/// <summary>
///
/// </summary>
/// <param name="isUpdate"></param>
/// <returns></returns>
private DataTable CreatePfamDnaRnaInteractTable(bool isUpdate)
{
string[] pfamDnaRnaCols = { "PdbID", "BuID", "ChainDomainID", "PfamID", "DnaRnaChain", "DnaRnaSymmetryString",
"AsymChain", "SymmetryString", "DnaRnaSeqID", "SeqID", "HmmSeqID" };
DataTable pfamDnaRnaTable = new DataTable("pfamDnaRnas");
foreach (string col in pfamDnaRnaCols)
{
pfamDnaRnaTable.Columns.Add(new DataColumn(col));
}
if (!isUpdate)
{
DbCreator dbCreate = new DbCreator();
string createTableString = "Create Table " + pfamDnaRnaTable.TableName + " ( " +
" PdbID CHAR(4) NOT NULL, " +
" BuID VARCHAR(8) NOT NULL, " +
" PfamID VARCHAR(40) NOT NULL, " +
" ChainDomainID INTEGER NOT NULL, " +
" DnaRnaChain CHAR(3) NOT NULL, " +
" DnaRnaSymmetryString VARCHAR(15), " +
" DnaRnaSeqID INTEGER NOT NULL, " +
" AsymChain CHAR(3) NOT NULL, " +
" SymmetryString VARCHAR(15), " +
" SeqID INTEGER NOT NULL, " +
" HmmSeqID INTEGER NOT NULL);";
dbCreate.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, pfamDnaRnaTable.TableName);
string createIndexString = "CREATE INDEX " + pfamDnaRnaTable.TableName + "_idx1 ON " + pfamDnaRnaTable.TableName + "(PdbID, ChainDomainID);";
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, pfamDnaRnaTable.TableName);
}
return(pfamDnaRnaTable);
}
/// <summary>
///
/// </summary>
private DataTable InitializeTable(bool isUpdate)
{
string[] pfamLigandColumns = { "PdbID", "AsymID", "ChainAsymID", "SeqID", "ChainSeqID", "Distance",
"Atom", "ChainAtom", "Residue", "ChainResidue" };
DataTable pfamLigandTable = new DataTable("ChainLigands");
foreach (string ligandCol in pfamLigandColumns)
{
pfamLigandTable.Columns.Add(new DataColumn(ligandCol));
}
if (!isUpdate)
{
DbCreator dbCreate = new DbCreator();
string createTableString = "Create Table " + pfamLigandTable.TableName + " (" +
" PdbID CHAR(4) NOT NULL, " +
" AsymID CHAR(3) NOT NULL, " +
// " Ligand CHAR(5) NOT NULL, " +
" ChainAsymID CHAR(3), " +
" SeqID INTEGER NOT NULL, " +
" ChainSeqID INTEGER NOT NULL, " +
" ATOM CHAR(4) NOT NULL, " +
" ChainATom CHAR(4), " +
" Residue CHAR(3), " +
" ChainResidue CHAR(3), " +
" Distance FLOAT" +
" );";
dbCreate.CreateTableFromString(ProtCidSettings.buCompConnection, createTableString, pfamLigandTable.TableName);
string createIndexString = "CREATE INDEX " + pfamLigandTable.TableName + "_idx1 ON " + pfamLigandTable.TableName + "(PdbID, AsymID)";
dbCreate.CreateIndex(ProtCidSettings.buCompConnection, createIndexString, pfamLigandTable.TableName);
}
return(pfamLigandTable);
}
private void InitializeDbTables()
{
DbCreator dbCreate = new DbCreator();
string createTableString = string.Format("CREATE Table {0} ( " +
" GroupSeqID INTEGER NOT NULL, " +
" SpaceGroup1 VARCHAR(30) NOT NULL, ASU1 VARCHAR(255) NOT NULL, PDBID1 CHAR(4) NOT NULL, " +
" NumOfInterfaces1 INTEGER NOT NULL, " +
" NumOfSgInterfaces1 INTEGER NOT NULL, NumOfSimInterfaces1 INTEGER NOT NULL, " +
" SpaceGroup2 VARCHAR(30) NOT NULL, ASU2 VARCHAR(255) NOT NULL, PDBID2 CHAR(4) NOT NULL, " +
" NumOfInterfaces2 INTEGER NOT NULL, " +
" NumOfSgInterfaces2 INTEGER NOT NULL, NumOfSimInterfaces2 INTEGER NOT NULL, " +
" MaxQ FLOAT NOT NULL, MinQ FLOAT NOT NULL, " +
" LeftMaxQ FLOAT NOT NULL, LeftMinQ FLOAT NOT NULL, Identity FLOAT NOT NULL, " +
" LeftMaxAsa1 FLOAT NOT NULL, LeftMaxAsa2 FLOAT NOT NULL);",
GroupDbTableNames.dbTableNames[GroupDbTableNames.ReduntCrystForms]);
dbCreate.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString,
GroupDbTableNames.dbTableNames[GroupDbTableNames.ReduntCrystForms]);
string indexString = string.Format("CREATE INDEX {0}_Idx1 ON {0} (PdbID1);",
GroupDbTableNames.dbTableNames[GroupDbTableNames.ReduntCrystForms]);
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, indexString,
GroupDbTableNames.dbTableNames[GroupDbTableNames.ReduntCrystForms]);
indexString = string.Format("CREATE INDEX {0}_Idx2 ON {0} (PdbID2);",
GroupDbTableNames.dbTableNames[GroupDbTableNames.ReduntCrystForms]);
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, indexString,
GroupDbTableNames.dbTableNames[GroupDbTableNames.ReduntCrystForms]);
}
private void InitializeDbTable()
{
DbCreator dbCreat = new DbCreator();
string createTableString = string.Format("CREATE TABLE {0} ( " +
" GroupSeqID INTEGER NOT NULL, " +
" CfGroupID INTEGER NOT NULL, " +
" PdbID CHAR(4) NOT NULL, " +
" SpaceGroup VARCHAR(30) NOT NULL, " +
" ASU VARCHAR(255) NOT NULL);",
GroupDbTableNames.dbTableNames[GroupDbTableNames.NonredundantCfGroups]);
dbCreat.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString,
GroupDbTableNames.dbTableNames[GroupDbTableNames.NonredundantCfGroups]);
string indexString = string.Format("Create Index {0}_pdb on {0} (PdbID);",
GroupDbTableNames.dbTableNames[GroupDbTableNames.NonredundantCfGroups]);
dbCreat.CreateIndex(ProtCidSettings.protcidDbConnection, indexString,
GroupDbTableNames.dbTableNames[GroupDbTableNames.NonredundantCfGroups]);
indexString = string.Format("Create Index {0}_groupcf on {0} (GroupSeqID, CfGroupID);",
GroupDbTableNames.dbTableNames[GroupDbTableNames.NonredundantCfGroups]);
dbCreat.CreateIndex(ProtCidSettings.protcidDbConnection, indexString,
GroupDbTableNames.dbTableNames[GroupDbTableNames.NonredundantCfGroups]);
}
/// <summary>
///
/// </summary>
/// <param name="isUpdate"></param>
private void CreateTables(bool isUpdate)
{
InitializeComHmmTable();
if (! isUpdate)
{
DbCreator dbCreate = new DbCreator ();
string dbCreateTableString = "Create Table " + tableName + " ( " +
"PfamID Varchar(40) Not Null, " +
"PdbID1 char(4) Not Null, " +
"ChainDomainID1 Integer Not Null, " +
"LigandChain1 char(3) Not Null, " +
"PdbID2 char(4) Not Null, " +
"ChainDomainID2 Integer Not Null, " +
"LigandChain2 char(3) Not Null, " +
"NumOfHmmSites1 Integer Not Null, " +
"NumOfHmmSites2 Integer Not Null, " +
"NumOfComHmmSites Integer Not Null, " +
"Jscore FLOAT Not Null);";
dbCreate.CreateTableFromString(ProtCidSettings.protcidDbConnection, dbCreateTableString, tableName);
string indexString = "Create Index PfamLigandComHmm_pfam on " + tableName + " (PfamID)";
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, indexString, tableName);
indexString = "Create Index PfamLigandComHmm_pdb on " + tableName + "(PdbID1, PdbID2)";
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, indexString, tableName);
indexString = "Create Index PfamLigandComHmm_pdb1 on " + tableName + "(PdbID1, ChainDomainID1)";
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, indexString, tableName);
indexString = "Create Index PfamLigandComHmm_pdb2 on " + tableName + "(PdbID2, ChainDomainID2)";
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, indexString, tableName);
}
}
/// <summary>
///
/// </summary>
/// <param name="isUpdate"></param>
/// <returns></returns>
private DataTable CreateTable(bool isUpdate)
{
string tableName = "PfamClansInPDB";
string[] clanColumns = { "ClanAcc", "NumPfams", "NumPfamsPdb", "NumPfamsPeptide", "NumPfamsDnaRna", "NumEntries", "NumUniprots" };
DataTable pfamClansPdbTable = new DataTable(tableName);
foreach (string col in clanColumns)
{
pfamClansPdbTable.Columns.Add(new DataColumn(col));
}
if (!isUpdate)
{
string createTableString = "Create Table " + tableName + " ( " +
" ClanAcc VARCHAR(10) NOT NULL, " +
" NumPfams Integer NOT NULL, " +
" NumPfamsPdb Integer NOT NULL, " +
" NumPfamsPeptide Integer NOT NULL, " +
" NumPfamsDnaRna Integer NOT NULL, " +
" NumEntries Integer NOT NULL, " +
" NumUniProts Integer NOT NULL " +
");";
DbCreator dbCreator = new DbCreator();
dbCreator.CreateTableFromString(ProtCidSettings.pdbfamDbConnection, createTableString, "PfamClansInPDB");
}
return(pfamClansPdbTable);
}
/// <summary>
/// Creates the database.
/// </summary>
public void CreateDatabase()
{
NotBusy = false;
Connecting(this, EventArgs.Empty);
DbCreator.Create(AsBuilder.ConnectionString, ConfigurationService.CurrentSchemaVersion);
NotBusy = true;
}
/// <summary>
/// Tests this instance.
/// </summary>
private void Test()
{
NotBusy = false;
Connecting(this, EventArgs.Empty);
DbCreator.Test(AsBuilder.ConnectionString);
NotBusy = true;
}
/// <summary>
///
/// </summary>
private void InitializeDbTables()
{
DbCreator dbCreate = new DbCreator();
if (dbCreate.IsTableExist(ProtCidSettings.protcidDbConnection, crystBuInterfaceCompTables[(int)BuType.PDB].TableName))
{
return;
}
string createTableString = string.Format("Create Table {0} ( " +
"PdbID CHAR(4) NOT NULL, InterfaceId INTEGER NOT NULL, " +
"BuID VARCHAR(8), BuInterfaceID INTEGER, QScore FLOAT);",
crystBuInterfaceCompTables[(int)BuType.PDB].TableName);
dbCreate.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, crystBuInterfaceCompTables[(int)BuType.PDB].TableName);
string indexString = string.Format("Create INDEX {0}_Idx1 " +
" ON {0} (PdbID, InterfaceID);", crystBuInterfaceCompTables[(int)BuType.PDB].TableName);
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, indexString, crystBuInterfaceCompTables[(int)BuType.PDB].TableName);
createTableString = string.Format("Create Table {0} ( " +
"PdbID CHAR(4) NOT NULL, InterfaceId INTEGER NOT NULL, " +
"BuID VARCHAR(8), BuInterfaceID INTEGER, QScore FLOAT);",
crystBuInterfaceCompTables[(int)BuType.PISA].TableName);
dbCreate.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, crystBuInterfaceCompTables[(int)BuType.PISA].TableName);
indexString = string.Format("Create INDEX {0}_Idx1 " +
" ON {0} (PdbID, InterfaceID);", crystBuInterfaceCompTables[(int)BuType.PISA].TableName);
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, indexString, crystBuInterfaceCompTables[(int)BuType.PISA].TableName);
}
public LoginViewModel()
{
db = new DbCreator();
db.CreateDbConnection();
LoginCommand = new RelayCommand(Login);
CloseCommand = new RelayCommand(Close);
}
/// <summary>
///
/// </summary>
/// <param name="isUpdate"></param>
private void CreateTables(bool isUpdate)
{
pfamLigandClusterTable = new DataTable(tableName);
string[] clusterCols = { "PfamID", "ClusterID", "PdbID", "ChainDomainID", "LigandChain", "LigandFileChain" };
foreach (string col in clusterCols)
{
pfamLigandClusterTable.Columns.Add(new DataColumn(col));
}
if (!isUpdate)
{
DbCreator dbCreate = new DbCreator();
string createTableString = "Create Table " + tableName + " ( " +
"PfamID varchar(40) NOT NULL, " +
"ClusterID Integer NOT NULL, " +
"PdbID char(4) Not Null, " +
"ChainDomainID Integer Not Null, " +
"LigandChain char(3) Not Null, " +
"LigandFileChain char(3) Not Null);";
dbCreate.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
string createIndexString = "Create Index " + tableName + "_cluster ON " + tableName + "(PfamID, ClusterID);";
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
createIndexString = "Create Index " + tableName + "_pdb ON " + tableName + "(PdbID, ChainDomainID);";
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
}
}
/// <summary>
///
/// </summary>
/// <param name="isUpdate"></param>
private void InitializeTables(bool isUpdate)
{
string tableName = "PdbPfamDomainFileInfo";
string[] tableCols = { "PdbID", "DomainID", "EntityID", "AsymChain", "SeqStart", "SeqEnd", "FileStart", "FileEnd" };
domainFileInfoTable = new DataTable(tableName);
foreach (string col in tableCols)
{
domainFileInfoTable.Columns.Add(new DataColumn(col));
}
if (!isUpdate)
{
DbCreator dbCreate = new DbCreator();
string createTableString = "CREATE TABLE " + tableName + " ( " +
"PdbID CHAR(4) NOT NULL, " +
"DomainID BIGINT NOT NULL, " +
"EntityID INTEGER NOT NULL, " +
"AsymChain CHAR(3) NOT NULL, " +
"SeqStart INTEGER NOT NULL, " +
"SeqEnd INTEGER NOT NULL, " +
"FileStart INTEGER NOT NULL, " +
"FileEnd INTEGER NOT NULL );";
dbCreate.CreateTableFromString(createTableString, tableName);
string createIndexString = "CREATE INDEX " + tableName + "_idx1 ON " + tableName + "(PdbID);";
dbCreate.CreateIndex(createIndexString, tableName);
createIndexString = "CREATE INDEX " + tableName + "_idx2 ON " + tableName + "(DomainID);";
dbCreate.CreateIndex(createIndexString, tableName);
}
}
/// <summary>
///
/// </summary>
/// <returns></returns>
private DataTable CreateTables(bool isUpdate)
{
DataTable pepInterfaceClusterStatTable = new DataTable("PfamPepClusterSumInfo");
string[] sumColumns = { "PfamID", "ClusterID", "NumEntries", "NumPepPfams", "NumUnpSeqs", "NumCFs",
"NumPepUnpSeqs", "NumPepSeqs", "SurfaceArea", "MinSeqIdentity", "ClusterInterface" };
foreach (string col in sumColumns)
{
pepInterfaceClusterStatTable.Columns.Add(new DataColumn(col));
}
if (!isUpdate)
{
DbCreator dbCreate = new DbCreator();
string createTableString = "Create Table " + pepInterfaceClusterStatTable.TableName + " ( " +
" PfamID VARCHAR(40) NOT NULL, " +
" ClusterID Integer Not NULL, " +
" NumEntries Integer NOT NULL, " +
" NumCFs Integer NOT NULL," +
" NumPepPfams Integer NOT NULL, " +
" NumUnpSeqs Integer NOT NULL, " +
" NumPepUnpSeqs Integer Not NULL, " +
" NumPepSeqs Integer Not NULL, " +
" SurfaceArea FLOAT, " +
" MinSeqIdentity FLOAT, " +
" ClusterInterface CHAR(10));";
dbCreate.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, pepInterfaceClusterStatTable.TableName);
}
return(pepInterfaceClusterStatTable);
}
/// <summary>
///
/// </summary>
private void InitializeResiduesContactsTables()
{
DbCreator dbCreator = new DbCreator();
string tableName = "SgInterfaceResidues";
string createTableString = "CREATE TABLE " + tableName + " ( " +
"PDBID CHAR(4) NOT NULL, " +
"INTERFACEID INTEGER NOT NULL, " +
"RESIDUE1 CHAR(3) NOT NULL, " +
"SEQID1 CHAR(5) NOT NULL, " +
"RESIDUE2 CHAR(3) NOT NULL, " +
"SEQID2 CHAR(5) NOT NULL, " +
"DISTANCE FLOAT NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
string createIdxString = string.Format("CREATE INDEX {0}_Idx1 ON {0} (PdbID, InterfaceID);", tableName);
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIdxString, tableName);
tableName = "SgInterfaceContacts";
createTableString = "CREATE TABLE " + tableName + " ( " +
"PDBID CHAR(4) NOT NULL, " +
"INTERFACEID INTEGER NOT NULL, " +
"RESIDUE1 CHAR(3) NOT NULL, " +
"SEQID1 CHAR(5) NOT NULL, " +
"RESIDUE2 CHAR(3) NOT NULL, " +
"SEQID2 CHAR(5) NOT NULL, " +
"DISTANCE FLOAT NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
createIdxString = string.Format("CREATE INDEX {0}_Idx1 ON {0} (PdbID, InterfaceID);", tableName);
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIdxString, tableName);
}
/// <summary>
///
/// </summary>
public static void InitializeGroupTable()
{
DbCreator dbCreator = new DbCreator();
string createTableString = "";
string createIndexString = "";
string tableName = ProtCidSettings.dataType + "HomoSeqInfo";
createTableString = "CREATE TABLE " + tableName + " ( " +
"GroupSeqID INTEGER NOT NULL, " +
"PdbID CHAR(4) NOT NULL, " +
"SpaceGroup VARCHAR(30) NOT NULL, " +
"ASU VARCHAR(50) NOT NULL, " +
"Method VARCHAR(100) NOT NULL, " +
"Resolution FLOAT NOT NULL, " +
"InPfam CHAR NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
createIndexString = string.Format("CREATE INDEX {0}_idx1 ON {0} (GroupSeqID);", tableName);
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
createIndexString = string.Format("CREATE INDEX {0}_idx2 ON {0} (PdbID);", tableName);
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
tableName = ProtCidSettings.dataType + "Groups";
createTableString = "CREATE TABLE " + tableName + " ( " +
"GroupSeqID INTEGER NOT NULL, " +
"EntryPfamArch BLOB Sub_Type TEXT NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
createIndexString = string.Format("CREATE INDEX {0}_idx1 ON {0} (GroupSeqID);", tableName);
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
}
public RegistViewModel()
{
db = new DbCreator();
db.CreateDbConnection();
RegistCommand = new RelayCommand(Regist);
CloseCommand = new RelayCommand(Close);
}
/// <summary>
///
/// </summary>
public static void InitializeDomainDbTables()
{
DbCreator dbCreator = new DbCreator();
string tableName = "";
string createTableString = "";
string createIndexString = "";
#region domain interfaces data
foreach (string buType in BuCompBuilder.buTypes)
{
if (buType == "asu")
{
tableName = buType + "PfamDomainInterfaces";
}
else
{
tableName = buType + "PfamBuDomainInterfaces";
}
createTableString = "CREATE TABLE " + tableName + " ( " +
"RelSeqID INTEGER NOT NULL, " +
"PdbID CHAR(4) NOT NULL, " +
"BUID VARCHAR(8) NOT NULL, " +
"InterfaceID INTEGER NOT NULL, " +
"DomainInterfaceID INTEGER NOT NULL, " +
"DomainID1 INTEGER NOT NULL, " +
"DomainID2 INTEGER NOT NULL, " +
"IsReversed CHAR(1) NOT NULL );";
dbCreator.CreateTableFromString(ProtCidSettings.buCompConnection, createTableString, tableName);
createIndexString = string.Format("CREATE INDEX {0}_Idx1 ON {0} (PdbID, BuID);", tableName);
dbCreator.CreateIndex(ProtCidSettings.buCompConnection, createIndexString, tableName);
if (buType == "asu")
{
tableName = "AsuIntraDomainInterfaces";
createTableString = "CREATE TABLE AsuIntraDomainInterfaces ( " +
"RelSeqID INTEGER NOT NULL, " +
"PdbID CHAR(4) NOT NULL, " +
"AsymChain CHAR(3) NOT NULL, " +
"DomainInterfaceID INTEGER NOT NULL, " +
"DomainID1 INTEGER NOT NULL, " +
"DomainID2 INTEGER NOT NULL, " +
"IsReversed CHAR(1) NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.buCompConnection, createTableString, tableName);
createIndexString = string.Format("CREATE INDEX AsuIntraDInterfaces_Idx1 ON {0} (PdbID, AsymChain);", tableName);
dbCreator.CreateIndex(ProtCidSettings.buCompConnection, createIndexString, tableName);
}
}
tableName = "PfamRelations";
createTableString = "CREATE TABLE " + tableName + " ( " +
"RelSeqID INTEGER NOT NULL, " +
"FamilyCode1 VARCHAR(15) NOT NULL, " +
"FamilyCode2 VARCHAR(15) NOT NULL );";
dbCreator.CreateTableFromString(ProtCidSettings.buCompConnection, createTableString, tableName);
createIndexString = string.Format("CREATE INDEX {0}_Idx1 ON {0} (RelSeqID);", tableName);
dbCreator.CreateIndex(ProtCidSettings.buCompConnection, createIndexString, tableName);
#endregion
}
protected override void OnStartup(StartupEventArgs e)
{
base.OnStartup(e);
MainWindow mv = new MainWindow();
this.MainWindow = mv;
this.ShutdownMode = ShutdownMode.OnMainWindowClose;
// 检测是否具备弹出登录窗口的条件
DbCreator db = new DbCreator();
db.CreateDbConnection();
bool isLogin = db.Init();
if (!isLogin)
{
RegistView registView = new RegistView();
bool? result = registView.ShowDialog();
// 如果注册成功，显示登录界面
if (result == true)
{
LoginView lw = new LoginView();
bool? ret = lw.ShowDialog();
string key = lw.PasswordBox.Password;
if (ret.Value == true)
{
mv = new MainWindow(true, key);
this.MainWindow = mv;
MainWindow.ShowDialog();
}
} // 若用户关闭注册窗口，则退出进程
else
{
MainWindow.Close();
}
}
else
{
LoginView loginView = new LoginView();
bool? resultLogin = loginView.ShowDialog();
string key = loginView.PasswordBox.Password;
// 登录成功，进入主界面
if (resultLogin.Value == true)
{
mv = new MainWindow(true, key);
this.MainWindow = mv;
MainWindow.ShowDialog();
} // 否则，退出进程
else
{
// 需要一个确认退出提示
MainWindow.Close();
}
}
}
public static void Executar()
{
var sqlConnection = DbCreator.Database(Database.SqlServer) // Retorna um Creator Concreto
.CreateConnector("minha connectionString") //Factory Method que retorna um produto concreto
.Connect();
var oracleConnection = DbCreator.Database(Database.Oracle) // Retorna um Creator Concreto
.CreateConnector("minha connectionString") //Factory Method que retorna um produto concreto
.Connect();
}
/// <summary>
///
/// </summary>
private void CreatProtBudBuTableInDb()
{
string[] buColumns = buQuery.BuTableColumns;
string createTableString = "Create Table " + buTableName + "( ";
string lowerCaseBuCol = "";
foreach (string buCol in buColumns)
{
lowerCaseBuCol = buCol.ToLower();
if (lowerCaseBuCol == "pdbid")
{
createTableString += "PdbID CHAR(4) NOT NULL, ";
}
else if (lowerCaseBuCol.IndexOf("buid") > -1)
{
createTableString += (buCol + " VARCHAR(10), ");
}
else if (lowerCaseBuCol.IndexOf("_entity") > -1 ||
lowerCaseBuCol.IndexOf("_asymid") > -1 ||
lowerCaseBuCol.IndexOf("_auth") > -1 ||
lowerCaseBuCol.IndexOf("_abc") > -1)
{
createTableString += (buCol + " BLOB SUB_TYPE TEXT NOT NULL, ");
}
else if (lowerCaseBuCol == "samebus")
{
createTableString += (buCol + " CHAR(9), ");
}
else if (lowerCaseBuCol == "dna" || lowerCaseBuCol == "rna" || lowerCaseBuCol == "ligands")
{
createTableString += (buCol + " CHAR(3), ");
}
else if (lowerCaseBuCol == "resolution")
{
createTableString += (buCol + " VARCHAR(32), ");
}
else if (lowerCaseBuCol == "names")
{
createTableString += (buCol + " BLOB SUB_TYPE TEXT NOT NULL, ");
}
}
createTableString = createTableString.TrimEnd(", ".ToCharArray());
createTableString += ");";
DbCreator dbCreat = new DbCreator();
dbCreat.CreateTableFromString(ProtCidSettings.pdbfamDbConnection, createTableString, buTableName);
string createIndexString = "Create Index " + buTableName + "_idx1 ON " + buTableName +
" ( PdbID, PdbBuID, PisaBuID);";
dbCreat.CreateIndex(ProtCidSettings.pdbfamDbConnection, createIndexString, buTableName);
}
/// <summary>
///
/// </summary>
/// <param name="isUpdate"></param>
/// <returns></returns>
public DataTable CreateHHAlignmentTable(bool isUpdate, string tableName)
{
string[] hhrAlignColumns = { "HitNo", "Query", "Hit", "QueryLength", "HitLength", "AlignLength",
"Identity", "Evalue", "PValue", "Score", "Similarity", "Prob",
"Sum_Probs", "QueryStart", "QueryEnd", "HitStart", "HitEnd",
"QueryAlignment", "HitAlignment" /*, "QueryConsensus", "HitConsensus",
* "QueryDssp", "HitDssp", "Confidence", "Match"*/};
DataTable pfamHHalignTable = new DataTable(tableName);
foreach (string hhCol in hhrAlignColumns)
{
pfamHHalignTable.Columns.Add(new DataColumn(hhCol));
}
if (!isUpdate)
{
DbCreator dbCreate = new DbCreator();
string createIndexString = "";
string createTableString = "CREATE TABLE " + tableName + " ( " +
"HitNO INTEGER NOT NULL, " +
"Query VARCHAR(32) NOT NULL," +
"Hit VARCHAR(32) NOT NULL, " +
"QueryLength INTEGER, " +
"HitLength INTEGER, " +
"AlignLength INTEGER, " +
"Identity FLOAT, " +
"EValue DOUBLE PRECISION, " +
"PValue DOUBLE PRECISION, " +
"Score DOUBLE PRECISION, " +
"Similarity FLOAT, " +
"Prob FLOAT, " +
"Sum_Probs FLOAT, " +
"QueryStart INTEGER, " + // for the input sequence
"QueryEnd INTEGER, " +
"HitStart INTEGER, " +
"HitEnd INTEGER, " +
"QueryAlignment BLOB Sub_Type 1, " +
"HitAlignment BLOB Sub_Type 1);";
/* "QueryConsensus BLOB Sub_Type 1, " +
* "HitConsensus BLOB Sub_Type 1, " +
* "QueryDssp BLOB Sub_Type 1, " +
* "HitDssp BLOB Sub_Type 1, " +
* "Confidence BLOB Sub_Type 1, " +
* "Match BLOB Sub_Type 1);"; */
dbCreate.CreateTableFromString(ProtCidSettings.alignmentDbConnection, createTableString, tableName);
createIndexString = "CREATE Index " + tableName + "_query ON " + tableName + "(Query)";
dbCreate.CreateIndex(ProtCidSettings.alignmentDbConnection, createIndexString, tableName);
createIndexString = "CREATE Index " + tableName + "_hit ON " + tableName + "(Hit)";
}
return(pfamHHalignTable);
}
public void TestWrite()
{
Connector.Add <MySqlConnection>(
"unit",
"database=Read",
"database=Write"
);
DbCreator creator = Connector.WriteInitor("unit");
Assert.NotNull(creator);
Assert.Equal("database=Write", creator().ConnectionString);
}
// Delete the database if the user confirms
public void DeleteDatabase()
{
NotBusy = false;
if (MessageBox.Show(
string.Format("Are you sure you want to delete database '{0}' on server: {1}?", AsBuilder.InitialCatalog, AsBuilder.DataSource),
"Delete SQL Server Database?",
MessageBoxButton.YesNo,
MessageBoxImage.Question) == MessageBoxResult.Yes)
{
Connecting(this, EventArgs.Empty);
DbCreator.Delete(AsBuilder.ConnectionString);
}
NotBusy = true;
}
/// <summary>
/// 泛型类型Emit初始化动态函数
/// </summary>
/// <param name="type">传入的数据库实例类型</param>
/// <param name="connection">传入的连接字符串</param>
/// <returns></returns>
internal static DbCreator DynamicCreateor(Type type, string connection)
{
DynamicMethod method = new DynamicMethod("Db" + Guid.NewGuid().ToString(), type, new Type[0]);
ILGenerator il = method.GetILGenerator();
#if NETSTANDARD1_3
ConstructorInfo ctor = info.DeclaringType.GetConstructor(null);
#else
ConstructorInfo ctor = type.GetConstructor(BindingFlags.Instance | BindingFlags.Public | BindingFlags.NonPublic, null, new Type[] { typeof(string) }, null);
#endif
il.Emit(OpCodes.Ldstr, connection);
il.Emit(OpCodes.Newobj, ctor);
il.Emit(OpCodes.Ret);
DbCreator function = (DbCreator)(method.CreateDelegate(typeof(DbCreator)));
return(function);
}
/// <summary>
///
/// </summary>
/// <param name="dataType"></param>
private void CreateDbRefTablesInDb(string dataType)
{
string createTableString = "";
string createIndexString = "";
DbCreator dbCreator = new DbCreator();
if (dataType == "sws")
{
createTableString = "CREATE TABLE " + dbRefTable.TableName + " ( " +
" PdbID CHAR(4) NOT NULL, " +
" RefID INTEGER NOT NULL, " +
" EntityID INTEGER NOT NULL, " +
// " AuthorChain CHAR(3) NOT NULL, " +
" DbAccession VARCHAR(15) NOT NULL, " +
" PRIMARY KEY (PdbID, RefID));";
}
else
{
createTableString = "CREATE TABLE " + dbRefTable.TableName + " ( " +
" PdbID CHAR(4) NOT NULL, " +
" RefID INTEGER NOT NULL, " +
" EntityID INTEGER NOT NULL, " +
// " AuthorChain CHAR(3) NOT NULL, " +
" DbAccession VARCHAR(15) NOT NULL, " +
" Isoform INTEGER NOT NULL, " +
" PRIMARY KEY (PdbID, RefID));";
}
dbCreator.CreateTableFromString(createTableString, dbRefTable.TableName);
createIndexString = "CREATE INDEX " + dbRefTable.TableName + "_idx1 ON " + dbRefTable.TableName + "(PdbID, EntityID);";
dbCreator.CreateIndex(createIndexString, dbRefTable.TableName);
createTableString = "CREATE TABLE" + dbRefSeqTable.TableName + " ( " +
" AlignID INTEGER NOT NULL, " +
" PdbID CHAR(4) NOT NULL, " +
" RefID INTEGER NOT NULL, " +
" AuthorChain CHAR(3) NOT NULL, " +
" DbAlignBeg INTEGER NOT NULL, " +
" DbAlignEnd INTEGER NOT NULL, " +
" AuthorAlignBeg INTEGER NOT NULL, " +
" AuthorAlignEnd INTEGER NOT NULL, " +
" SeqAlignBeg INTEGER NOT NULL, " +
" SeqAlignEnd INTEGER NOT NULL, " +
" PRIMARY KEY (PdbID, AlignID));";
dbCreator.CreateTableFromString(createTableString, dbRefSeqTable.TableName);
createIndexString = "CREATE INDEX " + dbRefSeqTable.TableName + "_idx1 ON " + dbRefSeqTable.TableName + "(PdbID, RefID);";
dbCreator.CreateIndex(createIndexString, dbRefSeqTable.TableName);
}
public void InitializeStatInfoTable(string type)
{
string[] statInfoCols = { "Category", "Single", "Pair", "Total" };
dbStatInfoTable = new DataTable(type + "StatInfo");
foreach (string statInfoCol in statInfoCols)
{
dbStatInfoTable.Columns.Add(new DataColumn(statInfoCol));
}
DbCreator dbCreate = new DbCreator();
string createTableString = "Create Table " + type + "StatInfo ( " +
" Category VARCHAR(30) NOT NULL, " +
" Single Integer NOT NULL, " +
" Pair Integer NOT NULL, " +
" Total Integer NOT NULL );";
dbCreate.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, type + "StatInfo");
}
/// <summary>
///
/// </summary>
/// <param name="isUpdate"></param>
private void CreateDbTable(bool isUpdate)
{
if (!isUpdate)
{
DbCreator dbCreate = new DbCreator();
string createTableString = "Create Table " + tableName + " ( " +
"PfamID varchar(40) NOT NULL, " +
"ClusterID Integer NOT NULL, " +
"PdbID char(4) Not Null, " +
"ChainDomainID Integer Not Null, " +
"LigandChain char(3) Not Null);";
dbCreate.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
string createIndexString = "Create Index " + tableName + "_cluster ON " + tableName + "(PfamID, ClusterID);";
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
createIndexString = "Create Index " + tableName + "_pdb ON " + tableName + "(PdbID, ChainDomainID);";
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
}
}
/// <summary>
///
/// </summary>
private void InitializeDbTable()
{
DbCreator dbCreator = new DbCreator();
if (!dbCreator.IsTableExist(ProtCidSettings.buCompConnection, domainInterfaceCompTable.TableName))
{
string createTableString = "CREATE TABLE " + domainInterfaceCompTable.TableName + " ( " +
"RelSeqID INTEGER NOT NULL, " +
"PdbID1 VARCHAR(4) NOT NULL, " +
"PdbID2 VARCHAR(4) NOT NULL, " +
"BuID1 VARCHAR(8) NOT NULL, " +
"BuID2 VARCHAR(8) NOT NULL, " +
"DomainInterfaceID1 INTEGER NOT NULL, " +
"DomainInterfaceID2 INTEGER NOT NULL, " +
"Qscore FLOAT NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.buCompConnection, createTableString, domainInterfaceCompTable.TableName);
}
}
static void Main(string[] args)
{
log.Info("Connection string : " + connectionString);
Console.WriteLine("Database Type : " + dbtype);
Console.WriteLine("Sleep Time : " + sleepTime);
Console.WriteLine("Service Host : " + predictionServiceHost + ":" + predictionServicePort);
Console.WriteLine(" ");
int sleep = 2000;
int.TryParse(sleepTime, out sleep);
Database dbStuff = new Database(DbCreator.Create(dbtype));
int cnt = 0;
int maxWait = 10;
while (true)
{
try
{
dbStuff.Connect(connectionString);
break;
}
catch (Exception e)
{
log.Error(e);
log.Warn("Cannot connect to DB... retrying in 10 seconds");
if (cnt++ < maxWait)
{
System.Threading.Thread.Sleep(10000);
}
else
{
break;
}
}
}
var gen = new PredictionsGenerator(dbStuff, mode, predictionServiceHost + ":" + predictionServicePort);
gen.Go();
}
// This method gets called by the runtime. Use this method to configure the HTTP request pipeline.
public void Configure(IApplicationBuilder app, IWebHostEnvironment env)
{
if (env.IsDevelopment())
{
app.UseDeveloperExceptionPage();
}
app.UseHttpsRedirection();
app.UseRouting();
app.UseAuthorization();
app.UseEndpoints(endpoints =>
{
endpoints.MapControllers();
});
DbCreator.CreateDb(app);
}