private void RunBakerCluster(string name, string dirName, string alignFile = null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
ClusterOutput output = null;
DistanceMeasure distance = null;
if (dcd == null)
{
distance = CreateMeasure(name, dirName, opt.threshold.hDistance, opt.threshold.hAtoms, opt.threshold.reference1Djury,
alignFile, opt.threshold.hammingProfile, null);
}
else
{
distance = CreateMeasureForDCD(dcd, opt.threshold.hDistance, opt.threshold.hAtoms, opt.threshold.reference1Djury,
opt.threshold.alignmentFileName, opt.threshold.hammingProfile, null);
}
ThresholdCluster bk = new ThresholdCluster(distance, opt.threshold.distThresh, opt.threshold.bakerNumberofStruct);
if (beginJob != null)
{
beginJob(currentProcessName, bk.ToString(), dirName, distance.ToString());
}
progressDic.Add(name, bk);
distance.InitMeasure();
DateTime cpuPart2 = DateTime.Now;
clType = bk.ToString();
output = bk.OrgClustering();
UpdateOutput(name, dirName, alignFile, output, distance.ToString(), cpuPart1, cpuPart2, bk);
}
private void RunFastHCluster(string name, string dirName, string alignFile = null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
ClusterOutput clustOut = null;
DistanceMeasure distance = null;
if (dcd == null)
{
distance = CreateMeasure(name, dirName, opt.hierarchical.distance, opt.hierarchical.atoms, opt.hierarchical.reference1DjuryFast,
alignFile, opt.hierarchical.hammingProfile, opt.hierarchical.jury1DProfileFast);
}
else
{
distance = CreateMeasureForDCD(dcd, opt.hierarchical.distance, opt.hierarchical.atoms, opt.hierarchical.reference1DjuryFast,
opt.hierarchical.alignmentFileName, opt.hierarchical.hammingProfile, opt.hierarchical.jury1DProfileFast);
}
FastDendrog km;
km = new FastDendrog(distance, opt.hierarchical, dirName);
if (beginJob != null)
{
beginJob(currentProcessName, km.ToString(), dirName, distance.ToString());
}
progressDic.Add(name, km);
distance.InitMeasure();
DateTime cpuPart2 = DateTime.Now;
clType = km.ToString();
clustOut = km.Run(new List <string>(distance.structNames.Keys));
UpdateOutput(name, dirName, alignFile, clustOut, distance.ToString(), cpuPart1, cpuPart2, km);
}
private void RunHierarchicalCluster(string name, string dirName, string alignFile = null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
DistanceMeasure distance = null;
//distance.CalcDistMatrix(distance.structNames);
// opt.hierarchical.atoms = PDB.PDBMODE.ALL_ATOMS;
if (dcd != null)
{
distance = CreateMeasureForDCD(dcd, opt.hierarchical.distance, opt.hierarchical.atoms, opt.hierarchical.reference1DjuryAglom,
opt.hierarchical.alignmentFileName, opt.hierarchical.hammingProfile, opt.hierarchical.jury1DProfileAglom);
}
else
{
distance = CreateMeasure(name, dirName, opt.hierarchical.distance, opt.hierarchical.atoms, opt.hierarchical.reference1DjuryAglom,
alignFile, opt.hierarchical.hammingProfile, opt.hierarchical.jury1DProfileAglom);
}
DebugClass.WriteMessage("Measure Created");
hierarchicalCluster hk = new hierarchicalCluster(distance, opt.hierarchical, dirName);
if (beginJob != null)
{
beginJob(currentProcessName, hk.ToString(), dirName, distance.ToString());
}
clType = hk.ToString();
ClusterOutput output;
progressDic.Add(name, hk);
distance.InitMeasure();
DateTime cpuPart2 = DateTime.Now;
output = hk.HierarchicalClustering(new List <string>(distance.structNames.Keys));
UpdateOutput(name, dirName, alignFile, output, distance.ToString(), cpuPart1, cpuPart2, hk);
}
public string UsedMeasure()
{
if (dist != null)
{
return(dist.ToString());
}
return("NONE");
}
private void RunKMeans(string name, string dirName, string alignFile = null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
ClusterOutput clustOut;
DistanceMeasure distance = null;
if (dcd == null)
{
distance = CreateMeasure(name, dirName, opt.kmeans.kDistance, opt.kmeans.kAtoms, opt.kmeans.reference1Djury,
alignFile, opt.kmeans.hammingProfile, opt.kmeans.jury1DProfile);
}
else
{
distance = CreateMeasureForDCD(dcd, opt.kmeans.kDistance, opt.kmeans.kAtoms, opt.kmeans.reference1Djury,
opt.kmeans.alignmentFileName, opt.kmeans.hammingProfile, opt.kmeans.jury1DProfile);
}
kMeans km;
km = new kMeans(distance, opt.kmeans.kMeans_init);
if (beginJob != null)
{
beginJob(currentProcessName, km.ToString(), dirName, distance.ToString());
}
progressDic.Add(name, km);
distance.InitMeasure();
DateTime cpuPart2 = DateTime.Now;
clType = km.ToString();
if ((int)opt.kmeans.maxK <= 1)
{
throw new Exception("k in k-Means must be bigger then 1, right now is: " + (int)opt.kmeans.maxK);
}
if (distance.structNames.Count < 10)
{
throw new Exception("Number of structures to cluster must be bigger then 10 right now is: " + distance.structNames.Count);
}
clustOut = km.kMeansLevel((int)opt.kmeans.maxK, opt.kmeans.maxIter, new List <string>(distance.structNames.Keys));
UpdateOutput(name, dirName, alignFile, clustOut, distance.ToString(), cpuPart1, cpuPart2, km);
GC.SuppressFinalize(distance);
}
private void RunHKMeans(string name, string dirName, string alignFile = null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
ClusterOutput clustOut = null;
DistanceMeasure distance = null;
if (dcd == null)
{
distance = CreateMeasure(name, dirName, opt.hierarchical.distance, opt.hierarchical.atoms, opt.hierarchical.reference1DjuryKmeans,
alignFile, opt.hierarchical.hammingProfile, opt.hierarchical.jury1DProfileKmeans);
}
else
{
distance = CreateMeasureForDCD(dcd, opt.hierarchical.distance, opt.hierarchical.atoms, opt.hierarchical.reference1DjuryKmeans,
opt.hierarchical.alignmentFileName, opt.hierarchical.hammingProfile, opt.hierarchical.jury1DProfileKmeans);
}
kMeans km;
km = new kMeans(distance, true);
if (beginJob != null)
{
beginJob(currentProcessName, km.ToString(), dirName, distance.ToString());
}
progressDic.Add(name, km);
DateTime cpuPart2 = DateTime.Now;
distance.InitMeasure();
clType = km.ToString();
km.BMIndex = opt.hierarchical.indexDB;
km.threshold = opt.hierarchical.numberOfStruct;
km.maxRepeat = opt.hierarchical.repeatTime;
km.maxK = opt.hierarchical.maxK;
clustOut = km.HierarchicalKMeans();
UpdateOutput(name, dirName, alignFile, clustOut, distance.ToString(), cpuPart1, cpuPart2, km);
}
private void Run3DJury(string name, string dirName, string alignFile = null, DCDFile dcd = null)
{
DateTime cpuStart = DateTime.Now;
ClusterOutput output;
DistanceMeasure distance = null;
if (alignFile != null)
{
distance = CreateMeasure(name, null, opt.other.oDistance, opt.other.oAtoms, opt.other.reference1Djury,
alignFile, opt.other.hammingProfile, opt.other.referenceProfile);
}
else
if (dirName != null)
{
distance = CreateMeasure(name, dirName, opt.other.oDistance, opt.other.oAtoms, opt.other.reference1Djury,
alignFile, opt.other.hammingProfile, opt.other.referenceProfile);
}
else
{
distance = CreateMeasureForDCD(dcd, opt.other.oDistance, opt.other.oAtoms, opt.other.reference1Djury,
opt.other.alignFileName, opt.other.hammingProfile, opt.other.referenceProfile);
}
Jury3D ju = new Jury3D(distance);
if (beginJob != null)
{
beginJob(currentProcessName, ju.ToString(), dirName, distance.ToString());
}
progressDic.Add(name, ju);
distance.InitMeasure();
clType = ju.ToString();
output = ju.Run3DJury();
UpdateOutput(name, dirName, alignFile, output, distance.ToString(), cpuStart, DateTime.Now, ju);
progressDic.Remove(name);
}