public void PrepareJury(List <KeyValuePair <string, string> > profiles, string profName, string profileFile)
{
al.Prepare(profiles, profName, profileFile);
stateAlign = al.GetStateAlign();
weights = al.r.GenerateWeights(wOpertion.MULT);
// maxProgress = 0.75;
}
public void PrepareJury(Alignment al)
{
this.al = al;
stateAlign = al.GetStateAlign();
weights = al.r.GenerateWeights(wOpertion.MULT);
}
public HTree(Alignment _al, HashCluster hCl)
{
al = _al;
stateAlign = al.GetStateAlign();
hCluster = hCl;
}
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);
}
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;
}