public AlignmentTestCase(double timeLimit, string v, string w, AlignmentFinder af, int expectedResult, bool subsequence = false) : base(timeLimit, null)
{
this.expectedResult = expectedResult;
this.v = v;
this.w = w;
this.af = af;
this.subsequence = subsequence;
}
static void Main(string[] args)
{
AlignmentFinder af1 = new AlignmentFinder();
AlignmentFinder af2 = new AlignmentFinder(ScoringMatrix.PAM250, -5);
TestSet unweightedTests = new TestSet();
unweightedTests.TestCases.Add(new AlignmentTestCase(1, "AGT", "AGT", af1, 0));
unweightedTests.TestCases.Add(new AlignmentTestCase(1, "CCCP", "AAAACCCPAAAAAAAAAA", af1, -14));
unweightedTests.TestCases.Add(new AlignmentTestCase(1, "AAACAC", "CACA", af1, -3));
unweightedTests.TestCases.Add(new AlignmentTestCase(1, "AGGCTACTTTCA", "GGCTACTATATCA", af1, -3));
unweightedTests.TestCases.Add(new AlignmentTestCase(1, "CCGCCT", "AGTGGGGTAAGA", af1, -10));
unweightedTests.TestCases.Add(new AlignmentTestCase(1, "AAAAAAAAAAAAAAAAAAAA", "AAGAAGAAGAAGAGAA", af1, -9));
unweightedTests.TestCases.Add(new AlignmentTestCase(1, "AAAAWWW", "WWWAAAA", af1, -6));
unweightedTests.TestCases.Add(new AlignmentTestCase(1, "WWSRWWW", "EWWW", af1, -4));
unweightedTests.TestCases.Add(new AlignmentTestCase(2, PheA, Dhv, af1, -397));
unweightedTests.TestCases.Add(new AlignmentTestCase(3, Yp0, Yp5, af1, -1137));
TestSet weightedTests = new TestSet();
weightedTests.TestCases.Add(new AlignmentTestCase(1, "AGT", "AGT", af2, 10));
weightedTests.TestCases.Add(new AlignmentTestCase(1, "CCCP", "AAAACCCPAAAAAAAAAA", af2, -28));
weightedTests.TestCases.Add(new AlignmentTestCase(1, "AAACAC", "CACA", af2, 6));
weightedTests.TestCases.Add(new AlignmentTestCase(1, "AGGCTACTTTCA", "GGCTACTATATCA", af2, 47));
weightedTests.TestCases.Add(new AlignmentTestCase(1, "CCGCCT", "AGTGGGGTAAGA", af2, -32));
weightedTests.TestCases.Add(new AlignmentTestCase(1, "AAAAAAAAAAAAAAAAAAAA", "AAGAAGAAGAAGAGAA", af2, 7));
weightedTests.TestCases.Add(new AlignmentTestCase(1, "AAAAWWW", "WWWAAAA", af2, 11));
weightedTests.TestCases.Add(new AlignmentTestCase(1, "WWSRWWW", "EWWW", af2, 36));
weightedTests.TestCases.Add(new AlignmentTestCase(2, PheA, Dhv, af2, 464));
weightedTests.TestCases.Add(new AlignmentTestCase(5, Yp0, Yp5, af2, 1062));
TestSet subsequenceTests = new TestSet();
subsequenceTests.TestCases.Add(new AlignmentTestCase(1, "AGT", "AGT", af2, 10, true));
subsequenceTests.TestCases.Add(new AlignmentTestCase(1, "CCCP", "AAAACCCPAAAAAAAAAA", af2, 42, true));
subsequenceTests.TestCases.Add(new AlignmentTestCase(1, "AAACAC", "CACA", af2, 26, true));
subsequenceTests.TestCases.Add(new AlignmentTestCase(1, "AGGCTACTTTCA", "CTAACT", af2, 30, true));
subsequenceTests.TestCases.Add(new AlignmentTestCase(1, "AGGCTACTTTCA", "CTCT", af2, 25, true));
subsequenceTests.TestCases.Add(new AlignmentTestCase(1, "AGGCTCTTTCA", "CTACT", af2, 25, true));
subsequenceTests.TestCases.Add(new AlignmentTestCase(1, "AAAAWWW", "WWWAAAA", af2, 51, true));
subsequenceTests.TestCases.Add(new AlignmentTestCase(1, "WSRWW", "EWWW", af2, 41, true));
subsequenceTests.TestCases.Add(new AlignmentTestCase(2, PheA, Dhv, af2, 658, true));
subsequenceTests.TestCases.Add(new AlignmentTestCase(5, Yp0, Yp5, af2, 1344, true));
Console.WriteLine("Część 1: bez wag dopasowań");
unweightedTests.PreformTests(true, false);
Console.WriteLine("Część 2: z wagami dopasowań");
weightedTests.PreformTests(true, false);
Console.WriteLine("Część 3: dopasowanie podciągów");
subsequenceTests.PreformTests(true, false);
}
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}");
}
