alg/tsf/test_tsf.cpp

   1 #define BOOST_TEST_DYN_LINK
   2 #define BOOST_TEST_MODULE test_tsf
   3 #include <boost/test/unit_test.hpp>
   4
   5 #include "trivial_filter.hpp"
   6
   7 BOOST_AUTO_TEST_CASE( test_nt_map )
   8 {
   9   BOOST_CHECK_EQUAL( nt_map('A'), A );
  10   BOOST_CHECK_EQUAL( nt_map('a'), A );
  11   BOOST_CHECK_EQUAL( nt_map('T'), T );
  12   BOOST_CHECK_EQUAL( nt_map('t'), T );
  13   BOOST_CHECK_EQUAL( nt_map('G'), G );
  14   BOOST_CHECK_EQUAL( nt_map('g'), G );
  15   BOOST_CHECK_EQUAL( nt_map('C'), C );
  16   BOOST_CHECK_EQUAL( nt_map('c'), C );
  17   BOOST_CHECK_EQUAL( nt_map('U'), U );
  18   BOOST_CHECK_EQUAL( nt_map('u'), U );
  19   BOOST_CHECK_EQUAL( nt_map('N'), N );
  20   BOOST_CHECK_EQUAL( nt_map('n'), N );
  21   BOOST_CHECK_EQUAL( nt_map('X'), X );
  22   BOOST_CHECK_EQUAL( nt_map('x'), X );
  23 }
  24
  25 BOOST_AUTO_TEST_CASE( test_generate_dna_pattern_1mer )
  26 {
  27   TSFLookupTable table(1,4);
  28   BOOST_CHECK( table.states() > 0);
  29
  30   const int failed_state =  TSFLookupTable::failed_state;
  31   const int accept_state = TSFLookupTable::accept_state;
  32
  33
  34   int a_state = table.next(TSFLookupTable::start_state, A);
  35   int t_state = table.next(TSFLookupTable::start_state, T);
  36   int g_state = table.next(TSFLookupTable::start_state, G);
  37   int c_state = table.next(TSFLookupTable::start_state, C);
  38
  39   BOOST_CHECK(a_state != t_state);
  40   BOOST_CHECK(a_state != g_state);
  41   BOOST_CHECK(a_state != c_state);
  42   BOOST_CHECK(t_state != g_state);
  43   BOOST_CHECK(t_state != c_state);
  44   BOOST_CHECK(g_state != c_state);
  45
  46   BOOST_CHECK_EQUAL( table.next(TSFLookupTable::start_state, A), a_state );
  47   BOOST_CHECK_EQUAL( table.next(a_state, A), a_state+1 );
  48   BOOST_CHECK_EQUAL( table.next(a_state, G), failed_state);
  49   BOOST_CHECK_EQUAL( table.next(a_state+1, A), a_state+2 );
  50   BOOST_CHECK_EQUAL( table.next(a_state+2, A), a_state+3 );
  51   BOOST_CHECK_EQUAL( table.next(a_state+3, A), a_state+3 );
  52   BOOST_CHECK_EQUAL( table.next(a_state+3, G), accept_state);
  53
  54   BOOST_CHECK_EQUAL( table.next(TSFLookupTable::start_state, G), g_state );
  55   BOOST_CHECK_EQUAL( table.next(g_state, G), g_state+1 );
  56   BOOST_CHECK_EQUAL( table.next(g_state, T), failed_state);
  57   BOOST_CHECK_EQUAL( table.next(g_state+1, G), g_state+2 );
  58   BOOST_CHECK_EQUAL( table.next(g_state+2, G), g_state+3 );
  59   BOOST_CHECK_EQUAL( table.next(g_state+3, G), g_state+3 );
  60   BOOST_CHECK_EQUAL( table.next(g_state+3, C), accept_state);
  61 }