public void BuildClanDomainInterfaces(int step)
{
ProtCidSettings.dataType = "pfam";
DomainInterfaceBuilder.InitializeThread();
DomainInterfaceTables.InitializeTables();
ProtCidSettings.progressInfo.Reset();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Retrieving domain-domain interactions.");
switch (step)
{
case 1:
ClanDomainInterfaceComp domainInterfaceComp = new ClanDomainInterfaceComp();
int relSeqId1 = 11619;
int relSeqId2 = 11642;
int clanSeqId = 398;
domainInterfaceComp.CompareRepDomainInterfaces2PfamRelations(clanSeqId, relSeqId1, relSeqId2);
break;
case 2:
ClanDomainInterfaceCluster clanInterfaceCluster = new ClanDomainInterfaceCluster();
clanInterfaceCluster.ClusterSuperDomainInterfaces();
break;
case 3: // output coordinate domain interfaces for each cluster
break;
default:
break;
}
}
/// <summary>
///
/// </summary>
public void ClusterUserDefinedGroupDomainInterfaces()
{
ProtCidSettings.dataType = "pfam";
DomainInterfaceBuilder.InitializeThread();
DomainInterfaceTables.InitializeTables();
ProtCidSettings.progressInfo.Reset();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Retrieving domain-domain interactions for user-defined group.");
// structure alignments between representative domains from PFAMs in a group
int groupSeqId = 100000;
/* Hashtable groupPfamHash = new Hashtable();
* string[] groupPfams = { "Integrase_Zn", "zf-H2C2" };
* groupPfamHash.Add(groupSeqId, groupPfams);
*
* PfamLib.DomainAlign.PfamDomainAlign domainAlign = new PfamLib.DomainAlign.PfamDomainAlign();
* domainAlign.AlignPfamDomainsForUserDefinedGroups(groupPfamHash);
*/
// calcuate the Q score between two different relations
groupSeqId = 100000;
Dictionary <int, int[]> groupRelationHash = new Dictionary <int, int[]> ();
List <int> relSeqIdList = new List <int> ();
relSeqIdList.Add(7956);
relSeqIdList.Add(15374);
int[] relSeqIds = new int[relSeqIdList.Count];
relSeqIdList.CopyTo(relSeqIds);
groupRelationHash.Add(groupSeqId, relSeqIds);
groupSeqId++;
relSeqIdList = new List <int> ();
relSeqIdList.Add(7954);
relSeqIdList.Add(15481);
relSeqIds = new int[relSeqIdList.Count];
relSeqIdList.CopyTo(relSeqIds);
groupRelationHash.Add(groupSeqId, relSeqIds);
Dictionary <string, string> pfamClanHash = new Dictionary <string, string> ();
pfamClanHash.Add("Integrase_Zn", "Zn_N");
pfamClanHash.Add("zf-H2C2", "Zn_N");
ClanDomainInterfaceComp domainInterfaceComp = new ClanDomainInterfaceComp();
domainInterfaceComp.CompareRepDomainInterfaces2PfamRelations(groupRelationHash, pfamClanHash);
}
