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 void Prepare(string profilesFile, string profName)
{
r.LoadProfiles(profName);
r.listFile = profilesFile;
DebugClass.WriteMessage("profiles gen started " + profName);
r.MakeProfiles();
DebugClass.WriteMessage("Prfofiles end");
}
public void LoadProfiles(string profileName)
{
if (File.Exists(profileName))
{
LoadTree(profileName);
if (masterNode == null)
{
DebugClass.WriteMessage("Ups no master node");
}
//SetupCodingAllNodes(masterNode);
}
else
{
throw new Exception("Profile: " + profileName + " not exists. Cannot be loaded!");
}
}
private void StartAlignment(Settings dirSettings, string profName, DCDFile dcd, string dirName, List <string> fileNames)
{
DebugClass.WriteMessage("Start align");
string refFile = null;
this.dirSettings = dirSettings;
// r = new ProfileTree();
r.LoadProfiles(profName);
if (dcd != null)
{
DebugClass.WriteMessage("profiles gen started");
r.PrepareProfiles(dcd);
}
else
if (dirName != null)
{
refFile = dirName + ".ref";
DebugClass.WriteMessage("profiles gen started");
r.PrepareProfiles(dirName);
DebugClass.WriteMessage("finished");
refSeq = ReadRefSeq(refFile);
}
else
{
maxV = fileNames.Count;
string name = fileNames[0];
if (fileNames[0].Contains("|"))
{
string[] aux = fileNames[0].Split('|');
name = aux[0];
}
refFile = Directory.GetParent(name).ToString() + ".ref";
DebugClass.WriteMessage("profiles gen started");
r.PrepareProfiles(fileNames);
DebugClass.WriteMessage("finished");
refSeq = ReadRefSeq(refFile);
}
DebugClass.WriteMessage("Prfofiles end");
}
public int GenerateActiveProfiles(Dictionary <string, profileNode> node, DCDFile dcd = null)
{
int activeProfiles = 0;
if (node == null)
{
node = masterNode;
}
if (profiles == null)
{
profiles = new Dictionary <string, Dictionary <string, protInfo> >();
}
DebugClass.WriteMessage("Profiling started");
foreach (var item in node.Values)
{
if (item.active)
{
Dictionary <string, protInfo> profString;
mgr.ResetProgress();
if (item.GetNumberofStates() == 0)
{
if (item.profProgram.Length > 0)
{
if (!profiles.ContainsKey(item.profName))
{
activeProfiles++;
if (File.Exists(item.OutFileName))
{
File.Delete(item.OutFileName);
}
GenerateProfile(item);
FileInfo f = new FileInfo(item.OutFileName);
if (!File.Exists(item.OutFileName) || f == null || f.Length == 0)
{
throw new Exception("Error: profile " + item.profName + " did not generate output " + item.OutFileName);
}
}
}
}
else
{
DebugClass.WriteMessage("Run profiling");
if (dcd == null)
{
mgr.RunProfile(item.internalName, listFile);
}
else
{
mgr.RunProfile(item.internalName, dcd);
}
activeProfiles++;
}
if (item.childrens.Count > 0)
{
activeProfiles += GenerateActiveProfiles(item.childrens);
}
else
{
if (!profiles.ContainsKey(item.profName))
{
if (item.GetNumberofStates() == 0)
{
profString = ReadProfile(item);
}
else
{
if (dcd == null)
{
profString = mgr.GetProfile(item, listFile);
}
else
{
profString = InternalProfilesManager.GetProfile(item, dcd);
}
}
if (profString != null && profString.Count > 0)
{
profiles.Add(item.profName, profString);
}
else
{
throw new Exception("For profile " + item.profName + " profiles has not been generated!");
}
}
}
profilesProgress.Add(mgr.ProgressUpdate());
}
}
progressObject = null;
return(activeProfiles);
}
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);
}
public void ReadOptionFile(string fileName)
{
if (File.Exists(fileName))
{
string line;
MemberInfo memB;
StreamReader r = new StreamReader(fileName);
// DebugClass.DebugOn();
DebugClass.WriteMessage("Start reading " + fileName);
while (!r.EndOfStream)
{
line = r.ReadLine();
if (line.Contains("#####"))
{
if (line.Contains("Parameters hierarchical"))
{
hierarchical.ReadOptionFile(r);
}
else
if (line.Contains("Parameters threshold"))
{
threshold.ReadOptionFile(r);
}
else
if (line.Contains("Parameters other"))
{
other.ReadOptionFile(r);
}
else
if (line.Contains("Parameters Hash"))
{
hash.ReadOptionFile(r);
}
else
if (line.Contains("Parameters kmeans"))
{
kmeans.ReadOptionFile(r);
}
}
line = line.Replace("# ", "#");
line = line.TrimEnd(new char [] { '\r', '\n' });
string[] strTab = line.Split('#');
if (strTab[1].Length == 0)
{
continue;
}
if (dicField.ContainsKey(strTab[0]))
{
if (dicField[strTab[0]].Contains("Generic.List"))
{
if (strTab[1].EndsWith(";"))
{
strTab[1] = strTab[1].Remove(strTab[1].Length - 1, 1);
}
string[] aux = strTab[1].Split(';');
if (strTab[0].Contains("dcd"))
{
dcdFiles.Clear();
foreach (var item in aux)
{
string[] tmp = item.Split(',');
DCDFile dcd = new DCDFile();
dcd.dcdFile = tmp[0];
dcd.pdbFile = tmp[1];
dcd.tempDir = tmp[2];
dcdFiles.Add(dcd);
}
}
else
{
if (strTab[0].Contains("prof"))
{
profileFiles.Clear();
foreach (var item in aux)
{
profileFiles.Add(item);
}
}
if (strTab[0].Contains("algorithm"))
{
clusterAlgorithm.Clear();
foreach (var item in aux)
{
clusterAlgorithm.Add((ClusterAlgorithm)Enum.Parse(typeof(ClusterAlgorithm), item));
}
}
if (strTab[0].Contains("data"))
{
dataDir.Clear();
foreach (var item in aux)
{
dataDir.Add(item);
}
}
continue;
}
}
memB = dicMem[strTab[0]];
string ww = memB.ReflectedType.GetField(memB.Name).FieldType.Name;
switch (ww)
{
case "string":
case "String":
memB.ReflectedType.GetField(memB.Name).SetValue(this, strTab[1]);
break;
case "Boolean":
memB.ReflectedType.GetField(memB.Name).SetValue(this, Convert.ToBoolean(strTab[1]));
break;
case "Single":
memB.ReflectedType.GetField(memB.Name).SetValue(this, Convert.ToSingle(strTab[1]));
break;
case "Int32":
memB.ReflectedType.GetField(memB.Name).SetValue(this, Convert.ToInt32(strTab[1]));
break;
case "Initialization":
memB.ReflectedType.GetField(memB.Name).SetValue(this, Enum.Parse(typeof(Initialization), strTab[1]));
break;
case "PDBMODE":
memB.ReflectedType.GetField(memB.Name).SetValue(this, Enum.Parse(typeof(PDB.PDBMODE), strTab[1]));
break;
case "ClusterAlgorithm":
memB.ReflectedType.GetField(memB.Name).SetValue(this, Enum.Parse(typeof(ClusterAlgorithm), strTab[1]));
break;
case "DistanceMeasures":
memB.ReflectedType.GetField(memB.Name).SetValue(this, Enum.Parse(typeof(DistanceMeasures), strTab[1]));
break;
case "AglomerativeType":
memB.ReflectedType.GetField(memB.Name).SetValue(this, Enum.Parse(typeof(AglomerativeType), strTab[1]));
break;
case "COL_SELECTION":
memB.ReflectedType.GetField(memB.Name).SetValue(this, Enum.Parse(typeof(COL_SELECTION), strTab[1]));
break;
}
//SetValue(this, strTab[1]);
}
else
{
DebugClass.WriteMessage("Not recognized: " + strTab[0]);
}
}
r.Close();
}
else
{
throw new Exception("Config file not found");
}
DebugClass.WriteMessage("Reading finished");
}
public void StartAll(object processParams)
{
ErrorBase.ClearErrors();
DebugClass.DebugOn();
string orgProcessName = ((ThreadParam)processParams).name;
currentProcessName = ((ThreadParam)processParams).name;
int counter = 1;
try
{
if (opt.profileFiles.Count == 0)
{
foreach (var alg in opt.clusterAlgorithm)
{
foreach (var item in opt.dataDir)
{
// if (tTimer != null)
// tTimer.Start();
currentProcessName = MakeName(processParams, alg, counter);
//if (beginJob != null)
// beginJob(currentProcessName, alg.ToString("g"), item, opt.GetDistanceMeasure(alg));
switch (alg)
{
case ClusterAlgorithm.uQlustTree:
RunHashDendrogCombine(currentProcessName, item);
break;
case ClusterAlgorithm.HashCluster:
RunHashCluster(currentProcessName, item);
break;
case ClusterAlgorithm.HierarchicalCluster:
RunHierarchicalCluster(currentProcessName, item);
break;
case ClusterAlgorithm.HKmeans:
RunHKMeans(currentProcessName, item);
break;
case ClusterAlgorithm.FastHCluster:
RunFastHCluster(currentProcessName, item);
break;
case ClusterAlgorithm.Kmeans:
RunKMeans(currentProcessName, item);
break;
case ClusterAlgorithm.BakerCluster:
RunBakerCluster(currentProcessName, item);
break;
case ClusterAlgorithm.Jury1D:
Run1DJury(currentProcessName, item);
break;
case ClusterAlgorithm.Jury3D:
Run3DJury(currentProcessName, item);
break;
case ClusterAlgorithm.Sift:
RunSift(currentProcessName, item);
break;
case ClusterAlgorithm.HTree:
RunHTree(currentProcessName, item);
break;
}
counter++;
}
foreach (var item in opt.dcdFiles)
{
// if (tTimer != null)
// tTimer.Start();
currentProcessName = MakeName(processParams, alg, counter);
//if (beginJob != null)
// beginJob(currentProcessName, opt.clusterAlgorithm.ToString(), item.dcdFile, opt.GetDistanceMeasure(alg));
switch (alg)
{
case ClusterAlgorithm.uQlustTree:
RunHashDendrog(currentProcessName, null, null, item);
break;
case ClusterAlgorithm.HashCluster:
RunHashCluster(currentProcessName, null, null, item);
break;
case ClusterAlgorithm.HierarchicalCluster:
RunHierarchicalCluster(currentProcessName, null, null, item);
break;
case ClusterAlgorithm.HKmeans:
RunHKMeans(currentProcessName, null, null, item);
break;
case ClusterAlgorithm.FastHCluster:
RunFastHCluster(currentProcessName, null, null, item);
break;
case ClusterAlgorithm.Kmeans:
RunKMeans(currentProcessName, null, null, item);
break;
case ClusterAlgorithm.BakerCluster:
RunBakerCluster(currentProcessName, null, null, item);
break;
case ClusterAlgorithm.Jury1D:
Run1DJury(currentProcessName, null, null, item);
break;
case ClusterAlgorithm.Jury3D:
Run3DJury(currentProcessName, null, null, item);
break;
case ClusterAlgorithm.Sift:
RunSift(currentProcessName, null, item);
break;
case ClusterAlgorithm.HTree:
RunHTree(currentProcessName, null, null, item);
break;
}
counter++;
}
}
}
else
{
foreach (var alg in opt.clusterAlgorithm)
{
foreach (var item in opt.profileFiles)
{
// if (tTimer != null)
// tTimer.Start();
currentProcessName = MakeName(processParams, alg, counter);
// if (beginJob != null)
// beginJob(currentProcessName, opt.clusterAlgorithm.ToString(), item, opt.GetDistanceMeasure(alg));
switch (alg)
{
case ClusterAlgorithm.uQlustTree:
RunHashDendrogCombine(currentProcessName, item, item);
//RunHashDendrog(currentProcessName, null, item);
break;
case ClusterAlgorithm.HashCluster:
RunHashCluster(currentProcessName, item, item);
break;
case ClusterAlgorithm.HierarchicalCluster:
RunHierarchicalCluster(currentProcessName, item, item);
break;
case ClusterAlgorithm.HKmeans:
RunHKMeans(currentProcessName, item, item);
break;
case ClusterAlgorithm.FastHCluster:
RunFastHCluster(currentProcessName, item, item);
break;
case ClusterAlgorithm.Kmeans:
RunKMeans(currentProcessName, item, item);
break;
case ClusterAlgorithm.BakerCluster:
RunBakerCluster(currentProcessName, item, item);
break;
case ClusterAlgorithm.Jury1D:
Run1DJury(currentProcessName, item, item);
break;
case ClusterAlgorithm.Jury3D:
Run3DJury(currentProcessName, item, item);
break;
case ClusterAlgorithm.HTree:
RunHTree(currentProcessName, item, item);
break;
}
counter++;
}
}
}
FinishThread(orgProcessName, false);
}
catch (Exception ex)
{
FinishThread(orgProcessName, true);
message(ex.Message);
}
DebugClass.DebugOff();
}
