text: // ==========================================================================
  //                 SeqAn - The Library for Sequence Analysis
  // ==========================================================================
  // Copyright (c) 2014, Knut Reinert, FU Berlin
  // All rights reserved.
  //
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  // modification, are permitted provided that the following conditions are met:
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  //     * 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.
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  // ==========================================================================
  // Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
  // ==========================================================================
  // Tests for reduced_aminoacid module
  // ==========================================================================
  
  #ifndef SEQAN_TESTS_REDUCED_ALPHABET_H_
  #define SEQAN_TESTS_REDUCED_ALPHABET_H_
  
  #include <seqan/basic.h>
  #include <seqan/sequence.h>
  #include <seqan/file.h>
  
  #include <seqan/reduced_aminoacid.h>
  #include <seqan/modifier.h>
  #include <seqan/index.h>
  
  using namespace seqan;
  
  #if 0
  SEQAN_DEFINE_TEST(test_reduced_aminoacid_cluster_red)
  {
      typedef SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<8> > >
              ReducedAminoAcid24to8;
      typedef SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<10> > >
              ReducedAminoAcid24to10;
      typedef SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<12> > >
              ReducedAminoAcid24to12;
  
      CharString str = "AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz*+#";
      String<AminoAcid> aas = "ARNDCQEGHILKMFPSTWYVBZX*";
  
      // N = 12
      {
          String<ReducedAminoAcid24to12> conv = str;
          SEQAN_ASSERT_EQ(
              CharString(conv),
              "AANNCCNNRRFFGGHHIISSRRIIIINNSSPPRRRRSSSSSSIIWWSSFFRR*SS");
          conv = aas;
          SEQAN_ASSERT_EQ(CharString(conv), "ARNNCRRGHIIRIFPSSWFINRS*");
      }
  
      // N = 10
      {
          String<ReducedAminoAcid24to10> conv = str;
          SEQAN_ASSERT_EQ(
              CharString(conv),
              "AANNCCNNRRFFGGHHIIAARRIIIINNAAPPRRRRAAAAAAIIFFAAFFRR*AA");
          conv = aas;
          SEQAN_ASSERT_EQ(CharString(conv), "ARNNCRRGHIIRIFPAAFFINRA*");
      }
  
      // N = 8
      {
          String<ReducedAminoAcid24to8> conv = str;
          SEQAN_ASSERT_EQ(
              CharString(conv),
              "AARRCCRRRRFFGGRRIIAARRIIIIRRAAPPRRRRAAAAAAIIFFAAFFRR*AA");
          conv = aas;
          SEQAN_ASSERT_EQ(CharString(conv), "ARRRCRRGRIIRIFPAAFFIRRA*");
      }
  }
  #endif
  
  SEQAN_DEFINE_TEST(test_reduced_aminoacid_murphy10)
  {
      typedef SimpleType<unsigned char, ReducedAminoAcid_<Murphy10> >
              ReducedAminoAcidMurphy10;
  
      CharString str = "AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz*+#";
      String<AminoAcid> aas = "ABCDEFGHIJKLMNOPQRSTUVWYZX*";
  
      // N = 10
      {
          String<ReducedAminoAcidMurphy10> conv = str;
          SEQAN_ASSERT_EQ(
              CharString(conv),
              "AABBCCBBBBFFGGHHIIIIKKIIIIBBAAPPBBKKSSSSAAIIFFAAFFBBFAA");
          conv = aas;
          SEQAN_ASSERT_EQ(CharString(conv), "ABCBBFGHIIKIIBAPBKSSAIFFBAF");
      }
  }
  
  template <typename TModString>
  void _testReducedAminoAcidMurphy10ModIteratorsImpl(TModString & conv)
  {
      typedef typename Iterator<TModString, Standard>::Type TIt;
      typedef typename Iterator<TModString, Rooted>::Type TItR;
  
      CharString toCharString = conv;
      SEQAN_ASSERT_EQ(toCharString,
                      "ABCBBFGHIIKIIBAPBKSSAIFFBAF");
  
      // iterating
      {
          unsigned c = 0;
          for (TIt it = begin(conv, Standard()), itEnd = end(conv, Standard());
               it != itEnd;
               ++it, ++c)
              SEQAN_ASSERT_EQ(char(*it), toCharString[c]);
      }
  
      // atBegin, atEnd, position (Standard)
      {
          TIt it = begin(conv, Standard());
          SEQAN_ASSERT(atBegin(it, conv));
          SEQAN_ASSERT_EQ(position(it, conv), 0u);
  
          it = end(conv, Standard());
          SEQAN_ASSERT(atEnd(it, conv));
          SEQAN_ASSERT_EQ(position(it, conv), length(conv));
      }
  
      // atBegin, atEnd, position (Rooted)
      {
          TItR it = begin(conv, Rooted());
          SEQAN_ASSERT(atBegin(it));
          SEQAN_ASSERT(atBegin(it, conv));
          SEQAN_ASSERT_EQ(position(it), 0u);
          SEQAN_ASSERT_EQ(position(it, conv), 0u);
  
          it = end(conv, Rooted());
          SEQAN_ASSERT(atEnd(it));
          SEQAN_ASSERT(atEnd(it, conv));
          SEQAN_ASSERT_EQ(position(it), length(conv));
          SEQAN_ASSERT_EQ(position(it, conv), length(conv));
      }
  }
  
  SEQAN_DEFINE_TEST(test_reduced_aminoacid_murphy10_moditerators)
  {
      typedef SimpleType<unsigned char, ReducedAminoAcid_<Murphy10> >
              ReducedAminoAcidMurphy10;
      typedef ModifiedString<String<AminoAcid>,
                             ModView<FunctorConvert<AminoAcid, ReducedAminoAcidMurphy10>>> TModString;
      String<AminoAcid> aas = "ABCDEFGHIJKLMNOPQRSTUVWYZX*";
  
      TModString conv(aas);
      _testReducedAminoAcidMurphy10ModIteratorsImpl(conv);
  
      TModString const conv2(aas);
      _testReducedAminoAcidMurphy10ModIteratorsImpl(conv2);
  
      Segment<TModString, InfixSegment> convinf = infix(conv, 0, length(conv));
      _testReducedAminoAcidMurphy10ModIteratorsImpl(convinf);
  
      Segment<TModString const, InfixSegment> conv2inf = infix(conv2, 0, length(conv));
      _testReducedAminoAcidMurphy10ModIteratorsImpl(conv2inf);
  }
  
  struct ReducedFMIndexConfig_
  {
      typedef size_t                                                 LengthSum;
      typedef WaveletTree<void, WTRDConfig<LengthSum> >              Bwt;
      typedef Levels<void, LevelsRDConfig<LengthSum, Alloc<>, 2> >   Sentinels;
  
      static const unsigned SAMPLING = 10;
  };
  
  SEQAN_DEFINE_TEST(test_reduced_aminoacid_murphy10_modview_fmindex)
  {
      typedef String<AminoAcid>                                               TOrigString;
      typedef StringSet<TOrigString, Owner<ConcatDirect<> > >                 TOrigSet;
  
      typedef SimpleType<unsigned char, ReducedAminoAcid_<Murphy10> >         ReducedAminoAcidMurphy10;
      typedef ModView<FunctorConvert<AminoAcid, ReducedAminoAcidMurphy10> >   TModView;
      typedef ModifiedString<TOrigString, TModView>                           TModString;
      typedef StringSet<TModString, Owner<ConcatDirect<> > >                  TModSet;
  
      typedef FMIndex<void, ReducedFMIndexConfig_>                            TFMIndex;
  
      TOrigSet origSet;
      appendValue(origSet, "ABCDEFGHIJKLMNOPQRSTUVWYZX*");
      appendValue(origSet, "ABABABABABABILMVILMVILMVABABABABAB");
      appendValue(origSet, "ABCDEFGHIJKLMNOPQRSTUVWYZX*LLLLL");
      reverse(origSet); // FM-Index is reversed o_O
  
      TModSet modSet(origSet);
      SEQAN_ASSERT_EQ(modSet[0], "FABFFIASSKBPABIIKIIHGFBBCBA");
      SEQAN_ASSERT_EQ(modSet[1], "BABABABABAIIIIIIIIIIIIBABABABABABA");
      SEQAN_ASSERT_EQ(modSet[2], "IIIIIFABFFIASSKBPABIIKIIHGFBBCBA");
  
      TOrigString query = "VVVVV";
      TModString modQuery(query);
      SEQAN_ASSERT_EQ(modQuery, "IIIII");
  
      Index<TModSet, TFMIndex> index(modSet);
      indexRequire(index, FibreSALF());         // instantiate
  
      // actual search is only done if lambdas are available
  #if defined(SEQAN_CXX11_STANDARD) && (!_MSC_VER || _MSC_VER >= 1700)
      typedef typename Iterator<Index<TModSet, TFMIndex>, TopDown<>>::Type TIndexIt;
  
      std::vector<std::pair<uint64_t, uint64_t>> hits;
      auto callback = [&] (TIndexIt & indexIt, int)
      {
          for (auto subjOcc : getOccurrences(indexIt))
          {
              // reverse positions again
              setSeqOffset(subjOcc,
                           length(origSet[getSeqNo(subjOcc)])
                           - getSeqOffset(subjOcc)
                           - length(query));
              hits.emplace_back(getSeqNo(subjOcc), getSeqOffset(subjOcc));
          }
      };
  
      Nothing nothing;
      _findImpl(nothing, index, modQuery, int(0), callback, Backtracking<Exact>());
  
      SEQAN_ASSERT_EQ(length(hits), 9u);
      SEQAN_ASSERT_EQ(std::get<0>(hits[0]), 1u); SEQAN_ASSERT_EQ(std::get<1>(hits[0]), 12u);
      SEQAN_ASSERT_EQ(std::get<0>(hits[1]), 2u); SEQAN_ASSERT_EQ(std::get<1>(hits[1]), 27u);
      for (unsigned i = 1; i < 7; ++i)
      {
          SEQAN_ASSERT_EQ(std::get<0>(hits[1+i]), 1u); SEQAN_ASSERT_EQ(std::get<1>(hits[1+i]), 12u +i);
      }
  #endif
  }
  
  #endif  // SEQAN_TESTS_REDUCED_ALPHABET_H_
  