private static void Run(Options options)
{
if (!ValidateOptions(options))
{
_printHelp = true;
return;
}
string sequence1 = File.ReadAllText(options.Sequence1Path);
string sequence2 = File.ReadAllText(options.Sequence2Path);
int[,] similiarityMatrix = null;
if (!string.IsNullOrWhiteSpace(options.SimiliarityMatrixPath))
{
similiarityMatrix = GetMatrix(options.SimiliarityMatrixPath, 5);
}
DNAMatcher matcher = new DNAMatcher(sequence1, sequence2, similiarityMatrix, options.PenaltyFunctionEnabled);
matcher.Verbose = options.Verbose;
string[] matching;
if (options.Verbose)
{
Console.WriteLine("Input sequences:");
Console.WriteLine(sequence1);
Console.WriteLine(sequence2);
Console.WriteLine();
}
if (similiarityMatrix != null)
{
if (options.PenaltyFunctionEnabled)
{
int similiarity = matcher.ComputeSimiliarityWithPenalty(out matching);
Console.WriteLine($"Optimal global similiarity (with penalty function): {similiarity}\n");
PrintMatching(matching);
}
else
{
int similiarity = matcher.Hirschberg(out matching);
Console.WriteLine($"Optimal global similiarity (Hirschberg): {similiarity}\n");
PrintMatching(matching);
}
}
}
private static void Run(Options options)
{
if (!ValidateOptions(options))
{
_printHelp = true;
return;
}
string sequence1 = File.ReadAllText(options.Sequence1Path);
string sequence2 = File.ReadAllText(options.Sequence2Path);
int[,] distanceMatrix = null;
int[,] similiarityMatrix = null;
IMatcher matcher;
if (options.IsRNA)
{
if (!string.IsNullOrWhiteSpace(options.DistanceMatrixPath))
{
distanceMatrix = GetMatrix(options.DistanceMatrixPath, 21);
}
if (!string.IsNullOrWhiteSpace(options.SimiliarityMatrixPath))
{
similiarityMatrix = GetMatrix(options.SimiliarityMatrixPath, 21);
}
matcher = new RNAMatcher(sequence1, sequence2, distanceMatrix, similiarityMatrix);
}
else
{
if (!string.IsNullOrWhiteSpace(options.DistanceMatrixPath))
{
distanceMatrix = GetMatrix(options.DistanceMatrixPath, 5);
}
if (!string.IsNullOrWhiteSpace(options.SimiliarityMatrixPath))
{
similiarityMatrix = GetMatrix(options.SimiliarityMatrixPath, 5);
}
matcher = new DNAMatcher(sequence1, sequence2, distanceMatrix, similiarityMatrix);
}
matcher.Verbose = options.Verbose;
string[] matching;
if (options.Verbose)
{
Console.WriteLine("Input sequences:");
Console.WriteLine(sequence1);
Console.WriteLine(sequence2);
Console.WriteLine();
}
if (distanceMatrix != null)
{
int editDistance = matcher.ComputeEditDistance(out matching);
Console.WriteLine($"Optimal edit distance: {editDistance}\n");
PrintMatching(matching);
}
if (similiarityMatrix != null)
{
int similiarity = matcher.ComputeSimiliarity(out matching);
Console.WriteLine($"Optimal global similiarity: {similiarity}\n");
PrintMatching(matching);
int localSimiliarity = matcher.ComputeLocalSimiliarity(out matching);
Console.WriteLine($"Optimal local similiarity: {localSimiliarity}\n");
PrintMatching(matching);
}
}
