2 #include <Sequence/Seq8.hpp> 3 #include <Sequence/SeqExceptions.hpp> 4 #include <boost/test/unit_test.hpp> 9 BOOST_AUTO_TEST_CASE( create_1 )
11 std::string seq(
"ATGCN");
14 BOOST_CHECK_EQUAL(seq.size(),s8.size());
16 for(
unsigned i = 0 ; i < seq.size() ; ++i )
18 BOOST_CHECK_EQUAL( seq[i],s8[i] );
21 BOOST_CHECK_EQUAL( seq, s8.unpack() );
24 BOOST_AUTO_TEST_CASE( create_2 )
26 std::string seq(
"ATGCNX");
28 Sequence::SeqException);
32 BOOST_AUTO_TEST_CASE( create_3 )
34 std::string seq(
"ATGCNW");
36 Sequence::SeqException);
40 BOOST_AUTO_TEST_CASE( assign_1 )
42 std::string seq(
"ATGCN");
46 BOOST_CHECK(s8==s8_2);
49 BOOST_AUTO_TEST_CASE( assign_2 )
51 std::string seq(
"ATGCN");
55 BOOST_CHECK(s8==s8_2);
58 BOOST_AUTO_TEST_CASE( assign_3 )
60 std::string seq(
"ATGCN");
64 BOOST_CHECK_EQUAL( s8.second.size(), 0 );
66 BOOST_CHECK_EQUAL(seq.size(),s8_2.size());
68 for(
unsigned i = 0 ; i < seq.size() ; ++i )
70 BOOST_CHECK_EQUAL( seq[i],s8_2[i] );
74 BOOST_AUTO_TEST_CASE( assign_4 )
76 std::string seq(
"ATGCN");
80 BOOST_CHECK_EQUAL( s8.second.size(), 0 );
82 BOOST_CHECK_EQUAL(seq.size(),s8_2.size());
84 for(
unsigned i = 0 ; i < seq.size() ; ++i )
86 BOOST_CHECK_EQUAL( seq[i],s8_2[i] );
91 BOOST_AUTO_TEST_CASE( IO_1 )
93 std::string seq(
"ATGCN");
99 std::istringstream i(o.str());
101 BOOST_CHECK( s8.first == s8_2.first );
102 BOOST_CHECK( s8.second == s8_2.second );
103 BOOST_CHECK_EQUAL( s8.unpack() , s8_2.unpack() );
105 BOOST_AUTO_TEST_SUITE_END()
const alphabet_t dna_alphabet
Alphabet for DNA sequences Valid DNA characters. Upper-case only. Only - is accepted as gap character...
const alphabet_t dna_poly_alphabet
Alphabet for polymorphism (SNP) analysis. 16 characters are used so that we may encode 2 nucleotides ...