public void TestStartNoGapAlgorithm(string matrix, string X, string Y, Func <int, double> penaltyFunc, double evaluation, string resultX, string resultY)
{
var similarityMatrix = new SimilarityMatrix(matrix);
var withGapPenalty = new WithGapPenalty(similarityMatrix, penaltyFunc);
var tuple = withGapPenalty.StartNoGapAlgorithm(X, Y);
Assert.AreEqual(evaluation, tuple.Item1);
Assert.AreEqual(resultX, tuple.Item2.Item1);
Assert.AreEqual(resultY, tuple.Item2.Item2);
}
static void Main(string[] args)
{
var arguments = args.Where(x => !x.StartsWith("-")).ToArray();
var options = args.Where(x => x.StartsWith("-")).ToArray();
// Display help message and quit program.
if (options.Any(x => x == "--help"))
{
Console.WriteLine("Syntax:\n");
Console.WriteLine(" SequencesAlignment [<matrixFilePath>] [<sequencesFilePath>] [--nogappenalty]");
return;
}
// Resolve path to file with matrix from arguments or ask user for the path.
string matrixFilePath = arguments.ElementAtOrDefault(0);
if (matrixFilePath == null)
{
Console.WriteLine("Path to file with similarity matrix:");
matrixFilePath = Console.ReadLine();
}
FileUtils fu = new FileUtils();
string matrixFileContent = fu.ReadContentFromFile(matrixFilePath);
SimilarityMatrix similarityMatrix = new SimilarityMatrix(matrixFileContent);
// Resolve path to file with sequences from arguments or ask user for two sequences.
string sequencesFilePath = arguments.ElementAtOrDefault(1);
string sequence1;
string sequence2;
if (sequencesFilePath == null)
{
Console.WriteLine("First sequences:");
sequence1 = Console.ReadLine();
Console.WriteLine("Second sequences:");
sequence2 = Console.ReadLine();
}
else
{
string[] sequences = fu.ReadSequencesFromFile(sequencesFilePath);
sequence1 = sequences[0];
sequence2 = sequences[1];
}
similarityMatrix.CheckSequenceCorrectness(sequence1);
similarityMatrix.CheckSequenceCorrectness(sequence2);
// Check whether user provided the --nogappenalty option.
bool isOptionB = options.Any(x => x == "--nogappenalty");
if (isOptionB)
{
Hirschberg h = new Hirschberg(similarityMatrix);
var results = h.StartAlgorithm(sequence1, sequence2);
double evaluation = similarityMatrix.Evaluate(results.Item1, results.Item2);
Console.WriteLine(results.Item1);
Console.WriteLine(results.Item2);
Console.WriteLine("Evaluation: " + evaluation);
}
else
{
WithGapPenalty p = new WithGapPenalty(similarityMatrix, x => x + 2);
var results = p.StartNoGapAlgorithm(sequence1, sequence2);
Console.WriteLine(results.Item2.Item1);
Console.WriteLine(results.Item2.Item2);
Console.WriteLine("Evaluation: " + results.Item1);
}
}