// ==========================================================================
//                 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: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
// Author: David Weese <david.weese@fu-berlin.de>
// ==========================================================================

#ifndef SEQAN_SEQUENCE_STRING_SET_BASE_H_
#define SEQAN_SEQUENCE_STRING_SET_BASE_H_

namespace seqan {

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

// ============================================================================
// Tags, Classes, Enums
// ============================================================================

template <typename TSpec = Default>
struct Owner {};

/*!
 * @class StringSet
 * @implements StringConcept
 * @implements TextConcept
 * @implements SegmentableConcept
 * @headerfile <seqan/sequence.h>
 * @brief A container class for a set of strings.
 *
 * @signature template <typename TString, typename TSpec>
 *            class StringSet;
 *
 * @tparam TString The type of the string to store in the string set.
 * @tparam TSpec   A tag for selecting the specialization of the string set.  Default: <tt>Owner&lt;Generous&gt;</tt>.
 *
 * String sets are containers for strings.  They have two advantages over a string of strings:
 *
 * First, they allow to express the common intent in Bioinformatics to have a list of strings, e.g. for the
 * chromosomes of a genome.  This facilitates writing generic data structures and algorithms to operate on single
 * strings and genomes which is captured by the @link TextConcept @endlink.
 *
 * Second, the @link DependentStringSet @endlink specialization allows one to create subsets of string sets without
 * storing copies of strings and identifying strings by a common id.
 *
 * @section Examples
 *
 * @include demos/dox/sequence/stringset.cpp
 *
 * The output is as follows:
 *
 * @include demos/dox/sequence/stringset.cpp.stdout
 */

template <typename TString, typename TSpec = Owner<> >
class StringSet;

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

// --------------------------------------------------------------------------
// Metafunction StringSpec
// --------------------------------------------------------------------------

template <typename TString, typename TSpec>
struct StringSpec<StringSet<TString, TSpec> > : StringSpec<TString> {};

// --------------------------------------------------------------------------
// Metafunction Concatenator
// --------------------------------------------------------------------------

/*!
 * @mfn StringSet#Concatenator
 * @brief Return the type of the concatenated sequence of all sequences in a StringSet.
 *
 * @signature Concatenator<TStringSet>::Type
 *
 * @tparam TStringSet The type of the string set.
 *
 * @return Type The resulting concatenator type.
 */

// TODO(holtgrew): Why is this specialized for all types?
template <typename TObject>
struct Concatenator
{
    typedef TObject Type;
};

template <typename TObject>
struct Concatenator<TObject const>
{
    typedef typename Concatenator<TObject>::Type const Type;
};

template <typename TString, typename TSpec >
struct Concatenator<StringSet<TString, TSpec> >
{
    typedef ConcatenatorManyToOne<StringSet<TString, TSpec> > Type;
};

// --------------------------------------------------------------------------
// Metafunction LengthSum
// --------------------------------------------------------------------------

/*!
 * @mfn StringSet#LengthSum
 * @brief Length sum type type in string set.
 *
 * @signature LengthSum<TStringSet>::Type
 *
 * @tparam TStringSet The @link StringSet @endlink to query for its length sum type.
 *
 * @return Type The resulting length sum type.
 */

// TODO(holtgrew): Complete documentation, part of TextConcept?

template <typename TString>
struct LengthSum
{
    typedef typename Size<TString>::Type Type;
};

template <typename TString, typename TSpec>
struct LengthSum<StringSet<TString, TSpec> >
{
    typedef typename Size<TString>::Type Type;
};

template <typename T>
struct LengthSum<T const> : LengthSum<T> {};

// --------------------------------------------------------------------------
// Metafunction StringSetLimits
// --------------------------------------------------------------------------

// TODO(holtgrew): Document these metafunctions.
// TODO(holtgrew): Default specializations necessary?
template <typename TString>
struct StringSetLimits
{
    typedef Nothing Type;
};

template <typename TString>
struct StringSetLimits<TString const>
{
    typedef typename StringSetLimits<TString>::Type const Type;
};

template <typename TString, typename TSpec>
struct StringSetLimits<StringSet<TString, TSpec> >
{
    typedef StringSet<TString, TSpec>               TStringSet_;
    typedef typename LengthSum<TStringSet_>::Type   Value_;
    typedef typename StringSpec<TStringSet_>::Type  TSpec_;

    typedef String<Value_, TSpec_>                  Type;
};

// --------------------------------------------------------------------------
// Metafunction StringSetPosition
// --------------------------------------------------------------------------

/*!
 * @mfn StringSet#StringSetPosition
 * @brief Returns position type in string set.
 *
 * @signature StringSetPosition<TStringSet>::Type
 *
 * @tparam TStringSet The @link StringSet @endlink to query for its position type.
 *
 * @return Type The position type of TStringSet.
 */

// TODO(holtgrew): Complete documentation, part of TextConcept?
// TODO(holtgrew): Default specializations necessary?
template <typename TString>
struct StringSetPosition
{
    typedef typename Size<TString>::Type Type;
};

template <typename TString>
struct StringSetPosition<TString const> : StringSetPosition<TString> {};

template <typename TString, typename TSpec>
struct StringSetPosition<StringSet<TString, TSpec> >
{
    typedef Pair<typename Size<StringSet<TString, TSpec> >::Type,
                 typename Size<TString>::Type,
                 Pack> Type;
};

// --------------------------------------------------------------------------
// Metafunction GetSequenceNo
// --------------------------------------------------------------------------

/*!
 * @mfn StringSet#GetSequenceByNo
 * @brief Type for getting sequence by number.
 *
 * @signature GetSequenceByNo<TStringSet>::Type
 *
 * @tparam TStringSet The StringSet to query for its sequence-by-number type.
 *
 * @return Type The given sequence-by-number type.
 */

// TODO(holtgrew): Complete documentation, part of TextConcept?
// TODO(holtgrew): Default specializations necessary?
template <typename TString>
struct GetSequenceByNo
{
    typedef TString & Type;
};

template <typename TString, typename TSpec>
struct GetSequenceByNo<StringSet<TString, TSpec> >
{
    typedef typename Reference< StringSet<TString, TSpec> >::Type Type;
};

template <typename TString, typename TSpec>
struct GetSequenceByNo<StringSet<TString, TSpec> const>
{
    typedef typename Reference< StringSet<TString, TSpec> const>::Type Type;
};

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

template < typename TString, typename TSpec >
struct Value< StringSet< TString, TSpec > >
{
    typedef TString Type;
};

template < typename TString, typename TSpec >
struct Value< StringSet< TString, TSpec > const>
{
    typedef TString const Type;
};

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

template < typename TString, typename TSpec, typename TIteratorSpec>
struct Iterator< StringSet< TString, TSpec >, TIteratorSpec>
{
    typedef Iter< StringSet< TString, TSpec >, PositionIterator> Type;
};

template < typename TString, typename TSpec, typename TIteratorSpec >
struct Iterator< StringSet< TString, TSpec> const, TIteratorSpec>
{
    typedef Iter< StringSet< TString, TSpec > const, PositionIterator> Type;
};

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

template <typename TString, typename TSpec>
struct Size< StringSet< TString, TSpec > >
    : Size<typename StringSetLimits< StringSet<TString, TSpec> >::Type > {};
// Default Size<T const> redirects to non-const.

// --------------------------------------------------------------------------
// Metafunction PrefixOnValue
// --------------------------------------------------------------------------

template <typename TString, typename TSpec>
struct PrefixOnValue< StringSet< TString, TSpec > >
    : Prefix<TString > {};

template <typename TString, typename TSpec>
struct PrefixOnValue<StringSet< TString, TSpec > const>
    : Prefix<TString const > {};

// --------------------------------------------------------------------------
// Metafunction SuffixOnValue
// --------------------------------------------------------------------------

template <typename TString, typename TSpec>
struct SuffixOnValue<StringSet< TString, TSpec> >
    : Suffix<TString> {};

template <typename TString, typename TSpec>
struct SuffixOnValue<StringSet< TString, TSpec> const>
    : Suffix<TString const> {};

// --------------------------------------------------------------------------
// Metafunction InfixOnValue
// --------------------------------------------------------------------------

template <typename TString, typename TSpec>
struct InfixOnValue<StringSet< TString, TSpec> >
    : Infix<TString> {};

template <typename TString, typename TSpec>
struct InfixOnValue<StringSet< TString, TSpec > const>
    : Infix< TString const > {};

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

template <typename TString, typename TSpec>
struct AllowsFastRandomAccess<StringSet<TString, TSpec> >
    : AllowsFastRandomAccess<TString> {};
// Default AllowsFastRandomAccess<T const> redirects to non-const.

// --------------------------------------------------------------------------
// Metafunction DefaultOverflowImplicit
// --------------------------------------------------------------------------

template < typename TString, typename TSpec >
struct DefaultOverflowImplicit<StringSet< TString, TSpec> >
{
    typedef Generous Type;
};

template < typename TString, typename TSpec >
struct DefaultOverflowImplicit<StringSet< TString, TSpec> const>
{
    typedef Generous Type;
};

// ----------------------------------------------------------------------------
// Concept StringConcept
// ----------------------------------------------------------------------------

template <typename TString, typename TSpec>
SEQAN_CONCEPT_IMPL((StringSet<TString, TSpec>), (StringConcept));           // resizable container

template <typename TString, typename TSpec>
SEQAN_CONCEPT_IMPL((StringSet<TString, TSpec> const), (ContainerConcept));  // read-only container

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


// --------------------------------------------------------------------------
// Function stringSetLimits()
// --------------------------------------------------------------------------

// TODO(holtgrew): Default implementation necessary?!
template <typename TStringSet>
inline typename StringSetLimits<TStringSet>::Type
stringSetLimits(TStringSet &)
{
    return typename StringSetLimits<TStringSet>::Type();
}

template <typename TString, typename TSpec>
inline typename StringSetLimits< StringSet<TString, TSpec> >::Type &
stringSetLimits(StringSet<TString, TSpec> & stringSet)
{
    if (!_validStringSetLimits(stringSet))
        _refreshStringSetLimits(stringSet);
    return stringSet.limits;
}

template <typename TString, typename TSpec>
inline typename StringSetLimits< StringSet<TString, TSpec> const>::Type &
stringSetLimits(StringSet<TString, TSpec> const & stringSet)
{
    if (!_validStringSetLimits(stringSet))
        _refreshStringSetLimits(const_cast< StringSet<TString, TSpec>& >(stringSet));
    return stringSet.limits;
}

// --------------------------------------------------------------------------
// Function getSeqNo()
// --------------------------------------------------------------------------

// TODO(holtgrew): Auto-sequences should go away!
template <typename TPosition>
inline TPosition
getSeqNo(TPosition const &, Nothing const &)
{
    return 0;
}

// TODO(holtgrew): Auto-sequences should go away!
template <typename TPosition>
inline TPosition
getSeqNo(TPosition const &)
{
    return 0;
}

// n sequences (position type is Pair)
template <typename T1, typename T2, typename TPack, typename TLimitsString>
inline T1 getSeqNo(Pair<T1, T2, TPack> const & pos, TLimitsString const &)
{
    return getValueI1(pos);
}

// n sequences (position type is Pair)
template <typename T1, typename T2, typename TPack>
inline T1 getSeqNo(Pair<T1, T2, TPack> const & pos)
{
    return getValueI1(pos);
}

// n sequences (position type is an integral type)
template <typename TPos, typename TLimitsString>
inline TPos getSeqNo(TPos const & pos, TLimitsString const & limits)
{
    typedef typename Iterator<TLimitsString const, Standard>::Type TIter;
    typedef typename Value<TLimitsString>::Type TSize;
    TIter _begin = begin(limits, Standard());
    TIter _upper = std::upper_bound(_begin, end(limits, Standard()), (TSize)pos) - 1;
    return difference(_begin, _upper);
}

// --------------------------------------------------------------------------
// Function getSeqOffset()
// --------------------------------------------------------------------------

// TODO(holtgrew): Auto-sequences should go away!
template <typename TPosition>
inline TPosition
getSeqOffset(TPosition const & pos, Nothing const &)
{
    return pos;
}

// TODO(holtgrew): Auto-sequences should go away!
template <typename TPosition>
inline TPosition
getSeqOffset(TPosition const & pos)
{
    return pos;
}

// n sequences (position type is Pair)
template <typename T1, typename T2, typename TPack, typename TLimitsString>
inline T2 getSeqOffset(Pair<T1, T2, TPack> const & pos, TLimitsString const &) {
    return getValueI2(pos);
}

// n sequences (position type is Pair)
template <typename T1, typename T2, typename TPack>
inline T2 getSeqOffset(Pair<T1, T2, TPack> const & pos) {
    return getValueI2(pos);
}

// n sequences (position type is an integral type)
template <typename TPos, typename TLimitsString>
inline TPos getSeqOffset(TPos const & pos, TLimitsString const & limits) {
    typedef typename Iterator<TLimitsString const, Standard>::Type TIter;
    typedef typename Value<TLimitsString>::Type TSize;
    TIter _begin = begin(limits, Standard());
    TIter _upper = std::upper_bound(_begin, end(limits, Standard()), (TSize)pos) - 1;
    return pos - *_upper;
}

// --------------------------------------------------------------------------
// Function setSeqOffset()
// --------------------------------------------------------------------------

// TODO(esiragusa): Implement a spec for global positions.
template <typename TPosition, typename TSeqOffset>
inline void
setSeqOffset(TPosition & pos, TSeqOffset seqOffset)
{
    pos = seqOffset;
}

template <typename T1, typename T2, typename TPack, typename TSeqOffset>
inline void
setSeqOffset(Pair<T1, T2, TPack> & pos, TSeqOffset seqOffset)
{
    setValueI2(pos, seqOffset);
}


// --------------------------------------------------------------------------
// Function posGlobalize()
// --------------------------------------------------------------------------

// any_position and no limits_string -> any_position
template <typename TPosition>
inline TPosition posGlobalize(TPosition const & pos, Nothing const &)
{
    return pos;
}

// local_position (0,x) and no limits_string -> global_position x
template <typename T1, typename T2, typename TPack>
inline T2 posGlobalize(Pair<T1, T2, TPack> const & pos, Nothing const &)
{
    return getSeqOffset(pos);
}

// any_position and no limits_string -> any_position
template <typename TLimitsString, typename TPosition>
inline TPosition posGlobalize(TPosition const & pos, TLimitsString const &)
{
    return pos;
}

// local_position and limits_string -> global_position
template <typename TLimitsString, typename T1, typename T2, typename TPack>
inline typename Value<TLimitsString>::Type
posGlobalize(Pair<T1, T2, TPack> const & pos, TLimitsString const & limits)
{
    return limits[getSeqNo(pos, limits)] + getSeqOffset(pos, limits);
}

// --------------------------------------------------------------------------
// Function posLocalToX()
// --------------------------------------------------------------------------

template <typename TDest, typename TLimitsString, typename T1, typename T2, typename TPack>
inline void
posLocalToX(TDest & dst, Pair<T1, T2, TPack> const & localPos, TLimitsString const & limits)
{
    dst = posGlobalize(localPos, limits);
}

template <typename TD1, typename TD2, typename TDPack, typename TLimitsString, typename T1, typename T2, typename TPack>
inline void
posLocalToX(Pair<TD1, TD2, TDPack> & dst, Pair<T1, T2, TPack> const & localPos, TLimitsString const &)
{
    dst = localPos;
}

// --------------------------------------------------------------------------
// Function posLocalize()
// --------------------------------------------------------------------------

// any_position and no limits_string -> any_position
template <typename TResult, typename TPosition>
inline void posLocalize(TResult & result, TPosition const & pos, Nothing const &) {
    result = pos;
}

template <typename T1, typename T2, typename TPack, typename TPosition>
inline void posLocalize(Pair<T1, T2, TPack> & result, TPosition const & pos, Nothing const &) {
    result.i1 = 0;
    result.i2 = pos;
}

// global_position and limits_string -> local_position
template <typename TResult, typename TSize, typename TSpec, typename TPosition>
inline void posLocalize(TResult & result, TPosition const & pos, String<TSize, TSpec> const & limits) {
    typedef typename Iterator<String<TSize, TSpec> const, Standard>::Type TIter;
    TIter _begin = begin(limits, Standard());
    TIter _upper = std::upper_bound(_begin, end(limits, Standard()), (TSize)pos) - 1;
    result.i1 = difference(_begin, _upper);
    result.i2 = pos - *_upper;
}

// local_position -> local_position
template <typename TResult, typename TSize, typename TSpec, typename T1, typename T2, typename TPack>
inline void posLocalize(TResult & result, Pair<T1, T2, TPack> const & pos, String<TSize, TSpec> const &/*limits*/) {
    result = pos;
}

// --------------------------------------------------------------------------
// Function prefix(); For local string set position.
// --------------------------------------------------------------------------

template < typename TString, typename TSpec, typename TPosition >
inline SEQAN_FUNC_DISABLE_IF(Is<IntegerConcept<TPosition> >,
                             typename PrefixOnValue<StringSet< TString, TSpec > >::Type)
prefix(StringSet< TString, TSpec > & me, TPosition const & pos)
{
    typedef StringSet<TString, TSpec>               TStringSet;
    typedef typename Size<TStringSet>::Type         TSetSize;
    typedef typename Size<TString>::Type            TStringSize;
    typedef Pair<TSetSize, TStringSize, Pack> TPair;

    TPair lPos;
    posLocalize(lPos, pos, stringSetLimits(me));
    return prefix(me[getSeqNo(lPos)], getSeqOffset(lPos));
}

template < typename TString, typename TSpec, typename TPosition >
inline SEQAN_FUNC_DISABLE_IF(Is<IntegerConcept<TPosition> >,
                             typename PrefixOnValue<StringSet< TString, TSpec > const>::Type)
prefix(StringSet< TString, TSpec > const & me, TPosition const & pos)
{
    typedef StringSet<TString, TSpec>               TStringSet;
    typedef typename Size<TStringSet>::Type         TSetSize;
    typedef typename Size<TString>::Type            TStringSize;
    typedef Pair<TSetSize, TStringSize, Pack> TPair;

    TPair lPos;
    posLocalize(lPos, pos, stringSetLimits(me));
    return prefix(me[getSeqNo(lPos)], getSeqOffset(lPos));
}

// --------------------------------------------------------------------------
// Function suffix(); For local string set position.
// --------------------------------------------------------------------------

template < typename TString, typename TSpec, typename TPosition >
inline SEQAN_FUNC_DISABLE_IF(Is<IntegerConcept<TPosition> >,
                             typename SuffixOnValue<StringSet< TString, TSpec > >::Type)
suffix(StringSet< TString, TSpec > & me, TPosition const & pos)
{
    typedef StringSet<TString, TSpec>               TStringSet;
    typedef typename Size<TStringSet>::Type         TSetSize;
    typedef typename Size<TString>::Type            TStringSize;
    typedef Pair<TSetSize, TStringSize, Pack> TPair;

    TPair lPos;
    posLocalize(lPos, pos, stringSetLimits(me));
    return suffix(me[getSeqNo(lPos)], getSeqOffset(lPos));
}

template < typename TString, typename TSpec, typename TPosition >
inline SEQAN_FUNC_DISABLE_IF(Is<IntegerConcept<TPosition> >,
                             typename SuffixOnValue<StringSet< TString, TSpec > const>::Type)
suffix(StringSet< TString, TSpec > const & me, TPosition const & pos)
{
    typedef StringSet<TString, TSpec>               TStringSet;
    typedef typename Size<TStringSet>::Type         TSetSize;
    typedef typename Size<TString>::Type            TStringSize;
    typedef Pair<TSetSize, TStringSize, Pack> TPair;

    TPair lPos;
    posLocalize(lPos, pos, stringSetLimits(me));
    return suffix(me[getSeqNo(lPos)], getSeqOffset(lPos));
}

// --------------------------------------------------------------------------
// Function infixWithLength(); For local string set position.
// --------------------------------------------------------------------------

template < typename TString, typename TSpec, typename TPosition, typename TSize >
inline SEQAN_FUNC_DISABLE_IF(Is<IntegerConcept<TPosition> >,
                             typename InfixOnValue<StringSet< TString, TSpec > >::Type)
infixWithLength(StringSet< TString, TSpec > & me, TPosition const & pos, TSize const length)
{
    typedef StringSet<TString, TSpec>               TStringSet;
    typedef typename Size<TStringSet>::Type         TSetSize;
    typedef typename Size<TString>::Type            TStringSize;
    typedef Pair<TSetSize, TStringSize, Pack> TPair;

    TPair lPos;
    posLocalize(lPos, pos, stringSetLimits(me));
    return infixWithLength(me[getSeqNo(lPos)], getSeqOffset(lPos), length);
}

template < typename TString, typename TSpec, typename TPosition, typename TSize >
inline SEQAN_FUNC_DISABLE_IF(Is<IntegerConcept<TPosition> >,
                             typename InfixOnValue<StringSet< TString, TSpec > const>::Type)
infixWithLength(StringSet< TString, TSpec > const & me, TPosition const & pos, TSize const length)
{
    typedef StringSet<TString, TSpec>               TStringSet;
    typedef typename Size<TStringSet>::Type         TSetSize;
    typedef typename Size<TString>::Type            TStringSize;
    typedef Pair<TSetSize, TStringSize, Pack> TPair;

    TPair lPos;
    posLocalize(lPos, pos, stringSetLimits(me));
    return infixWithLength(me[getSeqNo(lPos)], getSeqOffset(lPos), length);
}

// --------------------------------------------------------------------------
// Function infix(); For local string set position.
// --------------------------------------------------------------------------

template < typename TString, typename TSpec, typename TPosBeg, typename TPosEnd>
inline SEQAN_FUNC_DISABLE_IF(Is<IntegerConcept<TPosBeg> >,
                             typename InfixOnValue<StringSet< TString, TSpec > >::Type)
infix(StringSet<TString, TSpec > & me, TPosBeg const & posBegin, TPosEnd const & posEnd)
{
    typedef StringSet<TString, TSpec>               TStringSet;
    typedef typename Size<TStringSet>::Type         TSetSize;
    typedef typename Size<TString>::Type            TStringSize;
    typedef Pair<TSetSize, TStringSize, Pack> TPair;

    TPair localPosBegin, localPosEnd;
    posLocalize(localPosBegin, posBegin, stringSetLimits(me));
    posLocalize(localPosEnd, posEnd, stringSetLimits(me));
    return infix(me[getSeqNo(localPosBegin)], getSeqOffset(localPosBegin), getSeqOffset(localPosEnd));
}

template < typename TString, typename TSpec, typename TPosBeg, typename TPosEnd>
inline SEQAN_FUNC_DISABLE_IF(Is<IntegerConcept<TPosBeg> >,
                             typename InfixOnValue<StringSet< TString, TSpec > const>::Type)
infix(StringSet<TString, TSpec > const & me, TPosBeg const & posBegin, TPosEnd const & posEnd)
{
    typedef StringSet<TString, TSpec>               TStringSet;
    typedef typename Size<TStringSet>::Type         TSetSize;
    typedef typename Size<TString>::Type            TStringSize;
    typedef Pair<TSetSize, TStringSize, Pack> TPair;

    TPair localPosBegin, localPosEnd;
    posLocalize(localPosBegin, posBegin, stringSetLimits(me));
    posLocalize(localPosEnd, posEnd, stringSetLimits(me));
    return infix(me[getSeqNo(localPosBegin)], getSeqOffset(localPosBegin), getSeqOffset(localPosEnd));
}

// --------------------------------------------------------------------------
// Function posAtFirstLocal()
// --------------------------------------------------------------------------

template <typename TPos, typename TLimitsString>
inline bool posAtFirstLocal(TPos const & pos, TLimitsString const & limits) {
    return getSeqOffset(pos, limits) == 0;
}
template <typename TPos>
inline bool posAtFirstLocal(TPos const & pos) {
    return getSeqOffset(pos) == 0;
}

// --------------------------------------------------------------------------
// Function posAtEnd()
// --------------------------------------------------------------------------

template <typename T1, typename T2, typename TPack, typename TSequence, typename TSpec>
inline bool posAtEnd(Pair<T1, T2, TPack> const & pos, StringSet<TSequence, TSpec> const & stringSet) {
    return pos.i2 == sequenceLength(pos.i1, stringSet);
}
template <typename TPos, typename TSequence, typename TSpec>
inline bool posAtEnd(TPos pos, StringSet<TSequence, TSpec> const & stringSet) {
    return getSeqOffset(pos, stringSetLimits(stringSet)) == 0;
}
template <typename TPos, typename TSequence>
inline bool posAtEnd(TPos pos, TSequence const & seq) {
    return pos == length(seq);
}

// --------------------------------------------------------------------------
// Function posPrev()
// --------------------------------------------------------------------------

/*!
 * @defgroup PositionCalculation Position Calculation
 * @brief Position calculation functions.
 */

/*!
 * @fn PositionCalculation#posPrev
 * @headerfile <seqan/sequence.h>
 * @brief Returns a position where the local offset is decreased by one.
 *
 * @signature TPos posPrev(pos);
 *
 * @param[in] pos A position type, an integer with <tt>seqOfs</tt> or a pair <tt>(seqNo, seqOfs)</tt>.
 *
 * @return TPos The predecessor.  TPos is the type of <tt>pos</tt>.
 *
 * @see PositionCalculation#posNext
 * @see PositionCalculation#posInc
 * @see PositionCalculation#posAdd
 */

template <typename TPos>
inline TPos posPrev(TPos pos) {
    return pos - 1;
}

template <typename T1, typename T2, typename TPack>
inline Pair<T1, T2, TPack> posPrev(Pair<T1, T2, TPack> const & pos) {
    return Pair<T1, T2, TPack>(getValueI1(pos), getValueI2(pos) - 1);
}

// --------------------------------------------------------------------------
// Function posInc()
// --------------------------------------------------------------------------

/*!
 * @fn PositionCalculation#posInc
 * @headerfile <seqan/sequence.h>
 * @brief Increments the local offset of a position type.
 *
 * @signature void posInc(pos);
 *
 * @param[in,out] pos A position type, an integer with <tt>seqOfs</tt> or a pair <tt>(seqNo, seqOfs)</tt>.  In both
 *                    cases, <tt>seqOfs</tt> will be incremented by one.
 *
 * @see PositionCalculation#posNext
 * @see PositionCalculation#posPrev
 * @see PositionCalculation#posAdd
 */

template <typename TPos>
inline void posInc(TPos &pos) {
    ++pos;
}

template <typename TPos, typename TDelta>
inline void posInc(TPos &pos, TDelta delta) {
    pos += delta;
}

template <typename T1, typename T2, typename TPack>
inline void posInc(Pair<T1, T2, TPack> & pos) {
    ++pos.i2;
}

template <typename T1, typename T2, typename TPack, typename TDelta>
inline void posInc(Pair<T1, T2, TPack> & pos, TDelta delta) {
    pos.i2 += delta;
}

// --------------------------------------------------------------------------
// Function posNext()
// --------------------------------------------------------------------------

/*!
 * @fn PositionCalculation#posNext
 * @headerfile <seqan/sequence.h>
 * @brief Returns a position where the local offset is increased by one.
 *
 * @signature TPos posNext(pos);
 *
 * @param[in] pos A position type, an integer with <tt>seqOfs</tt> or a pair <tt>(seqNo, seqOfs)</tt>.
 *
 * @return TPos Returns a value of the same type as <tt>pos</tt> where <tt>seqOfs</tt> is increased by one.
 *
 * @see PositionCalculation#posInc
 * @see PositionCalculation#posPrev
 * @see PositionCalculation#posAdd
 */

template <typename TPos>
inline TPos posNext(TPos pos) {
    return pos + 1;
}

template <typename T1, typename T2, typename TPack>
inline Pair<T1, T2, TPack>
posNext(Pair<T1, T2, TPack> const & pos) {
    return Pair<T1, T2, TPack>(getValueI1(pos), getValueI2(pos) + 1);
}

// --------------------------------------------------------------------------
// Function posAdd()
// --------------------------------------------------------------------------

/*!
 * @fn PositionCalculation#posAdd
 * @headerfile <seqan/sequence.h>
 * @brief Returns a position where the local offset is increased by a value <tt>delta</tt>.
 *
 * @signature TPos posAdd(pos, delta);
 *
 * @param[in] pos   A position type, an integer with <tt>seqOfs</tt> or a pair <tt>(seqNo, seqOfs)</tt>.
 * @param[in] delta Increase the local offset of <tt>pos</tt> by this value.
 *
 * @return TPos Returns a value of the same type as <tt>pos</tt> where <tt>seqOfs</tt> is increased by <tt>delta</tt>.
 *
 * @see PositionCalculation#posInc
 * @see PositionCalculation#posPrev
 * @see PositionCalculation#posNext
 */

template <typename TPos, typename TDelta>
inline TPos posAdd(TPos pos, TDelta delta) {
    return pos + delta;
}

template <typename T1, typename T2, typename TPack, typename TDelta>
inline Pair<T1, T2, TPack>
posAdd(Pair<T1, T2, TPack> const & pos, TDelta delta) {
    return Pair<T1, T2, TPack>(getValueI1(pos), getValueI2(pos) + delta);
}


// --------------------------------------------------------------------------
// Function posAddAndCheck()
// --------------------------------------------------------------------------

/*!
 * @fn PositionCalculation#posAddAndCheck
 * @headerfile <seqan/sequence.h>
 * @brief Increases the local offset of a position by a value <tt>delta</tt> and check for overflow.
 *
 * @signature bool posAddAndCheck(pos, delta, text);
 *
 * @param[in,out] pos   A position type, an integer with <tt>seqOfs</tt> or a pair <tt>(seqNo, seqOfs)</tt>.
 * @param[in]     delta Increase the local offset of <tt>pos</tt> by this value.
 * @param[in]     text  The @link TextConcept text @endlink to use for checking.
 *
 * @see PositionCalculation#posAdd
 * @see PositionCalculation#posInc
 */

template <typename TPos, typename TDelta, typename TSequence>
inline bool posAddAndCheck(TPos & pos, TDelta delta, TSequence const & sequence) {
    return (pos += delta) < length(sequence);
}

template <typename TPos, typename TDelta, typename TSequence, typename TSpec>
inline bool posAddAndCheck(TPos & pos, TDelta delta, StringSet<TSequence, TSpec> const & stringSet)
{
    typedef StringSet<TSequence, TSpec> TStringSet;
    typedef typename StringSetLimits<TStringSet const>::Type TLimits;
    typedef typename Iterator<TLimits, Standard>::Type TIter;
    typedef typename Value<TLimits>::Type TSize;

    TLimits & limits = stringSetLimits(stringSet);
    TIter _end = end(limits, Standard());
    TIter _endMark = std::upper_bound(begin(limits, Standard()), _end, (TSize)pos);
    pos += delta;
    if (_endMark < _end)
        return pos < *_endMark;
    else
        return false;
}

template <typename T1, typename T2, typename TPack, typename TDelta, typename TSequence, typename TSpec>
inline bool
posAddAndCheck(Pair<T1, T2, TPack> & pos, TDelta delta, StringSet<TSequence, TSpec> const & stringSet) {
    return (pos.i2 += delta) < length(stringSet[pos.i1]);
}

// --------------------------------------------------------------------------
// Function posSub()
// --------------------------------------------------------------------------

/*!
 * @fn PositionCalculation#posSub
 * @headerfile <seqan/sequence.h>
 * @brief Returns a position where the local offset is decreased by a value <tt>delta</tt>.
 *
 * @signature TPos posSub(pos, delta);
 *
 * @param[in] pos   A position type, an integer with <tt>seqOfs</tt> or a pair <tt>(seqNo, seqOfs)</tt>.
 * @param[in] delta Decrease the local offset of <tt>pos</tt> by this value.
 *
 * @return TPos Returns a value of the same type as <tt>pos</tt> where <tt>seqOfs</tt> is decreased by <tt>delta</tt>.
 *
 * @see PositionCalculation#posAdd
 * @see PositionCalculation#posInc
 * @see PositionCalculation#posNext
 */

template <typename TA, typename TB>
inline TA posSub(TA a, TB b) {
    return a - b;
}

template <
    typename TA1, typename TA2, typename TAPack,
    typename TB1, typename TB2, typename TBPack
>
inline TA2
posSub(Pair<TA1, TA2, TAPack> const & a, Pair<TB1, TB2, TBPack> const & b) {
    return getValueI2(a) - getValueI2(b);
}

// --------------------------------------------------------------------------
// Function posLess()
// --------------------------------------------------------------------------

template <typename TPos>
inline bool posLess(TPos const & a, TPos const & b) {
    return a < b;
}

template <typename T1, typename T2, typename TPack>
inline bool posLess(Pair<T1, T2, TPack> const & a, Pair<T1, T2, TPack> const & b) {
    return
         (getValueI1(a) <  getValueI1(b)) ||
        ((getValueI1(a) == getValueI1(b)) && (getValueI2(a) < getValueI2(b)));
}

// --------------------------------------------------------------------------
// Function posCompare()
// --------------------------------------------------------------------------

template <typename TPos>
inline int posCompare(TPos const & a, TPos const & b) {
    if (a < b) return -1;
    if (a > b) return 1;
    return 0;
}

template <typename T1, typename T2, typename TPack>
inline int posCompare(Pair<T1, T2, TPack> const & a, Pair<T1, T2, TPack> const & b) {
    if (getValueI1(a) < getValueI1(b)) return -1;
    if (getValueI1(a) > getValueI1(b)) return 1;
    return posCompare(getValueI2(a), getValueI2(b));
}

// --------------------------------------------------------------------------
// Function suffixLength()
// --------------------------------------------------------------------------

template <typename TPos, typename TString>
inline typename Size<TString>::Type
suffixLength(TPos pos, TString const & string) {
    return length(string) - pos;
}

template <typename TPos, typename TString, typename TSpec>
inline typename Size<TString>::Type
suffixLength(TPos pos, StringSet<TString, TSpec> const & stringSet) {
    return length(stringSet[getSeqNo(pos, stringSetLimits(stringSet))]) - getSeqOffset(pos, stringSetLimits(stringSet));
}

// --------------------------------------------------------------------------
// Function countSequences()
// --------------------------------------------------------------------------

template <typename TString>
inline unsigned
countSequences(TString const &) {
    return 1;
}

template <typename TString, typename TSpec>
inline typename Size<StringSet<TString, TSpec> >::Type
countSequences(StringSet<TString, TSpec> const & stringSet) {
    return length(stringSet);
}

// --------------------------------------------------------------------------
// Function getSequenceByNo()
// --------------------------------------------------------------------------

template <typename TSeqNo, typename TString>
inline typename GetSequenceByNo<TString>::Type
getSequenceByNo(TSeqNo /*seqNo*/, TString & string)
{
    return string;
}

template <typename TSeqNo, typename TString, typename TSpec>
inline typename GetSequenceByNo< StringSet<TString, TSpec> >::Type
getSequenceByNo(TSeqNo seqNo, StringSet<TString, TSpec> & stringSet)
{
    return stringSet[seqNo];
}

template <typename TSeqNo, typename TString, typename TSpec>
inline typename GetSequenceByNo< StringSet<TString, TSpec> const>::Type
getSequenceByNo(TSeqNo seqNo, StringSet<TString, TSpec> const & stringSet)
{
    return stringSet[seqNo];
}

// --------------------------------------------------------------------------
// Function sequenceLength()
// --------------------------------------------------------------------------

template <typename TSeqNo, typename TText>
inline typename Size< typename GetSequenceByNo<TText const>::Type>::Type
sequenceLength(TSeqNo seqNo, TText const & text)
{
    return length(getSequenceByNo(seqNo, text));
}

// --------------------------------------------------------------------------
// Function _validStringSetLimits
// --------------------------------------------------------------------------

// TODO(holtgrew): Anti auto-stringset
template < typename T >
inline bool _validStringSetLimits(T const &) {
    return true;
}

template < typename TString, typename TSpec >
inline bool _validStringSetLimits(StringSet< TString, TSpec > const & me) {
    return me.limitsValid;
}

// --------------------------------------------------------------------------
// Function _refreshStringSetLimits
// --------------------------------------------------------------------------

template < typename T >
inline void _refreshStringSetLimits(T &) {}

template < typename TString, typename TSpec >
void _refreshStringSetLimits(StringSet< TString, TSpec > & me)
{
    typedef StringSet< TString, TSpec >                 TStringSet;
    typedef typename StringSetLimits<TStringSet>::Type  TLimits;

    typename Value<TLimits>::Type   sum = 0;
    typename Size<TStringSet>::Type len = length(me);
    typename Size<TStringSet>::Type i = 0;

//      SEQAN_ASSERT_EQ(length(me.limits), len + 1);
    resize(me.limits, len + 1, Generous());
    for(; i < len; ++i)
    {
        me.limits[i] = sum;
        sum += length(me[i]);
        SEQAN_ASSERT_LEQ(me.limits[i], sum);
    }
    me.limits[i] = sum;
    me.limitsValid = true;
}

// --------------------------------------------------------------------------
// Function _findIthNonZeroValue()
// --------------------------------------------------------------------------

// find the i-th non-zero value of a string me
template < typename TValue, typename TSpec, typename TPos >
inline typename Size< String<TValue, TSpec> >::Type
_findIthNonZeroValue(String<TValue, TSpec> const & me, TPos i)
{
    typename Iterator< String<TValue, TSpec> const, Standard >::Type it = begin(me, Standard());
    typename Iterator< String<TValue, TSpec> const, Standard >::Type itEnd = end(me, Standard());

    for(; it != itEnd; ++it)
        if (*it)
        {
            if (i)
                --i;
            else
                return position(it, me);
        }
    return length(me);
}

// --------------------------------------------------------------------------
// Function _countNonZeroValues()
// --------------------------------------------------------------------------

// count non-zero values before position i
template < typename TValue, typename TSpec, typename TPos >
inline typename Size< String<TValue, TSpec> >::Type
_countNonZeroValues(String<TValue, TSpec> const & me, TPos i)
{
    typename Iterator< String<TValue, TSpec> const, Standard >::Type it = begin(me, Standard());
    typename Iterator< String<TValue, TSpec> const, Standard >::Type itEnd = begin(me, Standard()) + i;
    typename Size< String<TValue, TSpec> >::Type counter = 0;

    for(; it != itEnd; ++it)
        if (*it) ++counter;
    return counter;
}

// --------------------------------------------------------------------------
// Function maxLength()
// --------------------------------------------------------------------------
// Returns the length of the longest string in the set.

template <typename TString, typename TSpec, typename TParallel>
inline typename Size<TString>::Type
maxLength(StringSet<TString, TSpec> const & me, Tag<TParallel> const & tag)
{
    typedef StringSet<TString, TSpec>               TStringSet;
    typedef typename Value<TStringSet const>::Type  TValue;

    return empty(me) ? 0 : length(maxElement(me, LengthLess<TValue>(), tag));
}

template <typename TString, typename TSpec>
inline typename Size<TString>::Type
maxLength(StringSet<TString, TSpec> const & me)
{
    return maxLength(me, Serial());
}

// --------------------------------------------------------------------------
// Function minLength()
// --------------------------------------------------------------------------
// Returns the length of the shortest string in the set.

template <typename TString, typename TSpec, typename TParallel>
inline typename Size<StringSet<TString, TSpec> const>::Type
minLength(StringSet<TString, TSpec> const & me, Tag<TParallel> const & tag)
{
    typedef StringSet<TString, TSpec>               TStringSet;
    typedef typename Value<TStringSet const>::Type  TValue;

    return empty(me) ? 0 : length(minElement(me, LengthLess<TValue>(), tag));
}

template <typename TString, typename TSpec>
inline typename Size<StringSet<TString, TSpec> const>::Type
minLength(StringSet<TString, TSpec> const & me)
{
    return minLength(me, Serial());
}

// --------------------------------------------------------------------------
// Function lengthSum()
// --------------------------------------------------------------------------

/*!
 * @fn StringSet#lengthSum
 * @brief Returns total length of all strings in the string set.
 *
 * @signature TSize lengthSum(s);
 *
 * @param[in] s The string set to get length sum of.
 *
 * @return TSize The sum of the lengths of all strings in the string set.
 */

template <typename TString>
inline typename LengthSum<TString>::Type
lengthSum(TString const & me)
{
    return length(me);
}

template <typename TString, typename TSpec>
inline typename LengthSum<StringSet<TString, TSpec> >::Type
lengthSum(StringSet<TString, TSpec> & me)
{
    if (!_validStringSetLimits(me))
        _refreshStringSetLimits(me);
    return back(stringSetLimits(me));
}

template < typename TString, typename TSpec >
inline typename LengthSum<StringSet<TString, TSpec> >::Type
lengthSum(StringSet<TString, TSpec> const & me)
{
    if (!_validStringSetLimits(me))
        _refreshStringSetLimits(me);
    return back(stringSetLimits(me));
}

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

/*!
 * @fn StringSet#clear
 * @headerfile <seqan/sequence.h>
 * @brief Clear the StringSet.
 *
 * @signature void clear(stringSet);
 *
 * @param[in,out] seedSet The StringSet to clear.
 */

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


template <typename TString, typename TSpec >
inline typename Size<StringSet<TString, TSpec > >::Type
length(StringSet<TString, TSpec > const & me)
{
    return length(me.strings);
}

// --------------------------------------------------------------------------
// Function resize()
// --------------------------------------------------------------------------

template <typename TString, typename TSpec, typename TSize, typename TExpand >
inline typename Size<StringSet<TString, TSpec > >::Type
resize(StringSet<TString, TSpec > & me, TSize new_size, Tag<TExpand> tag)
{
    resize(me.limits, new_size + 1, tag);
    me.limitsValid = (new_size == 0);

    //     the following would not work as changing the size of
    //     a single string cannot be recognized by the stringset
    //
    //        if (_validStringSetLimits(me))
    //            resize(me.limits, new_size + 1, back(me.limits), tag);

    return resize(me.strings, new_size, tag);
}

// --------------------------------------------------------------------------
// Function reserve()
// --------------------------------------------------------------------------

/*!
 * @fn StringSet#reserve
 * @brief Reserve memory for string set.
 *
 * @signature TSize reserve(s, newCapacity, tag);
 *
 * @param[in,out] s           The string set to reserve memory for.
 * @param[in]     newCapacity The target capacity.
 * @param[in]     tag         A tag to select the reservation strategy.
 */

template <typename TString, typename TSpec, typename TSize, typename TExpand>
inline typename Size<StringSet<TString, TSpec > >::Type
reserve(StringSet<TString, TSpec > & me,
        TSize const & new_capacity,
        Tag<TExpand> tag)
{
    reserve(me.limits, new_capacity + 1, tag);
    return reserve(me.strings, new_capacity, tag);
}

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

template <typename TString, typename TSpec, typename TSource, typename TExpand>
inline void
assign(StringSet<TString, TSpec> & target,
       TSource const & source,
       Tag<TExpand> tag)
{
    typedef typename Iterator<TSource const, Standard>::Type TSourceIterator;

    clear(target);
    reserve(target, length(source), tag);

    // we append each source string for target being a ConcatDirect StringSet
    TSourceIterator it = begin(source, Standard());
    TSourceIterator itEnd = end(source, Standard());
    for (; it != itEnd; ++it)
        appendValue(target, *it, tag);
}

template <typename TString, typename TSpec, typename TSource>
inline void
assign(StringSet<TString, TSpec> & target,
       TSource const & source)
{
    typedef StringSet<TString, TSpec> TTarget;
    assign(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
}

// --------------------------------------------------------------------------
// Function iter()
// --------------------------------------------------------------------------

template <typename TString, typename TSpec, typename TPos, typename TTag>
inline typename Iterator<StringSet<TString, TSpec >, Tag<TTag> const>::Type
iter(StringSet<TString, TSpec > & me,
     TPos pos,
     Tag<TTag> const &)
{
    typedef StringSet<TString, TSpec > TStringSet;
    typedef typename Iterator<TStringSet, Tag<TTag> const>::Type TIterator;
    typedef typename Position<TStringSet>::Type TPosition;
    return TIterator(me, (TPosition) pos);
}

template <typename TString, typename TSpec, typename TPos, typename TTag>
inline typename Iterator<StringSet<TString, TSpec > const, Tag<TTag> const>::Type
iter(StringSet<TString, TSpec > const & me,
     TPos pos,
     Tag<TTag> const &)
{
    typedef StringSet<TString, TSpec > const TStringSet;
    typedef typename Iterator<TStringSet, Tag<TTag> const>::Type TIterator;
    typedef typename Position<TStringSet>::Type TPosition;
    return TIterator(me, (TPosition) pos);
}

// --------------------------------------------------------------------------
// Function begin()
// --------------------------------------------------------------------------

template <typename TString, typename TSpec, typename TTag>
inline typename Iterator<StringSet<TString, TSpec >, Tag<TTag> const>::Type
begin(StringSet<TString, TSpec > & me,
      Tag<TTag> const & tag)
{
    return iter(me, 0, tag);
}

template <typename TString, typename TSpec, typename TTag>
inline typename Iterator<StringSet<TString, TSpec > const, Tag<TTag> const>::Type
begin(StringSet<TString, TSpec > const & me,
      Tag<TTag> const & tag)
{
    return iter(me, 0, tag);
}

// --------------------------------------------------------------------------
// Function end()
// --------------------------------------------------------------------------

template <typename TString, typename TSpec, typename TTag>
inline typename Iterator<StringSet<TString, TSpec >, Tag<TTag> const>::Type
end(StringSet<TString, TSpec > & me,
Tag<TTag> const & tag)
{
return iter(me, length(me), tag);
}

template <typename TString, typename TSpec, typename TTag>
inline typename Iterator<StringSet<TString, TSpec > const, Tag<TTag> const>::Type
end(StringSet<TString, TSpec > const & me,
Tag<TTag> const & tag)
{
return iter(me, length(me), tag);
}

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

// --------------------------------------------------------------------------
// Function getValueById()
// --------------------------------------------------------------------------

/*!
 * @mfn StringSet#Id
 * @brief Return the id type for the string set.
 * Note: Position is the same as id for all string sets but the @link DependentStringSet @endlink.
 *
 * @signature Id<TStringSet>::Type
 *
 * @tparam TStringSet The string set type to query for its id type.
 *
 * @return Type The resulting ID type.
 */

/*!
 * @fn StringSet#getValueById
 * @brief Get the value from a string set by its id.
 * Note: Position is the same as id for all string sets but the @link DependentStringSet @endlink.
 *
 * @signature TString getValueById(s, id);
 *
 * @param[in] s  The string set to get string from.
 * @param[in] id The id of the string to get.
 *
 * @return TString Reference to the string with the given id.
 */

// TODO(holtgrew): Why is there no generic implementation for StringSets??

// --------------------------------------------------------------------------
// Function valueById()
// --------------------------------------------------------------------------

/*!
 * @fn StringSet#valueById
 * @brief Get the value from a string set by its id.
 * Note: Position is the same as id for all string sets but the @link DependentStringSet @endlink.
 *
 * @signature TString valueById(s, id);
 *
 * @param[in] s  The string set to get string from.
 * @param[in] id The id of the string to get.
 *
 * @return TString Reference to the string with the given id.
 */

template<typename TString, typename TSpec, typename TId>
inline typename Reference<StringSet<TString, TSpec> >::Type
valueById(StringSet<TString, TSpec> & me,
        TId const id)
{
    return getValueById(me, id);
}

// --------------------------------------------------------------------------
// Function assignValueById()
// --------------------------------------------------------------------------

/*!
 * @fn StringSet#assignValue
 * @brief Set the member of a string set by the position.
 *
 * @signature void assignValue(set, pos, s);
 *
 * @param[in,out] set The string set to assign value in.
 * @param[in]     pos The position to modify value at.
 * @param[in]     s   The string to assign to the given position.
 */

/*!
 * @fn StringSet#assignValueById
 * @brief Set the member of a string set by its id.
 * Note: Position is the same as id for all string sets but the @link DependentStringSet @endlink.
 *
 * @signature TId assignValueById(set, s[, id]);
 *
 * @param[in] set The string set to assign value in.
 * @param[in] s   The string set to assign.
 * @param[in] id  The id of the string to set.  If omitted, <tt>s</tt> will be appended to <tt>set</tt>.
 *
 * @return TId The id of the new string in the string set.
 */

template<typename TString, typename TSpec, typename TString2>
inline typename Id<StringSet<TString, TSpec> >::Type
assignValueById(StringSet<TString, TSpec>& me,
                TString2& obj)
{
    appendValue(me, obj);
    SEQAN_ASSERT_EQ(length(me.limits), length(me) + 1);
    return length(me.strings) - 1;
}

template<typename TString, typename TSpec1, typename TSpec2, typename TId>
inline typename Id<StringSet<TString, TSpec1> >::Type
assignValueById(StringSet<TString, TSpec1>& dest,
                StringSet<TString, TSpec2>& source,
                TId id)
{
    return assignValueById(dest, getValueById(source, id), id);
}

// --------------------------------------------------------------------------
// Function removeValueById()
// --------------------------------------------------------------------------

/*!
 * @fn StringSet#removeValueById
 * @brief Remove a value from a string set by its id.
 * Note: Position is the same as id for all string sets but the @link DependentStringSet @endlink.
 *
 * @signature void removeValueById(set, id);
 *
 * @param[in,out] set The string to remove value in.
 * @param[in]     id  The id of the string to remove.
 */

// TODO(holtgrew): Why is there no generic implementation for StringSets??

// --------------------------------------------------------------------------
// Function positionToId()
// --------------------------------------------------------------------------

/*!
 * @fn StringSet#positionToId
 * @brief Convert a position/index in the string set to a string id.
 * Note: Position is the same as id for all string sets but the @link DependentStringSet @endlink.
 *
 * @signature Id positionToId(set, pos);
 *
 * @param[in] set The string to convert positions for.
 * @param[in] pos The position to convert.
 *
 * @return TId The resulting id.
 */

// TODO(holtgrew): Why is there no generic implementation for StringSets??

// --------------------------------------------------------------------------
// Function concat()
// --------------------------------------------------------------------------

/*!
 * @fn StringSet#concat
 * @brief Returns the concatenation sequence of all sequences in a string set.
 *
 * @signature TConcat concat(set);
 *
 * @param[in] set The string set to get the concatenation sequence for.
 *
 * @return TConcat The concatenation sequence.
 */

// TODO(holtgrew): Why default concat() for any class?
template <typename TString>
inline typename Concatenator<TString>::Type &
concat(TString & string)
{
    return string;
}

// TODO(holtgrew): Why default concat() for any class?
template <typename TString>
inline typename Concatenator<TString const>::Type &
concat(TString const & string)
{
    return string;
}

template <typename TString, typename TSpec>
inline typename Concatenator<StringSet<TString, TSpec> >::Type &
concat(StringSet<TString, TSpec> & me)
{
    me.concat.set = &me;
    return me.concat;
}

template <typename TString, typename TSpec>
inline typename Concatenator<StringSet<TString, TSpec> const>::Type &
concat(StringSet<TString, TSpec> const & constMe)
{
    StringSet<TString, TSpec> &me = const_cast<StringSet<TString, TSpec> &>(constMe);
    me.concat.set = &me;
    return me.concat;
}

// this function is deprecated and the return value is very ungeneric, e.g. doesn't work if strings are std::string
template <typename TStrings, typename TDelim>
[[deprecated]]
inline String<typename Value<typename Value<TStrings>::Type>::Type>
concat(TStrings const & strings, TDelim const & delimiter, bool ignoreEmptyStrings = false)
{
    String<typename Value<typename Value<TStrings>::Type>::Type> tmp;

    if (empty(strings))
        return tmp;

    if (ignoreEmptyStrings)
    {
        for (size_t i = 0; i < length(strings); ++i)
        {
            if (empty(strings[i]))
                continue;
            if (!empty(tmp))
                append(tmp, delimiter);
            append(tmp, strings[i]);
        }
    }
    else
    {
        tmp = front(strings);
        for (size_t i = 1; i < length(strings); ++i)
        {
            append(tmp, delimiter);
            append(tmp, strings[i]);
        }
    }
    return tmp;
}

// ----------------------------------------------------------------------------
// Function prefixSums<TValue>()
// ----------------------------------------------------------------------------

template <typename TValue, typename TPrefixSums, typename TText>
inline void prefixSums(TPrefixSums & sums, TText const & text)
{
    typedef typename Concatenator<TText const>::Type        TConcat;
    typedef typename Iterator<TConcat, Standard>::Type      TIter;

    resize(sums, ValueSize<TValue>::VALUE + 1, 0, Exact());

    // Compute symbol frequencies.
    TIter itEnd = end(concat(text), Standard());
    for (TIter it = begin(concat(text), Standard()); it != itEnd; goNext(it))
        sums[ordValue(static_cast<TValue>(*it)) + 1]++;

    // Cumulate symbol frequencies.
    partialSum(sums);
}

// --------------------------------------------------------------------------
// Function idToPosition()
// --------------------------------------------------------------------------

/*!
 * @fn StringSet#idToPosition
 * @brief Convert a string id to a position/index in the string set.
 * Note: Position is the same as id for all string sets but the @link DependentStringSet @endlink.
 *
 * @signature TPos idToPosition(set, id);
 *
 * @param[in] set The string to convert positions for.
 * @param[in] id  The id to convert.
 *
 * @return TPos The resulting position.
 */

// TODO(holtgrew): Why is there no generic implementation for StringSets??


// TODO(holtgrew): Should the following code be thrown away?

//template <typename TString, typename TSpec, typename TDestSpec, typename TIds, typename TLength>
//inline void
//subset(StringSet<TString, Owner<TSpec> >& source,
//    StringSet<TString, TDestSpec>& dest,
//    TIds ids,
//    TLength len)
//{
//}

//template <typename TString, typename TIds, typename TLength>
//inline void
//subset(StringSet<TString, Dependent<Generous> >& source,
//    StringSet<TString, Dependent<Generous> >& dest,
//    TIds ids,
//    TLength len)
//{
//    typedef StringSet<TString, Dependent<Generous> > TStringSet;
//    typedef typename Id<TStringSet>::Type TId;
//    typedef typename Size<TStringSet>::Type TSize;

//    clear(dest);
//    resize(dest.limits, len + 1);
//    dest.limitsValid = (len == 0);
//    resize(dest.strings, length(source.strings), (TString*) 0);
//    for(TSize i = 0; i < len; ++i)
//        dest.strings[ids[i]] = source.strings[ids[i]];
//}

//template <typename TString, typename TIds, typename TLength>
//inline void
//subset(StringSet<TString, Dependent<Tight> >& source,
//    StringSet<TString, Dependent<Tight> >& dest,
//    TIds ids,
//    TLength len)
//{
//    typedef StringSet<TString, Dependent<Tight> > TStringSet;
//    typedef typename Id<TStringSet>::Type TId;
//    typedef typename Size<TStringSet>::Type TSize;

//    clear(dest);
//    resize(dest.limits, len + 1);
//    dest.limitsValid = (len == 0);
//    TLength upperBound = length(source.ids);
//    for(TSize i=0;i<len;++i) {
//        TId id = ids[i];
//        if ((upperBound > id) &&
//            (source.ids[id] == id)) {
//                appendValue(dest.strings, source.strings[id]);
//                appendValue(dest.ids, id);
//        } else {
//            typedef String<TId> TIdString;
//            typedef typename Iterator<TIdString, Rooted>::Type TIter;
//            TIter it = begin(source.ids);
//            for(;!atEnd(it);goNext(it)) {
//                if (*it == id) {
//                    appendValue(dest.strings, source.strings[position(it)]);
//                    appendValue(dest.ids, id);
//                }
//            }
//        }
//    }
//}

//template <typename TString, typename TSpec, typename TIds>
//inline void
//subset(StringSet<TString, TSpec>& source,
//    StringSet<TString, TSpec>& dest,
//    TIds ids)
//{
//    subset(source, dest, ids, length(ids));
//}

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

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

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

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

// ----------------------------------------------------------------------------
// Function write() (works on any container of container)
// ----------------------------------------------------------------------------

template <typename TTarget, typename TSequences, typename TDelim>
inline SEQAN_FUNC_ENABLE_IF(And<Is<ContainerConcept<TSequences> >,
                                Is<ContainerConcept<typename Value<TSequences>::Type > > >, void)
write(TTarget & target, TSequences const & seqs, TDelim const & delimiter)
{
    typedef typename Iterator<TSequences const>::Type TSourceIt;

    if (SEQAN_UNLIKELY(empty(seqs)))
        return;
    for (TSourceIt it = begin(seqs, Standard()), itBack = (end(seqs, Standard()) - 1); it != itBack; ++it)
    {
        write(target, *it);
        write(target, delimiter);
    }
    write(target, back(seqs)); // no delimiter after last
}

template <typename TTarget, typename TSequences>
inline SEQAN_FUNC_ENABLE_IF(And<Is<ContainerConcept<TSequences> >,
                                Is<ContainerConcept<typename Value<TSequences>::Type > > >, void)
write(TTarget & target, TSequences const & seqs)
{
    write(target, seqs, '\n');
}

// ----------------------------------------------------------------------------
// Function append() (works on any container of container)
// ----------------------------------------------------------------------------

template <typename TSequences1, typename TSequences2, typename TExpand >
inline SEQAN_FUNC_ENABLE_IF(And<And<Is<ContainerConcept<TSequences1> >,
                                    Is<ContainerConcept<typename Value<TSequences1>::Type > > >,
                                And<Is<ContainerConcept<TSequences2> >,
                                    Is<ContainerConcept<typename Value<TSequences2>::Type > > > >, void)
append(TSequences1 & me, TSequences2 const & obj, Tag<TExpand>)
{
    typedef typename Iterator<TSequences2 const>::Type TSourceIt;

    typename Size<typename Value<TSequences1>::Type>::Type oldLength = length(me);
    resize(me, oldLength + length(obj), Tag<TExpand>());
    for (TSourceIt it = begin(obj, Standard()), itEnd = end(obj, Standard()); it != itEnd; ++it)
        assignValue(me, oldLength++, *it);
}

}  // namespace seqan

#endif  // #ifndef SEQAN_SEQUENCE_STRING_SET_BASE_H_
