text: // ==========================================================================
  //                 SeqAn - The Library for Sequence Analysis
  // ==========================================================================
  // Copyright (c) 2006-2016, Knut Reinert, FU Berlin
  // All rights reserved.
  //
  // Redistribution and use in source and binary forms, with or without
  // modification, are permitted provided that the following conditions are met:
  //
  //     * Redistributions of source code must retain the above copyright
  //       notice, this list of conditions and the following disclaimer.
  //     * Redistributions in binary form must reproduce the above copyright
  //       notice, this list of conditions and the following disclaimer in the
  //       documentation and/or other materials provided with the distribution.
  //     * Neither the name of Knut Reinert or the FU Berlin nor the names of
  //       its contributors may be used to endorse or promote products derived
  //       from this software without specific prior written permission.
  //
  // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
  // ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
  // FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
  // DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
  // SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
  // CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
  // LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
  // OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
  // DAMAGE.
  //
  // ==========================================================================
  // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
  // ==========================================================================
  // Test the interface of the Seed class for specializations Simple Seed and
  // Chained Seed.
  // ==========================================================================
  
  #include <seqan/basic.h>  // Includes testing infrastructure.
  #include <seqan/stream.h>   // Required to print strings in tests.
  
  #include <seqan/seeds.h>  // Include module under test.
  
  #include "seed_set_test_helpers.h"
  
  template <typename TSeedSpec>
  void testSeedsSeedBaseGettersSetters(TSeedSpec const &)
  {
      using namespace seqan;
  
      // Define Seed type and declare a variable.
      typedef Seed<TSeedSpec> TSeed;
      TSeed s(1, 2, 3);
  
      // Check values from construction.
      SEQAN_ASSERT_EQ(1u, beginPositionH(s));
      SEQAN_ASSERT_EQ(4u, endPositionH(s));
      SEQAN_ASSERT_EQ(2u, beginPositionV(s));
      SEQAN_ASSERT_EQ(5u, endPositionV(s));
      SEQAN_ASSERT_EQ(-1, lowerDiagonal(s));
      SEQAN_ASSERT_EQ(-1, upperDiagonal(s));
      SEQAN_ASSERT_EQ(-1, beginDiagonal(s));
      SEQAN_ASSERT_EQ(-1, endDiagonal(s));
  
      // Use setters from base class.
      setLowerDiagonal(s, 5);
      SEQAN_ASSERT_EQ(5, lowerDiagonal(s));
      setUpperDiagonal(s, 42);
      SEQAN_ASSERT_EQ(42, upperDiagonal(s));
  }
  
  template <typename TSeedSpec>
  void testSeedsSeedBaseBasicFunctions(TSeedSpec const &)
  {
      using namespace seqan;
  
      // Define Seed type and declare a variable.
      typedef Seed<TSeedSpec> TSeed;
      TSeed s(1, 2, 3);
  
      {  // test assign
          TSeed x;
          assign(x, s);
          SEQAN_ASSERT(x == s);
      }
  }
  
  template <typename TSeedSpec>
  void testSeedsSeedBaseAssign(TSeedSpec const &)
  {
      using namespace seqan;
      
      typedef Seed<TSeedSpec> TSeed;
      TSeed seed(0, 0, 3);
      setScore(seed, -3);
      
      // Via copy constructor.
      {
          TSeed seed2(seed);
          SEQAN_ASSERT(seed2 == seed);
          SEQAN_ASSERT_EQ(score(seed2), score(seed));
      }
      // Via operator=.
      {
          TSeed seed2;
          seed2 = seed;
          SEQAN_ASSERT(seed2 == seed);
          SEQAN_ASSERT_EQ(score(seed2), score(seed));
      }
      // Via assign().
      {
          TSeed seed2;
          assign(seed2, seed);
          SEQAN_ASSERT(seed2 == seed);
          SEQAN_ASSERT_EQ(score(seed2), score(seed));
      }
  }
  
  // Test constructors of the SimpleSeed specialization, as specified
  // for the base class Seed.
  SEQAN_DEFINE_TEST(test_seeds_seed_base_constructors_simple)
  {
      using namespace seqan;
      testSeedsSeedBaseConstructors(Simple());
  }
  
  // Test the metafunctions of the SimpleSeed specialization, as
  // specified for the base class Seed (none).
  SEQAN_DEFINE_TEST(test_seeds_seed_base_metafunctions_simple)
  {
      using namespace seqan;
  
      typedef Seed<Simple> TSeed;
  
      typedef typename Position<TSeed const>::Type TPosition SEQAN_UNUSED_TYPEDEF;
      typedef typename Position<TSeed>::Type TPosition SEQAN_UNUSED_TYPEDEF;
  
      typedef typename Size<TSeed const>::Type TSize SEQAN_UNUSED_TYPEDEF;
      typedef typename Size<TSeed>::Type TSize SEQAN_UNUSED_TYPEDEF;
  
      typedef typename Diagonal<TSeed const >::Type TDiagonal SEQAN_UNUSED_TYPEDEF;
      typedef typename Diagonal<TSeed>::Type TDiagonal SEQAN_UNUSED_TYPEDEF;
  }
  
  // Test the getters and seeters of the SimpleSeed specialization as
  // specified for the base class Seed.
  SEQAN_DEFINE_TEST(test_seeds_seed_base_getters_setters_simple)
  {
      using namespace seqan;
      testSeedsSeedBaseGettersSetters(Simple());
  }
  
  // Test the basic functions of the SimpleSeed specialization as
  // specified for the base class Seed.
  SEQAN_DEFINE_TEST(test_seeds_seed_base_basic_functions_simple)
  {
      using namespace seqan;
      testSeedsSeedBaseBasicFunctions(Simple());
  }
  
  // Test the assign function for the SimpleSeed specialization.
  SEQAN_DEFINE_TEST(test_seeds_seed_base_assign_simple)
  {
      using namespace seqan;
      testSeedsSeedBaseAssign(Simple());
  }
  
  // Test constructors of the ChainedSeed specialization, as specified
  // for the base class Seed.
  SEQAN_DEFINE_TEST(test_seeds_seed_base_constructors_chained)
  {
      using namespace seqan;
      testSeedsSeedBaseConstructors(ChainedSeed());
  }
  
  // Test the metafunctions of the ChainedSeed specialization, as
  // specified for the base class Seed (none).
  SEQAN_DEFINE_TEST(test_seeds_seed_base_metafunctions_chained)
  {
      using namespace seqan;
      // No metafunctions in base, intentionally left blank.
  }
  
  // Test the getters and seeters of the ChainedSeed specialization as
  // specified for the base class Seed.
  SEQAN_DEFINE_TEST(test_seeds_seed_base_getters_setters_chained)
  {
      using namespace seqan;
      testSeedsSeedBaseGettersSetters(ChainedSeed());
  }
  
  // Test the basic functions of the ChainedSeed specialization as
  // specified for the base class Seed.
  SEQAN_DEFINE_TEST(test_seeds_seed_base_basic_functions_chained)
  {
      using namespace seqan;
      testSeedsSeedBaseBasicFunctions(ChainedSeed());
  }
  
  // Test the assign function for the ChainedSeed specialization.
  SEQAN_DEFINE_TEST(test_seeds_seed_base_assign_chained)
  {
      using namespace seqan;
      testSeedsSeedBaseAssign(ChainedSeed());
  }
  
  SEQAN_BEGIN_TESTSUITE(test_seeds_seed_base)
  {
      SEQAN_CALL_TEST(test_seeds_seed_base_constructors_simple);
      SEQAN_CALL_TEST(test_seeds_seed_base_metafunctions_simple);
      SEQAN_CALL_TEST(test_seeds_seed_base_getters_setters_simple);
      SEQAN_CALL_TEST(test_seeds_seed_base_basic_functions_simple);
      SEQAN_CALL_TEST(test_seeds_seed_base_assign_simple);
      SEQAN_CALL_TEST(test_seeds_seed_base_constructors_chained);
      SEQAN_CALL_TEST(test_seeds_seed_base_metafunctions_chained);
      SEQAN_CALL_TEST(test_seeds_seed_base_getters_setters_chained);
      SEQAN_CALL_TEST(test_seeds_seed_base_basic_functions_chained);
      SEQAN_CALL_TEST(test_seeds_seed_base_assign_chained);
  }
  SEQAN_END_TESTSUITE
  