alg/tsf/test_tsf.cpp

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