/* 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 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;
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);
dist.InitMeasure();
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);
}
}
}