예제 #1
0
        /// <summary>
        ///
        /// </summary>
        /// <param name="pfamId"></param>
        private void DeleteObsoleteClusterData(string pfamId, List <string> updateEntryList)
        {
            string deleteString = string.Format("Delete From {0} Where PfamID = '{1}' AND PdbID In ({2});",
                                                tableName, pfamId, ParseHelper.FormatSqlListString(updateEntryList.ToArray()));

            dbUpdate.Delete(ProtCidSettings.protcidDbConnection, deleteString);
        }
예제 #2
0
 /// <summary>
 /// 
 /// </summary>
 /// <param name="updateEntries"></param>
 private void DeleteObsoleteData(string[] updateEntries)
 {
     string deleteString = "";
     for (int i = 0; i < updateEntries.Length; i += 300)
     {
         string[] subEntries = ParseHelper.GetSubArray(updateEntries, i, 300);
         deleteString = string.Format("Delete From {0} Where PdbID1 IN ({1}) OR PdbID2 IN ({1});", tableName, ParseHelper.FormatSqlListString (subEntries));
         dbUpdate.Delete(ProtCidSettings.protcidDbConnection, deleteString);
     }
 }
예제 #3
0
        /// <summary>
        ///
        /// </summary>
        /// <param name="obsoleteCrcCodes"></param>
        public void DeleteHHalignments(string[] obsoleteCrcCodes)
        {
            string deleteString = "";

            foreach (string crc in obsoleteCrcCodes)
            {
                deleteString = string.Format("Delete From hhglobal Where crc1 = '{0}' OR crc2 = '{0}';", crc);
                dbUpdate.Delete(localMysqlDbConnect, deleteString);
            }
        }
예제 #4
0
        /// <summary>
        /// /
        /// </summary>
        /// <param name="groupId"></param>
        /// <param name="repEntries"></param>
        private void DeleteOrigHomoEntriesNowRepEntries(int groupId, string[] repEntries)
        {
            string        queryString     = string.Format("Select Distinct PdbID2 From {0} Where GroupSeqID = {1};", HomoGroupTables.homoGroupTables[HomoGroupTables.HomoRepEntryAlign].TableName, groupId);
            DataTable     homoEntryTable  = ProtCidSettings.protcidQuery.Query(queryString);
            string        pdbId           = "";
            string        deleteString    = "";
            List <string> nowRepEntryList = new List <string>();

            foreach (DataRow homoEntryRow in homoEntryTable.Rows)
            {
                pdbId = homoEntryRow["PdbID2"].ToString();
                if (Array.IndexOf(repEntries, pdbId) > -1)
                {
                    nowRepEntryList.Add(pdbId);
                    deleteString = string.Format("Delete From {0} WHere PdbID2 = '{1}';", HomoGroupTables.homoGroupTables[HomoGroupTables.HomoRepEntryAlign].TableName, pdbId);
                    dbUpdate.Delete(ProtCidSettings.protcidDbConnection, deleteString);
                }
            }
        }
예제 #5
0
        /// <summary>
        ///
        /// </summary>
        /// <param name="updateEntries"></param>
        private void DeletePdbCrcRecords(string[] delEntries)
        {
            string   deleteString = "";
            DbUpdate dbDelete     = new DbUpdate();

            foreach (string pdbId in delEntries)
            {
                deleteString = string.Format("Delete From pdbcrcmap Where pdb = '{0}';", pdbId);
                dbDelete.Delete(localMysqlDbConnect, deleteString);
            }
        }
예제 #6
0
        /// <summary>
        ///
        /// </summary>
        public void RemoveObsoleteData()
        {
            StreamReader  lsFileReader = new StreamReader(@"D:\DbProjectData\PDB\newls-pdb.txt");
            string        line         = "";
            List <string> entryList    = new List <string> ();

            while ((line = lsFileReader.ReadLine()) != null)
            {
                entryList.Add(line.Substring(0, 4));
            }
            lsFileReader.Close();

            DbUpdate dbDelete              = new DbUpdate();
            string   deleteString          = "";
            string   crystInterfaceFileDir = @"D:\DbProjectData\InterfaceFiles_update\cryst";
            string   hashFolder            = "";

            foreach (string pdbId in entryList)
            {
                deleteString = string.Format("Delete From CrystEntryInterfaces Where PdbID = '{0}';", pdbId);
                dbDelete.Delete(ProtCidSettings.protcidDbConnection, deleteString);

                deleteString = string.Format("Delete From EntryInterfaceComp Where PdbID = '{0}';", pdbId);
                dbDelete.Delete(ProtCidSettings.protcidDbConnection, deleteString);

                deleteString = string.Format("Delete From DifEntryInterfaceComp " +
                                             "Where PdbID1 = '{0}' OR PdbID2 = '{0}';", pdbId);
                dbDelete.Delete(ProtCidSettings.protcidDbConnection, deleteString);

                deleteString = string.Format("Delete From FATCATALignments " +
                                             " Where QueryEntry = '{0}' OR HitEntry = '{0}';", pdbId);
                dbDelete.Delete(ProtCidSettings.alignmentDbConnection, deleteString);

                hashFolder = Path.Combine(crystInterfaceFileDir, pdbId.Substring(1, 2));
                string[] crystInterfaceFiles = Directory.GetFiles(hashFolder, pdbId + "*");
                foreach (string crystInterfaceFile in crystInterfaceFiles)
                {
                    File.Delete(crystInterfaceFile);
                }
            }
        }
예제 #7
0
        /// <summary>
        /// delete the alignment from database
        /// </summary>
        /// <param name="queryEntry"></param>
        /// <param name="queryChain"></param>
        /// <param name="hitEntry"></param>
        /// <param name="hitChain"></param>
        private void DeleteDbData(string queryEntry, string queryChain, string hitEntry, string hitChain)
        {
            string deleteString = string.Format("Delete From FatCatAlignments " +
                                                " Where (QueryEntry = '{0}' AND QueryChain = '{1}' AND " +
                                                " HitEntry = '{2}' AND HitChain = '{3}') " +
                                                " OR (QueryEntry = '{2}' AND QueryChain = '{3}' AND " +
                                                " HitEntry = '{0}' AND HitChain = '{1}');",
                                                queryEntry, queryChain, hitEntry, hitChain);

            dbUpdate.Delete(alignmentDbConnection, deleteString);


            /*      deleteString = string.Format("Delete From FatCatAlignments " +
             *        " Where QueryEntry = '{0}' AND QueryChain = '{1}' AND " +
             *        " HitEntry = '{2}' AND HitChain = '{3}';",
             *        hitEntry, hitChain, queryEntry, queryChain);
             *    dbUpdate.Delete (alignmentDbConnection, deleteString);*/
        }
예제 #8
0
        /// <summary>
        ///
        /// </summary>
        /// <param name="obsPdbId"></param>
        /// <param name="tableName"></param>
        /// <param name="dbDelete"></param>
        public void DeleteEntryInfoFromTable(string obsPdbId, string tableName, DbQuery dbQuery, DbUpdate dbDelete)
        {
            string    deleteString = "";
            string    queryString  = string.Format("Select First 1 * From {0};", tableName);
            DataTable dbTable      = dbQuery.Query(queryString);

            if (dbTable.Columns.Contains("PdbID"))
            {
                deleteString = string.Format("Delete From {0} Where PdbID = '{1}';", tableName, obsPdbId);
            }
            else if (dbTable.Columns.Contains("PdbID1"))
            {
                deleteString = string.Format("Delete From {0} Where PdbID1 = '{1}';", tableName, obsPdbId);
            }
            else if (dbTable.Columns.Contains("PdbID2"))
            {
                deleteString = string.Format("Delete From {0} Where PdbID2 = '{1}';", tableName, obsPdbId);
            }
            if (deleteString != "")
            {
                dbDelete.Delete(deleteString);
            }
        }
예제 #9
0
        /// <summary>
        ///
        /// </summary>
        /// <param name="pdbId"></param>
        private void DeleteObsoleteBuData(string pdbId)
        {
            string deleteString = string.Format("Delete From {0} Where PdbID = '{1}';", buTableName, pdbId);

            dbUpdate.Delete(ProtCidSettings.pdbfamDbConnection, deleteString);
        }
예제 #10
0
        /// <summary>
        ///
        /// </summary>
        /// <param name="pfamId"></param>
        private void DeletePfamLigandClusters(string pfamId)
        {
            string deleteString = string.Format("Delete From {0} Where PfamID = '{1}';", tableName, pfamId);

            dbUpdate.Delete(ProtCidSettings.protcidDbConnection, deleteString);
        }
예제 #11
0
        /// <summary>
        ///
        /// </summary>
        /// <param name="pdbId"></param>
        /// <param name="tableName"></param>
        private void DeletePdbEntryData(string pdbId, string tableName)
        {
            string deleteString = string.Format("Delete From {0} Where pdb_id = '{1}';", tableName, pdbId);

            dbUpdate.Delete(bamDbConnect, deleteString);
        }
예제 #12
0
        /// <summary>
        ///
        /// </summary>
        /// <param name="pdbId"></param>
        private void DeleteChainLigand(string pdbId)
        {
            string deleteString = string.Format("Delete From ChainLigands Where PdbID = '{0}';", pdbId);

            dbUpdate.Delete(ProtCidSettings.buCompConnection, deleteString);
        }
예제 #13
0
        /// <summary>
        ///
        /// </summary>
        /// <param name="seqCode"></param>
        private void DeleteUpdateHhAlignData(string seqCode)
        {
            string deleteString = string.Format("Delete From {0} Where Query = '{1}' OR Hit = '{1}';", hhAlignTableName, seqCode);

            dbUpdate.Delete(ProtCidSettings.alignmentDbConnection, deleteString);
        }