private void AlignProfile(string protName, string profileName, List <byte> prof)
{
List <byte> ll = new List <byte>(prof.Count);
int m = 0;
if (align == null || align[profileName] == null || !align[profileName].ContainsKey(protName))
{
foreach (var item in prof)
{
ll.Add(item);
}
}
else
{
string alignProfile = align[profileName][protName];
for (int i = 0; i < alignProfile.Length; i++)
{
if (alignProfile[i] == '-')
{
ll.Add(0);
continue;
}
if (m < prof.Count)
{
ll.Add(prof[m++]);
}
else
{
ErrorBase.AddErrors("Profile " + profileName + " for " + protName + " seems to be incorect");
}
}
}
protInfo tmp = new protInfo();
if (r.profiles[profileName].ContainsKey(protName))
{
tmp = r.profiles[profileName][protName];
tmp.alignment = ll;
r.profiles[profileName][protName] = tmp;
}
}
public Dictionary <string, List <byte> > CombineProfiles(string protName, Dictionary <string, Dictionary <string, protInfo> > pr)
{
if (protCombineStates == null)
{
protCombineStates = new Dictionary <string, List <byte> >();
}
if (combine == profileCombination.JOIN_STATES)
{
List <string> profName = new List <string>(pr.Keys);
List <string> states = new List <string>(pr[profName[0]][protName].alignment.Count);
protInfo info = pr[profName[0]][protName];
for (int i = 0; i < info.alignment.Count; i++)
{
string currentState = "";
foreach (var profileName in pr.Keys)
{
byte cc = pr[profileName][protName].alignment[i];
if (cc == 0)
{
currentState = "0";
break;
}
currentState += cc.ToString();
}
states.Add(currentState);
}
if (states.Count > 0)
{
//return states;
if (protCombineStates.Count > 0)
{
List <string> keys = new List <string>(protCombineStates.Keys);
if (states.Count == protCombineStates[keys[0]].Count)
{
AddItemsCombineStates(protName, states);
}
else
{
ErrorBase.AddErrors("Wrong alignment: " + protName);
}
}
else
{
AddItemsCombineStates(protName, states);
}
}
}
else
{
List <string> profNames = new List <string>(pr.Keys);
for (int i = 0; i < profNames.Count; i++)
{
List <string> codes = new List <string>();
foreach (var code in pr[profNames[i]][protName].alignment)
{
if (code != 0)
{
codes.Add(code.ToString() + "_" + i);
}
else
{
codes.Add("0");
}
AddItemsCombineStates(protName, codes);
codes.Clear();
}
}
}
return(protCombineStates);
}
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();
}
