void test2()
{
std::string string_a = "CAGCCCTAC";
std::string string_b = "CCTGTACCC";
std::vector<std::vector<int>> similarity = {
{+2, +0, +0, +0, -1},
{+0, +2, +0, +0, -1},
{+0, +0, +2, +0, -1},
{+0, +0, +0, +2, -1},
{-1, -1, -1, -1, +2}
};
Alignment alignment = Alignment(string_a, string_b, Alignment::STR_WEIGHTS(1, -1, -1), similarity,
[](int j) { return -(1); });
std::pair<std::string, std::string> result = alignment.global_alignment();
std::string expected_a = "CAGCCCTAC--";
std::string expected_b = "C--CTGTACCC";
if (result.first != expected_a || result.second != expected_b)
{
alignment.debugS();
this->testFailed("Test2");
}
}
void test1()
{
std::string string_a = "GCATGCA";
std::string string_b = "GATTACA";
std::vector<std::vector<int>> similarity = {
//A G C T -
{+2, +0, +0, +0, -1},
{+0, +2, +0, +0, -1},
{+0, +0, +2, +0, -1},
{+0, +0, +0, +2, -1},
{-1, -1, -1, -1, +2},
};
Alignment alignment = Alignment(string_a, string_b, Alignment::STR_WEIGHTS(1, -1, -1), similarity,
[](int j) { return -(j); });
std::pair<std::string, std::string> result = alignment.global_alignment();
std::string expected_a = "GCATG-CA";
std::string expected_b = "G-ATTACA";
std::cout << alignment.get_similarity();
if (result.first != expected_a || result.second != expected_b)
{
alignment.debugS();
this->testFailed("Test1");
}
}
void test0()
{
std::string string_a = "AGAGTCAATCCATAG";
std::string string_b = "CAGAGGTCCATCATG";
std::vector<std::vector<int>> similarity = {
//A G C T -
{+2, +0, +0, +0, -1},
{+0, +2, +0, +0, -1},
{+0, +0, +2, +0, -1},
{+0, +0, +0, +2, -1},
{-1, -1, -1, -1, +2},
};
Alignment alignment = Alignment(string_a, string_b, Alignment::STR_WEIGHTS(1, -1, -1), similarity);
std::pair<std::string, std::string> result = alignment.global_alignment();
std::string expected_a = "-AGAG-TCAATCCATAG";
std::string expected_b = "CAGAGGTCCATC-AT-G";
std::cout << alignment.get_similarity();
if (result.first != expected_a || result.second != expected_b)
{
alignment.debugS();
this->testFailed("Test0");
}
}
void test5()
{
std::string string_a = "GTATT";
std::string string_b = "TTT";
std::vector<std::vector<int>> similarity = {
//A G C T -
{+1, -1, -1, -1, -1},
{-1, +1, -1, -1, -1},
{-1, -1, +1, -1, -1},
{-1, -1, -1, +1, -1},
{-1, -1, -1, -1, +1}
};
Alignment alignment = Alignment(string_a, string_b, Alignment::STR_WEIGHTS(1, -1, -1), similarity,
[](int j) { return -(j+2); });
int result = alignment.get_similarity();
int expected_result = -3;
if (result != expected_result)
{
alignment.debugS();
this->testFailed("Test5");
}
}
void test4()
{
std::string string_a = "AGAGTCAATCCATAG";
std::string string_b = "CAGAGGTCCATCATG";
std::vector<std::vector<int>> similarity = {
{+2, +0, +0, +0, -1},
{+0, +2, +0, +0, -1},
{+0, +0, +2, +0, -1},
{+0, +0, +0, +2, -1},
{-1, -1, -1, -1, +2}
};
Alignment alignment = Alignment(string_a, string_b, Alignment::STR_WEIGHTS(1, -1, -1), similarity,
[](int j) { return -(j+2); });
std::pair<std::string, std::string> result = alignment.global_alignment();
std::string expected_a = "-AGAG-TCAATCCATAG";
std::string expected_b = "CAGAGGTCCATC-AT-G";
if (result.first != expected_a || result.second != expected_b)
{
alignment.debugS();
this->testFailed("Test4");
}
}
