static void Main(string[] args)
{
string strPath = Environment.GetFolderPath(Environment.SpecialFolder.DesktopDirectory);
string[] files = Directory.GetFiles(strPath + @"\Rosalind", "*.txt"); //Assumes only one txt file in this directory - the data set
string[] lines = { "" };
foreach (string file in files)
{
lines = File.ReadAllLines(file);
}
List <Fasta> fastaList = Fasta.DecodeFasta(lines);
string[] strings = new string[fastaList.Count];
for (int i = 0; i < fastaList.Count; i++)
{
strings[i] = fastaList[i].DNA;
}
ProfileMatrix matrix = new ProfileMatrix(strings);
Console.WriteLine(matrix.ConsensusString);
ProfileMatrix.OutputProfileMatrix(matrix);
Console.ReadLine();
}
public static void OutputProfileMatrix(ProfileMatrix matrix, bool align = true)
{
if (matrix.ProfileHeadings == null)
{
Console.WriteLine("Cannot output Matrix: No headings available.");
}
else
{
char[] headers = matrix.ProfileHeadings;
int[,] profileMatrix = matrix.Matrix;
int maxPadding = 3;
if (align)
{
maxPadding = 2;
for (int i = 0; i < profileMatrix.GetLength(0); i++)
{
for (int j = 0; j < profileMatrix.GetLength(1); j++)
{
if (profileMatrix[i, j].ToString().Length > maxPadding)
{
maxPadding = profileMatrix[i, j].ToString().Length;
}
}
}
}
for (int i = 0; i < matrix.ProfileHeadings.Length; i++)
{
Console.Write("{0}: ", matrix.ProfileHeadings[i]);
for (int j = 0; j < profileMatrix.GetLength(1); j++)
{
Console.Write(profileMatrix[i, j].ToString().PadRight(maxPadding));
}
Console.WriteLine();
}
}
}