private void button2_Click(object sender, EventArgs e)
{
if (Rmsd.Checked)
{
dist = DistanceMeasures.RMSD;
}
else
if (MaxSub.Checked)
{
dist = DistanceMeasures.MAXSUB;
}
else
{
dist = DistanceMeasures.GDT_TS;
}
if (jury1D.Checked)
{
profileName = jury1DSetup1.profileName;
if (profileName == null || profileName.Length == 0)
{
this.DialogResult = DialogResult.None;
}
}
else
{
profileName = null;
}
distThreshold = Convert.ToDouble(textBox1.Text, System.Globalization.CultureInfo.InvariantCulture);
consideredClusters = (int)numClusters.Value;
this.DialogResult = DialogResult.OK;
}
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 button3_Click(object sender, EventArgs e)
{
DistanceMeasures measure = distanceControl1.distDef;
List <string> refStructures = new List <string>();
dirName = textBox2.Text;
try
{
if (textBox1.Text != null && textBox1.Text.Length > 5 && File.Exists(textBox1.Text))
{
string[] tmp = textBox1.Text.Split(Path.DirectorySeparatorChar);
native = tmp[tmp.Length - 1];
}
currentV = 0;
ResultsForm fr = new ResultsForm();
Progress pr = new Progress(this, fr);
pr.Start();
pr.Show();
pr.Focus();
pr.BringToFront();
Thread startProg = new Thread(CalcStat);
startProg.Start();
}
catch (Exception ex)
{
MessageBox.Show("Exception: " + ex.Message);
}
}
BestModel FindBestToModel(List<string> targets,DistanceMeasures distance,string dirName,string alignFile,string profileName,string model)
{
BestModel vOut=new BestModel();
List<string> localNames = new List<string>(2);
List<string> fileNames = new List<string>(targets.Count);
foreach (var item in targets)
fileNames.Add(dirName + Path.DirectorySeparatorChar + item);
fileNames.Add(model);
//dist=PrepareDistance(distance,fileNames,alignFile,profileName);
string[] aux = model.Split(Path.DirectorySeparatorChar);
InitBestModel(distance, ref vOut);
foreach (var item in targets)
{
/* localNames.Clear();
localNames.Add(model);
localNames.Add(item);
dist = PrepareDistance(distance, fileNames, alignFile, profileName);*/
int value=0;
//value = dist.GetDistance(aux[aux.Length - 1], item);
value = GetDist(distance, dirName, model, item);
CheckBest(distance, value, item, ref vOut);
}
return vOut;
}
/* 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);
}
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);
}
string CLusterRepresent(DistanceMeasures distance,string dirName, List<string> targets,string alignFile, string profileName)
{
DistanceMeasure dist;
List<string> fileNames=new List<string>();
foreach (var item in targets)
fileNames.Add(dirName + Path.DirectorySeparatorChar + item);
dist = PrepareDistance(distance, fileNames, alignFile, profileName);
return dist.GetReferenceStructure(targets);
}
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 HashClusterDendrog(string dirName, string alignFile, HashCInput input, DistanceMeasures dMeasure, AglomerativeType linkageType, PDB.PDBMODE atoms, bool jury1d, string alignFileName,
string profileName = null, string refJuryProfile = null):base(dirName,alignFile,input)
{
this.dMeasure=dMeasure;
this.linkageType=linkageType;
this.atoms = atoms;
this.jury1d = jury1d;
this.profileName = profileName;
this.refJuryProfile = refJuryProfile;
this.dirName = dirName;
}
void InitBestModel(DistanceMeasures distance,ref BestModel model)
{
switch (distance)
{
case DistanceMeasures.HAMMING:
model.value = int.MinValue;
break;
case DistanceMeasures.MAXSUB:
case DistanceMeasures.RMSD:
case DistanceMeasures.GDT_TS:
model.value = int.MaxValue;
break;
}
}
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;
}
void CheckBest(DistanceMeasures distance,int value,string item,ref BestModel best)
{
switch (distance)
{
case DistanceMeasures.HAMMING:
if (best.value <= value)
{
best.value = value;
best.modelName = item;
}
break;
case DistanceMeasures.MAXSUB:
case DistanceMeasures.GDT_TS:
case DistanceMeasures.RMSD:
if (best.value >= value)
{
best.value=value;
best.modelName = item;
}
break;
}
}
int GetDist(DistanceMeasures distance,string dirName,string item1,string item2)
{
DistanceMeasure dist = null;
List<string> targets = new List<string>();
// targets.Add(dirName + Path.DirectorySeparatorChar + item1);
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);
}
void InitBestModel(DistanceMeasures distance,ref BestModel model)
{
switch (distance)
{
case DistanceMeasures.HAMMING:
model.value = int.MinValue;
break;
case DistanceMeasures.MAXSUB:
case DistanceMeasures.RMSD:
case DistanceMeasures.GDT_TS:
model.value = int.MaxValue;
break;
}
}
public void GetFraction(object param)
{
float fraction = 0;
float avrDiff=0;
int counter = 0;
int end;
DistanceMeasures distance=((fractionParams)param).distance;
string profileName = ((fractionParams)param).profileName;
double distThreshold = ((fractionParams)param).distThreshold;
int clustersNum = ((fractionParams)param).clustersNum;
results = new DataTable();
try
{
DataColumn col;
col=results.Columns.Add("Output", typeof(string));
col.AllowDBNull = true;
col=results.Columns.Add("Best Model", typeof(string));
col.AllowDBNull = true;
col=results.Columns.Add("Distance To Native", typeof(double));
col.AllowDBNull = true;
col=results.Columns.Add("Best found", typeof(string));
col.AllowDBNull = true;
col=results.Columns.Add("Distance to best model", typeof(double));
col.AllowDBNull = true;
maxV = output.Count;
foreach (var item in output)
{
string[] kkk = item.dirName.Split(Path.DirectorySeparatorChar);
List<List<string>> clusters = item.GetClusters(10);
List<string> list = new List<string>();
foreach (var cl in clusters)
foreach (var target in cl)
list.Add(target);
string native = item.dirName + ".pdb";
if (item.dirName.Contains("."))
{
string[] aux = item.dirName.Split('.');
native = aux[0] + ".pdb";
}
string fileBestModel = item.dirName + "_" + distance.ToString() + "_bestmodel.dat";
BestModel bestToNative;
if (!File.Exists(fileBestModel))
{
bestToNative = FindBestToModel(list, distance, item.dirName, "", "", native);
StreamWriter st = new StreamWriter(fileBestModel);
st.WriteLine(bestToNative.modelName + " " + bestToNative.value);
st.Close();
}
else
{
StreamReader st = new StreamReader(fileBestModel);
string line = st.ReadLine();
string[] aux = line.Split(' ');
bestToNative.modelName = aux[0];
bestToNative.value = Convert.ToInt32(aux[1], System.Globalization.CultureInfo.InvariantCulture);
st.Close();
}
if (bestToNative.value == int.MaxValue)
continue;
// list.Clear();
if (clusters.Count > 0)
clusters.Sort(delegate(List<string> first, List<string> second)
{ return second.Count.CompareTo(first.Count); });
string represent = "";
//And now best five
BestModel vOut = new BestModel();
InitBestModel(distance, ref vOut);
end = clustersNum;
if (clusters.Count < clustersNum)
end = clusters.Count;
for (int i = 0; i < end; i++)
//for (int i = 0; i < clusters.Count; i++)
{
if (profileName != null)
represent = CLusterRepresentJury(item.dirName, clusters[i], profileName)[0].Key;
else
{
if (item.juryLike != null)
represent = item.juryLike[i].Key;
else
{
/* if (clusters.Count > 1)
{
represent = CLusterRepresent(distance,item.dirName, clusters[i],"",profileName);
}
else*/
represent = clusters[i][0];
}
}
int vDist = GetDist(distance, item.dirName, bestToNative.modelName, represent);
//int vDist = GetDist(distance, item.dirName, native, represent);
CheckBest(distance, vDist, represent, ref vOut);
}
if (bestToNative.value == errorValue || vOut.value == errorValue)
{
if (bestToNative.value == errorValue && vOut.value != errorValue)
results.Rows.Add(item.name, bestToNative.modelName, double.NaN, vOut.modelName, vOut.value / 100.0);
else
if(bestToNative.value != errorValue && vOut.value == errorValue)
results.Rows.Add(item.name, bestToNative.modelName, bestToNative.value / 100.0, vOut.modelName, double.NaN);
else
results.Rows.Add(item.name, bestToNative.modelName, double.NaN, vOut.modelName, double.NaN);
}
else
results.Rows.Add(item.name, bestToNative.modelName, bestToNative.value / 100.0, vOut.modelName, vOut.value / 100.0);
if (vOut.value!=errorValue && vOut.value-bestToNative.value < distThreshold * 100)
//if (vOut.value != errorValue && vOut.value < distThreshold * 100)
{
fraction++;
}
if (vOut.value!=errorValue)
{
counter++;
avrDiff += vOut.value;
}
//dist = null;
GC.Collect();
currentV++;
}
avrDiff /= counter;
fraction /= counter;
results.Rows.Add(null, null, null, null, null);
results.Rows.Add("AVR:"," "+Math.Round(avrDiff / 100,2),null,"Fraction:",Math.Round(fraction,2));
}
catch(Exception ex)
{
exc = ex;
}
//Console.WriteLine("avrDiff=" + avrDiff + " fraction=" + fraction+" pearson="+Pearson());
currentV = maxV;
}
public void CalcStat()
{
List <string> fileNames = new List <string>();
List <string> refStructures = new List <string>();
DistanceMeasures measure = distanceControl1.distDef;
DistanceMeasure distTemp = null;
double distRes = 0;
maxV = selected.Count;
distList.Clear();
try
{
tableRes = new DataTable();
tableRes.Columns.Add("Cluster Size", typeof(int));
tableRes.Columns.Add("Reference structure", typeof(string));
tableRes.Columns.Add("Distance", typeof(double));
tableRes.Columns.Add("Hidden1", typeof(int));
tableRes.Columns.Add("Hidden2", typeof(string));
if (checkBoxSable.Checked)
{
tableRes.Columns.Add("Dist to Sable", typeof(double));
maxV *= 2;
}
if (checkBox1.Checked)
{
for (int i = 0; i < selected.Count; i++)
{
maxV += selected[i].Count;
}
}
fileNames.Add(textBox1.Text);
jury1D jury = new jury1D();
if (distanceControl1.reference)
{
jury.PrepareJury(dirName, alignFile, distanceControl1.referenceProfile);
}
refStructures.Clear();
selected.Sort(delegate(List <string> first, List <string> second)
{ return(first.Count.CompareTo(second.Count)); });
selected.Reverse();
// dataGridView1.Rows.Add(selected.Count);
for (int i = 0; i < selected.Count; i++)
{
string refD = selected[i][0];
ClusterOutput juryO = null;
if (distanceControl1.reference)
{
if (selected[i].Count > 5)
{
juryO = jury.JuryOptWeights(selected[i]);
if (juryO == null)
{
continue;
}
refD = juryO.juryLike[0].Key;
if (!fileNames.Contains(dirName + Path.DirectorySeparatorChar + juryO.juryLike[0].Key))
{
fileNames.Add(dirName + Path.DirectorySeparatorChar + juryO.juryLike[0].Key);
refStructures.Add(dirName + Path.DirectorySeparatorChar + refD);
}
}
else
if (!fileNames.Contains(dirName + Path.DirectorySeparatorChar + selected[i][0]))
{
fileNames.Add(dirName + Path.DirectorySeparatorChar + selected[i][0]);
refStructures.Add(dirName + Path.DirectorySeparatorChar + selected[i][0]);
}
}
else
{
dist = PrepareDistanceMeasure(selected[i], measure, dirName);
distTemp = dist;
refD = dist.GetReferenceStructure(selected[i]);
fileNames.Add(dirName + Path.DirectorySeparatorChar + refD);
refStructures.Add(dirName + Path.DirectorySeparatorChar + refD);
}
if (fileNames.Count == 2)
{
switch (measure)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(fileNames, alignFile, false, distanceControl1.profileName);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(fileNames, null, false);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(fileNames, null, false, distanceControl1.CAtoms);
break;
}
dist.InitMeasure();
distRes = Convert.ToDouble(String.Format("{0:0.00}", dist.GetDistance(native, refD) / 100.0));
}
fileNames.RemoveAt(fileNames.Count - 1);
if (checkBoxSable.Checked && refStructures.Count > 0)
{
tableRes.Rows.Add(selected[i].Count, refD, distRes, i, dirName, 0.0);
}
else
{
tableRes.Rows.Add(selected[i].Count, refD, distRes, i, dirName);
}
currentV++;
}
if (checkBoxSable.Checked && refStructures.Count > 0)
{
Dictionary <string, double> res = null;// SableDist(refStructures);
for (int i = 0; i < refStructures.Count; i++)
{
if (res.ContainsKey(Path.GetFileName(refStructures[i])))
{
DataRow dr = tableDist.Rows[i];
dr[5] = Convert.ToDouble(String.Format("{0:0.00}", res[Path.GetFileName(refStructures[i])]));
}
}
}
if (checkBox1.Checked)
{
CalculateDistToAll();
}
}
catch (Exception ex)
{
exc = ex;
}
}
BestModel FindBestToModel(List<string> targets,DistanceMeasures distance,string dirName,string alignFile,string profileName,string model)
{
BestModel vOut=new BestModel();
List<string> localNames = new List<string>(2);
List<string> fileNames = new List<string>(targets.Count);
foreach (var item in targets)
fileNames.Add(dirName + Path.DirectorySeparatorChar + item);
fileNames.Add(model);
//dist=PrepareDistance(distance,fileNames,alignFile,profileName);
string[] aux = model.Split(Path.DirectorySeparatorChar);
InitBestModel(distance, ref vOut);
foreach (var item in targets)
{
/* localNames.Clear();
localNames.Add(model);
localNames.Add(item);
dist = PrepareDistance(distance, fileNames, alignFile, profileName);*/
int value=0;
//value = dist.GetDistance(aux[aux.Length - 1], item);
value = GetDist(distance, dirName, model, item);
CheckBest(distance, value, item, ref vOut);
}
return vOut;
}
void CheckBest(DistanceMeasures distance,int value,string item,ref BestModel best)
{
switch (distance)
{
case DistanceMeasures.HAMMING:
if (best.value <= value)
{
best.value = value;
best.modelName = item;
}
break;
case DistanceMeasures.MAXSUB:
case DistanceMeasures.GDT_TS:
case DistanceMeasures.RMSD:
if (best.value >= value)
{
best.value=value;
best.modelName = item;
}
break;
}
}
string CLusterRepresent(DistanceMeasures distance,string dirName, List<string> targets,string alignFile, string profileName)
{
DistanceMeasure dist;
List<string> fileNames=new List<string>();
foreach (var item in targets)
fileNames.Add(dirName + Path.DirectorySeparatorChar + item);
dist = PrepareDistance(distance, fileNames, alignFile, profileName);
return dist.GetReferenceStructure(targets);
}
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 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);
}
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;
}
public void AddItemToList(string item,string clType,string dirName,DistanceMeasures measure)
{
int num;
if (dataGridView1.InvokeRequired)
dataGridView1.Invoke(new AddListBoxItem(AddItemToList), new object[] { item, clType, dirName, measure });
else
{
dataGridView1.Rows.Add(1);
num = dataGridView1.Rows.Count-1;
dataGridView1.Rows[num].DefaultCellStyle.ForeColor = Color.Red;
dataGridView1.Rows[num].Cells[0].Value = item;
dataGridView1.Rows[num].Cells[1].Value = clType;
dataGridView1.Rows[num].Cells[2].Value = measure;
dataGridView1.Rows[num].Cells[3].Value = dirName;
}
}
/* 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 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 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);
}
}
}
