private StatClust Calc(ClusterOutput outp,bool flag)
{
List <string> five=new List<string>();
List<string> listFiles = new List<string>();
//if (outp == null || outp.clusters == null)
// return null;
if(outp==null || outp.dirName==null)
return null;
string []aux=outp.dirName.Split(Path.DirectorySeparatorChar);
string native=aux[aux.Length-1]+".pdb";
string dirM = "";
for (int i = 0; i < aux.Length - 1; i++)
dirM += aux[i] + Path.DirectorySeparatorChar;
native = dirM + native;
if(!File.Exists(native))
return null;
five.Add(native);
// jury1D jury = new jury1D(outp.dirName, "", "C:\\data\\dcd\\SS_SA9internal.profiles");
// jury1D jury = new jury1D(outp.dirName, "", "C:\\data\\dcd\\SS3_SA9_jury_internal.profiles");
//jury1D jury = new jury1D(outp.dirName, "", "C:\\data\\dcd\\SS8_SA3_jury_internal.profiles");
jury1D jury;
// jury1D jury = new jury1D(outp.dirName, "", "C:\\data\\dcd\\SS_Contact_jury_internal.profiles");
if(outp.clusters!=null)
{
outp.clusters.Sort((a,b)=>b.Count.CompareTo(a.Count));
int end = outp.clusters.Count;
if (outp.clusters.Count > 5)
end = 5;
for (int i = 0; i < end; i++)
{
listFiles.Clear();
foreach (var item in outp.clusters[i])
{
listFiles.Add(outp.dirName + Path.DirectorySeparatorChar+item);
}
//
//
//Sift sift = new Sift(listFiles);
//ClusterOutput oo = sift.Shape();
if (flag)
{
DistanceMeasure distRmsd = new Rmsd(listFiles, "", false, uQlustCore.PDB.PDBMODE.ONLY_CA);
distRmsd.InitMeasure();
string strName = distRmsd.GetReferenceStructure(outp.clusters[i]);
five.Add(outp.dirName + Path.DirectorySeparatorChar + strName);
}
else
{
jury = new jury1D();
jury.PrepareJury(listFiles, "", "Z:\\dcd\\SS3_SA9_jury_internal.profiles");
ClusterOutput oo = jury.JuryOptWeights(outp.clusters[i]);
if (oo == null)
continue;
five.Add(outp.dirName + Path.DirectorySeparatorChar + oo.juryLike[0].Key);
}
//five.Add(outp.dirName + Path.DirectorySeparatorChar + outp.clusters[i][0]);
}
}
if (outp.hNode != null)
{
int end;
List<List<string>> cli=outp.hNode.GetClusters(10);
cli.Sort((a, b) => b.Count.CompareTo(a.Count));
outp.clusters = new List<List<string>>();
end = cli.Count;
if (cli.Count > 5)
end = 5;
for (int i = 0; i < end; i++)
{
// listFiles.Clear();
//foreach (var item in cli[i])
//{
//listFiles.Add(
//}
listFiles.Clear();
foreach (var item in cli[i])
{
listFiles.Add(outp.dirName + Path.DirectorySeparatorChar + item);
}
jury = new jury1D();
jury.PrepareJury(listFiles, "", "C:\\data\\dcd\\SS8_SA3_jury_internal.profiles");
outp.clusters.Add(cli[0]); //jury
ClusterOutput oo = jury.JuryOptWeights(cli[i]);
if (oo == null)
continue;
five.Add(outp.dirName + Path.DirectorySeparatorChar + cli[i][0]);
//five.Add(outp.dirName + Path.DirectorySeparatorChar + strName);
}
}
if (outp.juryLike != null)
{
int end = outp.juryLike.Count;
if (outp.juryLike.Count > 5)
end = 5;
for (int i = 0; i < end; i++)
five.Add(outp.dirName + Path.DirectorySeparatorChar + outp.juryLike[i].Key);
}
// DistanceMeasure dist;
// dist = new Rmsd(five, "", false, PDB.PDBMODE.ONLY_CA);
// dist = new MaxSub(five, "", false);
Dictionary<string, double> cc = ReadScore(aux[aux.Length - 1]);
if (cc == null)
return null ;
StatClust stCLust = new StatClust();
string[] tt1 = native.Split(Path.DirectorySeparatorChar);
stCLust.native = tt1[tt1.Length - 1];
for (int i = 1; i < five.Count; i++)
{
string[] tt2 = five[i].Split(Path.DirectorySeparatorChar);
// double rmsd = dist.GetDistance(tt1[tt1.Length-1], tt2[tt2.Length-1]) /100.0;
double rmsd=0;
if (cc.ContainsKey(tt2[tt2.Length-1]))
rmsd = cc[tt2[tt2.Length - 1]];
if (rmsd > stCLust.rmsd)
{
if (outp.juryLike != null)
stCLust.size = outp.juryLike.Count;
else
stCLust.size = outp.clusters[i - 1].Count;
stCLust.rmsd = rmsd;
string[] dd = five[i].Split(Path.DirectorySeparatorChar);
stCLust.reference = dd[dd.Length-1];
}
}
if (stCLust.rmsd < 1000)
{
avrSum += stCLust.rmsd;
avrCount++;
}
if (outp.hNode != null)
{
outp.clusters.Clear();
outp.clusters = null;
}
return stCLust;
}
private void button2_Click(object sender, EventArgs e)
{
string[] aux;
if(checkBox1.Checked)
{
if(jury1DSetup1.profileName==null || jury1DSetup1.profileName.Length==0)
{
MessageBox.Show("Profile name for 1djury must be specified!");
this.DialogResult = DialogResult.None;
return;
}
jury1D jury = new jury1D();
jury.PrepareJury(structures, "",jury1DSetup1.profileName);
List <string> prep=new List<string>();
foreach (var item in structures)
{
aux = item.Split(Path.DirectorySeparatorChar);
prep.Add(aux[aux.Length - 1]);
}
ClusterOutput oc=jury.JuryOptWeights(prep);
for(int i=0;i<selectBest1.bestNumber;i++)
bestJuryStructures.Add(oc.juryLike[i].Key);
}
this.DialogResult = DialogResult.OK;
if (selectBest1.getFileName != null && File.Exists(selectBest1.getFileName))
{
DistanceMeasures measure = selectBest1.measure;
structures.Add(selectBest1.getFileName);
DistanceMeasure dist = null;
switch (measure)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(structures, "", false, selectBest1.hammingProfile);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(structures, "", false);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(structures, "", false, selectBest1.CAtoms);
break;
}
List<KeyValuePair<string, int>> distList = new List<KeyValuePair<string, int>>();
aux = selectBest1.getFileName.Split(Path.DirectorySeparatorChar);
string native = aux[aux.Length - 1];
foreach (var item in structures)
{
aux = item.Split(Path.DirectorySeparatorChar);
int val = dist.GetDistance(native, aux[aux.Length - 1]);
distList.Add(new KeyValuePair<string, int>(aux[aux.Length - 1], val));
}
distList.Sort((firstPair, nextPair) =>
{
return firstPair.Value.CompareTo(nextPair.Value);
});
for (int i = 0; i < selectBest1.bestNumber; i++)
{
bestStructures.Add(distList[i].Key);
}
}
}
private DistanceMeasure CreateMeasure(string processName, string dirName,DistanceMeasures measure,PDB.PDBMODE atoms,bool jury1d,string alignFileName,
string profileName=null,string refJuryProfile=null)
{
DistanceMeasure dist=null;
switch(measure)
{
case DistanceMeasures.HAMMING:
if (alignFileName != null)
dist = new JuryDistance(alignFileName, jury1d, profileName, refJuryProfile);
else
dist = new JuryDistance(dirName, alignFileName, jury1d, profileName, refJuryProfile);
break;
case DistanceMeasures.COSINE:
if (alignFileName != null)
dist = new CosineDistance(alignFileName, jury1d, profileName, refJuryProfile);
else
dist = new CosineDistance(dirName, alignFileName, jury1d, profileName, refJuryProfile);
break;
case DistanceMeasures.RMSD:
if (dirName == null)
throw new Exception("RMSD and MAXSUB measures cannot be used for aligned profiles!");
dist = new Rmsd(dirName, alignFileName, jury1d, atoms, refJuryProfile);
break;
case DistanceMeasures.MAXSUB:
if (dirName == null)
throw new Exception("RMSD and MAXSUB measures cannot be used for aligned profiles!");
dist = new MaxSub(dirName, alignFileName, jury1d, refJuryProfile);
break;
case DistanceMeasures.GDT_TS:
if (dirName == null)
throw new Exception("RMSD and MAXSUB measures cannot be used for aligned profiles!");
dist = new GDT_TS(dirName, alignFileName, jury1d, refJuryProfile);
break;
}
return dist;
}
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 Dictionary<string,double> SableDist(List<string> refStructures)
{
StreamReader sableFile = new StreamReader(textBox3.Text);
string line = sableFile.ReadLine();
string prefix=refStructures[0];
protInfo pr_SS=new protInfo();
protInfo pr_SA = new protInfo();
string seq, ss, sa;
if(prefix.Contains("\\"))
{
string []aux=prefix.Split('\\');
prefix=aux[aux.Length-2];
}
while (line !=null)
{
if(line.StartsWith("Query:"))
{
string[] aux = line.Split(' ');
aux = aux[1].Split('.');
if (prefix.Contains(aux[0]))
{
pr_SS.sequence = sableFile.ReadLine();
string ww=sableFile.ReadLine();
pr_SS.profile = new List<byte>();
for (int i = 0; i < ww.Length;i++ )
pr_SS.profile.Add(ww[i].ToString());
line = sableFile.ReadLine();
pr_SA.sequence = pr_SS.sequence;
pr_SA.profile = new List<string>(Regex.Replace(sableFile.ReadLine(),@"\s+"," ").Trim().Split(' '));
for (int i = 0; i < pr_SA.profile.Count; i++)
pr_SA.profile[i] = (Convert.ToInt16(pr_SA.profile[i]) / 10).ToString();
}
}
line = sableFile.ReadLine();
}
sableFile.Close();
Settings set=new Settings();
set.Load();
Alignment al=new Alignment(refStructures,set,"H:\\profiels\\SS3_SA9_internal.profiles");
al.MyAlign(null);
al.AddStructureToAlignment("sable_res","SS", ref pr_SS);
al.AddStructureToAlignment("sable_res", "SA", ref pr_SA);
Dictionary<string, Dictionary<string, protInfo>> allProf = new Dictionary<string, Dictionary<string, protInfo>>();
allProf.Add("SS", new Dictionary<string, protInfo>());
allProf["SS"].Add("sable_res", pr_SS);
allProf.Add("SA", new Dictionary<string, protInfo>());
allProf["SA"].Add("sable_res", pr_SA);
Dictionary<string,List<string>> protCombineStates = al.CombineProfiles("sable_res", allProf);
JuryDistance dist = new JuryDistance(al, false);
Dictionary<string, double> distRes = new Dictionary<string, double>();
foreach (var item in refStructures)
{
distRes.Add(Path.GetFileName(item), dist.GetDistance("sable_res",Path.GetFileName(item)));
currentV++;
}
return distRes;
}*/
private DistanceMeasure PrepareDistanceMeasure(List <string> cluster,DistanceMeasures measure,string dirName)
{
DistanceMeasure distRes=null;
List<string> clustFiles = new List<string>();
foreach (var item in cluster)
clustFiles.Add(dirName + Path.DirectorySeparatorChar + item);
switch (measure)
{
case DistanceMeasures.HAMMING:
distRes = new JuryDistance(clustFiles, alignFile, true, distanceControl1.profileName);
break;
case DistanceMeasures.MAXSUB:
{
distRes = new MaxSub(clustFiles, alignFile, distanceControl1.reference);
}
break;
case DistanceMeasures.RMSD:
distRes = new Rmsd(clustFiles, alignFile, distanceControl1.reference, distanceControl1.CAtoms, distanceControl1.referenceProfile);
break;
}
distRes.InitMeasure();
return distRes;
}
private void SaveAll()
{
DistanceMeasure dist=null;
Settings set = new Settings();
set.Load();
string[] files;
if (set.extension.Length > 0)
files = Directory.GetFiles(directory, set.extension);
else
files = Directory.GetFiles(directory);
List<string> fileList = new List<string>(2);
StreamWriter r = new StreamWriter(saveFile);
maxV = files.Length;
foreach (var item in files)
{
fileList.Clear();
fileList.Add(item);
fileList.Add(markStructure);
switch (distanceControl1.distDef)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(fileList, null, false, distanceControl1.profileName, distanceControl1.referenceProfile);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(fileList, null, false, distanceControl1.CAtoms, null);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(fileList, null, false, null);
break;
case DistanceMeasures.GDT_TS:
dist = new GDT_TS(fileList, null, false, null);
break;
}
dist.InitMeasure();
try
{
int val = dist.GetDistance(Path.GetFileName(fileList[1]), Path.GetFileName(fileList[0]));
currentV++;
if (val < int.MaxValue)
r.WriteLine(fileList[0] + " " + (double)val / 100);
else
r.WriteLine(fileList[0] + " NaN");
}
catch (Exception ex)
{
exc = ex;
}
}
r.Close();
currentV = maxV;
}