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); }