public override void PerformTestCase()
{
if (!subsequence)
{
result = af.FindAlignment(v, w, out al);
}
else
{
result = af.FindSubsequenceAlignment(v, w, out al);
}
}
private static void DebugTest(string v, string w, AlignmentFinder af, bool subsequence)
{
Console.WriteLine("------------------------");
Console.WriteLine($"v={v}");
Console.WriteLine($"w={w}");
Alignment al;
int sc;
if (!subsequence)
{
sc = af.FindAlignment(v, w, out al);
}
else
{
sc = af.FindSubsequenceAlignment(v, w, out al);
}
Console.WriteLine($"av={al.AlignedV}");
Console.WriteLine($"aw={al.AlignedW}");
Console.WriteLine($"returned={sc}");
int score = 0;
int n = al.AlignedV.Length;
for (int i = 0; i < n; ++i)
{
if (al.AlignedV[i] != '-' && al.AlignedW[i] != '-')
{
score += af.Matrix[al.AlignedV[i], al.AlignedW[i]];
}
else if (al.AlignedV[i] == '-' && al.AlignedW[i] == '-')
{
throw new ArgumentException("aligned gaps found");
}
else
{
score += af.Epsilon;
}
}
Console.WriteLine($"computed={score}");
}