private DistanceMeasure CreateMeasureForDCD(DCDFile dcd, DistanceMeasures measure, PDB.PDBMODE atoms, bool jury1d, string alignFileName,
string profileName = null, string refJuryProfile = null)
{
DistanceMeasure dist = null;
switch (measure)
{
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(dcd, alignFileName, true, profileName, refJuryProfile);
}
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(dcd, alignFileName, jury1d, atoms, refJuryProfile);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(dcd, alignFileName, jury1d, refJuryProfile);
break;
case DistanceMeasures.GDT_TS:
dist = new GDT_TS(dcd, alignFileName, jury1d, refJuryProfile);
break;
}
dist.InitMeasure();
return(dist);
}
public void MakeProfiles(DCDFile dcd = null)
{
int active = 0;
List <profileNode> prof = GetActiveProfiles();
if (prof == null)
{
return;
}
profilesNum = GetActiveProfiles().Count;
profilesProgress = new List <double>(profilesNum);
active = GenerateActiveProfiles(masterNode, dcd);
foreach (var item in profiles)
{
foreach (var it in item.Value)
{
if (it.Value.profile.Count == 0)
{
throw new Exception("Failed to generate profiles!");
}
}
}
if (active == 0)
{
throw new Exception("Error: there are no active profiles!");
}
}
void RunHTree(string name, string dirName, string alignmentFile = null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
HashCluster hCluster;
if (dcd != null)
{
hCluster = new HashCluster(dcd, opt.hash);
}
else
if (alignmentFile != null)
{
hCluster = new HashCluster("", alignmentFile, opt.hash);
}
else
{
hCluster = new HashCluster(dirName, null, opt.hash);
}
HTree h = new HTree(dirName, alignmentFile, hCluster);
beginJob(currentProcessName, h.ToString(), dirName, "HAMMING");
progressDic.Add(name, h);
hCluster.InitHashCluster();
DateTime cpuPart2 = DateTime.Now;
ClusterOutput output = new ClusterOutput();
output = h.RunHTree();
UpdateOutput(name, dirName, alignmentFile, output, "NONE", cpuPart1, cpuPart2, h);
}
protected void InitMeasure(DCDFile dcd, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
{
base.InitMeasure(dcd, alignFile, flag, refJuryProfile);
DCDReader readDCD = new DCDReader(dcd);
pdbs = new PDBFiles();
readDCD.DCDPrepareReading(dcd.dcdFile, dcd.pdbFile);
int counter = 0;
bool cont = true;
do
{
MemoryStream mStream = new MemoryStream();
StreamWriter wStream = new StreamWriter(mStream);
cont=readDCD.ReadAndSavePDB(wStream);
string name = "Model" + counter++;
mStream.Position = 0;
pdbs.AddPDB(mStream, allAtoms, name);
}
while(cont);
readDCD.FinishDCDReading();
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(alignFile);
structNames = CheckAvailableStructures();
atomDic=pdbs.MakeAllAtomsDic();
}
public HashCluster(DCDFile dcd, HashCInput input)
{
this.dcd = dcd;
this.input = input;
currentV = 0;
maxV = 4;
threadNumbers = dirSettings.numberOfCores;
}
public HashClusterDendrog(DCDFile dcd, HashCInput input, HierarchicalCInput dendrogOpt) : base(dcd, input)
{
this.dMeasure = dendrogOpt.distance;
this.linkageType = dendrogOpt.linkageType;
this.atoms = dendrogOpt.atoms;
this.jury1d = dendrogOpt.reference1DjuryH;
this.profileName = dendrogOpt.hammingProfile;
this.refJuryProfile = dendrogOpt.jury1DProfileH;
hier = dendrogOpt;
}
public Rmsd(DCDFile dcd, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
{
order = true;
dirSettings.Load();
this.dcd = dcd;
this.alignFile=alignFile;
this.flag=flag;
this.allAtoms=allAtoms;
this.refJuryProfile = refJuryProfile;
}
public HashClusterDendrog(DCDFile dcd, HashCInput input,DistanceMeasures dMeasure, AglomerativeType linkageType,PDB.PDBMODE atoms,bool jury1d,string alignFileName,
string profileName=null,string refJuryProfile=null):base(dcd,input)
{
this.dMeasure=dMeasure;
this.linkageType=linkageType;
this.atoms = atoms;
this.jury1d = jury1d;
this.profileName = profileName;
this.refJuryProfile = refJuryProfile;
}
private void Run1DJury(string name, string dirName, string alignFile = null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
ClusterOutput output;
jury1D ju = new jury1D();
if (beginJob != null)
{
beginJob(currentProcessName, ju.ToString(), dirName, "NONE");
}
progressDic.Add(name, ju);
//DistanceMeasure distance = CreateMeasure();
if (opt.other.alignGenerate)
{
opt.other.alignFileName = "";
}
if (alignFile != null)
{
ju.PrepareJury(alignFile, opt.other.juryProfile);
}
else
if (dcd != null)
{
ju.PrepareJury(dcd, alignFile, opt.other.juryProfile);
}
else
{
ju.PrepareJury(dirName, alignFile, opt.other.juryProfile);
}
clType = ju.ToString();
DateTime cpuPart2 = DateTime.Now;
//jury1D ju = new jury1D(opt.weightHE,opt.weightC,(JuryDistance) distance);
//output = ju.JuryOpt(new List<string>(ju.stateAlign.Keys));
if (ju.alignKeys != null)
{
output = ju.JuryOptWeights(ju.alignKeys);
}
else
{
UpadateJobInfo(name, true, false);
throw new Exception("Alignment is epmty! Check errors");
}
UpdateOutput(name, dirName, alignFile, output, ju.ToString(), cpuPart1, cpuPart2, ju);
}
public void PrepareProfiles(DCDFile dcd)
{
profiles = new Dictionary <string, Dictionary <string, protInfo> >();
RemoveOutFiles();
MakeProfiles(dcd);
if (File.Exists(listFile))
{
File.Delete(listFile);
}
}
private void RunSift(string name, string dirName, DCDFile dcd = null)
{
DateTime cpuStart = DateTime.Now;
ClusterOutput output = null;
Sift s = new Sift();
if (beginJob != null)
{
beginJob(currentProcessName, s.ToString(), dirName, "NONE");
}
progressDic.Add(name, s);
clType = s.ToString();
output = s.RunSift(dirName);
UpdateOutput(name, dirName, null, output, "Sift", cpuStart, DateTime.Now, s);
}
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 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");
}
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");
}
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 void Prepare(DCDFile dcd, Settings dirSettings, string profName)
{
StartAlignment(dirSettings, profName, dcd, null, null);
}
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);
}
public DCDReader(DCDFile dcdFile)
{
this.dcdFile = dcdFile;
}
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);
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.linkageType,dirName);
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 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 RunHashDendrog(string name, string dirName, string alignmentFile = null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
HashCluster hk = null;
if (dcd != null)
{
hk = new HashCluster(dcd, opt.hash);
}
else
if (alignmentFile != null)
{
hk = new HashCluster("", alignmentFile, opt.hash);
}
else
{
hk = new HashCluster(dirName, null, opt.hash);
}
progressDic.Add(name, hk);
hk.InitHashCluster();
DateTime cpuPart2 = DateTime.Now;
ClusterOutput output;
output = hk.RunHashDendrog();
UpdateOutput(name, dirName, alignmentFile, output, "NONE", cpuPart1, cpuPart2, hk);
}
private DistanceMeasure CreateMeasureForDCD(DCDFile dcd, DistanceMeasures measure, PDB.PDBMODE atoms, bool jury1d, string alignFileName,
string profileName = null, string refJuryProfile = null)
{
DistanceMeasure dist=null;
switch (measure)
{
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(dcd, alignFileName, true, profileName, refJuryProfile);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(dcd, alignFileName, jury1d, atoms, refJuryProfile);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(dcd, alignFileName, jury1d, refJuryProfile);
break;
case DistanceMeasures.GDT_TS:
dist = new GDT_TS(dcd, alignFileName, jury1d, refJuryProfile);
break;
}
dist.InitMeasure();
return dist;
}
private void Run1DJury(string name, string dirName, string alignFile=null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
ClusterOutput output;
jury1D ju=new jury1D();
progressDic.Add(name,ju);
//DistanceMeasure distance = CreateMeasure();
if (opt.other.alignGenerate)
opt.other.alignFileName = "";
if (alignFile != null)
ju.PrepareJury(alignFile, opt.other.juryProfile);
else
if (dcd != null)
ju.PrepareJury(dcd, alignFile, opt.other.juryProfile);
else
ju.PrepareJury(dirName, alignFile, opt.other.juryProfile);
clType = ju.ToString();
DateTime cpuPart2 = DateTime.Now;
//jury1D ju = new jury1D(opt.weightHE,opt.weightC,(JuryDistance) distance);
//output = ju.JuryOpt(new List<string>(ju.stateAlign.Keys));
if (ju.alignKeys != null)
{
output = ju.JuryOptWeights(ju.alignKeys);
}
else
{
UpadateJobInfo(name, true, false);
throw new Exception("Alignment is epmty! Check errors");
}
UpdateOutput(name, dirName,alignFile, output,ju.ToString(), cpuPart1,cpuPart2, ju);
}
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);
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);
}
void PrepareForDCD(DCDFile dcd, HashCInput input)
{
dirSettings.Load();
this.dcd = dcd;
al = new Alignment();
al.Prepare(dcd, dirSettings, input.profileName);
al.MyAlign(alignFile);
stateAlign = al.GetStateAlign();
if (input.regular)
{
if (input.profileName == input.profileNameReg)
stateAlignReg = stateAlign;
else
{
Alignment alReg = new Alignment();
alReg.Prepare(dcd, dirSettings, input.profileNameReg);
alReg.MyAlign(alignFile);
stateAlignReg = alReg.GetStateAlign();
}
}
this.input = input;
}
public MaxSub(DCDFile dcd, string alignFile, bool flag, string refJuryProfile = null)
: base(dcd, alignFile, flag, PDBMODE.ONLY_CA,refJuryProfile)
{
order = true;
maxSimilarity = 0.0;
}
private void RunHashCluster(string name, string dirName, string alignmentFile = null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
HashCluster hk = null;
if (dcd != null)
{
hk = new HashCluster(dcd, opt.hash);
}
else
if (alignmentFile != null)
{
hk = new HashCluster("", alignmentFile, opt.hash);
}
else
{
hk = new HashCluster(dirName, null, opt.hash);
}
progressDic.Add(name, hk);
if (beginJob != null)
{
beginJob(currentProcessName, hk.ToString(), dirName, "HAMMING");
}
hk.InitHashCluster();
DateTime cpuPart2 = DateTime.Now;
ClusterOutput output;
output = hk.RunHashCluster();
UpdateOutput(name, dirName, alignmentFile, output, "HAMMING", cpuPart1, cpuPart2, hk);
}
public JuryDistance(DCDFile dcd, string alignFile, bool flag, string profileName, string refJuryProfile = null)
:base(dcd, alignFile, flag, profileName, refJuryProfile)
{
}
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);
}
public void PrepareJury(DCDFile dcd, string alignFile, string profile = null)
{
currentProfile = profile;
al.Prepare(dcd, set, currentProfile);
CommonConstr(alignFile, profile);
}
private void RunHashDendrogCombine(string name, string dirName, string alignmentFile = null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
HashClusterDendrog hk = null;
if (dcd != null)
hk = new HashClusterDendrog(dcd, opt.hierarchical.hash, opt.hierarchical.distance, opt.hierarchical.linkageType, opt.hierarchical.atoms, opt.hierarchical.reference1DjuryH,
opt.hierarchical.alignmentFileName, opt.hierarchical.hammingProfile, opt.hierarchical.jury1DProfileH);
else
if (alignmentFile != null)
hk = new HashClusterDendrog(null, alignmentFile, opt.hierarchical.hash, opt.hierarchical.distance, opt.hierarchical.linkageType, opt.hierarchical.atoms, opt.hierarchical.reference1DjuryH,
opt.hierarchical.alignmentFileName, opt.hierarchical.hammingProfile, opt.hierarchical.jury1DProfileH);
else
hk = new HashClusterDendrog(dirName, null, opt.hierarchical.hash, opt.hierarchical.distance, opt.hierarchical.linkageType, opt.hierarchical.atoms, opt.hierarchical.reference1DjuryH,
opt.hierarchical.alignmentFileName, opt.hierarchical.hammingProfile, opt.hierarchical.jury1DProfileH);
ClusterOutput output;
progressDic.Add(name, hk);
hk.InitHashCluster();
DateTime cpuPart2 = DateTime.Now;
output = hk.RunHashDendrogCombine();
UpdateOutput(name, dirName,alignmentFile, output, hk.UsedMeasure(), cpuPart1, cpuPart2, hk);
}
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);
}
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);
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 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 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);
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);
}
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");
}
private void RunSift(string name, string dirName,DCDFile dcd = null)
{
DateTime cpuStart = DateTime.Now;
ClusterOutput output = null;
Sift s = new Sift();
progressDic.Add(name, s);
clType = s.ToString();
output=s.RunSift(dirName);
UpdateOutput(name, dirName, null,output, "Sift",cpuStart,DateTime.Now, s);
}
public void Prepare(DCDFile dcd,Settings dirSettings, string profName)
{
StartAlignment(dirSettings, profName, dcd, null, null);
}
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);
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 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");
}
private void RunHashCluster(string name, string dirName, string alignmentFile=null,DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
HashCluster hk = null;
if (dcd != null)
hk = new HashCluster(dcd, opt.hash);
else
if(alignmentFile!=null)
hk = new HashCluster("", alignmentFile, opt.hash);
else
hk = new HashCluster(dirName, null, opt.hash);
progressDic.Add(name, hk);
hk.InitHashCluster();
DateTime cpuPart2 = DateTime.Now;
ClusterOutput output;
output = hk.RunHashCluster();
UpdateOutput(name, dirName,alignmentFile, output, "NONE", cpuPart1, cpuPart2, hk);
}
private void RunHashDendrogCombine(string name, string dirName, string alignmentFile = null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
HashClusterDendrog hk = null;
if (dcd != null)
{
hk = new HashClusterDendrog(dcd, opt.hash, opt.hierarchical);
}
else
if (alignmentFile != null)
{
hk = new HashClusterDendrog(null, alignmentFile, opt.hash, opt.hierarchical);
}
else
{
hk = new HashClusterDendrog(dirName, null, opt.hash, opt.hierarchical);
}
ClusterOutput output;
if (beginJob != null)
{
beginJob(currentProcessName, hk.ToString(), dirName, "NONE");
}
progressDic.Add(name, hk);
hk.InitHashCluster();
DateTime cpuPart2 = DateTime.Now;
output = hk.RunHashDendrogCombine();
UpdateOutput(name, dirName, alignmentFile, output, hk.UsedMeasure(), cpuPart1, cpuPart2, hk);
}
