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);
}
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);
}
public ClusterOutput DendrogUsingMeasures(List <string> structures)
{
jury1D juryLocal = new jury1D();
juryLocal.PrepareJury(al);
ClusterOutput outC = null;
Dictionary <string, List <int> > dic;
//Console.WriteLine("Start after jury " + Process.GetCurrentProcess().PeakWorkingSet64);
maxV = refPoints * 20 * 4;
currentV = 0;
dic = PrepareKeys(structures, false);
//DebugClass.DebugOn();
// input.relClusters = input.reqClusters;
// input.perData = 90;
if (dic.Count > input.relClusters)
{
if (!input.combine)
{
dic = HashEntropyCombine(dic, structures, input.relClusters);
}
else
{
dic = Rpart(dic, structures, false);
}
//dic = FastCombineKeysNew(dic, structures, false);
}
Dictionary <string, int> xx = ReadLeafs();
dic = SelectClusters(xx, dic);
maxV = 3;
currentV = 1;
//Console.WriteLine("Entropy ready after jury " + Process.GetCurrentProcess().PeakWorkingSet64);
DebugClass.WriteMessage("Entropy ready");
//Alternative way to start of UQclust Tree must be finished
//input.relClusters = 10000;
//dic = FastCombineKeys(dic, structures, true);
DebugClass.WriteMessage("dic size" + dic.Count);
currentV++;
//Console.WriteLine("Combine ready after jury " + Process.GetCurrentProcess().PeakWorkingSet64);
DebugClass.WriteMessage("Combine Keys ready");
Dictionary <string, string> translateToCluster = new Dictionary <string, string>(dic.Count);
List <string> structuresToDendrogram = new List <string>(dic.Count);
List <string> structuresFullPath = new List <string>(dic.Count);
DebugClass.WriteMessage("Number of clusters: " + dic.Count);
int cc = 0;
List <string> order = new List <string>(dic.Keys);
order.Sort(delegate(string a, string b)
{
if (dic[b].Count == dic[a].Count)
{
for (int i = 0; i < a.Length; i++)
{
if (a[i] != b[i])
{
if (a[i] == '0')
{
return(-1);
}
else
{
return(1);
}
}
}
}
return(dic[b].Count.CompareTo(dic[a].Count));
});
foreach (var item in order)
{
if (dic[item].Count > 2)
{
List <string> cluster = new List <string>(dic[item].Count);
foreach (var str in dic[item])
{
cluster.Add(structures[str]);
}
ClusterOutput output = juryLocal.JuryOptWeights(cluster);
structuresToDendrogram.Add(output.juryLike[0].Key);
if (alignFile == null)
{
structuresFullPath.Add(dirName + Path.DirectorySeparatorChar + output.juryLike[0].Key);
}
else
{
structuresFullPath.Add(output.juryLike[0].Key);
}
translateToCluster.Add(output.juryLike[0].Key, item);
}
else
{
structuresToDendrogram.Add(structures[dic[item][0]]);
if (alignFile == null)
{
structuresFullPath.Add(dirName + Path.DirectorySeparatorChar + structures[dic[item][0]]);
}
else
{
structuresFullPath.Add(structures[dic[item][0]]);
}
translateToCluster.Add(structures[dic[item][0]], item);
}
cc++;
}
currentV++;
DebugClass.WriteMessage("Jury finished");
switch (dMeasure)
{
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(structuresFullPath, alignFile, true, profileName, refJuryProfile);
}
break;
case DistanceMeasures.COSINE:
dist = new CosineDistance(structuresFullPath, alignFile, jury1d, profileName, refJuryProfile);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(structuresFullPath, "", jury1d, atoms, refJuryProfile);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(structuresFullPath, "", jury1d, refJuryProfile);
break;
}
// return new ClusterOutput();
DebugClass.WriteMessage("Start hierarchical");
//Console.WriteLine("Start hierarchical " + Process.GetCurrentProcess().PeakWorkingSet64);
currentV = maxV;
hk = new hierarchicalCluster(dist, hier, dirName);
dist.InitMeasure();
//Now just add strctures to the leaves
outC = hk.HierarchicalClustering(structuresToDendrogram);
DebugClass.WriteMessage("Stop hierarchical");
List <HClusterNode> hLeaves = outC.hNode.GetLeaves();
foreach (var item in hLeaves)
{
if (translateToCluster.ContainsKey(item.setStruct[0]))
{
foreach (var str in dic[translateToCluster[item.setStruct[0]]])
{
if (item.setStruct[0] != structures[str])
{
item.setStruct.Add(structures[str]);
}
}
item.consistency = CalcClusterConsistency(item.setStruct);
}
else
{
throw new Exception("Cannot add structure. Something is wrong");
}
}
outC.hNode.RedoSetStructures();
outC.runParameters = hier.GetVitalParameters();
outC.runParameters += input.GetVitalParameters();
return(outC);
}
private void CalculateDistToAll()
{
tableDist = new DataTable();
tableDist.Columns.Add("Reference structure", typeof(string));
tableDist.Columns.Add("Distance", typeof(double));
tableDist.Columns.Add("Cluster size", typeof(int));
List <string> fileNames=new List<string>();
if (textBox1.Text != null && textBox1.Text.Length > 5 && File.Exists(textBox1.Text))
{
fileNames.Add(textBox1.Text);
string[] tmp = textBox1.Text.Split(Path.DirectorySeparatorChar);
native = tmp[tmp.Length - 1];
}
bestStr = float.MaxValue;
foreach (var item in selected)
{
foreach (var lItem in item)
{
fileNames.Add(dirName+Path.DirectorySeparatorChar+lItem);
switch (distanceControl1.distDef)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(fileNames, alignFile, false, distanceControl1.profileName);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(fileNames, alignFile, false);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(fileNames, alignFile, false, distanceControl1.CAtoms);
break;
}
dist.InitMeasure();
float distF = float.MaxValue;
if (distanceControl1.distDef != DistanceMeasures.HAMMING)
{
if (!dist.pdbs.molDic.ContainsKey(native) || !dist.pdbs.molDic.ContainsKey(lItem))
continue;
if (dist.pdbs.molDic[native].mol.Chains[0].chainSequence.Length > dist.pdbs.molDic[lItem].mol.Chains[0].chainSequence.Length)
distF = dist.GetDistance(native, lItem) / 100.0f;
else
distF = dist.GetDistance(lItem, native) / 100.0f;
}
else
distF=dist.GetDistance(native, lItem) / 100.0f;
tableDist.Rows.Add(lItem, Convert.ToDouble(String.Format("{0:0.00}", distF)),item.Count);
distList.Add(lItem, distF);
if (bestStr > distF)
bestStr = distF;
fileNames.RemoveAt(fileNames.Count - 1);
currentV++;
}
}
}
public void CalcStat()
{
List<string> fileNames = new List<string>();
List<string> refStructures = new List<string>();
DistanceMeasures measure = distanceControl1.distDef;
DistanceMeasure distTemp = null;
double distRes=0;
maxV = selected.Count;
distList.Clear();
try
{
tableRes = new DataTable();
tableRes.Columns.Add("Cluster Size", typeof(int));
tableRes.Columns.Add("Reference structure", typeof(string));
tableRes.Columns.Add("Distance", typeof(double));
tableRes.Columns.Add("Hidden1", typeof(int));
tableRes.Columns.Add("Hidden2", typeof(string));
if (checkBoxSable.Checked)
{
tableRes.Columns.Add("Dist to Sable", typeof(double));
maxV *= 2;
}
if (checkBox1.Checked)
{
for (int i = 0; i < selected.Count; i++)
maxV += selected[i].Count;
}
fileNames.Add(textBox1.Text);
jury1D jury = new jury1D();
if (distanceControl1.reference)
jury.PrepareJury(dirName, alignFile, distanceControl1.referenceProfile);
refStructures.Clear();
selected.Sort(delegate(List<string> first, List<string> second)
{ return first.Count.CompareTo(second.Count); });
selected.Reverse();
// dataGridView1.Rows.Add(selected.Count);
for (int i = 0; i < selected.Count; i++)
{
string refD = selected[i][0];
ClusterOutput juryO = null;
if (distanceControl1.reference)
{
if (selected[i].Count > 5)
{
juryO = jury.JuryOptWeights(selected[i]);
if (juryO == null)
continue;
refD = juryO.juryLike[0].Key;
if (!fileNames.Contains(dirName + Path.DirectorySeparatorChar + juryO.juryLike[0].Key))
{
fileNames.Add(dirName + Path.DirectorySeparatorChar + juryO.juryLike[0].Key);
refStructures.Add(dirName + Path.DirectorySeparatorChar + refD);
}
}
else
if (!fileNames.Contains(dirName + Path.DirectorySeparatorChar + selected[i][0]))
{
fileNames.Add(dirName + Path.DirectorySeparatorChar + selected[i][0]);
refStructures.Add(dirName + Path.DirectorySeparatorChar + selected[i][0]);
}
}
else
{
dist = PrepareDistanceMeasure(selected[i], measure, dirName);
distTemp = dist;
refD = dist.GetReferenceStructure(selected[i]);
fileNames.Add(dirName + Path.DirectorySeparatorChar + refD);
refStructures.Add(dirName + Path.DirectorySeparatorChar + refD);
}
if (fileNames.Count == 2)
{
switch (measure)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(fileNames, alignFile, false, distanceControl1.profileName);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(fileNames, null, false);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(fileNames, null, false, distanceControl1.CAtoms);
break;
}
dist.InitMeasure();
distRes = Convert.ToDouble(String.Format("{0:0.00}", dist.GetDistance(native, refD) / 100.0));
}
fileNames.RemoveAt(fileNames.Count - 1);
if (checkBoxSable.Checked && refStructures.Count > 0)
tableRes.Rows.Add(selected[i].Count, refD, distRes, i, dirName, 0.0);
else
tableRes.Rows.Add(selected[i].Count, refD, distRes, i, dirName);
currentV++;
}
if (checkBoxSable.Checked && refStructures.Count > 0)
{
Dictionary<string, double> res = null;// SableDist(refStructures);
for (int i = 0; i < refStructures.Count; i++)
{
if (res.ContainsKey(Path.GetFileName(refStructures[i])))
{
DataRow dr = tableDist.Rows[i];
dr[5] = Convert.ToDouble(String.Format("{0:0.00}", res[Path.GetFileName(refStructures[i])]));
}
}
}
if (checkBox1.Checked)
{
CalculateDistToAll();
}
}
catch(Exception ex)
{
exc = ex;
}
}
private void CalculateDistToAll()
{
tableDist = new DataTable();
tableDist.Columns.Add("Reference structure", typeof(string));
tableDist.Columns.Add("Distance", typeof(double));
tableDist.Columns.Add("Cluster size", typeof(int));
List <string> fileNames = new List <string>();
if (textBox1.Text != null && textBox1.Text.Length > 5 && File.Exists(textBox1.Text))
{
fileNames.Add(textBox1.Text);
string[] tmp = textBox1.Text.Split(Path.DirectorySeparatorChar);
native = tmp[tmp.Length - 1];
}
bestStr = float.MaxValue;
foreach (var item in selected)
{
foreach (var lItem in item)
{
fileNames.Add(dirName + Path.DirectorySeparatorChar + lItem);
switch (distanceControl1.distDef)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(fileNames, alignFile, false, distanceControl1.profileName);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(fileNames, alignFile, false);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(fileNames, alignFile, false, distanceControl1.CAtoms);
break;
}
dist.InitMeasure();
float distF = float.MaxValue;
if (distanceControl1.distDef != DistanceMeasures.HAMMING)
{
if (!dist.pdbs.molDic.ContainsKey(native) || !dist.pdbs.molDic.ContainsKey(lItem))
{
continue;
}
if (dist.pdbs.molDic[native].mol.Chains[0].chainSequence.Length > dist.pdbs.molDic[lItem].mol.Chains[0].chainSequence.Length)
{
distF = dist.GetDistance(native, lItem) / 100.0f;
}
else
{
distF = dist.GetDistance(lItem, native) / 100.0f;
}
}
else
{
distF = dist.GetDistance(native, lItem) / 100.0f;
}
tableDist.Rows.Add(lItem, Convert.ToDouble(String.Format("{0:0.00}", distF)), item.Count);
distList.Add(lItem, distF);
if (bestStr > distF)
{
bestStr = distF;
}
fileNames.RemoveAt(fileNames.Count - 1);
currentV++;
}
}
}
public void CalcStat()
{
List <string> fileNames = new List <string>();
List <string> refStructures = new List <string>();
DistanceMeasures measure = distanceControl1.distDef;
DistanceMeasure distTemp = null;
double distRes = 0;
maxV = selected.Count;
distList.Clear();
try
{
tableRes = new DataTable();
tableRes.Columns.Add("Cluster Size", typeof(int));
tableRes.Columns.Add("Reference structure", typeof(string));
tableRes.Columns.Add("Distance", typeof(double));
tableRes.Columns.Add("Hidden1", typeof(int));
tableRes.Columns.Add("Hidden2", typeof(string));
if (checkBoxSable.Checked)
{
tableRes.Columns.Add("Dist to Sable", typeof(double));
maxV *= 2;
}
if (checkBox1.Checked)
{
for (int i = 0; i < selected.Count; i++)
{
maxV += selected[i].Count;
}
}
fileNames.Add(textBox1.Text);
jury1D jury = new jury1D();
if (distanceControl1.reference)
{
jury.PrepareJury(dirName, alignFile, distanceControl1.referenceProfile);
}
refStructures.Clear();
selected.Sort(delegate(List <string> first, List <string> second)
{ return(first.Count.CompareTo(second.Count)); });
selected.Reverse();
// dataGridView1.Rows.Add(selected.Count);
for (int i = 0; i < selected.Count; i++)
{
string refD = selected[i][0];
ClusterOutput juryO = null;
if (distanceControl1.reference)
{
if (selected[i].Count > 5)
{
juryO = jury.JuryOptWeights(selected[i]);
if (juryO == null)
{
continue;
}
refD = juryO.juryLike[0].Key;
if (!fileNames.Contains(dirName + Path.DirectorySeparatorChar + juryO.juryLike[0].Key))
{
fileNames.Add(dirName + Path.DirectorySeparatorChar + juryO.juryLike[0].Key);
refStructures.Add(dirName + Path.DirectorySeparatorChar + refD);
}
}
else
if (!fileNames.Contains(dirName + Path.DirectorySeparatorChar + selected[i][0]))
{
fileNames.Add(dirName + Path.DirectorySeparatorChar + selected[i][0]);
refStructures.Add(dirName + Path.DirectorySeparatorChar + selected[i][0]);
}
}
else
{
dist = PrepareDistanceMeasure(selected[i], measure, dirName);
distTemp = dist;
refD = dist.GetReferenceStructure(selected[i]);
fileNames.Add(dirName + Path.DirectorySeparatorChar + refD);
refStructures.Add(dirName + Path.DirectorySeparatorChar + refD);
}
if (fileNames.Count == 2)
{
switch (measure)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(fileNames, alignFile, false, distanceControl1.profileName);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(fileNames, null, false);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(fileNames, null, false, distanceControl1.CAtoms);
break;
}
dist.InitMeasure();
distRes = Convert.ToDouble(String.Format("{0:0.00}", dist.GetDistance(native, refD) / 100.0));
}
fileNames.RemoveAt(fileNames.Count - 1);
if (checkBoxSable.Checked && refStructures.Count > 0)
{
tableRes.Rows.Add(selected[i].Count, refD, distRes, i, dirName, 0.0);
}
else
{
tableRes.Rows.Add(selected[i].Count, refD, distRes, i, dirName);
}
currentV++;
}
if (checkBoxSable.Checked && refStructures.Count > 0)
{
Dictionary <string, double> res = null;// SableDist(refStructures);
for (int i = 0; i < refStructures.Count; i++)
{
if (res.ContainsKey(Path.GetFileName(refStructures[i])))
{
DataRow dr = tableDist.Rows[i];
dr[5] = Convert.ToDouble(String.Format("{0:0.00}", res[Path.GetFileName(refStructures[i])]));
}
}
}
if (checkBox1.Checked)
{
CalculateDistToAll();
}
}
catch (Exception ex)
{
exc = ex;
}
}
public ClusterOutput DendrogUsingMeasures(List<string> structures)
{
jury1D juryLocal = new jury1D();
juryLocal.PrepareJury(al);
ClusterOutput outC = null;
Dictionary<string, List<int>> dic;
//Console.WriteLine("Start after jury " + Process.GetCurrentProcess().PeakWorkingSet64);
maxV = 4;
currentV = 0;
dic = PrepareKeys(structures,false);
currentV++;
//DebugClass.DebugOn();
//dic = HashEntropyCombine(dic, structures,input.reqClusters);
//Console.WriteLine("Entropy ready after jury " + Process.GetCurrentProcess().PeakWorkingSet64);
DebugClass.WriteMessage("Entropy ready");
//Alternative way to start of UQclust Tree must be finished
//input.relClusters = 10000;
input.relClusters = input.reqClusters;
input.perData = 90;
//dic = FastCombineKeys(dic, structures, false);
dic = FastCombineKeys(dic, structures, true);
DebugClass.WriteMessage("dic size" + dic.Count);
currentV++;
//Console.WriteLine("Combine ready after jury " + Process.GetCurrentProcess().PeakWorkingSet64);
DebugClass.WriteMessage("Combine Keys ready");
Dictionary<string, string> translateToCluster = new Dictionary<string, string>(dic.Count);
List<string> structuresToDendrogram = new List<string>(dic.Count);
List<string> structuresFullPath = new List<string>(dic.Count);
DebugClass.WriteMessage("Number of clusters: "+dic.Count);
int cc = 0;
foreach (var item in dic)
{
if (item.Value.Count > 2)
{
List<string> cluster = new List<string>(item.Value.Count);
foreach (var str in item.Value)
cluster.Add(structures[str]);
ClusterOutput output = juryLocal.JuryOptWeights(cluster);
structuresToDendrogram.Add(output.juryLike[0].Key);
if(alignFile==null)
structuresFullPath.Add(dirName + Path.DirectorySeparatorChar + output.juryLike[0].Key);
else
structuresFullPath.Add(output.juryLike[0].Key);
translateToCluster.Add(output.juryLike[0].Key, item.Key);
}
else
{
structuresToDendrogram.Add(structures[item.Value[0]]);
if(alignFile==null)
structuresFullPath.Add(dirName + Path.DirectorySeparatorChar + structures[item.Value[0]]);
else
structuresFullPath.Add(structures[item.Value[0]]);
translateToCluster.Add(structures[item.Value[0]], item.Key);
}
cc++;
}
currentV++;
DebugClass.WriteMessage("Jury finished");
switch (dMeasure)
{
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(structuresFullPath, alignFile, true, profileName, refJuryProfile);
break;
case DistanceMeasures.COSINE:
dist = new CosineDistance(structuresFullPath, alignFile, jury1d, profileName, refJuryProfile);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(structuresFullPath, "", jury1d, atoms, refJuryProfile);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(structuresFullPath, "", jury1d, refJuryProfile);
break;
}
// return new ClusterOutput();
DebugClass.WriteMessage("Start hierarchical");
//Console.WriteLine("Start hierarchical " + Process.GetCurrentProcess().PeakWorkingSet64);
currentV = maxV;
hk = new hierarchicalCluster(dist, linkageType, dirName);
dist.InitMeasure();
//Now just add strctures to the leaves
outC = hk.HierarchicalClustering(structuresToDendrogram);
DebugClass.WriteMessage("Stop hierarchical");
List<HClusterNode> hLeaves = outC.hNode.GetLeaves();
foreach(var item in hLeaves)
{
if (translateToCluster.ContainsKey(item.setStruct[0]))
{
foreach (var str in dic[translateToCluster[item.setStruct[0]]])
if (item.setStruct[0] != structures[str])
item.setStruct.Add(structures[str]);
}
else
throw new Exception("Cannot add structure. Something is wrong");
}
outC.hNode.RedoSetStructures();
return outC;
}
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;
}
int GetDist(DistanceMeasures distance,string dirName,string item1,string item2)
{
DistanceMeasure dist = null;
List<string> targets = new List<string>();
// targets.Add(dirName + Path.DirectorySeparatorChar + item1);
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);
}