public List <INPUTMODE> GetModes()
{
Dictionary <INPUTMODE, int> dic = new Dictionary <INPUTMODE, int>();
List <INPUTMODE> modes = new List <INPUTMODE>();
foreach (var item in masterNode)
{
profileNode n = InternalProfilesManager.GetNode(item.Value.internalName);
if (n == null)
{
return(null);
}
Type t = Type.GetType(InternalProfilesManager.internalList[n]);
InternalProfileBase c = Activator.CreateInstance(t) as InternalProfileBase;
foreach (var it in c.destination)
{
if (!dic.ContainsKey(it))
{
dic.Add(it, 1);
}
else
{
dic[it]++;
}
}
}
foreach (var item in dic)
{
if (item.Value == masterNode.Keys.Count)
{
modes.Add(item.Key);
}
}
return(modes);
}
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();
}
}
}
static void Main(string[] args)
{
bool errors = false;
bool times = false;
bool binary = false;
bool progress = false;
bool automaticProfiles = false;
string configFileName = "";
Options opt = new Options();
ClusterVis clusterOut = new ClusterVis();
try
{
InternalProfilesManager.InitProfiles();
}
catch (Exception ex)
{
Console.WriteLine("Some of the profiles are not available: ", ex.Message);
}
//Console.WriteLine(Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location));
/*foreach(var item in InternalProfilesManager.internalList)
* {
* Console.WriteLine("profile=" + item);
* }*/
if (args.Length == 0)
{
Console.WriteLine("Following argument is required:");
Console.WriteLine("-f configuration_file");
Console.WriteLine("Following options may be specified");
Console.WriteLine("-e \n\t show all errors");
Console.WriteLine("-m \n\t set the input mode\n\tRNA or PROTEIN [default PROTEIN]");
Console.WriteLine("-n \n\t number of cores to be used");
Console.WriteLine("-t \n\tshow time information");
Console.WriteLine("-a \n\tgenerate automatic profiles (can be used only when aligned profile is set in configuration file)");
Console.WriteLine("-b \n\tSave results to binary file (readable by GUI version)");
Console.WriteLine("-p \n\tShow progres bar");
return;
}
Settings set = new Settings();
set.Load();
if (set.profilesDir == null || set.profilesDir.Length == 0)
{
set.profilesDir = "generatedProfiles";
// set.Save();
}
set.mode = INPUTMODE.PROTEIN;
for (int i = 0; i < args.Length; i++)
{
switch (args[i])
{
case "-f":
if (i + 1 >= args.Length)
{
Console.WriteLine("After -f option you have to provide configuration file");
return;
}
if (!File.Exists(args[i + 1]))
{
Console.WriteLine("File " + args[i + 1] + " does not exist");
return;
}
configFileName = args[i + 1];
i++;
break;
case "-b":
binary = true;
break;
case "-n":
if (args.Length > i)
{
int num;
try
{
num = Convert.ToInt32(args[++i]);
set.numberOfCores = num;
}
catch (Exception ex)
{
Console.WriteLine("Wrong definition of number of cores: " + ex.Message);
return;
}
}
else
{
Console.WriteLine("Number of cores has been not provided");
}
break;
case "-m":
if (args.Length > i)
{
set.Load();
i++;
if (args[i] == "PROTEIN")
{
set.mode = INPUTMODE.PROTEIN;
}
else
if (args[i] == "RNA")
{
set.mode = INPUTMODE.RNA;
}
else
if (args[i] == "USER")
{
set.mode = INPUTMODE.USER_DEFINED;
}
else
{
Console.WriteLine("Incorrect mode:" + args[i]);
return;
}
}
else
{
Console.WriteLine("No mode specified");
}
break;
case "-e":
errors = true;
break;
case "-t":
times = true;
break;
case "-a":
automaticProfiles = true;
break;
case "-p":
progress = true;
break;
default:
if (args[i].Contains("-"))
{
Console.WriteLine("Unknown option " + args[i]);
}
break;
}
}
set.Save();
if (configFileName.Length == 0)
{
Console.WriteLine("Configurarion file has been not provided!");
return;
}
string[] aux = null;
try
{
Console.WriteLine("Configuration file " + configFileName);
opt.ReadOptionFile(configFileName);
if (automaticProfiles)
{
opt.GenerateAutomaticProfiles(null);
}
aux = args[0].Split('.');
manager.opt = opt;
manager.message = ErrorMessage;
if (progress)
{
TimeIntervalTerminal.InitTimer(UpdateProgress);
TimeIntervalTerminal.Start();
}
manager.RunJob("");
manager.WaitAllNotFinished();
UpdateProgress(null, null);
if (progress)
{
TimeIntervalTerminal.Stop();
}
Console.Write("\r ");
}
catch (Exception ex)
{
Console.WriteLine("Exception : " + ex.Message);
}
if (manager.clOutput.Count > 0)
{
foreach (var item in manager.clOutput.Keys)
{
clusterOut.output = manager.clOutput[item];
string clustName = manager.clOutput[item].clusterType;
if (clustName.Contains(":"))
{
clustName = clustName.Replace(':', '-');
}
clusterOut.output.SaveTxt(clustName + "_" + opt.outputFile);
//clusterOut.SCluster(clustName+"_"+opt.outputFile);
if (binary)
{
string fileName = opt.outputFile + "_" + item + ".cres";
StreamWriter file = new StreamWriter(fileName);
file.Close();
ClusterOutput.Save(opt.outputFile + "_" + item + ".cres0", clusterOut.output);
}
}
}
if (times)
{
foreach (var item in manager.clOutput)
{
Console.WriteLine(item.Value.dirName + " " + item.Value.measure + " " + item.Value.time);
}
}
if (errors)
{
foreach (var item in ErrorBase.GetErrors())
{
Console.WriteLine(item);
}
}
Console.WriteLine();
}
public ProfileTree()//(string profileFile)
{
mgr = new InternalProfilesManager();
progressObject = mgr;
set.Load();
}
public int GenerateActiveProfiles(Dictionary <string, profileNode> node, DCDFile dcd = null)
{
int activeProfiles = 0;
if (node == null)
{
node = masterNode;
}
if (profiles == null)
{
profiles = new Dictionary <string, Dictionary <string, protInfo> >();
}
DebugClass.WriteMessage("Profiling started");
foreach (var item in node.Values)
{
if (item.active)
{
Dictionary <string, protInfo> profString;
mgr.ResetProgress();
if (item.GetNumberofStates() == 0)
{
if (item.profProgram.Length > 0)
{
if (!profiles.ContainsKey(item.profName))
{
activeProfiles++;
if (File.Exists(item.OutFileName))
{
File.Delete(item.OutFileName);
}
GenerateProfile(item);
FileInfo f = new FileInfo(item.OutFileName);
if (!File.Exists(item.OutFileName) || f == null || f.Length == 0)
{
throw new Exception("Error: profile " + item.profName + " did not generate output " + item.OutFileName);
}
}
}
}
else
{
DebugClass.WriteMessage("Run profiling");
if (dcd == null)
{
mgr.RunProfile(item.internalName, listFile);
}
else
{
mgr.RunProfile(item.internalName, dcd);
}
activeProfiles++;
}
if (item.childrens.Count > 0)
{
activeProfiles += GenerateActiveProfiles(item.childrens);
}
else
{
if (!profiles.ContainsKey(item.profName))
{
if (item.GetNumberofStates() == 0)
{
profString = ReadProfile(item);
}
else
{
if (dcd == null)
{
profString = mgr.GetProfile(item, listFile);
}
else
{
profString = InternalProfilesManager.GetProfile(item, dcd);
}
}
if (profString != null && profString.Count > 0)
{
profiles.Add(item.profName, profString);
}
else
{
throw new Exception("For profile " + item.profName + " profiles has not been generated!");
}
}
}
profilesProgress.Add(mgr.ProgressUpdate());
}
}
progressObject = null;
return(activeProfiles);
}
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();
}
}
}
public AdvancedVersion(Form parent = null)
{
InitializeComponent();
this.parent = parent;
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();
if (!Directory.Exists(setCheck.profilesDir))
{
MessageBox.Show("Directory for generated profiles:" + setCheck.profilesDir + " cannot be found\n You must provide correct directory!");
SetSettings(false);
}
}
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();
}
public StartForm()
{
InitializeComponent();
InternalProfilesManager.RemoveProfilesFile();
List <InternalProfileBase> profiles = InternalProfilesManager.InitProfiles();
}
