/// <summary>
/// insert data into database
/// </summary>
private void InsertDataIntoDb()
{
dbInsert.InsertDataIntoDBtables(ProtCidSettings.protcidDbConnection, HomoGroupTables.homoGroupTables[HomoGroupTables.HomoSeqInfo]);
InsertAlignmentData();
HomoGroupTables.ClearTables();
}
/// <summary>
///
/// </summary>
/// <param name="groupSeqId"></param>
private void InsertUpdateDataIntoDb(int groupSeqId)
{
UpdateAlignmentData(groupSeqId);
DeletePfamHomoGroupInfo(groupSeqId);
dbInsert.InsertDataIntoDBtables(ProtCidSettings.protcidDbConnection, HomoGroupTables.homoGroupTables[HomoGroupTables.HomoSeqInfo]);
HomoGroupTables.ClearTables();
}
public void ClassifyHomoEntries(string[] entryList)
{
InitializeTables();
DeleteObsHomoGroupDataInDb(groupSeqNum);
AddEntryDataToTable(entryList, groupSeqNum);
RetrieveRepEntries();
dbInsert.InsertDataIntoDBtables(ProtCidSettings.protcidDbConnection, HomoGroupTables.homoGroupTables);
HomoGroupTables.ClearTables();
}
/// <summary>
/// initialize tables
/// </summary>
/// <param name="isUpdate"></param>
protected void InitializeTables(bool isUpdate)
{
// create tables in memory
HomoGroupTables.InitializeTables();
if (!isUpdate)
{
HomoGroupTables.InitializeAllGroupDbTables();
// reuse the alignments data
// HomoGroupTables.InitializeGroupTable();
// HomoGroupTables.AddFlagColumn ();
}
}
/// <summary>
/// classify pfam group into subgroups based on
/// number of entities and domain families
/// </summary>
/// <param name="entryList"></param>
private void UpdateEntryPfamArchGroupTables(int groupSeqId, string[] groupEntries)
{
AddEntryDataToTable(groupEntries, groupSeqId);
UpdateHomoGroupRepAlignTables();
DeletePfamHomoGroupInfo(groupSeqId);
dbInsert.InsertDataIntoDBtables(ProtCidSettings.protcidDbConnection, HomoGroupTables.homoGroupTables[HomoGroupTables.HomoSeqInfo]);
HomoGroupTables.ClearTables();
entryAlignment.entryEntityFamilyTable.Clear();
}
/// <summary>
/// used for user-defined groups
/// </summary>
/// <param name="entryList"></param>
/// <param name="groupName"></param>
public void ClassifyHomoEntries(string[] entryList, string groupName)
{
InitializeTables();
DeleteObsHomoGroupDataInDb(groupSeqNum);
DataRow familyRow = HomoGroupTables.homoGroupTables[HomoGroupTables.FamilyGroups].NewRow();
familyRow["GroupSeqId"] = groupSeqNum;
familyRow["FamilyString"] = groupName;
HomoGroupTables.homoGroupTables[HomoGroupTables.FamilyGroups].Rows.Add(familyRow);
AddEntryDataToTable(entryList, groupSeqNum);
RetrieveRepEntries();
dbInsert.InsertDataIntoDBtables(ProtCidSettings.protcidDbConnection, HomoGroupTables.homoGroupTables);
HomoGroupTables.ClearTables();
}
/// <summary>
///
/// </summary>
/// <param name="pdbId1"></param>
/// <param name="pdbId2"></param>
public DataTable GetEntryAlignmentInfoFromAlignmentsTables(string pdbId1, string pdbId2)
{
if (HomoGroupTables.homoGroupTables == null)
{
HomoGroupTables.InitializeTables();
}
HomoGroupTables.homoGroupTables[HomoGroupTables.HomoRepEntryAlign].Clear();
string[] homoEntries = new string[1];
homoEntries[0] = pdbId2;
entryAlignment.RetrieveRepEntryAlignment(pdbId1, homoEntries, -1);
GetHomoEntryAlignAsymInfo(ref HomoGroupTables.homoGroupTables[HomoGroupTables.HomoRepEntryAlign]);
return(HomoGroupTables.homoGroupTables[HomoGroupTables.HomoRepEntryAlign]);
// return alignInfoTable;
}
/// <summary>
///
/// </summary>
/// <param name="updateGroups"></param>
public void UpdateGroupMissingEntryAlignments(int[] updateGroups)
{
HomoGroupTables.InitializeTables();
InitializeEntityCrcRepTable();
delDataWriter = new StreamWriter("DeletedAlignData.txt", true);
delDataWriter.WriteLine(DateTime.Today.ToShortDateString());
ProtCidSettings.progressInfo.ResetCurrentProgressInfo();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Retrieve rep entries alignments info in each group.");
ProtCidSettings.progressInfo.currentOperationLabel = "Alignments info";
string tableName = ProtCidSettings.dataType + "HomoGroupEntryAlign";
ProtCidSettings.logWriter.WriteLine(tableName);
ProtCidSettings.logWriter.WriteLine("Retrieve rep entries alignments info in each group.");
ProtCidSettings.progressInfo.ResetCurrentProgressInfo();
ProtCidSettings.progressInfo.progStrQueue.Enqueue(tableName);
ProtCidSettings.progressInfo.totalOperationNum = updateGroups.Length;
ProtCidSettings.progressInfo.totalStepNum = updateGroups.Length;
foreach (int groupId in updateGroups)
{
ProtCidSettings.progressInfo.currentFileName = groupId.ToString();
ProtCidSettings.progressInfo.currentOperationNum++;
ProtCidSettings.progressInfo.currentStepNum++;
try
{
DataTable missingAlignTable = GetMissingAlignTable(groupId, tableName);
if (missingAlignTable.Rows.Count == 0)
{
continue;
}
string[] groupEntries = GetGroupAlignEntries(missingAlignTable);
SetEntryPdbCrcMapTable(groupEntries);
UpdateMissingAlignEntryTable(groupId, missingAlignTable, entityCrcRepTable);
}
catch (Exception ex)
{
ProtCidSettings.logWriter.WriteLine(groupId + " " + ex.Message);
ProtCidSettings.logWriter.Flush();
ProtCidSettings.progressInfo.progStrQueue.Enqueue(groupId + " " + ex.Message);
}
}
ProtCidSettings.progressInfo.progStrQueue.Enqueue(tableName + " Done!");
tableName = ProtCidSettings.dataType + "HomoRepEntryAlign";
ProtCidSettings.logWriter.WriteLine(tableName);
ProtCidSettings.logWriter.WriteLine("Retrieve rep entries alignments info in each group.");
ProtCidSettings.progressInfo.ResetCurrentProgressInfo();
ProtCidSettings.progressInfo.progStrQueue.Enqueue(tableName);
ProtCidSettings.progressInfo.totalOperationNum = updateGroups.Length;
ProtCidSettings.progressInfo.totalStepNum = updateGroups.Length;
foreach (int groupId in updateGroups)
{
ProtCidSettings.progressInfo.currentFileName = groupId.ToString();
ProtCidSettings.progressInfo.currentOperationNum++;
ProtCidSettings.progressInfo.currentStepNum++;
try
{
DataTable missingAlignTable = GetMissingAlignTable(groupId, tableName);
if (missingAlignTable.Rows.Count == 0)
{
continue;
}
string[] groupEntries = GetGroupAlignEntries(missingAlignTable);
SetEntryPdbCrcMapTable(groupEntries);
UpdateMissingAlignEntryTable(groupId, missingAlignTable, entityCrcRepTable);
}
catch (Exception ex)
{
ProtCidSettings.logWriter.WriteLine(groupId + " " + ex.Message);
ProtCidSettings.logWriter.Flush();
ProtCidSettings.progressInfo.progStrQueue.Enqueue(groupId + " " + ex.Message);
}
}
delDataWriter.Close();
ProtCidSettings.progressInfo.progStrQueue.Enqueue(tableName + " Done!");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.logWriter.WriteLine("Done!");
}
/// <summary>
/// initialize tables
/// </summary>
/// <param name="isUpdate"></param>
protected void InitializeTables()
{
// create tables in memory
HomoGroupTables.InitializeTables();
GetDuplicateSgHash();
}
