public void BuildChainInterfaceClusters(int operationStep)
{
ProtCidSettings.dataType = "pfam";
DbBuilderHelper.Initialize();
switch (operationStep)
{
case 1:
try
{
ChainGroupsClassifier chainGroupClassifier = new ChainGroupsClassifier();
chainGroupClassifier.CombineFamilyGroups();
}
catch (Exception ex)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Classify chain relations error: " +
ex.Message);
ProtCidSettings.logWriter.WriteLine("Classify chain relations error: " +
ex.Message);
ProtCidSettings.logWriter.Flush();
}
break;
// goto case 2;
case 2:
ChainGroupRepEntryComp interGroupRepEntryComp = new ChainGroupRepEntryComp();
interGroupRepEntryComp.CompareTwoEntries("5uvz", "2dww");
interGroupRepEntryComp.CompareInterGroupRepEntryInterfacesInChainGroups();
// interGroupRepEntryComp.PrintMissingAlignInterGroupRepEntries();
Alignments.GroupEntryAlignments groupAlign = new Alignments.GroupEntryAlignments();
groupAlign.GetRepChainPairsToBeAligned();
// interGroupRepEntryComp.CompareMissingEntryPairs();
break;
// goto case 3;
case 3:
ChainInterfaceCluster interfaceCluster = new ChainInterfaceCluster();
interfaceCluster.ClusterChainGroupInterfaces();
/* int[] abSuperGroupIds = { 744};
* interfaceCluster.UpdateSuperGroups(abSuperGroupIds); */
break;
// goto case 4;
case 4:
ChainClusterStat superClusterStat = new ChainClusterStat();
// superClusterStat.PrintChainClusterTextFilesFromDb ();
superClusterStat.PrintSupergroupInterfaceClusters("pfam");
// goto case 5;
break;
case 5:
InterfaceFilesReverser interfaceFileReverse = new InterfaceFilesReverser();
// interfaceFileReverse.UpdateIsSymmetry();
string clusterReverseFileList = interfaceFileReverse.ReverseClusterInterfaceFiles();
#if DEBUG
/////////////////////////////////////
// the clusterReverseFileList is still a problem, file not exist exception, probably due to change the current directory
// but I can not detect where the problem is.
// should fix it.
////////////////////////////////////
ProtCidSettings.progressInfo.progStrQueue.Enqueue("The current working directory: " + System.Environment.CurrentDirectory);
ProtCidSettings.logWriter.WriteLine("The current working directory: " + System.Environment.CurrentDirectory);
FileInfo fileInfo = new FileInfo(clusterReverseFileList);
ProtCidSettings.logWriter.WriteLine("The directory of clusterReverseFileList file: " + fileInfo.DirectoryName);
#endif
clusterReverseFileList = Path.Combine(ProtCidSettings.applicationStartPath, clusterReverseFileList);
ChainClusterCompress clusterFileCompress = new ChainClusterCompress();
clusterFileCompress.CompressClusterInterfaceFiles(clusterReverseFileList);
// copy the interface files for those not in any clusters
// save disk space in the web server
clusterFileCompress.RetrieveCrystInterfaceFilesNotInClusters(false);
InterfaceImageGen imageGen = new InterfaceImageGen();
imageGen.GenerateInterfaceImages();
// goto case 6;
break;
case 6:
SeqFastaGenerator seqFastaGen = new SeqFastaGenerator();
seqFastaGen.WriteSequencesToFastaFiles();
break;
// goto case 7;
case 7:
BiolUnitSumInfo buSumInfo = new BiolUnitSumInfo();
// buSumInfo.UpdateBiolUnits();
buSumInfo.RetrieveBiolUnits();
break;
default:
break;
}
DbBuilderHelper.UpdateIndexes("PfamSuper", ProtCidSettings.protcidDbConnection);
ProtCidSettings.progressInfo.threadFinished = true;
}
/// <summary>
///
/// </summary>
/// <param name="userGroupName"></param>
/// <param name="userGroupSeqId"></param>
/// <param name="userEntries"></param>
public void FindInterfaceClustersInUserGroup(string userGroupName, int userGroupSeqId, string[] userEntries)
{
ProtCidSettings.progressInfo.Reset();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Clutering interfaces in the user group");
ProtCidSettings.progressInfo.progStrQueue.Enqueue(userGroupName + " " + userGroupSeqId.ToString());
Dictionary <int, string[]> updatedGroupHash = GetUpdatedGroups(userEntries);
Dictionary <int, Dictionary <int, string[]> > updateSuperGroupHash = new Dictionary <int, Dictionary <int, string[]> > ();
updateSuperGroupHash.Add(userGroupSeqId, updatedGroupHash);
Dictionary <int, string> superGroupNameHash = new Dictionary <int, string> ();
superGroupNameHash.Add(userGroupSeqId, userGroupName);
List <int> updateSuperGroupList = new List <int> (updateSuperGroupHash.Keys);
int[] updateSuperGroups = new int[updateSuperGroupList.Count];
updateSuperGroupList.CopyTo(updateSuperGroups);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Updating Super Groups.");
ChainGroupsClassifier superGroupClassifier = new ChainGroupsClassifier();
superGroupClassifier.AddChainRelGroupsBasedOnPfam(updateSuperGroupHash, superGroupNameHash);
// clear the any existing file to make sure the file containing only those from
// the comparison between groups.
string nonAlignedPairFile = "NonAlignedEntryPairs.txt";
if (File.Exists(nonAlignedPairFile))
{
// before delete, make a copy
File.Copy(nonAlignedPairFile, Path.Combine(ProtCidSettings.dirSettings.fatcatPath, nonAlignedPairFile));
File.Delete(nonAlignedPairFile);
}
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Updating the interface comparisons between groups.");
ChainGroupRepEntryComp interGroupRepEntryComp = new ChainGroupRepEntryComp();
interGroupRepEntryComp.UpdateEntryComparisonInSuperGroups(updateSuperGroupHash);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Updating super groups clustering.");
ChainInterfaceCluster interfaceCluster = new ChainInterfaceCluster();
interfaceCluster.ClusterUserDefinedGroupInterfaces(updateSuperGroups);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Updating the summary data.");
ChainClusterStat superClusterStat = new ChainClusterStat();
superClusterStat.UpdateSupergroupInterfaceClustersSumInfo(updateSuperGroups, userEntries, "pfam", false);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Updating tar interface files.");
InterfaceFilesReverser interfaceFileReverse = new InterfaceFilesReverser();
string updateClusterReverseListFile = interfaceFileReverse.ReverseClusterInterfaceFiles(updateSuperGroupHash);
// string updateClusterReverseListFile = "ReverseInterfacesInCluster.txt";
ChainClusterCompress clusterFileCompress = new ChainClusterCompress();
clusterFileCompress.CompressGroupClusterInterfaceFiles(updateSuperGroups, updateClusterReverseListFile);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Updating sequence files.");
SeqFastaGenerator seqFastaGen = new SeqFastaGenerator();
seqFastaGen.UpdateSeqFastaFiles(updateSuperGroups);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
}
