRO46,47) to 3 peptides, 1 of which is evidenced by an ambiguous spectrum = 3 additional peptides
// 1 protein (PRO48) to 1 peptide evidenced by the ambiguous spectrum above and 1 extra peptide = 1 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHHKKKKK@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHHKKKK@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HKKKKK@{0}/1 KKKKKM@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("KKKKKMMMMM@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO49) to 3 peptides, 1 of which is evidenced by an ambiguous spectrum = 3 additional peptides
// 2 proteins (PRO50,51) to 1 peptide evidenced by the ambiguous spectrum above and 1 extra peptide = 1 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("LLLLLNNNNN@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("LLLLLNNNN@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("LNNNNN@{0}/1 NNNNNQ@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("NNNNNQQQQQ@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO52) to 3 peptides, 2 of which are evidenced by ambiguous spectra = 3 additional peptides
// 1 protein (PRO53) to 1 peptide evidenced by an ambiguous spectrum above and 1 extra peptide = 1 additional peptides
// 1 protein (PRO54) to 1 peptide evidenced by the other ambiguous spectrum above and 1 extra peptide = 1 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("MMMMMPPPPP@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("MPPPPP@{0}/1 PRRRRR@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("PPPPPRRRRR@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("MPPPP@{0}/1 PRRRRP@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("PPPPRRRRP@{0}/1 AAAAAAAAAA@{0}/8", charge)),
// PRO55 -> QQQQSSSS, SSSSUUUU = 2 additional peptides
// PRO56 -> UUUUYYYY, SSSSUUUU = 2 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("QQQQSSSS@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("SSSSUUUU@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("UUUUYYYY@{0}/1 AAAAAAAAAA@{0}/8", charge)),
// PRO57 -> RRRRTTTT, WWWWZZZZ, TTTTWWWW = 3 additional peptides
// PRO58 -> ZZZZBBBB, WWWWZZZZ, TTTTWWWW = 3 additional peptides
// PRO59 -> RRRRTTTT, ZZZZBBBB, TTTTWWWW = 3 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("RRRRTTTT@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("WWWWZZZZ@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("TTTTWWWW@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("ZZZZBBBB@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// PRO60 -> AAAADDDD, DDDDGGGG, GGGGKKKK = 3 additional peptides
// PRO61 -> DDDDGGGG, GGGGKKKK, KKKKNNNN = 3 additional peptides
// PRO62 -> AAAADDDD, KKKKNNNN = 0 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("AAAADDDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDGGGG@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("GGGGKKKK@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("KKKKNNNN@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// PRO63 -> BBBBEEEE, EEEEHHHH = 2 additional peptides
// PRO64 -> EEEEHHHH, HHHHLLLL = 0 additional peptides
// PRO65 -> HHHHLLLL, LLLLPPPP = 2 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBEEEE@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("EEEEHHHH@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHLLLL@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("LLLLPPPP@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// PRO66 -> CCCCFFFF, CFFFFI, FFFFIIII = 3 additional peptides
// PRO67 -> FFFFIIII, FIIIIM, IIIIMMMM = 1 additional peptides
// PRO68 -> IIIIMMMM, IMMMMQ, MMMMQQQQ = 3 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("CCCCFFFF@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("CFFFFI@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("FFFFIIII@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("FIIIIM@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("IIIIMMMM@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("IMMMMQ@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("MMMMQQQQ@{0}/1 AAAAAAAAAA@{0}/8", charge)),
// PRO69 -> NNNNRRRR, RRRRUUUU, RRRRUUU = 3 additional peptides
// PRO70 -> RRRRUUUU, RRRRUUU, UUUUZZZZ = 0 additional peptides
// PRO71 -> UUUUZZZZ, UZZZZC, ZZZZCCCC = 3 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("NNNNRRRR@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("RRRRUUUU@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("RRRRUUU@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("UUUUZZZZ@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("UZZZZC@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("ZZZZCCCC@{0}/1 BBBBBBBBBB@{0}/8", charge)),
};
TestModel.CreateTestData(session, testPsmSummary);
}
var dataFilter = new DataFilter()
{
MaximumQValue = 1,
MinimumDistinctPeptides = 0,
MinimumSpectra = 0,
MinimumAdditionalPeptides = 1
};
dataFilter.ApplyBasicFilters(session);
// clear session so objects are loaded from database
session.Clear();
var additionalPeptidesByProteinId = new Map<long, int>();
foreach (object[] row in session.CreateSQLQuery("SELECT ProteinId, AdditionalMatches FROM AdditionalMatches").List<object[]>())
additionalPeptidesByProteinId[Convert.ToInt64(row[0])] = Convert.ToInt32(row[1]);
// 1 protein to 1 peptide to 1 spectrum = 1 additional peptide
Assert.AreEqual(1, additionalPeptidesByProteinId[1]);
// 1 protein to 1 peptide to 2 spectra = 1 additional peptide
Assert.AreEqual(1, additionalPeptidesByProteinId[2]);
// 1 protein to 2 peptides to 1 spectrum (each) = 2 additional peptides
Assert.AreEqual(2, additionalPeptidesByProteinId[3]);
// 1 protein to 2 peptides to 2 spectra (each) = 2 additional peptides
Assert.AreEqual(2, additionalPeptidesByProteinId[4]);
// 2 proteins to 1 peptide to 1 spectrum = 1 additional peptide (ambiguous protein group)
Assert.AreEqual(1, additionalPeptidesByProteinId[5]);
Assert.AreEqual(1, additionalPeptidesByProteinId[6]);
// 2 proteins to 1 peptide to 2 spectra = 1 additional peptide (ambiguous protein group)
Assert.AreEqual(1, additionalPeptidesByProteinId[7]);
Assert.AreEqual(1, additionalPeptidesByProteinId[8]);
// 2 proteins to 2 peptides to 1 spectrum (each) = 2 additional peptides (ambiguous protein group)
Assert.AreEqual(2, additionalPeptidesByProteinId[9]);
Assert.AreEqual(2, additionalPeptidesByProteinId[10]);
// 2 proteins to 2 peptides to 2 spectra (each) = 2 additional peptides (ambiguous protein group)
Assert.AreEqual(2, additionalPeptidesByProteinId[11]);
Assert.AreEqual(2, additionalPeptidesByProteinId[12]);
// 1 protein to 2 peptides to 1 spectrum (each) = 2 additional peptide
// 1 protein to 1 of the above peptides = 0 additional peptides (subsumed protein)
// 1 protein to the other above peptide = 0 additional peptides (subsumed protein)
Assert.AreEqual(2, additionalPeptidesByProteinId[13]);
Assert.AreEqual(0, additionalPeptidesByProteinId[14]);
Assert.AreEqual(0, additionalPeptidesByProteinId[15]);
// 1 protein to 2 peptides to 1 spectrum (each) = 2 additional peptide
// 2 proteins to 1 of the above peptides = 0 additional peptides (subsumed ambiguous protein group)
Assert.AreEqual(2, additionalPeptidesByProteinId[16]);
Assert.AreEqual(0, additionalPeptidesByProteinId[17]);
Assert.AreEqual(0, additionalPeptidesByProteinId[18]);
// 2 proteins to 2 peptides to 1 spectrum (each) = 2 additional peptide (ambiguous protein group)
// 1 protein to 1 of the above peptides = 0 additional peptides (subsumed protein)
// 1 protein to the other above peptide = 0 additional peptides (subsumed protein)
Assert.AreEqual(2, additionalPeptidesByProteinId[19]);
Assert.AreEqual(2, additionalPeptidesByProteinId[20]);
Assert.AreEqual(0, additionalPeptidesByProteinId[21]);
Assert.AreEqual(0, additionalPeptidesByProteinId[22]);
// 2 proteins to 2 peptides to 1 spectrum (each) = 2 additional peptides (ambiguous protein group)
// 2 proteins to 1 of the above peptides = 0 additional peptides (subsumed ambiguous protein group)
Assert.AreEqual(2, additionalPeptidesByProteinId[23]);
Assert.AreEqual(2, additionalPeptidesByProteinId[24]);
Assert.AreEqual(0, additionalPeptidesByProteinId[25]);
Assert.AreEqual(0, additionalPeptidesByProteinId[26]);
// 1 protein to 3 peptides to 1 spectrum (each) = 3 additional peptides
// 1 protein to 1 of the above peptides and 1 extra peptide to 1 spectrum = 1 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[27]);
Assert.AreEqual(1, additionalPeptidesByProteinId[28]);
// 1 protein to 3 peptides to 1 spectrum (each) = 3 additional peptides
// 2 proteins to 1 of the above peptides and 1 extra peptide to 1 spectrum = 1 additional peptides (ambiguous protein group)
Assert.AreEqual(3, additionalPeptidesByProteinId[29]);
Assert.AreEqual(1, additionalPeptidesByProteinId[30]);
Assert.AreEqual(1, additionalPeptidesByProteinId[31]);
// 2 proteins to 3 peptides to 1 spectrum (each) = 3 additional peptides (ambiguous protein group)
// 1 protein to 1 of the above peptides and 1 extra peptide to 1 spectrum = 1 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[32]);
Assert.AreEqual(3, additionalPeptidesByProteinId[33]);
Assert.AreEqual(1, additionalPeptidesByProteinId[34]);
// 2 proteins to 3 peptides to 1 spectrum (each) = 3 additional peptides (ambiguous protein group)
// 2 proteins to 1 of the above peptides and 1 extra peptide to 1 spectrum = 1 additional peptides (ambiguous protein group)
Assert.AreEqual(3, additionalPeptidesByProteinId[35]);
Assert.AreEqual(3, additionalPeptidesByProteinId[36]);
Assert.AreEqual(1, additionalPeptidesByProteinId[37]);
Assert.AreEqual(1, additionalPeptidesByProteinId[38]);
// 1 protein (PRO39) to 5 peptides = 5 additional peptides
// 1 protein (PRO40) to 4 of the above peptides = 0 additional peptides
// 1 protein (PRO41) to 3 of the above peptides and 1 extra peptides = 1 additional peptides
// 1 protein (PRO42) to 2 of the above peptides and 2 extra peptides = 2 additional peptides
// 1 protein (PRO43) to 1 of the above peptides and 3 extra peptides = 3 additional peptides
Assert.AreEqual(5, additionalPeptidesByProteinId[39]);
Assert.AreEqual(0, additionalPeptidesByProteinId[40]);
Assert.AreEqual(1, additionalPeptidesByProteinId[41]);
Assert.AreEqual(2, additionalPeptidesByProteinId[42]);
Assert.AreEqual(3, additionalPeptidesByProteinId[43]);
// 1 protein (PRO44) to 3 peptides, 1 of which is evidenced by an ambiguous spectrum = 3 additional peptides
// 1 protein (PRO45) to 1 peptide evidenced by the ambiguous spectrum above and 1 extra peptide = 1 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[44]);
Assert.AreEqual(1, additionalPeptidesByProteinId[45]);
// 2 proteins (PRO46,47) to 3 peptides, 1 of which is evidenced by an ambiguous spectrum = 3 additional peptides
// 1 protein (PRO48) to 1 peptide evidenced by the ambiguous spectrum above and 1 extra peptide = 1 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[46]);
Assert.AreEqual(3, additionalPeptidesByProteinId[47]);
Assert.AreEqual(1, additionalPeptidesByProteinId[48]);
// 1 protein (PRO49) to 3 peptides, 1 of which is evidenced by an ambiguous spectrum = 3 additional peptides
// 2 proteins (PRO50,51) to 1 peptide evidenced by the ambiguous spectrum above and 1 extra peptide = 1 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[49]);
Assert.AreEqual(1, additionalPeptidesByProteinId[50]);
Assert.AreEqual(1, additionalPeptidesByProteinId[51]);
// 1 protein (PRO52) to 3 peptides, 2 of which are evidenced by ambiguous spectra = 3 additional peptides
// 1 protein (PRO53) to 1 peptide evidenced by an ambiguous spectrum above and 1 extra peptide = 1 additional peptides
// 1 protein (PRO54) to 1 peptide evidenced by the other ambiguous spectrum above and 1 extra peptide = 1 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[52]);
Assert.AreEqual(1, additionalPeptidesByProteinId[53]);
Assert.AreEqual(1, additionalPeptidesByProteinId[54]);
// PRO55 -> QQQQSSSS, SSSSUUUU = 2 additional peptides
// PRO56 -> UUUUYYYY, SSSSUUUU = 2 additional peptides
Assert.AreEqual(2, additionalPeptidesByProteinId[55]);
Assert.AreEqual(2, additionalPeptidesByProteinId[56]);
// PRO57 -> RRRRTTTT, WWWWZZZZ, TTTTWWWW = 3 additional peptides
// PRO58 -> QQQQKKKK, WWWWZZZZ, TTTTWWWW = 3 additional peptides
// PRO59 -> RRRRTTTT, TTTTZZZZ, TTTTWWWW = 3 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[57]);
Assert.AreEqual(3, additionalPeptidesByProteinId[58]);
Assert.AreEqual(3, additionalPeptidesByProteinId[59]);
// PRO60 -> AAAADDDD, DDDDGGGG, GGGGKKKK = 3 additional peptides
// PRO61 -> DDDDGGGG, GGGGKKKK, KKKKNNNN = 3 additional peptides
// PRO62 -> AAAADDDD, KKKKNNNN = 0 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[60]);
Assert.AreEqual(3, additionalPeptidesByProteinId[61]);
Assert.AreEqual(0, additionalPeptidesByProteinId[62]);
// PRO63 -> BBBBEEEE, EEEEHHHH = 2 additional peptides
// PRO64 -> EEEEHHHH, HHHHLLLL = 0 additional peptides
// PRO65 -> HHHHLLLL, LLLLPPPP = 2 additional peptides
Assert.AreEqual(2, additionalPeptidesByProteinId[63]);
Assert.AreEqual(0, additionalPeptidesByProteinId[64]);
Assert.AreEqual(2, additionalPeptidesByProteinId[65]);
// PRO66 -> CCCCFFFF, CFFFFI, FFFFIIII = 3 additional peptides
// PRO67 -> FFFFIIII, FIIIIM, IIIIMMMM = 1 additional peptides
// PRO68 -> IIIIMMMM, IMMMMQ, MMMMQQQQ = 3 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[66]);
Assert.AreEqual(1, additionalPeptidesByProteinId[67]);
Assert.AreEqual(3, additionalPeptidesByProteinId[68]);
// PRO69 -> NNNNRRRR, RRRRUUUU, RRRRUUU = 3 additional peptides
// PRO70 -> RRRRUUUU, RRRRUUU, UUUUZZZZ = 0 additional peptides
// PRO71 -> UUUUZZZZ, UZZZZC, ZZZZCCCC = 3 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[69]);
Assert.AreEqual(0, additionalPeptidesByProteinId[70]);
Assert.AreEqual(3, additionalPeptidesByProteinId[71]);
// test that the MinimumAdditionalPeptidesPerProtein filter is applied correctly;
// proteins filtered out by it should cascade to PeptideInstances, Peptides, and PSMs
dataFilter.MinimumAdditionalPeptides = 1;
dataFilter.ApplyBasicFilters(session);
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO55"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO56"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO57"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO58"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO59"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO60"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO61"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO62"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO62"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "AAAADDDD"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "KKKKNNNN"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO63"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO64"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO65"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO64"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "EEEEHHHH"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "HHHHLLLL"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO66"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO67"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO68"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO69"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO70"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO71"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO70"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "RRRRUUUU"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "RRRRUUU"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "UUUUZZZZ"));
dataFilter.MinimumAdditionalPeptides = 2;
dataFilter.ApplyBasicFilters(session);
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO55"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO56"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO57"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO58"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO59"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO60"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO61"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO62"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO62"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO63"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO64"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO65"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO64"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO66"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO67"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO68"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO67"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "FIIIIM"));
Assert.IsNull(session.UniqueResult<PeptideSpectrumMatch>(o => o.Peptide.Sequence == "FIIIIM"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO69"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO70"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO71"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO70"));
dataFilter.MinimumAdditionalPeptides = 3;
dataFilter.ApplyBasicFilters(session);
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO55"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO56"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO55"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO56"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "QQQQSSSS"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "SSSSUUUU"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "UUUUYYYY"));
Assert.IsNull(session.UniqueResult<PeptideSpectrumMatch>(o => o.Peptide.Sequence == "QQQQSSSS"));
Assert.IsNull(session.UniqueResult<PeptideSpectrumMatch>(o => o.Peptide.Sequence == "SSSSUUUU"));
Assert.IsNull(session.UniqueResult<PeptideSpectrumMatch>(o => o.Peptide.Sequence == "UUUUYYYY"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO57"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO58"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO59"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO60"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO61"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO62"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO62"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO63"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO64"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO65"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO63"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO64"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO65"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "BBBBEEEE"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "EEEEHHHH"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "HHHHLLLL"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "LLLLPPPP"));
Assert.IsNull(session.UniqueResult<PeptideSpectrumMatch>(o => o.Peptide.Sequence == "BBBBEEEE"));
Assert.IsNull(session.UniqueResult<PeptideSpectrumMatch>(o => o.Peptide.Sequence == "EEEEHHHH"));
Assert.IsNull(session.UniqueResult<PeptideSpectrumMatch>(o => o.Peptide.Sequence == "HHHHLLLL"));
Assert.IsNull(session.UniqueResult<PeptideSpectrumMatch>(o => o.Peptide.Sequence == "LLLLPPPP"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO66"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO67"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO68"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO67"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO69"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO70"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO71"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO70"));
dataFilter.MinimumAdditionalPeptides = 4;
dataFilter.ApplyBasicFilters(session);
Assert.AreEqual(1, session.Query<Protein>().Count());
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO39"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession != "PRO39"));
var remainingPeptides = new string[] { "BBBBBDDDDD", "BBBBDDDD", "BBBBDDD", "BBBDD", "BBDD" };
Assert.AreEqual(5, session.Query<Peptide>().Count());
Assert.AreEqual(5, session.Query<Peptide>().Count(o => remainingPeptides.Contains(o.Sequence)));
Assert.AreEqual(0, session.Query<Peptide>().Count(o => !remainingPeptides.Contains(o.Sequence)));
Assert.AreNotEqual(0, session.Query<PeptideSpectrumMatch>().Count(o => remainingPeptides.Contains(o.Peptide.Sequence)));
Assert.AreEqual(0, session.Query<PeptideSpectrumMatch>().Count(o => !remainingPeptides.Contains(o.Peptide.Sequence)));
dataFilter.MinimumAdditionalPeptides = 5;
dataFilter.ApplyBasicFilters(session);
Assert.AreEqual(1, session.Query<Protein>().Count());
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO39"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession != "PRO39"));
dataFilter.MinimumAdditionalPeptides = 6;
dataFilter.ApplyBasicFilters(session);
Assert.AreEqual(0, session.Query<Protein>().Count());
Assert.AreEqual(0, session.Query<PeptideInstance>().Count());
Assert.AreEqual(0, session.Query<Peptide>().Count());
Assert.AreEqual(0, session.Query<PeptideSpectrumMatch>().Count());
session.Close();
}
private SecondCache(NHibernate.ISessionFactory factory)
{
this._factory = factory;
}
public void TestFilteredQueries ()
{
// each protein in the test scenarios is created from simple repeating motifs
var testProteinSequences = new string[]
{
createSimpleProteinSequence("A", 20), // PRO1
createSimpleProteinSequence("B", 20),
createSimpleProteinSequence("C", 20),
createSimpleProteinSequence("D", 20),
createSimpleProteinSequence("E", 20), // PRO5
createSimpleProteinSequence("E", 21),
createSimpleProteinSequence("F", 20),
createSimpleProteinSequence("F", 21),
createSimpleProteinSequence("G", 20),
createSimpleProteinSequence("G", 21), // PRO10
createSimpleProteinSequence("H", 20),
createSimpleProteinSequence("H", 21),
createSimpleProteinSequence("AAAABBBBCCCC", 24),
createSimpleProteinSequence("AAAABBBB", 24),
createSimpleProteinSequence("BBBBCCCC", 24), // PRO15
createSimpleProteinSequence("BBBBBDDDDD", 20),
createSimpleProteinSequence("BBBBDDDD", 24),
createSimpleProteinSequence("ZBBBBDDD", 24),
createSimpleProteinSequence("YBBBDDD", 20),
createSimpleProteinSequence("WBBDD", 21), // PRO20
createSimpleProteinSequence("DDDDDFFFFF", 20),
createSimpleProteinSequence("FFFFFHHHHH", 20),
createSimpleProteinSequence("HHHHHKKKKK", 20),
createSimpleProteinSequence("HHHHHKKKKK", 30),
createSimpleProteinSequence("KKKKKMMMMM", 20), // PRO25
createSimpleProteinSequence("LLLLLNNNNN", 20),
createSimpleProteinSequence("NNNNNQQQQQ", 20),
createSimpleProteinSequence("NNNNNQQQQQ", 30),
createSimpleProteinSequence("MMMMMPPPPP", 20),
createSimpleProteinSequence("PPPPPRRRRR", 20), // PRO30
createSimpleProteinSequence("PPPPPRRRR", 24),
createSimpleProteinSequence("QQQQSSSSUUUU", 24),
createSimpleProteinSequence("SSSSUUUUYYYY", 24),
createSimpleProteinSequence("RRRRTTTTWWWWZZZZ", 32),
createSimpleProteinSequence("TTTTWWWWZZZZBBBB", 32), // PRO35
createSimpleProteinSequence("RRRRTTTTZZZZBBBBTTTTWWWW", 24),
createSimpleProteinSequence("AAAADDDDGGGGKKKK", 32),
createSimpleProteinSequence("DDDDGGGGKKKKNNNN", 32),
createSimpleProteinSequence("AAAADDDDKKKKNNNN", 32),
createSimpleProteinSequence("BBBBEEEEHHHH", 24), // PRO40
createSimpleProteinSequence("EEEEHHHHLLLL", 24),
createSimpleProteinSequence("HHHHLLLLPPPP", 24),
createSimpleProteinSequence("CCCCFFFFIIII", 24),
createSimpleProteinSequence("FFFFIIIIMMMM", 24),
createSimpleProteinSequence("IIIIMMMMQQQQ", 24), // PRO45
createSimpleProteinSequence("NNNNRRRRUUUU", 24),
createSimpleProteinSequence("RRRRUUUUZZZZ", 24),
createSimpleProteinSequence("UUUUZZZZCCCC", 24),
};
string idpDbName = System.Reflection.MethodInfo.GetCurrentMethod().Name + ".idpDB";
File.Delete(idpDbName);
var log = new StringWriter();
Console.SetOut(log);
sessionFactory = SessionFactoryFactory.CreateSessionFactory(idpDbName, new SessionFactoryConfig { CreateSchema = true, WriteSqlToConsoleOut = true});
var session = sessionFactory.OpenSession();
TestModel.CreateTestProteins(session, testProteinSequences);
const int analysisCount = 2;
const int sourceCount = 1;
const int chargeCount = 2;
int totalPSMs = 0;
for (int analysis = 1; analysis <= analysisCount; ++analysis)
for (int source = 1; source <= sourceCount; ++source)
for (int charge = 1; charge <= chargeCount; ++charge)
{
int scan = 0;
List<SpectrumTuple> testPsmSummary = new List<SpectrumTuple>()
{
// Columns: Group Source Spectrum Analysis Score Q List of Peptide@Charge/ScoreDivider
// 1 protein (PRO1) to 1 peptide to 1 spectrum = 1 additional peptide
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("AAAAAAAAAA@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO2) to 1 peptide to 2 spectra = 1 additional peptide
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBBBBBBB@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBBBBBBB@{0}/1 CCCCCCCCCC@{0}/8", charge)),
// 1 protein (PRO3) to 2 peptides to 1 spectrum (each) = 2 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("CCCCCCCCCC@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("CCCCCCCCC@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO4) to 2 peptides to 2 spectra (each) = 2 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDDDDDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDDDDDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDDDDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDDDDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins (PRO5,6) to 1 peptide to 1 spectrum = 1 additional peptide (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("EEEEEEEEEE@{0}/1 AAAAAAAAAA@{0}/8", charge)),
// 2 proteins (PRO7,8) to 1 peptide to 2 spectra = 1 additional peptide (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("FFFF[C1H2]FFFFFF@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("FFFFFFFFFF@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins (PRO9,10) to 2 peptides to 1 spectrum (each) = 2 additional peptides (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("GGGGGGGGGG@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("GGGGGGGGG@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins (PRO11,12) to 2 peptides to 2 spectra (each) = 2 additional peptides (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHH[O1]HHHHH@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHHH[O1]HHHH@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("[O1]HHHHHHHHH@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("[O1]HHHHHHHHH@{0}/1 BBBBBBBBBB@{0}/8", charge)),
};
totalPSMs += scan;
TestModel.CreateTestData(session, testPsmSummary);
}
var dataFilter = new DataFilter()
{
MaximumQValue = 1,
MinimumDistinctPeptides = 1,
MinimumSpectra = 1,
MinimumAdditionalPeptides = 1
};
dataFilter.ApplyBasicFilters(session);
// clear session so objects are loaded from database
session.Clear();
// test with default DistinctMatchFormat (charge state and modifications distinct)
{
var peptideRows = IDPicker.Forms.PeptideTableForm.DistinctPeptideRow.GetRows(session, dataFilter);
int row = 0;
Assert.AreEqual(12, peptideRows.Count);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "AAAAAAAAAA"), peptideRows[row].Peptide);
Assert.AreEqual(2, peptideRows[row].DistinctMatches);
Assert.AreEqual(1, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "BBBBBBBBBB"), peptideRows[row].Peptide);
Assert.AreEqual(2, peptideRows[row].DistinctMatches);
Assert.AreEqual(2, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "CCCCCCCCCC"), peptideRows[row].Peptide);
Assert.AreEqual(2, peptideRows[row].DistinctMatches);
Assert.AreEqual(1, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "CCCCCCCCC"), peptideRows[row].Peptide);
Assert.AreEqual(2, peptideRows[row].DistinctMatches);
Assert.AreEqual(1, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "DDDDDDDDDD"), peptideRows[row].Peptide);
Assert.AreEqual(2, peptideRows[row].DistinctMatches);
Assert.AreEqual(2, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "DDDDDDDDD"), peptideRows[row].Peptide);
Assert.AreEqual(2, peptideRows[row].DistinctMatches);
Assert.AreEqual(2, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "EEEEEEEEEE"), peptideRows[row].Peptide);
Assert.AreEqual(2, peptideRows[row].DistinctMatches);
Assert.AreEqual(1, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "FFFFFFFFFF"), peptideRows[row].Peptide);
Assert.AreEqual(4, peptideRows[row].DistinctMatches);
Assert.AreEqual(2, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "GGGGGGGGGG"), peptideRows[row].Peptide);
Assert.AreEqual(2, peptideRows[row].DistinctMatches);
Assert.AreEqual(1, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "GGGGGGGGG"), peptideRows[row].Peptide);
Assert.AreEqual(2, peptideRows[row].DistinctMatches);
Assert.AreEqual(1, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "HHHHHHHHHH"), peptideRows[row].Peptide);
Assert.AreEqual(4, peptideRows[row].DistinctMatches);
Assert.AreEqual(2, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "HHHHHHHHH"), peptideRows[row].Peptide);
Assert.AreEqual(2, peptideRows[row].DistinctMatches);
Assert.AreEqual(2, peptideRows[row++].Spectra);
}
// test with charge state and analysis indistinct and modifications distinct
{
dataFilter.DistinctMatchFormat.IsChargeDistinct = false;
dataFilter.DistinctMatchFormat.IsAnalysisDistinct = false;
dataFilter.ApplyBasicFilters(session);
var peptideRows = IDPicker.Forms.PeptideTableForm.DistinctPeptideRow.GetRows(session, dataFilter);
int row = 0;
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "AAAAAAAAAA"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(1, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "BBBBBBBBBB"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(2, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "CCCCCCCCCC"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(1, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "CCCCCCCCC"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(1, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "DDDDDDDDDD"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(2, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "DDDDDDDDD"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(2, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "EEEEEEEEEE"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(1, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "FFFFFFFFFF"), peptideRows[row].Peptide);
Assert.AreEqual(2, peptideRows[row].DistinctMatches);
Assert.AreEqual(2, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "GGGGGGGGGG"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(1, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "GGGGGGGGG"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(1, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "HHHHHHHHHH"), peptideRows[row].Peptide);
Assert.AreEqual(2, peptideRows[row].DistinctMatches);
Assert.AreEqual(2, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "HHHHHHHHH"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(2, peptideRows[row++].Spectra);
}
// test with charge state, analysis, and modifications indistinct
{
dataFilter.DistinctMatchFormat.IsChargeDistinct = false;
dataFilter.DistinctMatchFormat.IsAnalysisDistinct = false;
dataFilter.DistinctMatchFormat.AreModificationsDistinct = false;
dataFilter.ApplyBasicFilters(session);
var peptideRows = IDPicker.Forms.PeptideTableForm.DistinctPeptideRow.GetRows(session, dataFilter);
int row = 0;
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "AAAAAAAAAA"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(1, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "BBBBBBBBBB"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(2, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "CCCCCCCCCC"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(1, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "CCCCCCCCC"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(1, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "DDDDDDDDDD"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(2, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "DDDDDDDDD"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(2, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "EEEEEEEEEE"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(1, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "FFFFFFFFFF"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(2, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "GGGGGGGGGG"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(1, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "GGGGGGGGG"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(1, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "HHHHHHHHHH"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(2, peptideRows[row++].Spectra);
Assert.AreEqual(session.UniqueResult<Peptide>(o => o.Sequence == "HHHHHHHHH"), peptideRows[row].Peptide);
Assert.AreEqual(1, peptideRows[row].DistinctMatches);
Assert.AreEqual(2, peptideRows[row++].Spectra);
}
session.Close();
}
public UserRepository(NHibernate.ISessionFactory northwindWithSecurity, AuthorizationRepositoryFactory authorizationRepositoryFactory)
{
_authorizationRepositoryFactory = authorizationRepositoryFactory;
_northwindWithSecurity = northwindWithSecurity;
}
public void TestBasicFilters ()
{
string[] testProteinSequences = new string[]
{
"PEPTIDERPEPTIDEKPEPTIDE",
"DERPEPTIDEKPEPTIDE",
"TIDERPEPTIDEKPEP",
"ELVISKLIVESRTHANKYAVERYMUCH",
"ELVISISRCKNRLLKING",
"THEQUICKBRWNFXJUMPSVERTHELAZYDG",
};
string idpDbName = System.Reflection.MethodInfo.GetCurrentMethod().Name + ".idpDB";
File.Delete(idpDbName);
sessionFactory = SessionFactoryFactory.CreateSessionFactory(idpDbName, new SessionFactoryConfig { CreateSchema = true });
var session = sessionFactory.OpenSession();
TestModel.CreateTestProteins(session, testProteinSequences);
int numSources = 2;
int numAnalyses = 2;
for (int source = 1; source <= numSources; ++source)
for (int analysis = 1; analysis <= numAnalyses; ++analysis)
{
int scan = 0;
List<SpectrumTuple> testPsmSummary = new List<SpectrumTuple>()
{
// Group Score Q List of Peptide@Charge/ScoreDivider
// not enough passing peptides for DERPEPTIDEKPEPTIDE or TIDERPEPTIDEKPEP
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 2, "PEPTIDEK@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 2, "PEPTIDEK@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 2, "PEPTIDEK@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 2, "PEPTIDEK@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 2, "DERPEPTIDEK@1/1 PEPTIDER@1/2"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 2, "DERPEPTIDEK@1/1 PEPTIDER@1/2"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 2, "DERPEPTIDEK@1/1 PEPTIDER@1/2"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 2, "DERPEPTIDEK@1/1 PEPTIDER@1/2"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 2, "TIDER@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 2, "TIDER@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 2, "TIDER@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 2, "TIDER@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 1, "PEPTIDEK@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 1, "DERPEPTIDEK@1/1 PEPTIDER@1/2"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 1, "TIDER@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 1, "PEPTIDER@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 1, "PEPTIDER@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 1, "PEPTIDER@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 1, "PEPTIDER@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 1, "PEPTIDER@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "PEPTIDERPEPTIDEK@1/1 PEPTIDEK@1/2"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "PEPTIDERPEPTIDEK@1/1 PEPTIDEK@1/2"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "PEPTIDERPEPTIDEK@1/1 PEPTIDEK@1/2"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "PEPTIDERPEPTIDEK@1/1 PEPTIDEK@1/2"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "PEPTIDERPEPTIDEK@1/1 PEPTIDEK@1/2"),
// not enough distinct peptides for ELVISKLIVESRTHANKYAVERYMUCH
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "ELVISKLIVESR@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "ELVISKLIVESR@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "ELVISKLIVESR@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "ELVISKLIVESR@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "ELVISKLIVESR@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "ELVISKLIVESR@1/1"),
// not enough spectra for ELVISISRCKNRLLKING
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "ELVISISR@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "ELVISISR@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "ELVISISR@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "ELVISISR@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "ELVISISR@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "CKNRLLKING@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "CKNRLLKING@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "CKNRLLKING@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "CKNRLLKING@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "CKNRLLKING@1/1"),
// not enough spectra for distinct peptide THEQUICK
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "THEQUICK@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "THEQUICK@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "THEQU[H3C2N1O1]ICK@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "THEQU[H3C2N1O1]ICK@1/1"),
// not enough spectra for distinct matches THEQUICK@2 and THEQUICK@3
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "THEQUICK@2/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "THEQUICK@3/1"),
};
TestModel.CreateTestData(session, testPsmSummary);
}
// Spectral counts must be multiplied by numSources.
// Distinct Matches:
// PEPTIDEK(+1): 1 spectrum
// DERPEPTIDEK(+1): 1 spectrum
// TIDER(+1): 1 spectrum
// PEPTIDER(+1): 5 spectra
// PEPTIDERPEPTIDEK(+1): 5 spectra
// ELVISKLIVESR(+1): 6 spectra
// ELVISISR(+1): 5 spectra
// CKNRLLKING(+1): 5 spectra
// THEQUICK(+1): 2 spectra
// THEQUICK(+2): 1 spectrum
// THEQUICK(+3): 1 spectrum
// THEQU[H3C2N1O1]ICK(+1): 2 spectra
// Proteins:
// PEPTIDERPEPTIDEKPEPTIDE: 5 distinct peptides over 13 (passing) spectra
// DERPEPTIDEKPEPTIDE: 2 distinct peptides, 2 spectra
// TIDERPEPTIDEKPEP: 3 distinct peptides, 3 spectra
// ELVISKLIVESRTHANKYAVERYMUCH: 1 distinct peptide, 6 spectra
// ELVISISRCKNRLLKING: 2 distinct peptides, 10 spectra
// THEQUICKBRWNFXJUMPSVERTHELAZYDG: 1 distinct peptide, 6 spectra
var dataFilter = new DataFilter()
{
MaximumQValue = 1,
MinimumDistinctPeptides = 1,
MinimumSpectra = 1,
MinimumAdditionalPeptides = 0
};
dataFilter.ApplyBasicFilters(session);
// clear session so objects are loaded from database
session.Clear();
for (int sourceId = 1; sourceId <= numSources; ++sourceId)
for (int analysisId = 1; analysisId <= numAnalyses; ++analysisId)
{
string source = "Source " + sourceId.ToString();
string analysis = "Engine " + analysisId.ToString();
var sourceAnalysisPSMs = session.Query<PeptideSpectrumMatch>().Where(o => o.Analysis.Software.Name == analysis && o.Spectrum.Source.Name == source);
// test that PSMs with QValue > MaximumQValue are filtered out
Assert.AreEqual(0, sourceAnalysisPSMs.Count(o => o.QValue > 1));
}
// test that non-rank-1 PSMs are filtered out
Assert.AreEqual(0, session.Query<PeptideSpectrumMatch>().Where(o => o.Rank > 1).Count());
// test that nothing else is filtered out
Assert.AreEqual(6, session.Query<Protein>().Count());
Assert.AreEqual(9, session.Query<Peptide>().Count());
Assert.AreEqual(35 * (numSources + numAnalyses), session.Query<PeptideSpectrumMatch>().Count());
dataFilter.MinimumDistinctPeptides = 3;
dataFilter.MinimumSpectra = 1;
dataFilter.ApplyBasicFilters(session);
session.Clear();
// test that proteins without at least MinimumPeptidesPerProtein peptides are filtered out
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Sequence == "PEPTIDERPEPTIDEKPEPTIDE"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Sequence == "TIDERPEPTIDEKPEP"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Sequence == "DERPEPTIDEKPEPTIDE"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Sequence == "ELVISKLIVESRTHANKYAVERYMUCH"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Sequence == "ELVISISRCKNRLLKING"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Sequence == "THEQUICKBRWNFXJUMPSVERTHELAZYDG"));
// test that protein filters cascade to peptide instances
Assert.AreEqual(5, session.Query<PeptideInstance>().Count(o => o.Protein.Sequence == "PEPTIDERPEPTIDEKPEPTIDE"));
Assert.AreEqual(3, session.Query<PeptideInstance>().Count(o => o.Protein.Sequence == "TIDERPEPTIDEKPEP"));
Assert.AreEqual(0, session.Query<PeptideInstance>().Count(o => o.Protein.Sequence == "DERPEPTIDEKPEPTIDE"));
Assert.AreEqual(0, session.Query<PeptideInstance>().Count(o => o.Protein.Sequence == "ELVISKLIVESRTHANKYAVERYMUCH"));
Assert.AreEqual(0, session.Query<PeptideInstance>().Count(o => o.Protein.Sequence == "ELVISISRCKNRLLKING"));
Assert.AreEqual(0, session.Query<PeptideInstance>().Count(o => o.Protein.Sequence == "THEQUICKBRWNFXJUMPSVERTHELAZYDG"));
// test that protein filters cascade to peptides
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "PEPTIDEK"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "DERPEPTIDEK"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "TIDER"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "PEPTIDER"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "PEPTIDERPEPTIDEK"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "ELVISKLIVESR"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "ELVISISR"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "CKNRLLKING"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "THEQUICK"));
// test that protein filters cascade to PSMs
Assert.AreEqual(13 * (numSources + numAnalyses), session.Query<PeptideSpectrumMatch>().Count());
dataFilter.MinimumDistinctPeptides = 1;
dataFilter.MinimumSpectra = 4 * numSources;
dataFilter.ApplyBasicFilters(session);
session.Clear();
// test that proteins without at least MinimumSpectraPerProtein spectra are filtered out
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Sequence == "PEPTIDERPEPTIDEKPEPTIDE"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Sequence == "TIDERPEPTIDEKPEP"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Sequence == "DERPEPTIDEKPEPTIDE"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Sequence == "ELVISKLIVESRTHANKYAVERYMUCH"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Sequence == "ELVISISRCKNRLLKING"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Sequence == "THEQUICKBRWNFXJUMPSVERTHELAZYDG"));
dataFilter.MinimumDistinctPeptides = 1;
dataFilter.MinimumSpectra = 1;
dataFilter.MinimumSpectraPerDistinctMatch = 2 * numSources;
dataFilter.ApplyBasicFilters(session);
session.Clear();
// test that distinct matches without at least MinimumSpectraPerDistinctMatch spectra are filtered out
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "PEPTIDER"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "PEPTIDERPEPTIDEK"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "ELVISKLIVESR"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "ELVISISR"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "CKNRLLKING"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "THEQUICK"));
Assert.AreEqual(4 * (numSources + numAnalyses), session.Query<PeptideSpectrumMatch>().Count(o => o.Peptide.Sequence == "THEQUICK" && o.Charge == 1));
Assert.AreEqual(0, session.Query<PeptideSpectrumMatch>().Count(o => o.Charge == 2));
Assert.AreEqual(0, session.Query<PeptideSpectrumMatch>().Count(o => o.Charge == 3));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "PEPTIDEK"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "DERPEPTIDEK"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "TIDER"));
// test that peptide filters cascade to proteins
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Sequence == "ELVISKLIVESRTHANKYAVERYMUCH"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Sequence == "THEQUICKBRWNFXJUMPSVERTHELAZYDG"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Sequence == "PEPTIDERPEPTIDEKPEPTIDE"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Sequence == "ELVISISRCKNRLLKING"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Sequence == "TIDERPEPTIDEKPEP"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Sequence == "DERPEPTIDEKPEPTIDE"));
dataFilter.MinimumSpectraPerDistinctMatch = 1;
dataFilter.MinimumSpectraPerDistinctPeptide = 6 * numSources;
dataFilter.ApplyBasicFilters(session);
session.Clear();
// test that distinct peptides without at least MinimumSpectraPerDistinctPeptide spectra are filtered out
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "ELVISKLIVESR"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "THEQUICK"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "PEPTIDER"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "PEPTIDERPEPTIDEK"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "ELVISISR"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "CKNRLLKING"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "PEPTIDEK"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "DERPEPTIDEK"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "TIDER"));
// test that peptide filters cascade to proteins
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Sequence == "ELVISKLIVESRTHANKYAVERYMUCH"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Sequence == "THEQUICKBRWNFXJUMPSVERTHELAZYDG"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Sequence == "PEPTIDERPEPTIDEKPEPTIDE"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Sequence == "TIDERPEPTIDEKPEP"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Sequence == "DERPEPTIDEKPEPTIDE"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Sequence == "ELVISISRCKNRLLKING"));
// test that peptide filters cascade to peptide instances
Assert.AreEqual(1, session.Query<PeptideInstance>().Count(o => o.Protein.Sequence == "ELVISKLIVESRTHANKYAVERYMUCH"));
Assert.AreEqual(1, session.Query<PeptideInstance>().Count(o => o.Protein.Sequence == "THEQUICKBRWNFXJUMPSVERTHELAZYDG"));
Assert.AreEqual(0, session.Query<PeptideInstance>().Count(o => o.Protein.Sequence == "PEPTIDERPEPTIDEKPEPTIDE"));
Assert.AreEqual(0, session.Query<PeptideInstance>().Count(o => o.Protein.Sequence == "TIDERPEPTIDEKPEP"));
Assert.AreEqual(0, session.Query<PeptideInstance>().Count(o => o.Protein.Sequence == "DERPEPTIDEKPEPTIDE"));
Assert.AreEqual(0, session.Query<PeptideInstance>().Count(o => o.Protein.Sequence == "ELVISISRCKNRLLKING"));
dataFilter.MinimumSpectraPerDistinctMatch = 1;
dataFilter.MinimumSpectraPerDistinctPeptide = 1;
dataFilter.MaximumProteinGroupsPerPeptide = 1;
dataFilter.ApplyBasicFilters(session);
session.Clear();
// test that distinct peptides linking to more than MaximumProteinGroupsPerPeptide protein groups are filtered out
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "ELVISKLIVESR"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "THEQUICK"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "ELVISISR"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "CKNRLLKING"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "PEPTIDER"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "PEPTIDERPEPTIDEK"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "PEPTIDEK"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "DERPEPTIDEK"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "TIDER"));
// test that MaximumProteinGroupsPerPeptide filter cascades to proteins
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Sequence == "PEPTIDERPEPTIDEKPEPTIDE"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Sequence == "ELVISKLIVESRTHANKYAVERYMUCH"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Sequence == "ELVISISRCKNRLLKING"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Sequence == "THEQUICKBRWNFXJUMPSVERTHELAZYDG"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Sequence == "TIDERPEPTIDEKPEP"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Sequence == "DERPEPTIDEKPEPTIDE"));
session.Close();
}
public CustomerDemographicRepository(NHibernate.ISessionFactory northwind)
{
_northwind = northwind;
}
public EntityTypeRepository(NHibernate.ISessionFactory northwindWithSecurity)
{
_northwindWithSecurity = northwindWithSecurity;
}
/// <summary>
/// This method use a lock to syncronize the factory creation.
/// </summary>
private void CheckFactory()
{
if (mFactory != null) return;
lock (mSyncObj)
{
if (mFactory != null) return;
var configuration = CreateNHibernateConfiguration(ConfigurationFlags.Default);
mFactory = configuration.BuildSessionFactory();
}
}
public PermissionRepository(NHibernate.ISessionFactory northwindWithSecurity, PermissionsBuilderServiceFactory permissionBuilderServiceFactory, PermissionsServiceFactory permissionsServiceFactory)
{
_northwindWithSecurity = northwindWithSecurity;
_permissionBuilderServiceFactory = permissionBuilderServiceFactory;
_permissionsServiceFactory = permissionsServiceFactory;
}
public void TestCoverage ()
{
string[] testProteinSequences = new string[]
{
"PEPTIDERPEPTIDEKELVISPEPTIDE",
"DERPEPTIDEKELVISPEPTIDE",
"TIDERELVISPEPTIDEKPEP",
"ELVISKLIVESRTHANKYAVERYMUCH",
"ELVISISRCKNRLLKING",
};
string idpDbName = System.Reflection.MethodInfo.GetCurrentMethod().Name + ".idpDB";
File.Delete(idpDbName);
sessionFactory = SessionFactoryFactory.CreateSessionFactory(idpDbName, new SessionFactoryConfig { CreateSchema = true });
var session = sessionFactory.OpenSession();
TestModel.CreateTestProteins(session, testProteinSequences);
int numSources = 2;
int numAnalyses = 2;
for (int source = 1; source <= numSources; ++source)
for (int analysis = 1; analysis <= numAnalyses; ++analysis)
{
int scan = 0;
List<SpectrumTuple> testPsmSummary = new List<SpectrumTuple>()
{
// Group Score Q List of Peptide@Charge/ScoreDivider
// PEPTIDERPEPTIDEKELVISPEPTIDE
// ------- ------- ------- (PEPTIDE)
// -------- (PEPTIDER)
// ----- (TIDER)
// -------- (PEPTIDEK)
// ----------- (DERPEPTIDEK)
// ---------------- (PEPTIDERPEPTIDEK)
// 3334455444444443000001111111 (23/28 covered)
// DERPEPTIDEKELVISPEPTIDE
// ------- ------- (PEPTIDE)
// -------- (PEPTIDEK)
// ----------- (DERPEPTIDEK)
// 11133333332000001111111 (18/23 covered)
// TIDERELVISPEPTIDEKPEP
// ------- (PEPTIDE)
// -------- (PEPTIDEK)
// ----- (TIDER)
// 111110000022222221000 (13/21 covered)
new SpectrumTuple("/", source, ++scan, analysis, 42, 0, "PEPTIDE@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, 42, 0, "PEPTIDER@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, 42, 0, "PEPTIDERPEPTIDEK@1/1 PEPTIDEK@1/2"),
new SpectrumTuple("/", source, ++scan, analysis, 42, 0, "PEPTIDEK@1/1 TIDEK@1/2"),
new SpectrumTuple("/", source, ++scan, analysis, 42, 0, "DERPEPTIDEK@1/1 PEPTIDEKPEP@1/2"),
new SpectrumTuple("/", source, ++scan, analysis, 42, 0, "TIDER@1/1"),
// ELVISKLIVESRTHANKYAVERYMUCH
// ------------ (ELVISLIVESR)
// ------------ (E[N-1H-3]LVISLIVESR)
// 222222222222000000000000000 (12/27 covered)
new SpectrumTuple("/", source, ++scan, analysis, 42, 0, "ELVISKLIVESR@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, 42, 0, "E[N-1H-3]LVISKLIVESR@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, 42, 0, "ELVISKLIVESR@1/1"),
// ELVISISRCKNRLLKING
// -------- (ELVISISR)
// ------------ (ELVISISRCKNR)
// ---------- (CKNRLLKING)
// 222222222222111111 (18/18 covered)
new SpectrumTuple("/", source, ++scan, analysis, 42, 0, "ELVISISR@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, 42, 0, "ELVISISRCKNR@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, 42, 0, "CKNRLLKING@1/1"),
};
TestModel.CreateTestData(session, testPsmSummary);
}
var dataFilter = new DataFilter()
{
MaximumQValue = 1,
MinimumDistinctPeptides = 1,
MinimumSpectra = 1,
MinimumAdditionalPeptides = 0
};
dataFilter.ApplyBasicFilters(session);
// clear session so objects are loaded from database
session.Clear();
Protein pro;
const double epsilon = 1e-9;
// PEPTIDERPEPTIDEKELVISPEPTIDE
// 3334455444444443000001111111 (23/28 covered)
pro = session.UniqueResult<Protein>(o => o.Sequence == "PEPTIDERPEPTIDEKELVISPEPTIDE");
Assert.AreEqual(100 * 23.0 / 28, pro.Coverage, epsilon);
CollectionAssert.AreEqual(createProteinCoverageMask("3334455444444443000001111111"), pro.CoverageMask.ToArray());
// DERPEPTIDEKELVISPEPTIDE
// 11133333332000001111111 (18/23 covered)
pro = session.UniqueResult<Protein>(o => o.Sequence == "DERPEPTIDEKELVISPEPTIDE");
Assert.AreEqual(100 * 18.0 / 23, pro.Coverage, epsilon);
CollectionAssert.AreEqual(createProteinCoverageMask("11133333332000001111111"), pro.CoverageMask.ToArray());
// TIDERELVISPEPTIDEKPEP
// 111110000011111111000 (13/21 covered)
pro = session.UniqueResult<Protein>(o => o.Sequence == "TIDERELVISPEPTIDEKPEP");
Assert.AreEqual(100 * 13.0 / 21, pro.Coverage, epsilon);
CollectionAssert.AreEqual(createProteinCoverageMask("111110000022222221000"), pro.CoverageMask.ToArray());
// ELVISKLIVESRTHANKYAVERYMUCH
// 222222222222000000000000000 (12/27 covered)
pro = session.UniqueResult<Protein>(o => o.Sequence == "ELVISKLIVESRTHANKYAVERYMUCH");
Assert.AreEqual(100 * 12.0 / 27, pro.Coverage, epsilon);
// TODO: make modifications add depth to sequence coverage?
//CollectionAssert.AreEqual(createProteinCoverageMask("222222222222000000000000000"), pro.CoverageMask.ToArray());
// ELVISISRCKNRLLKING
// 222222222222111111 (18/18 covered)
pro = session.UniqueResult<Protein>(o => o.Sequence == "ELVISISRCKNRLLKING");
Assert.AreEqual(100 * 18 / 18, pro.Coverage, epsilon);
CollectionAssert.AreEqual(createProteinCoverageMask("222222222222111111"), pro.CoverageMask.ToArray());
}
public SystemController(NHibernate.ISessionFactory sessionFactory)
{
// TODO: Complete member initialization
this.sessionFactory = sessionFactory;
}
public OrderRepository(NHibernate.ISessionFactory northwind)
{
_northwind = northwind;
}
public void TestProteinGroups ()
{
string[] testProteinSequences = new string[]
{
"PEPTIDERPEPTIDEKPEPTIDE",
"DERPEPTIDEKPEPTIDE",
"TIDERPEPTIDEKPEP",
"ELVISKLIVESRTHANKYAVERYMUCH",
"ELVISISRCKNRLLKING",
};
string idpDbName = System.Reflection.MethodInfo.GetCurrentMethod().Name + ".idpDB";
File.Delete(idpDbName);
sessionFactory = SessionFactoryFactory.CreateSessionFactory(idpDbName, new SessionFactoryConfig { CreateSchema = true });
var session = sessionFactory.OpenSession();
TestModel.CreateTestProteins(session, testProteinSequences);
int numSources = 2;
int numAnalyses = 2;
for (int source = 1; source <= numSources; ++source)
for (int analysis = 1; analysis <= numAnalyses; ++analysis)
{
int scan = 0;
List<SpectrumTuple> testPsmSummary = new List<SpectrumTuple>()
{
// Group Score Q List of Peptide@Charge/ScoreDivider
// PEPTIDERPEPTIDEKPEPTIDE in protein group: DERPEPTIDEK,PEPTIDEK,PEPTIDERPEPTIDEK,TIDEK
// DERPEPTIDEKPEPTIDE in protein group: DERPEPTIDEK,PEPTIDEK,TIDEK
// TIDERPEPTIDEKPEP in protein group: DERPEPTIDEK,PEPTIDEK,TIDEK
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 2, "PEPTIDER@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 1, "PEPTIDEK@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 1, "PEPTIDERPEPTIDEK@1/1 PEPTIDEK@1/2"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 2, "PEPTIDERPEPTIDEK@1/1 PEPTIDEK@1/2"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 1, "DERPEPTIDEK@1/1 PEPTIDER@1/2"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 2, "TIDER@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 1, "TIDEK@1/1"),
// ELVISKLIVESRTHANKYAVERYMUCH in protein group: ELVIS,ELVISK,ELVISKLIVESR
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "ELVIS@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "ELVISK@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "ELVISKLIVESR@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 2, "LIVESR@1/1"),
// ELVISISRCKNRLLKING in protein group: CKNRLLKING,ELVIS,ELVISISR
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "ELVISISR@1/1"),
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "CKNRLLKING@1/1"),
};
TestModel.CreateTestData(session, testPsmSummary);
}
var dataFilter = new DataFilter()
{
MaximumQValue = 1,
MinimumDistinctPeptides = 2,
MinimumSpectra = 3 * numSources,
MinimumAdditionalPeptides = 0
};
dataFilter.ApplyBasicFilters(session);
// clear session so objects are loaded from database
session.Clear();
Assert.AreEqual(1, session.UniqueResult<Protein>(o => o.Sequence == "PEPTIDERPEPTIDEKPEPTIDE").ProteinGroup);
Assert.AreEqual(2, session.UniqueResult<Protein>(o => o.Sequence == "DERPEPTIDEKPEPTIDE").ProteinGroup);
Assert.AreEqual(2, session.UniqueResult<Protein>(o => o.Sequence == "TIDERPEPTIDEKPEP").ProteinGroup);
Assert.AreEqual(4, session.UniqueResult<Protein>(o => o.Sequence == "ELVISKLIVESRTHANKYAVERYMUCH").ProteinGroup);
Assert.AreEqual(3, session.UniqueResult<Protein>(o => o.Sequence == "ELVISISRCKNRLLKING").ProteinGroup);
Assert.AreEqual(2, session.Query<Protein>().Where(o => o.ProteinGroup == 2).Count());
session.Close();
}
public EmployeeRepository(NHibernate.ISessionFactory northwind)
{
_northwind = northwind;
}
public void TestAminoAcidOffsets ()
{
string[] testProteinSequences = new string[]
{
"PEPTIDERPEPTIDEKPEPTIDE",
"DERPEPTIDEKPEPTIDE",
"TIDERPEPTIDEKPEP",
"ELVISKLIVESRTHANKYAVERYMUCH",
"ELVISISRCKNRLLKING",
};
string idpDbName = System.Reflection.MethodInfo.GetCurrentMethod().Name + ".idpDB";
File.Delete(idpDbName);
sessionFactory = SessionFactoryFactory.CreateSessionFactory(idpDbName, new SessionFactoryConfig { CreateSchema = true });
var session = sessionFactory.OpenSession();
TestModel.CreateTestProteins(session, testProteinSequences);
int numSources = 2;
int numAnalyses = 2;
for (int source = 1; source <= numSources; ++source)
for (int analysis = 1; analysis <= numAnalyses; ++analysis)
{
int scan = 0;
List<SpectrumTuple> testPsmSummary = new List<SpectrumTuple>()
{
// Group Score Q List of Peptide@Charge/ScoreDivider
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "PEPTIDER@1/1"), // [0,7]
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "PEPTIDEK@1/1"), // [8,15] [5,12]
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "PEPTIDERPEPTIDEK@2/1"), // [0,15]
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "PEPTIDERPEPTIDEK@3/1"), // [0,15]
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "DERPEPTIDEK@1/1"), // [0,10] [5,14]
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "TIDER@1/1"), // [0,4] [3,7]
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "TIDEK@2/1"), // [6,10] [8,12] [10,14]
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "TIDEK@3/1"), // [6,10] [8,12] [10,14]
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "ELVIS@1/1"), // [0,4]
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "ELVISK@1/1"), // [0,5]
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "ELVISKLIVESR@1/1"), // [0,11]
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "LIVESR@1/1"), // [5,11]
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "ELVISISR@1/1"), // [0,7]
new SpectrumTuple("/", source, ++scan, analysis, scan*2, 0, "CKNRLLKING@1/1"), // [8,18]
};
TestModel.CreateTestData(session, testPsmSummary);
}
var dataFilter = new DataFilter() { MinimumAdditionalPeptides = 0 };
dataFilter.ApplyBasicFilters(session);
// clear session so objects are loaded from database
session.Clear();
// get all peptides at the protein N-terminus
dataFilter.AminoAcidOffset = new List<int> { 0 };
Assert.AreEqual(8, Convert.ToInt32(session.CreateQuery("SELECT COUNT(DISTINCT pi.Peptide) " + dataFilter.GetFilteredQueryString(DataFilter.FromProtein)).UniqueResult()));
// get all peptides of PEPTIDERPEPTIDEKPEPTIDE at the N-terminus
dataFilter.Protein = new List<Protein> { session.UniqueResult<Protein>(o => o.Sequence == "PEPTIDERPEPTIDEKPEPTIDE") };
Assert.AreEqual(2, Convert.ToInt32(session.CreateQuery("SELECT COUNT(DISTINCT pi.Peptide) " + dataFilter.GetFilteredQueryString(DataFilter.FromProtein)).UniqueResult()));
// get all peptides of PEPTIDERPEPTIDEKPEPTIDE that cover offset 8 (PEPTIDERPEPTIDEK, DERPEPTIDEK, PEPTIDEK)
dataFilter.AminoAcidOffset = new List<int> { 8 };
Assert.AreEqual(3, Convert.ToInt32(session.CreateQuery("SELECT COUNT(DISTINCT pi.Peptide) " + dataFilter.GetFilteredQueryString(DataFilter.FromProtein)).UniqueResult()));
// get all peptides of PEPTIDERPEPTIDEKPEPTIDE that cover offset 3 or 8 (PEPTIDER, PEPTIDERPEPTIDEK, DERPEPTIDEK, TIDER, PEPTIDEK)
dataFilter.AminoAcidOffset = new List<int> { 3, 8 };
Assert.AreEqual(5, Convert.ToInt32(session.CreateQuery("SELECT COUNT(DISTINCT pi.Peptide) " + dataFilter.GetFilteredQueryString(DataFilter.FromProtein)).UniqueResult()));
// get all peptides of PEPTIDERPEPTIDEKPEPTIDE at the C-terminus
dataFilter.AminoAcidOffset = new List<int> { Int32.MaxValue };
Assert.AreEqual(0, Convert.ToInt32(session.CreateQuery("SELECT COUNT(DISTINCT pi.Peptide) " + dataFilter.GetFilteredQueryString(DataFilter.FromProtein)).UniqueResult()));
// get all peptides at the protein C-terminus
dataFilter.Protein = null;
Assert.AreEqual(1, Convert.ToInt32(session.CreateQuery("SELECT COUNT(DISTINCT pi.Peptide) " + dataFilter.GetFilteredQueryString(DataFilter.FromProtein)).UniqueResult()));
// get all peptides at either protein terminus
dataFilter.AminoAcidOffset = new List<int> { 0, Int32.MaxValue };
Assert.AreEqual(9, Convert.ToInt32(session.CreateQuery("SELECT COUNT(DISTINCT pi.Peptide) " + dataFilter.GetFilteredQueryString(DataFilter.FromProtein)).UniqueResult()));
session.Close();
}
static Context()
{
log4net.Config.XmlConfigurator.Configure();
SessionFactory = new NHibernate.Cfg.Configuration().Configure().BuildSessionFactory();
}