int GetDist(DistanceMeasures distance,string dirName,string item1,string item2)
{
DistanceMeasure dist = null;
List<string> targets = new List<string>();
if(!item1.Contains(dirName))
targets.Add(dirName + Path.DirectorySeparatorChar + item1);
else
targets.Add(item1);
targets.Add(dirName + Path.DirectorySeparatorChar + item2);
switch (distance)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(targets, "", false, "");
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(targets, "", false);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(targets, "", false, PDB.PDBMODE.ONLY_CA);
break;
case DistanceMeasures.GDT_TS:
dist = new GDT_TS(targets, "", false);
break;
}
dist.InitMeasure();
return GetDist(dist, item1, item2);
}
/* 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 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);
}
DistanceMeasure PrepareDistance(DistanceMeasures distance,List <string> targets,string alignFile,string profileName)
{
DistanceMeasure dist=null;
switch (distance)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(targets, alignFile, false, profileName);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(targets, alignFile, false);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(targets, alignFile, false, PDB.PDBMODE.ONLY_CA);
break;
case DistanceMeasures.GDT_TS:
dist = new GDT_TS(targets, alignFile, false);
break;
}
dist.InitMeasure();
return dist;
}
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;
}
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);
}
}
}
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.TANIMOTO:
if (alignFileName != null)
{
dist = new Tanimoto(alignFileName, jury1d, profileName, refJuryProfile);
}
else
{
dist = new Tanimoto(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);
}
