private void uniProtToolStripMenuItem_Click(object sender, EventArgs e) { DomainInterfaceBuilder.InitializeThread(); UnpInteractionStr unpDomainInter = new UnpInteractionStr(); unpDomainInter.BuildUnpInteractionNetTable(); }
/// <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; }