/// <summary>
///
/// </summary>
/// <param name="stepNum"></param>
public void BuildDomainInterfaces(int stepNum)
{
InitializeThread();
DomainInterfaceTables.InitializeTables();
ProtCidSettings.progressInfo.Reset();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Retrieving domain-domain interactions.");
/* ProtCidSettings.progressInfo.progStrQueue.Enqueue("Creating database tables.");
* DomainInterfaceTables.InitializeDbTables();
* ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done.");
*/
switch (stepNum)
{
case 1:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Detecting domain-domain interactions from cryst chain interfaces.");
DomainClassifier domainClassifier = new DomainClassifier();
domainClassifier.RetrieveDomainInterfaces();
ProtCidSettings.progressInfo.currentOperationIndex++;
// goto case 1;
break;
case 2:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Write domain interface files.");
DomainInterfaceWriter domainInterfaceWriter = new DomainInterfaceWriter();
domainInterfaceWriter.WriteDomainInterfaceFiles();
// domainInterfaceWriter.UpdateDomainInterfaceFiles();
// domainInterfaceWriter.WriteMultiChainDomainInterfaces();
ProtCidSettings.progressInfo.currentOperationIndex++;
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Calculate SAs of domain interface files.");
DomainInterfaceSA interfaceSa = new DomainInterfaceSA();
// interfaceSa.UpdateDomainInterfaceSAs();
interfaceSa.CalculateDomainInterfaceSAs();
ProtCidSettings.progressInfo.currentOperationIndex++;
// goto case 2;
break;
case 3:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Comparing domain interfaces.");
PfamDomainInterfaceComp domainComp = new PfamDomainInterfaceComp();
domainComp.CompareDomainInterfaces();
/* domainComp.SynchronizeDomainChainInterfaceComp();
* domainComp.CompareSpecificDomainInterfaces ();
* domainComp.UpdateMultiChainDomainInterfaces();
*/
ProtCidSettings.progressInfo.currentOperationIndex++;
break;
case 4:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Comparing entry domain interfaces.");
DomainInterfaceBuComp.CrystBuDomainInterfaceComp domainInterfaceComp =
new InterfaceClusterLib.DomainInterfaces.DomainInterfaceBuComp.CrystBuDomainInterfaceComp();
// int[] relSeqIds = {10515 };
// domainInterfaceComp.UpdateCrystBuDomainInterfaceComp(relSeqIds);
domainInterfaceComp.CompareCrystBuDomainInterfaces();
ProtCidSettings.progressInfo.currentOperationIndex++;
break;
case 5:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Cluster domain interfaces.");
DomainInterfaceCluster interfaceCluster = new DomainInterfaceCluster();
int[] relSeqIds = { 2 };
interfaceCluster.UpdateDomainInterfaceClusters(relSeqIds);
// interfaceCluster.ClusterDomainInterfaces();
// interfaceCluster.ClusterLeftRelations();
break;
// goto case 4;
case 6:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Print Domain Interface Cluster Info.");
DomainClusterStat clusterStat = new DomainClusterStat();
int[] updateRelSeqIds = { 2 };
clusterStat.UpdateDomainClusterInfo(updateRelSeqIds);
// clusterStat.PrintDomainClusterInfo();
// clusterStat.PrintDomainDbSumInfo("PfamDomain");
// clusterStat.AddNumCFsToIPfamInPdbMetaData();
// clusterStat.PrintPartialDomainClusterInfo();
// clusterStat.GetPfamDomainSumInfo();
/* DomainInterfaceStatInfo statInfo = new DomainInterfaceStatInfo();
* // statInfo.PrintPepInteractingHmmSites();
* // statInfo.GetPfamPepInterfaceClusterInfo();
* // statInfo.PrintPepLigandHmmSites ();
* statInfo.PrintPfamDomainRelationInfo();
* // statInfo.GetGenAsymChainDomainInterfaces();*/
break;
// goto case 7;
case 7:
PfamClusterFilesCompress clusterFileCompress = new PfamClusterFilesCompress();
clusterFileCompress.CompressPfamClusterChainInterfaceFiles();
clusterFileCompress.RetrieveCrystInterfaceFilesNotInClusters(true);
DomainSeqFasta seqFasta = new DomainSeqFasta();
seqFasta.PrintClusterDomainSequences();
DomainInterfaceImageGen imageGen = new DomainInterfaceImageGen();
imageGen.GenerateDomainInterfaceImages();
PfamRelNetwork pfamNetWriter = new PfamRelNetwork();
pfamNetWriter.GeneratePfamNetworkGraphmlFiles();
// build the unp-unp interaction table based on pdb domain interfaces
UnpInteractionStr unpInteract = new UnpInteractionStr();
unpInteract.BuildUnpInteractionNetTable();
break;
case 8: // about peptide interfaces
PfamPeptideInterfaces pepInterfaces = new PfamPeptideInterfaces();
pepInterfaceBuilder.BuildPfamPeptideInterfaces();
break;
case 9:
// ligandInteractBuilder.AddClusterInfoToPfamDomainAlign();
ligandInteractBuilder.BuildPfamLigandInteractions();
break;
default:
break;
}
ProtCidSettings.logWriter.Close();
ProtCidSettings.progressInfo.threadFinished = true;
}
