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();
}
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 StartForm()
{
InitializeComponent();
InternalProfilesManager.RemoveProfilesFile();
List <InternalProfileBase> profiles = InternalProfilesManager.InitProfiles();
}
