// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2018, 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: David Weese <david.weese@fu-berlin.de>
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================

#ifndef SEQAN_MODIFIER_MODIFIER_STRING_H_
#define SEQAN_MODIFIER_MODIFIER_STRING_H_

namespace seqan
{

// ==========================================================================
// Forwards
// ==========================================================================

template <typename T> struct InnermostHost_;
template <typename TType, typename TTestType> struct IsConstructible;
template <typename TType, typename TTestType> struct IsAnInnerHost;

// ==========================================================================
// Classes
// ==========================================================================

// --------------------------------------------------------------------------
// Class ModifierString
// --------------------------------------------------------------------------

/*!
 * @class ModifiedString
 * @implements ContainerConcept
 * @headerfile <seqan/modifier.h>
 * @brief Allows you to generate modified versions of a string in a non-inplace way.
 *
 * @signature template <typename THost[, typename TSpec]>
 *            class ModifiedString;
 *
 * @tparam THost The host sequence.
 * @tparam TSpec The specialization tag, defaults to <tt>void</tt>.
 *
 * <tt>THost</tt> can also be a modified string, so you can create nest modified strings to create custom combinations.
 *
 * @section Examples
 *
 * @subsection Using ModReverseString
 *
 * @include demos/dox/modifier/modified_string.cpp
 *
 * The output is als follows:
 *
 * @include demos/dox/modifier/modified_string.cpp.stdout
 *
 * @subsection Using a custom functor for ModViewString
 *
 * @include demos/dox/modifier/modified_string_mod_view.cpp
 *
 * The output is as follows:
 *
 * @include demos/dox/modifier/modified_string_mod_view.cpp.stdout
 *
 * @subsection Using nested modified strings.
 *
 * @include demos/dox/modifier/modified_string_nested.cpp
 *
 * The output is as follows:
 *
 * @include demos/dox/modifier/modified_string_nested.cpp.stdout
 */

template <typename THost, typename TSpec = void>
class ModifiedString
{
public:
    typedef typename Pointer_<THost>::Type       THostPointer_;
    typedef typename Cargo<ModifiedString>::Type TCargo_;

    mutable THostPointer_ _host;
    TCargo_ _cargo;

    // Default constructor.
    ModifiedString() :
        _host(),
        _cargo()
    {}

    // Construct with the actual host.
    explicit
    ModifiedString(typename Parameter_<THost>::Type host) :
        _host(_toPointer(host)),
        _cargo()
    {}

    // Constructor for creating a ModifiedString with const host from a non-const host.
    template <typename THost_>
    explicit
    ModifiedString(THost_ & host,
                   SEQAN_CTOR_ENABLE_IF(IsConstructible<THost, THost_>)) :
            _host(_toPointer(host)),
            _cargo()
    {
        ignoreUnusedVariableWarning(dummy);
    }

    // Constructor for an inner host type; forward host to hosted type.
    template <typename THost_>
    explicit
    ModifiedString(THost_ && host,
                   SEQAN_CTOR_ENABLE_IF(IsAnInnerHost<
                                            typename RemoveReference<THost>::Type,
                                            typename RemoveReference<THost_>::Type >)) :
            _host(std::forward<THost_>(host)),
            _cargo()
    {
        ignoreUnusedVariableWarning(dummy);
    }

    template <typename TPos>
    inline typename Reference<ModifiedString>::Type
    operator[](TPos pos)
    {
        return value(*this, pos);
    }

    template <typename TPos>
    inline typename Reference<ModifiedString const>::Type
    operator[](TPos pos) const
    {
        return value(*this, pos);
    }

    ModifiedString & operator= (THost & other)
    {
        assign(*this, other);
        return *this;
    }
};

// ==========================================================================
// Metafunctions
// ==========================================================================

// --------------------------------------------------------------------------
// Metafunction InnermostHost_
// --------------------------------------------------------------------------

// TODO(holtgrew): Test me!

// This metafunction returns the innermost host type for a ModifiedString cascade.

// Recurse down const/non-const.

template <typename TType, typename TTestType>
struct IsConstructible:
    If<IsLightWeight<TType>,
       IsSameType<TType const, TTestType const>,
       Or<IsSameType<TType, TTestType>,
          IsSameType<TType, TTestType const> > > {};

template <typename TType, typename TTestType>
struct IsAnInnerHost: False {};

template <typename THost, typename TSpec, typename TTestType>
struct IsAnInnerHost<ModifiedString<THost, TSpec>, TTestType>:
    If<IsConstructible<THost, TTestType>,
       True,
       IsAnInnerHost<THost, TTestType> > {};

template <typename THost, typename TSpec, typename TTestType>
struct IsAnInnerHost<ModifiedString<THost, TSpec> const, TTestType>:
    IsAnInnerHost<ModifiedString<THost, TSpec>, TTestType> {};


template <typename THost, typename TInnerSpec, typename TOuterSpec>
struct InnermostHost_<ModifiedString<ModifiedString<THost, TInnerSpec> const, TOuterSpec> >
{
    typedef THost Type;
};

template <typename THost, typename TInnerSpec, typename TOuterSpec>
struct InnermostHost_<ModifiedString<ModifiedString<THost, TInnerSpec>, TOuterSpec> >
{
    typedef THost Type;
};

// Recursion stop.

template <typename THost, typename TSpec>
struct InnermostHost_<ModifiedString<THost, TSpec> const>
{
    typedef THost Type;
};

template <typename THost, typename TSpec>
struct InnermostHost_<ModifiedString<THost, TSpec> >
{
    typedef THost Type;
};

// --------------------------------------------------------------------------
// Metafunction Spec
// --------------------------------------------------------------------------

template < typename THost, typename TSpec >
struct Spec< ModifiedString<THost, TSpec> >
{
    typedef TSpec Type;
};

template < typename THost, typename TSpec >
struct Spec< ModifiedString<THost, TSpec> const >
{
    typedef TSpec Type;
};

// --------------------------------------------------------------------------
// Metafunction Value
// --------------------------------------------------------------------------

// use Value, GetValue, Reference, Size, ... from corresponding iterator
template < typename THost, typename TSpec >
struct Value< ModifiedString<THost, TSpec> >:
    Value< typename Iterator< ModifiedString<THost, TSpec>, Rooted >::Type > {};

template < typename THost, typename TSpec >
struct Value< ModifiedString<THost, TSpec> const >:
    Value< typename Iterator< ModifiedString<THost, TSpec> const, Rooted >::Type > {};

// --------------------------------------------------------------------------
// Metafunction GetValue
// --------------------------------------------------------------------------

template < typename THost, typename TSpec >
struct GetValue< ModifiedString<THost, TSpec> >:
    GetValue< typename Iterator< ModifiedString<THost, TSpec>, Rooted >::Type > {};

template < typename THost, typename TSpec >
struct GetValue< ModifiedString<THost, TSpec> const >:
    GetValue< typename Iterator< ModifiedString<THost, TSpec> const, Rooted >::Type > {};

// --------------------------------------------------------------------------
// Metafunction Reference
// --------------------------------------------------------------------------

template < typename THost, typename TSpec >
struct Reference< ModifiedString<THost, TSpec> >:
    Reference< typename Iterator< ModifiedString<THost, TSpec>, Rooted >::Type > {};

template < typename THost, typename TSpec >
struct Reference< ModifiedString<THost, TSpec> const >:
    Reference< typename Iterator< ModifiedString<THost, TSpec> const, Rooted >::Type > {};

// --------------------------------------------------------------------------
// Metafunction Size
// --------------------------------------------------------------------------

template < typename THost, typename TSpec >
struct Size< ModifiedString<THost, TSpec> >:
    Size< typename Iterator< ModifiedString<THost, TSpec>, Rooted >::Type > {};

// --------------------------------------------------------------------------
// Metafunction Position
// --------------------------------------------------------------------------

template < typename THost, typename TSpec >
struct Position< ModifiedString<THost, TSpec> >:
    Position< typename Iterator< ModifiedString<THost, TSpec>, Rooted >::Type > {};

// --------------------------------------------------------------------------
// Metafunction Difference
// --------------------------------------------------------------------------

template < typename THost, typename TSpec >
struct Difference< ModifiedString<THost, TSpec> >:
    Difference< typename Iterator< ModifiedString<THost, TSpec>, Rooted >::Type > {};

// --------------------------------------------------------------------------
// Metafunction Iterator
// --------------------------------------------------------------------------

template <typename THost, typename TSpec>
struct Iterator<ModifiedString<THost, TSpec>, Standard>
{
    typedef ModifiedIterator<typename Iterator<THost, Standard>::Type, TSpec> Type;
};
template <typename THost, typename TSpec>
struct Iterator<ModifiedString<THost, TSpec>, Rooted>
{
    typedef ModifiedIterator<typename Iterator<THost, Rooted>::Type, TSpec> Type;
};

// TODO(holtgrew): Should the result of Iterator<> be a const iterator for const ModifiedString objects?
//          weese: I chose more lenient variant (A), i.e. constness is not propagated upwards.

// VARIANT A: const ModifiedString does not propagate its constness upwards
template <typename THost, typename TSpec >
struct Iterator<ModifiedString<THost, TSpec> const, Standard>
{
    typedef ModifiedIterator<typename Iterator<THost, Standard>::Type, TSpec> Type;
};
template <typename THost, typename TSpec >
struct Iterator<ModifiedString<THost, TSpec> const, Rooted>
{
    typedef ModifiedIterator<typename Iterator<THost, Rooted>::Type, TSpec> Type;
};

// VARIANT B: const ModifiedString propagates its constness upwards
//template <typename THost, typename TSpec >
//struct Iterator<ModifiedString<THost, TSpec> const, Standard>
//{
//    typedef ModifiedIterator<typename Iterator<THost const, Standard>::Type, TSpec> Type;
//};
//template <typename THost, typename TSpec >
//struct Iterator<ModifiedString<THost, TSpec> const, Rooted>
//{
//    typedef ModifiedIterator<typename Iterator<THost const, Rooted>::Type, TSpec> Type;
//};

// --------------------------------------------------------------------------
// Metafunction Host
// --------------------------------------------------------------------------

template <typename T>
struct ConvertArrayToPointer
{
    typedef T Type;
};

template <typename T, int SIZE>
struct ConvertArrayToPointer<T[SIZE]>
{
    typedef T* Type;
};

template <typename THost, typename TSpec >
struct Host<ModifiedString<THost, TSpec> > {
    typedef typename ConvertArrayToPointer<THost>::Type Type;
};

// VARIANT A: const ModifiedString does not propagate its constness upwards
template <typename THost, typename TSpec >
struct Host<ModifiedString<THost, TSpec> const > {
    typedef typename ConvertArrayToPointer<THost>::Type Type;
};

// VARIANT B: const ModifiedString propagates its constness upwards
//template <typename THost, typename TSpec >
//struct Host<ModifiedString<THost, TSpec> const > {
//    typedef typename ConvertArrayToPointer<THost const>::Type Type;
//};

// --------------------------------------------------------------------------
// Metafunction Parameter_
// --------------------------------------------------------------------------

// don't uncomment this, it would cause the Segment() c'tor to take the address
// of a temporary copy of the ModifiedString

template <typename THost, typename TSpec >
struct Parameter_<ModifiedString<THost, TSpec> > {
    typedef ModifiedString<THost, TSpec> Type;
};

template <typename THost, typename TSpec >
struct Parameter_<ModifiedString<THost, TSpec> const > {
    typedef ModifiedString<THost, TSpec> Type;
};

// --------------------------------------------------------------------------
// Metafunction Pointer_
// --------------------------------------------------------------------------

template <typename THost, typename TSpec >
struct Pointer_<ModifiedString<THost, TSpec> >
{
    typedef ModifiedString<THost, TSpec> Type;
};

template <typename THost, typename TSpec >
struct Pointer_<ModifiedString<THost, TSpec> const > : Pointer_<ModifiedString<THost, TSpec> >
{};

// --------------------------------------------------------------------------
// Metafunction IsSequence
// --------------------------------------------------------------------------

template <typename THost, typename TSpec >
struct IsSequence<ModifiedString<THost, TSpec> > : True
{};

// ----------------------------------------------------------------------------
// Concept ContainerConcept
// ----------------------------------------------------------------------------

template <typename THost, typename TSpec>
SEQAN_CONCEPT_IMPL((ModifiedString<THost, TSpec>), (ContainerConcept));

template <typename THost, typename TSpec>
SEQAN_CONCEPT_IMPL((ModifiedString<THost, TSpec> const), (ContainerConcept));

// --------------------------------------------------------------------------
// Metafunction AllowsFastRandomAccess
// --------------------------------------------------------------------------

template <typename THost, typename TSpec >
struct AllowsFastRandomAccess<ModifiedString<THost, TSpec> > : AllowsFastRandomAccess<THost>
{};

// ==========================================================================
// Functions
// ==========================================================================

// --------------------------------------------------------------------------
// Function _copyCargo
// --------------------------------------------------------------------------

template <typename TDest, typename TSource>
inline void _copyCargoImpl(TDest &, TSource &, False const)
{}

template <typename TDest, typename TSource>
inline void _copyCargoImpl(TDest & me, TSource & _origin, True const)
{
    cargo(me) = cargo(_origin);
}

template <typename TDest, typename TSource>
inline void _copyCargo(TDest & me, TSource & _origin)
{
    _copyCargoImpl(me, _origin, typename IsSameType<
                   typename RemoveConst_<typename Cargo<TDest>::Type >::Type,
                   typename RemoveConst_<typename Cargo<TSource>::Type>::Type >::Type());
}

// --------------------------------------------------------------------------
// Function _toPointer()
// --------------------------------------------------------------------------

template <typename THost, typename TSpec>
inline typename Pointer_<ModifiedString<THost, TSpec> >::Type
_toPointer(ModifiedString<THost, TSpec> & me)
{
    return me;
}

template <typename THost, typename TSpec>
inline typename Pointer_<ModifiedString<THost, TSpec> const >::Type
_toPointer(ModifiedString<THost, TSpec> const & me)
{
    return me;
}

// --------------------------------------------------------------------------
// Function _toParameter()
// --------------------------------------------------------------------------

template <typename THost, typename TSpec>
inline typename Parameter_<ModifiedString<THost, TSpec> >::Type
_toParameter(ModifiedString<THost, TSpec> & me)
{
    return me;
}

template <typename THost, typename TSpec>
inline typename Parameter_<ModifiedString<THost, TSpec> const >::Type
_toParameter(ModifiedString<THost, TSpec> const & me)
{
    return me;
}

// --------------------------------------------------------------------------
// Function host()
// --------------------------------------------------------------------------

template <typename THost, typename TSpec>
inline typename Host<ModifiedString<THost, TSpec> >::Type &
host(ModifiedString<THost, TSpec> & me)
{
    return _referenceCast<typename Host<ModifiedString<THost, TSpec> >::Type &>(me._host);
}

template <typename THost, typename TSpec>
inline typename Host<ModifiedString<THost, TSpec> const>::Type &
host(ModifiedString<THost, TSpec> const & me)
{
    return _referenceCast<typename Host<ModifiedString<THost, TSpec> const>::Type &>(me._host);
}

// --------------------------------------------------------------------------
// Function setHost()
// --------------------------------------------------------------------------

template <typename THost, typename TSpec>
inline void setHost(ModifiedString<THost, TSpec> & me, THost & host)
{
    me._host = _toPointer(host);
}

template <typename THost, typename TSpec>
inline void setHost(ModifiedString<THost, TSpec> & me, THost const & host)
{
    me._host = _toPointer(host);
}

// --------------------------------------------------------------------------
// Function cargo()
// --------------------------------------------------------------------------

template <typename THost, typename TSpec>
inline typename Reference<typename Cargo<ModifiedString<THost, TSpec> >::Type >::Type
cargo(ModifiedString<THost, TSpec> & me)
{
    return me._cargo;
}

template <typename THost, typename TSpec>
inline typename Reference<typename Cargo<ModifiedString<THost, TSpec> const>::Type >::Type
cargo(ModifiedString<THost, TSpec> const & me)
{
    return me._cargo;
}

// --------------------------------------------------------------------------
// Function value()
// --------------------------------------------------------------------------

template <typename THost, typename TSpec, typename TPos>
inline typename Reference<ModifiedString<THost, TSpec> >::Type
value(ModifiedString<THost, TSpec> & me, TPos pos)
{
    return value(begin(me, Standard()) + pos);
}

template <typename THost, typename TSpec, typename TPos>
inline typename Reference<ModifiedString<THost, TSpec> const>::Type
value(ModifiedString<THost, TSpec> const & me, TPos pos)
{
    return value(begin(me, Standard()) + pos);
}

// --------------------------------------------------------------------------
// Function length()
// --------------------------------------------------------------------------

template <typename THost, typename TSpec>
inline typename Size<ModifiedString<THost, TSpec> >::Type
length(ModifiedString<THost, TSpec> const & me)
{
    return length(host(me));
}

// --------------------------------------------------------------------------
// Function begin()
// --------------------------------------------------------------------------
//
//template <typename THost, typename TSpec>
//inline typename Iterator<ModifiedString<THost, TSpec> const>::Type
//begin(ModifiedString<THost, TSpec> const & me)
//{
//    typedef typename Iterator<ModifiedString<THost, TSpec> const>::Type TResult;
//    TResult tmp(begin(host(me)));
//    _copyCargo(tmp, me);
//    return tmp;
//}
//
//template <typename THost, typename TSpec>
//inline typename Iterator<ModifiedString<THost, TSpec> >::Type
//begin(ModifiedString<THost, TSpec> & me)
//{
//    typedef typename Iterator<ModifiedString<THost, TSpec> >::Type TResult;
//    TResult tmp(begin(host(me)));
//    _copyCargo(tmp, me);
//    return tmp;
//}

template <typename THost, typename TSpec, typename TTagSpec>
inline typename Iterator<ModifiedString<THost, TSpec> const, Tag<TTagSpec> const>::Type
begin(ModifiedString<THost, TSpec> const & me, Tag<TTagSpec> const tag_)
{
    typedef typename Iterator<ModifiedString<THost, TSpec> const, Tag<TTagSpec> const>::Type TResult;
    TResult tmp(begin(host(me), tag_));
    _copyCargo(tmp, me);
    return tmp;
}

template <typename THost, typename TSpec, typename TTagSpec>
inline typename Iterator<ModifiedString<THost, TSpec>, Tag<TTagSpec> const>::Type
begin(ModifiedString<THost, TSpec> & me, Tag<TTagSpec> const tag_)
{
    typedef typename Iterator<ModifiedString<THost, TSpec>, Tag<TTagSpec> const>::Type TResult;
    TResult tmp(begin(host(me), tag_));
    _copyCargo(tmp, me);
    return tmp;
}

// --------------------------------------------------------------------------
// Function end()
// --------------------------------------------------------------------------
//
//template < typename THost, typename TSpec >
//inline typename Iterator< ModifiedString<THost, TSpec> const >::Type
//end(ModifiedString<THost, TSpec> const & me)
//{
//    typedef typename Iterator<ModifiedString<THost, TSpec> >::Type TResult;
//    TResult tmp(end(host(me)));
//    _copyCargo(tmp, me);
//    return tmp;
//}
//
//template < typename THost, typename TSpec >
//inline typename Iterator< ModifiedString<THost, TSpec> >::Type
//end(ModifiedString<THost, TSpec> & me)
//{
//    typedef typename Iterator<ModifiedString<THost, TSpec> const>::Type TResult;
//    TResult tmp(end(host(me)));
//    _copyCargo(tmp, me);
//    return tmp;
//}

template < typename THost, typename TSpec, typename TTagSpec >
inline typename Iterator< ModifiedString<THost, TSpec> const, Tag<TTagSpec> const >::Type
end(ModifiedString<THost, TSpec> const & me, Tag<TTagSpec> const tag_)
{
    typedef typename Iterator<ModifiedString<THost, TSpec> const, Tag<TTagSpec> const>::Type TResult;
    TResult tmp(end(host(me), tag_));
    _copyCargo(tmp, me);
    return tmp;
}

template < typename THost, typename TSpec, typename TTagSpec >
inline typename Iterator< ModifiedString<THost, TSpec>, Tag<TTagSpec> const >::Type
end(ModifiedString<THost, TSpec> & me, Tag<TTagSpec> const tag_)
{
    typedef typename Iterator<ModifiedString<THost, TSpec>, Tag<TTagSpec> const>::Type TResult;
    TResult tmp(end(host(me), tag_));
    _copyCargo(tmp, me);
    return tmp;
}

// --------------------------------------------------------------------------
// Function operator==()
// --------------------------------------------------------------------------

template <typename THost, typename TSpec, typename TRight >
inline bool
operator==(ModifiedString<THost, TSpec> const & left,
           TRight const & right)
{
    typename Comparator<ModifiedString<THost, TSpec> >::Type _lex(left, right);
    return isEqual(_lex);
}

template <typename TLeftValue, typename THost, typename TSpec >
inline bool
operator==(TLeftValue * left,
           ModifiedString<THost, TSpec> const & right)
{
    typename Comparator<ModifiedString<THost, TSpec> >::Type _lex(left, right);
    return isEqual(_lex);
}

// --------------------------------------------------------------------------
// Function operator!=()
// --------------------------------------------------------------------------

template <typename THost, typename TSpec, typename TRight >
inline bool
operator!=(ModifiedString<THost, TSpec> const & left,
           TRight const & right)
{
    typename Comparator<ModifiedString<THost, TSpec> >::Type _lex(left, right);
    return isNotEqual(_lex);
}

template <typename TLeftValue, typename THost, typename TSpec >
inline bool
operator!= (TLeftValue * left,
            ModifiedString<THost, TSpec> const & right)
{
    typename Comparator<ModifiedString<THost, TSpec> >::Type _lex(left, right);
    return isNotEqual(_lex);
}

// --------------------------------------------------------------------------
// Function operator<()
// --------------------------------------------------------------------------

template <typename THost, typename TSpec, typename TRight>
inline bool
operator<(ModifiedString<THost, TSpec> const & left,
          TRight const & right)
{
    return isLess(left, right, typename DefaultPrefixOrder<ModifiedString<THost, TSpec> >::Type());
}

template <typename TLeftValue, typename THost, typename TSpec >
inline bool
operator<(TLeftValue * left,
          ModifiedString<THost, TSpec> const & right)
{
    return isLess(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
}

// --------------------------------------------------------------------------
// Function operator<=()
// --------------------------------------------------------------------------

template <typename THost, typename TSpec, typename TRight>
inline bool
operator<=(ModifiedString<THost, TSpec> const & left,
           TRight const & right)
{
    return isLessOrEqual(left, right, typename DefaultPrefixOrder<ModifiedString<THost, TSpec> >::Type());
}

template <typename TLeftValue, typename THost, typename TSpec >
inline bool
operator<=(TLeftValue * left,
           ModifiedString<THost, TSpec> const & right)
{
    return isLessOrEqual(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
}

// --------------------------------------------------------------------------
// Function operator>()
// --------------------------------------------------------------------------

template <typename THost, typename TSpec, typename TRight>
inline bool
operator>(ModifiedString<THost, TSpec> const & left,
          TRight const & right)
{
    return isGreater(left, right, typename DefaultPrefixOrder<ModifiedString<THost, TSpec> >::Type());
}

template <typename TLeftValue, typename THost, typename TSpec >
inline bool
operator>(TLeftValue * left,
          ModifiedString<THost, TSpec> const & right)
{
    return isGreater(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
}

// --------------------------------------------------------------------------
// Function operator>=()
// --------------------------------------------------------------------------

template <typename THost, typename TSpec, typename TRight>
inline bool
operator>=(ModifiedString<THost, TSpec> const & left,
           TRight const & right)
{
    return isGreaterOrEqual(left, right, typename DefaultPrefixOrder<ModifiedString<THost, TSpec> >::Type());
}

template <typename TLeftValue, typename THost, typename TSpec >
inline bool
operator>=(TLeftValue * left,
           ModifiedString<THost, TSpec> const & right)
{
    return isGreaterOrEqual(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
}

// --------------------------------------------------------------------------
// Function operator<<()
// --------------------------------------------------------------------------

template < typename TStream, typename THost, typename TSpec >
inline TStream &
operator<<(TStream & target, ModifiedString<THost, TSpec> const & source)
{
    typename DirectionIterator<TStream, Output>::Type it = directionIterator(target, Output());
    write(it, source);
    return target;
}

// --------------------------------------------------------------------------
// Function operator>>()
// --------------------------------------------------------------------------

template < typename TStream, typename THost, typename TSpec >
inline TStream &
operator>>(TStream & source, ModifiedString<THost, TSpec> & target)
{
    typename DirectionIterator<TStream, Input>::Type it = directionIterator(source, Input());;
    read(it, target);
    return source;
}

// --------------------------------------------------------------------------
// Function getObjectId()
// --------------------------------------------------------------------------

template <typename THost, typename TSpec>
inline void const *
getObjectId(ModifiedString<THost, TSpec> & me)
{
    return getObjectId(host(me));
}

template <typename THost, typename TSpec>
inline void const *
getObjectId(ModifiedString<THost, TSpec> const & me)
{
    return getObjectId(host(me));
}

// ----------------------------------------------------------------------------
// Function assign()
// ----------------------------------------------------------------------------

template <typename THost, typename TSpec, typename TOtherHost, typename TOtherSpec>
inline void assign(ModifiedString<THost, TSpec> & me, ModifiedString<TOtherHost, TOtherSpec> const & other)
{
    setHost(me, host(other));
    assign(cargo(me), cargo(other));
}

// --------------------------------------------------------------------------
// Function open()
// --------------------------------------------------------------------------

template <typename THost, typename TSpec >
inline bool
open(ModifiedString<THost, TSpec> &, const char *, int)
{
    return true; // NOOP; this has to be done manually right now
}

template <typename THost, typename TSpec, typename TSpec2>
inline bool
open(StringSet<ModifiedString<THost, TSpec>, Owner<ConcatDirect<TSpec2> > > &,
     const char *,
     int)
{
    return true; // NOOP; this has to be done manually right now
}

// --------------------------------------------------------------------------
// Function save()
// --------------------------------------------------------------------------

template <typename THost, typename TSpec >
inline bool
save(ModifiedString<THost, TSpec> const &, const char *, int)
{
    return true; // NOOP; this has to be done manually right now
}

template <typename THost, typename TSpec, typename TSpec2>
inline bool
save(StringSet<ModifiedString<THost, TSpec>, Owner<ConcatDirect<TSpec2> > > const &,
     const char *,
     int)
{
    return true; // NOOP; this has to be done manually right now
}

// --------------------------------------------------------------------------
// Function clear()
// --------------------------------------------------------------------------

template <typename THost, typename TSpec >
inline void clear(ModifiedString<THost, TSpec> &)
{}

}  // namespace seqan

#endif  // SEQAN_MODIFIER_MODIFIER_STRING_H_