libseqan2-dev 2.3.2+dfsg2-4ubuntu2 / usr / include / seqan / stream / tokenization.h

// ==========================================================================
//                 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: David Weese <david.weese@fu-berlin.de>
// ==========================================================================
// Tokenization.
// ==========================================================================

#ifndef SEQAN_STREAM_TOKENIZATION_H_
#define SEQAN_STREAM_TOKENIZATION_H_

namespace seqan {

// ============================================================================
// Functors
// ============================================================================

// ----------------------------------------------------------------------------
// Functor IsInAlphabet
// ----------------------------------------------------------------------------

template <typename TValue>
struct IsInAlphabet
{
    template <typename TInValue>
    bool operator() (TInValue const & inVal) const
    {
        TValue val = inVal;
        return convert<TInValue>(val) == toUpperValue(inVal);
    }

    bool operator() (TValue const &) const
    {
        return true;
    }
};

// ----------------------------------------------------------------------------
// Functor IsInRange
// ----------------------------------------------------------------------------

template <char FIRST_CHAR, char LAST_CHAR>
struct IsInRange
{
    template <typename TValue>
    bool operator() (TValue const & val) const
    {
        return FIRST_CHAR <= val && val <= LAST_CHAR;
    }
};

template <char FIRST_CHAR, char LAST_CHAR, typename TContext>
struct ExceptionMessage<IsInRange<FIRST_CHAR, LAST_CHAR>, TContext>
{
    static const std::string VALUE;
};

template <char FIRST_CHAR, char LAST_CHAR, typename TContext>
const std::string ExceptionMessage<IsInRange<FIRST_CHAR, LAST_CHAR>, TContext>::VALUE =
    std::string("Character in range'") + FIRST_CHAR + "' to '" + LAST_CHAR + "' expected.";

// ----------------------------------------------------------------------------
// Functor EqualsChar
// ----------------------------------------------------------------------------

template <char VALUE>
struct EqualsChar
{
    template <typename TValue>
    bool operator() (TValue const & val) const
    {
        return val == VALUE;
    }
};

template <char CHAR, typename TContext>
struct ExceptionMessage<EqualsChar<CHAR>, TContext>
{
    static const std::string VALUE;
};

template <char CHAR, typename TContext>
const std::string ExceptionMessage<EqualsChar<CHAR>, TContext>::VALUE = std::string("Character '") + CHAR + "' expected.";

// ----------------------------------------------------------------------------
// Functor EqualsDynamicValue
// ----------------------------------------------------------------------------

template <typename TValue>
struct EqualsDynamicValue
{
    TValue val;

    EqualsDynamicValue(TValue const & val) :
        val(val)
    {}

    template <typename TValue2>
    bool operator() (TValue2 const & v) const
    {
        return v == val;
    }
};

template <typename TValue, typename TContext>
inline std::string const &
getExceptionMessage(EqualsDynamicValue<TValue> const & func, TContext const &)
{
    return std::string("Character '") + func.val + "' expected.";
}

// ----------------------------------------------------------------------------
// Composite Functors
// ----------------------------------------------------------------------------
// Don't use isblank() or isspace() as it they seem to be slower than our functors (due to inlining)

typedef EqualsChar<'\t'>                                        IsTab;
typedef EqualsChar<' '>                                         IsSpace;
typedef OrFunctor<IsSpace, IsTab>                               IsBlank;
typedef OrFunctor<EqualsChar<'\n'>, EqualsChar<'\r'> >          IsNewline;
typedef OrFunctor<IsBlank, IsNewline>                           IsWhitespace;
typedef IsInRange<'!', '~'>                                     IsGraph;
typedef OrFunctor<IsInRange<'a', 'z'>, IsInRange<'A', 'Z'> >    IsAlpha;
typedef IsInRange<'0', '9'>                                     IsDigit;
typedef OrFunctor<IsAlpha, IsDigit>                             IsAlphaNum;

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

// ----------------------------------------------------------------------------
// Function _skipUntil(); Element-wise
// ----------------------------------------------------------------------------

template <typename TFwdIterator, typename TStopFunctor, typename TChunk>
inline void _skipUntil(TFwdIterator &iter, TStopFunctor &stopFunctor, TChunk)
{
    for (; !atEnd(iter) && !stopFunctor(*iter); ++iter) ;
}

// ----------------------------------------------------------------------------
// Function _skipUntil(); Chunked
// ----------------------------------------------------------------------------

template <typename TFwdIterator, typename TStopFunctor, typename TValue>
inline void _skipUntil(TFwdIterator &iter, TStopFunctor &stopFunctor, Range<TValue*> *)
{
    typedef typename Value<TFwdIterator>::Type TIValue;

    for (; !atEnd(iter); )
    {
        Range<TIValue const *> ichunk;
        getChunk(ichunk, iter, Input());
        SEQAN_ASSERT(!empty(ichunk));

        const TIValue* SEQAN_RESTRICT ptr = ichunk.begin;

        for (; ptr != ichunk.end; ++ptr)
        {
            if (SEQAN_UNLIKELY(stopFunctor(*ptr)))
            {
                iter += ptr - ichunk.begin;    // advance input iterator
                return;
            }
        }

        iter += ptr - ichunk.begin;            // advance input iterator
    }
}

// ----------------------------------------------------------------------------
// Function skipUntil()
// ----------------------------------------------------------------------------

template <typename TFwdIterator, typename TStopFunctor>
inline void skipUntil(TFwdIterator &iter, TStopFunctor &stopFunctor)
{
    typedef typename Chunk<TFwdIterator>::Type* TIChunk;

    _skipUntil(iter, stopFunctor, TIChunk());
}

template <typename TFwdIterator, typename TStopFunctor>
inline void skipUntil(TFwdIterator &iter, TStopFunctor const &stopFunctor)
{
    typedef typename Chunk<TFwdIterator>::Type* TIChunk;

    TStopFunctor stopFunctor_ = stopFunctor;
    _skipUntil(iter, stopFunctor_, TIChunk());
}

// ----------------------------------------------------------------------------
// Function skipOne()
// ----------------------------------------------------------------------------

template <typename TFwdIterator, typename TFunctor>
inline void skipOne(TFwdIterator &iter, TFunctor &functor)
{
    AssertFunctor<TFunctor, ParseError> asserter(functor);

    if (SEQAN_UNLIKELY(atEnd(iter)))
        throw UnexpectedEnd();

    asserter(*iter);
    ++iter;
}

template <typename TFwdIterator, typename TFunctor>
inline void skipOne(TFwdIterator &iter, TFunctor const &functor)
{
    TFunctor func(functor);
    skipOne(iter, func);
}

template <typename TFwdIterator>
inline void skipOne(TFwdIterator &iter)
{
    True func;
    skipOne(iter, func);
}

// ----------------------------------------------------------------------------
// Function _readUntil(); Element-wise
// ----------------------------------------------------------------------------

template <typename TTarget, typename TFwdIterator, typename TStopFunctor, typename TIgnoreFunctor, typename TIChunk, typename TOChunk>
inline void
_readUntil(TTarget &target, TFwdIterator &iter, TStopFunctor &stopFunctor, TIgnoreFunctor &ignoreFunctor, TIChunk, TOChunk)
{
    typename RemoveConst<typename Value<TFwdIterator>::Type>::Type val;
    for (; !atEnd(iter); ++iter)
    {
        if (SEQAN_UNLIKELY(stopFunctor(val = *iter)))
            return;
        if (SEQAN_LIKELY(!ignoreFunctor(val)))
            writeValue(target, val);
    }
}

// ----------------------------------------------------------------------------
// Function _readUntil(); Chunked
// ----------------------------------------------------------------------------

template <typename TTarget, typename TFwdIterator, typename TStopFunctor, typename TIgnoreFunctor, typename TIValue, typename TOValue>
inline void _readUntil(TTarget &target,
                       TFwdIterator &iter,
                       TStopFunctor &stopFunctor,
                       TIgnoreFunctor &ignoreFunctor,
                       Range<TIValue*> *,
                       Range<TOValue*> *)
{
    Range<TOValue*> ochunk(NULL, NULL);
    TOValue* SEQAN_RESTRICT optr = NULL;

    Range<TIValue*> ichunk;
    for (; !atEnd(iter); )
    {
        getChunk(ichunk, iter, Input());
        const TIValue* SEQAN_RESTRICT iptr = ichunk.begin;
        SEQAN_ASSERT(iptr < ichunk.end);

        for (; iptr != ichunk.end; ++iptr)
        {
            if (SEQAN_UNLIKELY(stopFunctor(*iptr)))
            {
                iter += iptr - ichunk.begin;               // advance input iterator
                advanceChunk(target, optr - ochunk.begin); // extend target string size
                return;
            }

            if (SEQAN_UNLIKELY(ignoreFunctor(*iptr)))
                continue;

            // construct values in reserved memory
            if (SEQAN_UNLIKELY(optr == ochunk.end))
            {
                advanceChunk(target, optr - ochunk.begin);
                // reserve memory for the worst-case
                // TODO(weese):Document worst-case behavior
                reserveChunk(target, length(ichunk), Output());
                getChunk(ochunk, target, Output());
                optr = ochunk.begin;
                SEQAN_ASSERT(optr < ochunk.end);
            }
            *optr++ = *iptr;
        }
        iter += iptr - ichunk.begin;                       // advance input iterator
    }
    advanceChunk(target, optr - ochunk.begin);
}

// ----------------------------------------------------------------------------
// Function readUntil()
// ----------------------------------------------------------------------------

template <typename TTarget, typename TFwdIterator, typename TStopFunctor, typename TIgnoreFunctor>
inline void readUntil(TTarget &target, TFwdIterator &iter, TStopFunctor &stopFunctor, TIgnoreFunctor &ignoreFunctor)
{
    typedef typename Chunk<TFwdIterator>::Type*         TIChunk;
    typedef typename Iterator<TTarget, Rooted>::Type    TTargetIter;
    typedef typename Chunk<TTargetIter>::Type*          TOChunk;

    _readUntil(target, iter, stopFunctor, ignoreFunctor, TIChunk(), TOChunk());
}

template <typename TTarget, typename TFwdIterator, typename TStopFunctor, typename TIgnoreFunctor>
inline void
readUntil(TTarget &target, TFwdIterator &iter, TStopFunctor const &stopFunctor, TIgnoreFunctor const &ignoreFunctor)
{
    TStopFunctor stopFunctor_ = stopFunctor;
    TIgnoreFunctor ignoreFunctor_ = ignoreFunctor;
    readUntil(target, iter, stopFunctor_, ignoreFunctor_);
}

// ----------------------------------------------------------------------------
// Function readUntil(); Not ignoring
// ----------------------------------------------------------------------------

template <typename TTarget, typename TFwdIterator, typename TStopFunctor>
inline void readUntil(TTarget &target, TFwdIterator &iter, TStopFunctor const &stopFunctor)
{
    readUntil(target, iter, stopFunctor, False());
}

template <typename TTarget, typename TFwdIterator, typename TStopFunctor>
inline void readUntil(TTarget &target, TFwdIterator &iter, TStopFunctor &stopFunctor)
{
    False noAssertFunc;
    readUntil(target, iter, stopFunctor, noAssertFunc);
}

// ----------------------------------------------------------------------------
// Function readOne()
// ----------------------------------------------------------------------------

template <typename TTarget, typename TFwdIterator, typename TFunctor>
inline void readOne(TTarget & target, TFwdIterator &iter, TFunctor &functor)
{
    if (SEQAN_UNLIKELY(atEnd(iter)))
        throw UnexpectedEnd();

    AssertFunctor<TFunctor, ParseError> asserter(functor);

    asserter(*iter);
    target = *iter;
    ++iter;
}

template <typename TTarget, typename TFwdIterator, typename TFunctor>
inline void readOne(TTarget & target, TFwdIterator &iter, TFunctor const &functor)
{
    TFunctor func(functor);
    readOne(target, iter, func);
}

template <typename TTarget, typename TFwdIterator>
inline void readOne(TTarget & target, TFwdIterator &iter)
{
    if (SEQAN_UNLIKELY(atEnd(iter)))
        throw UnexpectedEnd();

    target = *iter;
    ++iter;
}

// ----------------------------------------------------------------------------
// Function readRawByte()
// ----------------------------------------------------------------------------

//TODO(singer) to be revised
template <typename TValue, typename TFwdIterator>
inline void readRawPod(TValue & value, TFwdIterator &srcIter)
{
    write((char*)&value, srcIter, sizeof(TValue));
}

// ----------------------------------------------------------------------------
// Function readLine()
// ----------------------------------------------------------------------------

template <typename TTarget, typename TFwdIterator>
inline void readLine(TTarget &target, TFwdIterator &iter)
{
    readUntil(target, iter, IsNewline());

    // consume "\r\n.", "\r[!\n]" or "\n."

    if (SEQAN_UNLIKELY(atEnd(iter)))
        return;

    // If the current character is Line Feed ('\r') then this can be an ANSI or a Mac line ending.
    if (*iter == '\r')
    {
        ++iter;     // consume the found newline
        if (SEQAN_UNLIKELY(atEnd(iter)))
            return;
    }

    // Unix Carriage Return ('\n') is the simplest case.
    if (*iter == '\n')
        ++iter;     // consume the found newline
}

// ----------------------------------------------------------------------------
// Function skipLine()
// ----------------------------------------------------------------------------

template <typename TFwdIterator>
inline void skipLine(TFwdIterator &iter)
{
    skipUntil(iter, IsNewline());

    // consume "\r\n.", "\r[!\n]" or "\n."

    if (SEQAN_UNLIKELY(atEnd(iter)))
        return;

    // If the current character is Line Feed ('\r') then this can be an ANSI or a Mac line ending.
    if (*iter == '\r')
    {
        ++iter;     // consume the found newline
        if (SEQAN_UNLIKELY(atEnd(iter)))
            return;
    }

    // Unix Carriage Return ('\n') is the simplest case.
    if (*iter == '\n')
        ++iter;     // consume the found newline
}

// ----------------------------------------------------------------------------
// Function writeWrappedString()
// ----------------------------------------------------------------------------

template <typename TTarget, typename TSequence, typename TSize>
inline void writeWrappedString(TTarget & target, TSequence const & seq, TSize lineLength)
{
    typedef typename Size<TSequence>::Type TSeqSize;
    typedef typename Iterator<TSequence const, Rooted>::Type TIter;

    TIter iter = begin(seq, Rooted());
    TSeqSize charsLeft = length(seq);
    TSeqSize charsPerLine;
    TSeqSize lineLength_ = (lineLength == 0)? maxValue<TSeqSize>() : lineLength;

    do
    {
        charsPerLine = std::min(charsLeft, lineLength_);
        write(target, iter, charsPerLine);
        writeValue(target, '\n');
        charsLeft -= charsPerLine;
    }
    while (charsLeft != 0);
}

// ----------------------------------------------------------------------------
// Function findFirst()
// ----------------------------------------------------------------------------

template <typename TContainer, typename TFunctor>
inline typename Position<TContainer>::Type
findFirst(TContainer const &cont, TFunctor const &func)
{
    typename Iterator<TContainer const, Rooted>::Type iter = begin(cont, Rooted());
    skipUntil(iter, func);
    return iter - begin(cont, Rooted());
}

template <typename TContainer>
inline typename Position<TContainer>::Type
findFirst(TContainer const &cont, typename Value<TContainer>::Type const &val)
{
    EqualsDynamicValue<typename Value<TContainer>::Type> func(val);
    return findFirst(cont, func);
}

// ----------------------------------------------------------------------------
// Function findLast()
// ----------------------------------------------------------------------------

template <typename TContainer, typename TFunctor>
inline typename Position<TContainer>::Type
findLast(TContainer const &cont, TFunctor const &func)
{
    typedef ModifiedString<TContainer const, ModReverse> TRevContainer;

    SEQAN_CONCEPT_ASSERT((IntegerConcept<typename Position<TContainer>::Type>));

    // search from back to front
    TRevContainer rev(cont);
    typename Iterator<TRevContainer, Rooted>::Type iter = begin(rev, Rooted());
    skipUntil(iter, func);

    if (atEnd(iter))
        return -1;

    return host(iter) - begin(cont, Rooted());
}

template <typename TContainer>
inline typename Position<TContainer>::Type
findLast(TContainer const &cont, typename Value<TContainer>::Type const &val)
{
    EqualsDynamicValue<typename Value<TContainer>::Type> func(val);
    return findLast(cont, func);
}

// ----------------------------------------------------------------------------
// Function cropAfterFirst(); crop after first occurrence (including it)
// ----------------------------------------------------------------------------

template <typename TContainer, typename TFunctor>
inline void
cropAfterFirst(TContainer &cont, TFunctor const &func)
{
    resize(cont, findFirst(cont, func));
}

// ----------------------------------------------------------------------------
// Function cropAfterLast(); crop after last occurrence (excluding it)
// ----------------------------------------------------------------------------

template <typename TContainer, typename TFunctor>
inline void
cropAfterLast(TContainer &cont, TFunctor const &func)
{
    resize(cont, findLast(cont, func) + 1);
}

// ----------------------------------------------------------------------------
// Function cropBeforeFirst(); crop before first occurrence (excluding it)
// ----------------------------------------------------------------------------

template <typename TContainer, typename TFunctor>
inline void
cropBeforeFirst(TContainer &cont, TFunctor const &func)
{
    erase(cont, 0, findFirst(cont, func));
}

// ----------------------------------------------------------------------------
// Function cropBeforeLast(); crop before first occurrence (including it)
// ----------------------------------------------------------------------------

template <typename TContainer, typename TFunctor>
inline void
cropBeforeLast(TContainer &cont, TFunctor const &func)
{
    erase(cont, 0, findLast(cont, func) + 1);
}
// ----------------------------------------------------------------------------
// Function cropOuter(); crop after last occurrence (excluding it)
// ----------------------------------------------------------------------------

template <typename TContainer, typename TFunctor>
inline void
cropOuter(TContainer &cont, TFunctor const &func)
{
    cropAfterLast(cont, NotFunctor<TFunctor>(func));
    cropBeforeFirst(cont, NotFunctor<TFunctor>(func));
}

// --------------------------------------------------------------------------
// Function strSplit()
// --------------------------------------------------------------------------

/*!
 * @fn StringSet#strSplit
 * @brief Split a sequence using a delimiter and append the results to a target string set
 *
 * @signature void strSplit(result, sequence[, sep[, allowEmptyStrings[, maxSplit]]]);
 *
 * @param[out] result           The resulting string set (can be any ContainerOfContainer, also STL)
 * @param[in]  sequence         The sequence to split.
 * @param[in]  sep              The splitter to use (default <tt>' '</tt>).
 * @param[in]  allowEmptyString Whether or not to allow empty strings (<tt>bool</tt>, defaults to <tt>true</tt> iff
 *                              <tt>sep</tt> is given).
 * @param[in]  maxSplit         The maximal number of split operations to do if given.
 */

template <typename TResult, typename TSequence, typename TFunctor, typename TSize>
inline SEQAN_FUNC_ENABLE_IF(And<Is<ContainerConcept<TResult> >,
                                Is<ContainerConcept<typename Value<TResult>::Type > > >, void)
strSplit(TResult & result,
         TSequence const & sequence,
         TFunctor const & sep,
         bool const allowEmptyStrings,
         TSize maxSplit)
{
    typedef typename Iterator<TSequence const, Standard>::Type TIter;
    typedef std::conditional_t<Is<StlContainerConcept<TResult>>::VALUE,
                               TSequence,
                               decltype(infix(sequence, 0, 1))> TResultValue;

    TIter itBeg = begin(sequence, Standard());
    TIter itEnd = end(sequence, Standard());
    TIter itFrom = itBeg;

    if (maxSplit == 0)
    {
        appendValue(result, sequence);
        return;
    }

    for (TIter it = itBeg; it != itEnd; ++it)
        if (sep(getValue(it)))
        {
            if (allowEmptyStrings || itFrom != it)
            {
                appendValue(result, static_cast<TResultValue>(infix(sequence, itFrom - itBeg, it - itBeg)));
                if (--maxSplit == 0)
                {
                    if (!allowEmptyStrings)
                    {
                        while (it != itEnd && sep(getValue(it)))
                            ++it;
                    }
                    else
                        ++it;

                    if (it != itEnd)
                        appendValue(result, static_cast<TResultValue>(infix(sequence, itFrom - itBeg, it - itBeg)));

                    return;
                }
            }
            itFrom = it + 1;
        }

    if (allowEmptyStrings || itFrom != itEnd)
        appendValue(result, static_cast<TResultValue>(infix(sequence, itFrom - itBeg, itEnd - itBeg)));
}

template <typename TResult, typename TSequence, typename TFunctor>
inline SEQAN_FUNC_ENABLE_IF(And<Is<ContainerConcept<TResult> >,
                                Is<ContainerConcept<typename Value<TResult>::Type > > >, void)
strSplit(TResult & result, TSequence const & sequence, TFunctor const & sep, bool const allowEmptyStrings)
{
    strSplit(result, sequence, sep, allowEmptyStrings, maxValue<typename Size<TSequence>::Type>());
}

template <typename TResult, typename TSequence, typename TFunctor>
inline SEQAN_FUNC_ENABLE_IF(And<Is<ContainerConcept<TResult> >,
                                Is<ContainerConcept<typename Value<TResult>::Type > > >, void)
strSplit(TResult & result, TSequence const & sequence, TFunctor const & sep)
{
    strSplit(result, sequence, sep, true);
}

template <typename TResult, typename TSequence>
inline SEQAN_FUNC_ENABLE_IF(And<Is<ContainerConcept<TResult> >,
                                Is<ContainerConcept<typename Value<TResult>::Type > > >, void)
strSplit(TResult & result, TSequence const & sequence)
{
    strSplit(result, sequence, EqualsChar<' '>(), false);
}

}  // namespace seqan

#endif  // #ifndef SEQAN_STREAM_TOKENIZATION_H_