public HashCluster(Dictionary<string, List<byte>> profiles, Alignment _al, HashCInput input)
{
this.input = input;
stateAlign = profiles;
currentV = 0;
al = _al;
maxV = 4;
threadNumbers = dirSettings.numberOfCores;
}
public void InitHashCluster()
{
if(dcd!=null)
PrepareForDCD(dcd, input);
else
if(alignFile!=null && alignFile.Length>0)
{
al = new Alignment();
al.Prepare(alignFile, input.profileName);
// al.Prepare(profiles, profName, input.profileName);
al.MyAlign(alignFile);
//al.CombineAll();
stateAlign = al.GetStateAlign();
//AddErrors(al.errors);
// stateAlign = al.GetStateAlign();
if (input.regular)
{
if (input.profileName == input.profileNameReg)
stateAlignReg = stateAlign;
else
{
Alignment alReg = new Alignment();
if (alignFile != null)
alReg.Prepare(alignFile, input.profileNameReg);
else
alReg.Prepare(dirName, dirSettings, input.profileNameReg);
alReg.MyAlign(alignFile);
stateAlignReg = alReg.GetStateAlign();
}
}
}
if(stateAlign==null)
PrepareForPDB(dirName, alignFile, input);
}
protected Dictionary <byte,int>[] JuryConsensusStates(Alignment alUse,List<string> structNames)
{
jury1D juryLocal = new jury1D();
juryLocal.PrepareJury(alUse,stateAlign);
Dictionary <byte ,int>[] cons=new Dictionary<byte,int>[columns.Length];
ClusterOutput output = juryLocal.JuryOptWeights(structNames);
if (output == null)
return null;
int i = 0;
string result;
if (structNames.Contains("consensus"))
result = "consensus";
else
result = output.juryLike[0].Key;
foreach (var item in stateAlign[result])
{
cons[i] = new Dictionary<byte, int>();
cons[i++].Add(item, 0);
}
return cons;
}
void PrepareForPDB(string dirName, string alignFile,HashCInput input)
{
dirSettings.Load();
this.dirName = dirName;
al = new Alignment();
if (alignFile != null)
al.Prepare(alignFile, input.profileName);
else
{
al.Prepare(dirName, dirSettings, input.profileName);
}
al.MyAlign(alignFile);
stateAlign = al.GetStateAlign();
if (input.regular)
{
if (input.profileName == input.profileNameReg)
stateAlignReg = stateAlign;
else
{
Alignment alReg = new Alignment();
if(alignFile!=null)
alReg.Prepare(alignFile, input.profileNameReg);
else
alReg.Prepare(dirName, dirSettings, input.profileNameReg);
alReg.MyAlign(alignFile);
stateAlignReg = alReg.GetStateAlign();
}
}
this.input = input;
}
void PrepareForDCD(DCDFile dcd, HashCInput input)
{
dirSettings.Load();
this.dcd = dcd;
al = new Alignment();
al.Prepare(dcd, dirSettings, input.profileName);
al.MyAlign(alignFile);
stateAlign = al.GetStateAlign();
if (input.regular)
{
if (input.profileName == input.profileNameReg)
stateAlignReg = stateAlign;
else
{
Alignment alReg = new Alignment();
alReg.Prepare(dcd, dirSettings, input.profileNameReg);
alReg.MyAlign(alignFile);
stateAlignReg = alReg.GetStateAlign();
}
}
this.input = input;
}