int GetDist(DistanceMeasures distance,string dirName,string item1,string item2)
{
DistanceMeasure dist = null;
List<string> targets = new List<string>();
if(!item1.Contains(dirName))
targets.Add(dirName + Path.DirectorySeparatorChar + item1);
else
targets.Add(item1);
targets.Add(dirName + Path.DirectorySeparatorChar + item2);
switch (distance)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(targets, "", false, "");
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(targets, "", false);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(targets, "", false, PDB.PDBMODE.ONLY_CA);
break;
case DistanceMeasures.GDT_TS:
dist = new GDT_TS(targets, "", false);
break;
}
dist.InitMeasure();
return GetDist(dist, item1, item2);
}
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);
}
DistanceMeasure PrepareDistance(DistanceMeasures distance,List <string> targets,string alignFile,string profileName)
{
DistanceMeasure dist=null;
switch (distance)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(targets, alignFile, false, profileName);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(targets, alignFile, false);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(targets, alignFile, false, PDB.PDBMODE.ONLY_CA);
break;
case DistanceMeasures.GDT_TS:
dist = new GDT_TS(targets, alignFile, false);
break;
}
dist.InitMeasure();
return dist;
}
private void SaveAll()
{
DistanceMeasure dist = null;
Settings set = new Settings();
set.Load();
string[] files;
if (set.extension.Length > 0)
{
files = Directory.GetFiles(directory, set.extension);
}
else
{
files = Directory.GetFiles(directory);
}
List <string> fileList = new List <string>(2);
StreamWriter r = new StreamWriter(saveFile);
maxV = files.Length;
foreach (var item in files)
{
fileList.Clear();
fileList.Add(item);
fileList.Add(markStructure);
switch (distanceControl1.distDef)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(fileList, null, false, distanceControl1.profileName, distanceControl1.referenceProfile);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(fileList, null, false, distanceControl1.CAtoms, null);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(fileList, null, false, null);
break;
case DistanceMeasures.GDT_TS:
dist = new GDT_TS(fileList, null, false, null);
break;
}
dist.InitMeasure();
try
{
int val = dist.GetDistance(Path.GetFileName(fileList[1]), Path.GetFileName(fileList[0]));
currentV++;
if (val < int.MaxValue)
{
r.WriteLine(fileList[0] + " " + (double)val / 100);
}
else
{
r.WriteLine(fileList[0] + " NaN");
}
}
catch (Exception ex)
{
exc = ex;
}
}
r.Close();
currentV = maxV;
}
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);
}