public HashClusterDendrog(DCDFile dcd, HashCInput input, HierarchicalCInput dendrogOpt) : base(dcd, input)
{
this.dMeasure = dendrogOpt.distance;
this.linkageType = dendrogOpt.linkageType;
this.atoms = dendrogOpt.atoms;
this.jury1d = dendrogOpt.reference1DjuryH;
this.profileName = dendrogOpt.hammingProfile;
this.refJuryProfile = dendrogOpt.jury1DProfileH;
hier = dendrogOpt;
}
public HashClusterDendrog(string dirName, string alignFile, HashCInput input, DistanceMeasures dMeasure, AglomerativeType linkageType, PDB.PDBMODE atoms, bool jury1d, string alignFileName,
string profileName = null, string refJuryProfile = null):base(dirName,alignFile,input)
{
this.dMeasure=dMeasure;
this.linkageType=linkageType;
this.atoms = atoms;
this.jury1d = jury1d;
this.profileName = profileName;
this.refJuryProfile = refJuryProfile;
this.dirName = dirName;
}
private DistanceMeasure CreateMeasure(string processName, string dirName, DistanceMeasures measure, PDB.PDBMODE atoms, bool jury1d, string alignFileName,
string profileName = null, string refJuryProfile = null)
{
DistanceMeasure dist = null;
switch (measure)
{
case DistanceMeasures.HAMMING:
if (alignFileName != null)
{
dist = new JuryDistance(alignFileName, jury1d, profileName, refJuryProfile);
}
else
{
dist = new JuryDistance(dirName, alignFileName, jury1d, profileName, refJuryProfile);
}
break;
case DistanceMeasures.TANIMOTO:
if (alignFileName != null)
{
dist = new Tanimoto(alignFileName, jury1d, profileName, refJuryProfile);
}
else
{
dist = new Tanimoto(dirName, alignFileName, jury1d, profileName, refJuryProfile);
}
break;
case DistanceMeasures.COSINE:
if (alignFileName != null)
{
dist = new CosineDistance(alignFileName, jury1d, profileName, refJuryProfile);
}
else
{
dist = new CosineDistance(dirName, alignFileName, jury1d, profileName, refJuryProfile);
}
break;
case DistanceMeasures.RMSD:
if (dirName == null)
{
throw new Exception("RMSD and MAXSUB measures cannot be used for aligned profiles!");
}
dist = new Rmsd(dirName, alignFileName, jury1d, atoms, refJuryProfile);
break;
case DistanceMeasures.MAXSUB:
if (dirName == null)
{
throw new Exception("RMSD and MAXSUB measures cannot be used for aligned profiles!");
}
dist = new MaxSub(dirName, alignFileName, jury1d, refJuryProfile);
break;
case DistanceMeasures.GDT_TS:
if (dirName == null)
{
throw new Exception("RMSD and MAXSUB measures cannot be used for aligned profiles!");
}
dist = new GDT_TS(dirName, alignFileName, jury1d, refJuryProfile);
break;
}
return(dist);
}
private DistanceMeasure CreateMeasureForDCD(DCDFile dcd, DistanceMeasures measure, PDB.PDBMODE atoms, bool jury1d, string alignFileName,
string profileName = null, string refJuryProfile = null)
{
DistanceMeasure dist = null;
switch (measure)
{
case DistanceMeasures.HAMMING:
if (refJuryProfile == null || !jury1d)
{
throw new Exception("Sorry but for jury measure you have to define 1djury profile to find reference structure");
}
else
{
dist = new JuryDistance(dcd, alignFileName, true, profileName, refJuryProfile);
}
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(dcd, alignFileName, jury1d, atoms, refJuryProfile);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(dcd, alignFileName, jury1d, refJuryProfile);
break;
case DistanceMeasures.GDT_TS:
dist = new GDT_TS(dcd, alignFileName, jury1d, refJuryProfile);
break;
}
dist.InitMeasure();
return(dist);
}