public ThresholdCForm(ThresholdCInput obj,bool flag,List<string> profiles=null)
{
InitializeComponent();
if (profiles != null)
{
button3.Visible = true;
profileFile = profiles[0];
}
else
button3.Visible = false;
if (flag)
distanceControl1.FreezDist();
Settings set = new Settings();
set.Load();
if (set.mode == INPUTMODE.RNA)
distanceControl1.HideAtoms = true;
if (obj != null)
{
numericUpDown1.Value = (decimal)obj.distThresh;
minCluster.Value = (decimal)obj.bakerNumberofStruct;
distanceControl1.profileName = obj.hammingProfile;
distanceControl1.distDef = obj.hDistance;
distanceControl1.CAtoms = obj.hAtoms;
}
}
public SelectBestToNatiive(List <string> structures)
{
InitializeComponent();
Settings set = new Settings();
set.Load();
if (set.mode == INPUTMODE.RNA)
selectBest1.HideAtoms = true;
this.structures = new List<string>(structures);
}
public KMeansForm(KmeansInput obj, bool flag,INPUTMODE inputmode,List<string> profiles=null)
{
InitializeComponent();
this.inputmode = inputmode;
if (profiles != null)
{
button3.Visible = true;
profileFile = profiles[0];
}
else
button3.Visible = false;
distanceControl1.changedProfile = juryChanged;
Settings set = new Settings();
set.Load();
if (set.mode == INPUTMODE.RNA)
distanceControl1.HideAtoms = true;
jury1DSetup1.profileNameChanged = juryChanged;
if (flag)
distanceControl1.FreezDist();
if (obj != null)
{
kmeansMaxK.Value = (decimal)obj.maxK;
if (obj.kMeans_init == Initialization.Jury1D)
{
juryRadio.Checked = true;
randomRadio.Checked = false;
}
else
{
juryRadio.Checked = false;
randomRadio.Checked = true;
}
distanceControl1.distDef = obj.kDistance;
distanceControl1.CAtoms = obj.kAtoms;
distanceControl1.profileName = obj.hammingProfile;
jury1DSetup1.profileName = obj.jury1DProfile;
numericUpDown1.Value = obj.maxIter;
distanceControl1.reference = obj.reference1Djury;
distanceControl1.referenceProfile = obj.jury1DProfile;
}
}
public ClusterStat(ClusterOutput output,string winName)
{
this.output = output;
this.alignFile = output.alignFile;// output[0].loadableProfile;
InitializeComponent();
Settings set = new Settings();
set.Load();
if (set.mode == INPUTMODE.RNA)
distanceControl1.HideAtoms = true;
dataGridView2.Columns[1].ValueType=typeof(Double);
this.Text = winName;
if (output == null)
return;
if (output!=null && output.hNode != null)
button2.Visible = true;
else
{
button3.Enabled = true;
if(output.clusters!=null)
selected = output.clusters;
else
if (output.juryLike != null)
{
selected = new List<List<string>>();
List<string> n = new List<string>();
foreach (var item in output.juryLike)
n.Add(item.Key);
selected.Add(n);
}
}
string fileName = output.dirName + ".pdb";
if (File.Exists(fileName))
textBox1.Text = fileName;
if (Directory.Exists(output.dirName))
{
dirName = output.dirName;
textBox2.Text = dirName;
}
fileName=output.dirName+Path.DirectorySeparatorChar+Path.GetFileName(output.dirName);
if (File.Exists(fileName))
textBox3.Text = fileName;
}
public RankingCForm(RankingCInput obj,ClusterAlgorithm alg,bool flag,INPUTMODE inputMode,List<string> profFiles=null)
{
this.alg = alg;
this.inputMode = inputMode;
InitializeComponent();
if (profFiles != null)
{
profileFile = profFiles[0];
button3.Visible = true;
}
else
button3.Visible = false;
Settings set = new Settings();
set.Load();
if (set.mode == INPUTMODE.RNA)
distanceControl1.HideAtoms = true;
if (flag)
{
distanceControl1.FreezDist();
sift.Enabled = false;
if (sift.Checked)
{
jury1d.Checked = true;
}
}
switch(alg)
{
case ClusterAlgorithm.Jury1D:
jury1d.Checked = true;
jury3d.Checked = false;
sift.Checked = false;
break;
case ClusterAlgorithm.Jury3D:
jury1d.Checked = false;
jury3d.Checked = true;
sift.Checked = false;
break;
case ClusterAlgorithm.Sift:
jury1d.Checked = false;
jury3d.Checked = false;
sift.Checked = true;
break;
default:
jury1d.Checked = true;
jury3d.Checked = false;
sift.Checked = false;
break;
}
if (obj != null)
{
distanceControl1.distDef = obj.oDistance;
distanceControl1.CAtoms = obj.oAtoms;
distanceControl1.profileName = obj.hammingProfile;
jury1DSetup1.profileName = obj.juryProfile;
distanceControl1.referenceProfile = obj.referenceProfile;
distanceControl1.reference = obj.reference1Djury;
}
if(jury1d.Checked)
distanceControl1.Enabled = false;
}
public Form1()
{
InitializeComponent();
InternalProfilesManager.RemoveProfilesFile();
System.Windows.Forms.DataGridViewCellStyle dataGridViewCellStyle1 = new System.Windows.Forms.DataGridViewCellStyle();
System.OperatingSystem osinfo=System.Environment.OSVersion;
DebugClass.WriteMessage("system: " + osinfo.VersionString+" "+Environment.Is64BitOperatingSystem);
profiles=InternalProfilesManager.InitProfiles();
manager.beginJob = AddItemToList;
manager.updateJob = UpdateListBox;
manager.message = ErrorMessage;
TimeInterval.InitTimer(UpdateProgress);
/* this.toolsToolStripMenuItem.DropDownItems.Remove(this.best5ToolStripMenuItem);
this.toolsToolStripMenuItem.DropDownItems.Remove(this.compareBest5ToolStripMenuItem);
this.toolsToolStripMenuItem.DropDownItems.Remove(this.best5RmsdCenterToolStripMenuItem);*/
/*string[] dirs = Directory.GetDirectories("Y:\\casp10","T065*");
foreach (var item in dirs)
{
string[] Files = Directory.GetFiles(item);
List<string> ddd = new List<string>(Files);
Rmsd rmsd = new Rmsd(ddd, "", false, PDB.PDBMODE.ONLY_CA);
List <string> kk =new List<string>();
foreach(var nn in Files)
{
string[] aux = nn.Split(Path.DirectorySeparatorChar);
kk.Add(aux[aux.Length - 1]);
}
string []aa=item.Split(Path.DirectorySeparatorChar);
rmsd.DistStat(kk,aa[aa.Length-1]);
}*/
/* List <string> ddd=new List<string>();
ddd.Add("y:\\TASSER_decoys\\1af7.pdb");
ddd.Add("y:\\TASSER_decoys\\1af7\\d1216.pdb");
DistanceMeasure maxsub = new MaxSub(ddd, "", false);
double cc = maxsub.GetDistance("1af7.pdb","d1216.pdb");*/
try
{
manager.opt.ReadDefaultFile();
}
catch (Exception ex)
{
MessageBox.Show("Error: " + ex.Message);
}
Settings setCheck = new Settings();
try
{
setCheck.Load();
}
catch
{
MessageBox.Show("First you have to set options!");
SetSettings(false);
}
foreach (var item in Enum.GetValues(typeof(INPUTMODE)))
{
comboBox1.Items.Add(item);
}
comboBox1.SelectedItem = setCheck.mode;
foreach (var item in manager.opt.dataDir)
listBox1.Items.Add((string)item);
foreach (var item in manager.opt.dcdFiles)
listBox1.Items.Add(item);
foreach (var item in manager.opt.profileFiles)
listBox1.Items.Add(item+" profiles");
if (manager.opt.profileFiles.Count > 0)
{
radioButton1.Enabled = false;
radioButton2.Enabled = false;
radioButton3.Enabled = false;
radioButton4.Checked = true;
}
SetDataDirOptions();
}
private void setingsToolStripMenuItem_Click(object sender, EventArgs e)
{
SetSettings(true);
Settings setCheck = new Settings();
setCheck.Load();
InternalProfilesManager.RemoveProfilesFile();
foreach (var item in profiles)
{
item.ClearProfiles();
item.LoadProfiles();
if (item.GetMode().Contains(setCheck.mode))
item.AddInternalProfiles();
}
}
private void comboBox1_SelectedIndexChanged(object sender, EventArgs e)
{
if ((INPUTMODE)comboBox1.SelectedItem == INPUTMODE.PROTEIN || (INPUTMODE)comboBox1.SelectedItem == INPUTMODE.RNA)
{
radioButton4.Visible = false;
radioButton1.Visible = true;
radioButton2.Checked = true;
radioButton2.Visible = true;
radioButton3.Visible = true;
}
else
{
// radioButton4.Visible = true;
radioButton4.Checked = true;
radioButton1.Visible = false;
radioButton2.Visible = false;
radioButton3.Visible = false;
}
listBox1.Items.Clear();
Settings s = new Settings();
s.Load();
s.mode = (INPUTMODE)comboBox1.SelectedItem;
s.Save();
}
public HierarchicalCForm(HierarchicalCInput obj,ClusterAlgorithm alg,INPUTMODE mode,bool flag,List<string> profiles)
{
this.alg = alg;
objCopy = obj;
this.mode = mode;
InitializeComponent();
if (profiles != null)
{
button3.Visible = true;
profileFile = profiles[0];
}
else
button3.Visible = false;
userHash1.regularizationOff();
SizeHeight = this.Size.Height;
distanceControl1.refChanged = ReferanceCheckChanged;
//distanceControl1.FreezeCAtoms();
Settings set = new Settings();
set.Load();
if (set.mode == INPUTMODE.RNA)
distanceControl1.HideAtoms = true;
foreach (var item in Enum.GetValues(typeof(AglomerativeType)))
comboBox1.Items.Add(Enum.GetName(typeof(AglomerativeType),item));
if (obj != null)
{
comboBox1.SelectedItem=Enum.GetName(typeof(AglomerativeType),obj.linkageType);
numericBox1.Text = obj.numInitNodes.ToString();
DBIndex.Value = (decimal)obj.indexDB;
threshold.Value = (decimal)obj.numberOfStruct;
maxRepeat.Value = (decimal)obj.repeatTime;
maxK.Value = (decimal)obj.maxK;
switch (alg)
{
case ClusterAlgorithm.FastHCluster:
AglomRadio.Checked = false;
FastHClusterRadio.Checked = true;
KmeansRadio.Checked = false;
userHash1.Visible = false;
radioButton3.Checked = false;
groupBox1.Visible = true;
if (radioButton1.Checked)
if (distanceControl1.reference)
jury1DSetup3.Visible = false;
else
jury1DSetup3.Visible = true;
this.Size = new Size(this.Size.Width, SizeHeight / 2 + SizeHeight / 4);
distanceControl1.reference = obj.reference1DjuryFast;
distanceControl1.referenceProfile = obj.consensusProfile;
userHash1.profRefFile = obj.jury1DProfileFast;
break;
case ClusterAlgorithm.HKmeans:
AglomRadio.Checked = false;
FastHClusterRadio.Checked = false;
KmeansRadio.Checked = true;
groupBox1.Visible = false;
radioButton3.Checked = false;
userHash1.Visible = false;
this.Size = new Size(this.Size.Width, SizeHeight / 2 + SizeHeight/3);
distanceControl1.reference = obj.reference1DjuryKmeans;
distanceControl1.referenceProfile = obj.jury1DProfileKmeans;
break;
case ClusterAlgorithm.uQlustTree:
userHash1.Visible = true;
AglomRadio.Checked = false;
FastHClusterRadio.Checked = false;
KmeansRadio.Checked = false;
groupBox1.Visible = false;
radioButton3.Checked = true;
this.Size = new Size(this.Size.Width, SizeHeight);
distanceControl1.reference = obj.reference1DjuryH;
distanceControl1.referenceProfile = obj.jury1DProfileH;
break;
default://Aglomerative
AglomRadio.Checked = true;
FastHClusterRadio.Checked = false;
KmeansRadio.Checked = false;
groupBox1.Visible = false;
userHash1.Visible = false;
radioButton3.Checked = false;
distanceControl1.reference = obj.reference1DjuryAglom;
distanceControl1.referenceProfile = obj.jury1DProfileAglom;
break;
}
distanceControl1.distDef = obj.distance;
distanceControl1.CAtoms = obj.atoms;
distanceControl1.profileName = obj.hammingProfile;
jury1DSetup3.profileName = obj.consensusProfile;
checkBox2.Checked = obj.ItMeans;
numericUpDown1.Value = obj.ItNum;
if (obj.HConsensus)
{
radioButton1.Checked = false;
radioButton2.Checked = true;
}
else
{
radioButton1.Checked = true;
radioButton2.Checked = false;
}
if (flag)
{
distanceControl1.FreezDist();
// distanceControl1.distDef = DistanceMeasures.HAMMING;
}
// distanceControl1.CAtoms = PDB.PDBMODE.ONLY_CA;
userHash1.SetHash(obj.hash);
}
}
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 EditProfile(string Path, bool edit,profileType type)
{
ProfileDefinitionForm profDef = null ;
InternalProfileForm internalDef = null;
profileNode node = null;
profileNode newNode = null;
DialogResult res=DialogResult.Cancel;
if (edit)
{
node = treeProfiles.FindNode(Path);
if (node.internalName!=null)
{
internalDef = new InternalProfileForm(node,filter);
res = internalDef.ShowDialog();
if (res == DialogResult.OK)
{
newNode = internalDef.localNode;
toolSave.Enabled = true;
toolStripButton6.Enabled = true;
}
}
else
{
profDef = new ProfileDefinitionForm(node);
res = profDef.ShowDialog();
if (res == DialogResult.OK)
{
newNode = profDef.profile;
toolSave.Enabled = true;
toolStripButton6.Enabled = true;
}
}
}
else
{
if (Path == null)
Path = "Profiles";
if (type == profileType.EXTERNAL)
{
profDef = new ProfileDefinitionForm();
res = profDef.ShowDialog();
if (res == DialogResult.OK)
{
node = profDef.profile;
node.internalName = null;
toolSave.Enabled = true;
toolStripButton6.Enabled = true;
}
}
else
{
Settings set=new Settings();
set.Load();
InternalProfilesManager manager = new InternalProfilesManager();
List<profileNode> validProfiles = new List<profileNode>();
foreach (var item in InternalProfilesManager.internalList.Keys)
if (manager.CheckAccessibility(item, set.mode))
validProfiles.Add(item);
ListInternal intr = new ListInternal(validProfiles);
res = intr.ShowDialog();
if (res == DialogResult.OK)
{
InternalProfileForm intForm;
profileNode localNode = InternalProfilesManager.GetNode(intr.selectedProfile);
if(localNode.profName.Contains("Load"))
intForm = new InternalProfileForm(localNode,filter,false);
else
intForm = new InternalProfileForm(localNode,filter);
res = intForm.ShowDialog();
if (res == DialogResult.OK)
{
node = intForm.localNode;
node.profProgram = intr.selectedProfile;
newNode = node;
toolSave.Enabled = true;
toolStripButton6.Enabled = true;
}
}
}
}
if (res == DialogResult.OK)
{
if (node != null && File.Exists(node.OutFileName))
File.Delete(node.OutFileName);
//profChanged = true;
if (!edit)
{
//profChanged = true;
Regex exp = new Regex("^/");
TreeNode nodeT;//= new TreeNode(profDef.profile.profName);
string nPath = "";
if (Path != null)
nPath = exp.Replace(Path, "");
if (profilesView.SelectedNode == null)
{
nodeT = profilesView.Nodes[0].Nodes.Add(node.profName);
profilesView.Nodes[0].Expand();
}
else
{
nodeT = profilesView.SelectedNode.Nodes.Add(node.profName);
profilesView.SelectedNode.Expand();
}
nodeT.Tag = newNode;
Regex exp2 = new Regex("^Profiles");
Path = exp2.Replace(Path, "");
treeProfiles.AdddNode(Path, node);
}
else
{
profilesView.SelectedNode.Text = node.profName;
treeProfiles.RemoveNode(Path);
Regex exp2 = new Regex("^Profiles");
Path = exp2.Replace(Path, "");
treeProfiles.AdddNode(ParentPath(Path),newNode);
node.CopyNode(newNode);
ShowTree();
}
}
}