//Creators
public static Alphabet AlphabetByOrder(string[] sample, string alpha, int bitLength)
{
if (sample.Length == 0)
throw new Exception();
var a = new List<String>();
int[] ii = new int[bitLength];
while (true)
{
var s = "";
for (int i = 0; i < bitLength; i++)
s += alpha[ii[i]];
a.Add(s);
ii[0]++;
if (ii[0] < alpha.Length)
continue;
int index = 0;
bool done = false, cont = false;
while (ii[index] >= alpha.Length)
{
ii[index] = 0;
if (index + 1 >= ii.Length)
{
done = true;
break;
}
ii[index + 1]++;
if (ii[index + 1] >= alpha.Length)
index++;
else
{
cont = true;
break;
}
}
if (cont)
continue;
if (done)
break;
break;
}
var r = new Alphabet();
for (int i = 0; i < sample.Length; i++)
for (int j = 0; j < sample[i].Length - bitLength; j++)
{
var s = "";
for (int k = 0; k < bitLength; k++)
s += sample[i][j + k];
r.AddMessageSample(s, a);
}
r.UpdateInfo();
return r;
}
private static void TEST(string id, string f)
{
var testSeqStateLength = 2;
var avgWindowLength = 5;
//Base Sequences
var text = Management.GetTextFromFile(f);
List<string> heads, seqs;
//var f = Management.GetTextFromFile(@"C:\Users\Ryan\Desktop\VSSD\vs projects\EvoMathProj\resources\data\ORFs.fasta");
//var f = Management.GetTextFromFile(@"C:\Users\Ryan\Desktop\VSSD\vs projects\EvoMathProj\resources\data\dj1.fasta");
CommandLibrary.StateSequence.FastaFileToArrays(text, out heads, out seqs);
var baseAlpha = new Alphabet(new int[] { 1, 2, 3 });
baseAlpha.AddMessageSamples(seqs, null);
baseAlpha.UpdateInfo();
//Test seq
var testSeqIndex = -1;
for (int i = 0; i < heads.Count; i++)
if (heads[i].Contains(id))
{
testSeqIndex = i;
break;
}
if (testSeqIndex == -1)
return;
var testSeq = seqs[testSeqIndex];
var testSeqFinal = new List<double>();
var outputFileText = new List<string>();
//var testSeqAlpha = new Alphabet(new int[] { 2 });
for (int i = 0; i < testSeq.Length - (testSeqStateLength - 1); i += 1)
{
var curTestWord = "";
var curTestSeqInd = new List<double>();
var curTestSeqIndCum = 1.0;
for (int j = 0; j < testSeqStateLength; j++)
{
curTestWord += testSeq[j + i];
curTestSeqInd.Add(baseAlpha.GetStateProbability("" + testSeq[j + i]));
curTestSeqIndCum *= curTestSeqInd[curTestSeqInd.Count - 1];
}
var probOfWord = baseAlpha.GetStateProbability(curTestWord);
var y1 = (curTestSeqIndCum - probOfWord);
var y2 = Math.Sqrt(y1 * y1);
testSeqFinal.Add(y2);
var valPI = 0.0;
var valER = 0.0;
if (testSeqFinal.Count >= avgWindowLength)
{
valPI = 1.0;
var count = 0;
for (int j = testSeqFinal.Count - (avgWindowLength); j < testSeqFinal.Count; j++)
{
valPI *= testSeqFinal[j];
valER += testSeqFinal[j];
count++;
}
Math.Pow(valPI, 1.0 / count);
Math.Sqrt(valER / count);
}
outputFileText.Add(
(i + 1) + "," + testSeq[i] + "," + curTestWord + "," +
probOfWord + "," + curTestSeqIndCum + "," + y1 + "," +
y2 + "," + valER);
//valPI);
continue;
}
if (File.Exists(@"C:\Users\Ryan\Desktop\VSSD\vs projects\EvoMathProj\resources\data\InfoOut.csv"))
File.Delete(@"C:\Users\Ryan\Desktop\VSSD\vs projects\EvoMathProj\resources\data\InfoOut.csv");
Management.WriteTextToFile(@"C:\Users\Ryan\Desktop\VSSD\vs projects\EvoMathProj\resources\data\InfoOut.csv", outputFileText.ToArray<string>(), false);
return;
}
