public AppConsole(RichTextBox screen, AppForm a)
: base(screen, a)
{
string arg_31_0 = "@#$B";
CommandConsole.ArgClass[] array = new CommandConsole.ArgClass[4];
array[2] = new CommandLibrary.StateSequence(new char?('$'));
this.CLF = new CommandConsole(arg_31_0, array, true, Program.ConsoleWorkingDirectory, AppConsole.InitStrings);
this.CLF.OnWorkingDirectoryChanged += new CommandPromptWrapper.DirectoryChangedEvent(this.CLF_OnWorkingDirectoryChanged);
a.ConsoleTextBox.Lines = new string[]
{
" "
};
a.ConsoleTextBox.KeyDown += new KeyEventHandler(this.richTextBox1_KeyDown);
a.ConsoleTextBox.KeyUp += new KeyEventHandler(this.richTextBox1_KeyUp);
a.ConsoleTextBox.MouseUp += new MouseEventHandler(this.richTextBox1_MouseUp);
}
public AppWorking(Type t, String msg, AppForm par, BackgroundWorker bgw)
{
InitializeComponent();
parent = par;
worker = bgw;
this.loadMsg = msg;
this.labelMsg.Text = msg;
this.labelPercent.Text = "0%";
worker.WorkerSupportsCancellation = true;
this.Init(t);
par.Enabled = false;
this.CenterToScreen();
this.Show();
this.BringToFront();
this.Focus();
}
public AppBase(RichTextBox screen, AppForm a)
{
this._parentForm = a;
this._screen = screen;
}
//Constructor
public AppBLAST(RichTextBox screen, AppForm a)
: base(screen, a)
{
}
//Constructor
public AppSQL(RichTextBox screen, AppForm a)
: base(screen, a)
{
}
public AppWorking(String msg, AppForm par, BackgroundWorker bgw)
: this(Type.Base, msg, par, bgw)
{
}
static void Main(string[] args)
{
/*
var s = "and del from not while " +
"as elif global or with " +
"assert else if pass yield " +
"break except import print " +
"class exec in raise " +
"continue finally is return " +
"def for lambda try";
var ss = s.Split(new string[] { " " }, StringSplitOptions.RemoveEmptyEntries);
var sss = "";
foreach (string si in ss)
sss += "\"" + si + "\"" + ", ";
var ssss = sss.Remove(sss.Length - 2, 2);
while (ssss.Contains("\\"))
ssss = ssss.Remove(ssss.IndexOf("\\"));
var cd = Environment.CurrentDirectory;
if (Program.HandleArgs(args))
return;
/*
//Expression e = new Expression();
string[] orfs = Management.GetTextFromFile(@"C:\Users\Ryan\Desktop\VSSD\vs projects\EvoMathProj\ORFs.txt");
string[] engl = Management.GetTextFromFile(@"C:\Users\Ryan\Desktop\VSSD\vs projects\EvoMathProj\English.txt");
//string[] engl = Management.GetTextFromFile(@"C:\Users\Ryan\Desktop\VSSD\vs projects\EvoMathProj\Decameron.txt");
string[] fsts = new string[(int)(orfs.Length / 2.0)], seqs = new string[(int)(orfs.Length / 2.0)];
for (int i = 0; i < orfs.Length; i++)
if ((i + 2) % 2 == 0)
fsts[(int)(i / 2.0)] = orfs[i];
else
seqs[(int)(i / 2.0)] = orfs[i];
String dnaA = "ACGT";
for (int i = 0; false &&
i < seqs.Length; i++)
{
var s = "";
for (int j = 0; j < 1000; j++)
{
s += dnaA[Program.R.Next(dnaA.Length)];
}
seqs[i] = s;
}
seqs = InfoMath.PrepareSample(seqs, true, true, true, true);
engl = InfoMath.PrepareSample(engl, false, true, false, false);
var seqA = new Alphabet(seqs, dnaA);
//var englA = new Alphabet(engl, " ABCDEFGHIJKLMNOPQRSTUVWXYZ.");
//var engl2A = Alphabet.AlphabetByOrder(engl, " ABCDEFGHIJKLMNOPQRSTUVWXYZ.", 2);
//var seq2A = Alphabet.AlphabetByOrder(seqs, "ACGT", 2);
//var seq3A = Alphabet.AlphabetByOrder(seqs, "ACGT", 3);
//var p1 = seqA.MyInfo.GetStateProbability("ATG");
//var p2 = seq2A.MyInfo.GetStateProbability("ATG");
//var p3 = seq3A.MyInfo.GetStateProbability("ATG");
// var p4 = seq3A.MyInfo.GetStateProbability("A");
*/
var t = Management.GetTextFromFile(@"C:\Users\Ryan\Desktop\VSSD\vs projects\EvoMathProj\resources\data\dj-1.fasta");
for (int i = 0; i < t.Length; i++)
{
while(t[i].Contains(","))
{
t[i] = t[i].Replace(",", ";");
}
}
Management.WriteTextToFile(@"C:\Users\Ryan\Desktop\VSSD\vs projects\EvoMathProj\resources\data\dj-1.fasta", t, false);
var l = CommandLibrary.StateSequence.FastaToCSV(@"C:\Users\Ryan\Desktop\VSSD\vs projects\EvoMathProj\resources\data\dj-1.fasta");
Management.WriteTextToFile(@"C:\Users\Ryan\Desktop\VSSD\vs projects\EvoMathProj\resources\data\dj-1.csv", l.ToArray<string>(), false);
//Program.TEST(">Contig100.revised.gene1.mrna", @"C:\Users\Ryan\Desktop\VSSD\vs projects\EvoMathProj\resources\data\ORFs.fasta");
//Program.TEST("31543380", @"C:\Users\Ryan\Desktop\VSSD\vs projects\EvoMathProj\resources\data\dj1.fasta");
//var l2 = Program.CreateFastaCSV(@"C:\Users\Ryan\Desktop\VSSD\vs projects\EvoMathProj\resources\data\dj1.fasta");
//Management.WriteTextToFile(@"C:\Users\Ryan\Desktop\VSSD\vs projects\EvoMathProj\resources\data\CHOPPED-dj-1.csv", l2.ToArray<string>(), false);
Application.ApplicationExit += Application_ApplicationExit;
Application.EnableVisualStyles();
Application.SetCompatibleTextRenderingDefault(false);
Program.MainForm = new AppForm();
Program.HandleArgs(args, Program.MainForm);
Application.Run(Program.MainForm);
return;
}
private static void HandleArgs(string[] args, AppForm f)
{
//f.AppConsole.CLF.RunCommandLine("$a(orfs.txt) /literal /DNA", @"C:\Users\Ryan\Desktop\VSSD\vs projects\EvoMathProj");
//while (!f.AppConsole.CLF.IsDone)
//{
//}
//f.AppConsole.CLF.RunCommandLine("$a.stats()", @"C:\Ryan\ProteinProj\ProjectFiles");
//throw new NotImplementedException();
}
