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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, 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>
// ==========================================================================
// Shortcuts for certain often-used string types.
// ==========================================================================
#ifndef SEQAN_HEADER_SEQUENCE_SHORTCUTS_H
#define SEQAN_HEADER_SEQUENCE_SHORTCUTS_H
namespace seqan2
{
//////////////////////////////////////////////////////////////////////////////
/*!
* @typedef CharString
* @headerfile <seqan/sequence.h>
* @brief An AllocString with char alphabet.
*
* You can efficiently cast a CharString to <tt>char *</tt> using <tt>toCString</tt>.
*
* @signature typedef String<char> CharString;
*/
typedef String<char, Alloc<void> > CharString;
//____________________________________________________________________________
/*!
* @typedef CharIterator
* @headerfile <seqan/sequence.h>
* @brief An iterator overa a @link CharString @endlink.
*
* @signature typedef Iterator<CharString, Rooted>::Type CharIterator;
*/
typedef Iterator<CharString, Rooted>::Type CharIterator;
//////////////////////////////////////////////////////////////////////////////
/*!
* @typedef UnicodeString
* @headerfile <seqan/sequence.h>
* @brief An AllocString with wchar_t alphabet.
*
* @signature typedef String<wchar_t> CharString;
*/
typedef String<wchar_t, Alloc<void> > UnicodeString;
//____________________________________________________________________________
typedef Iterator<UnicodeString, Rooted>::Type UnicodeIterator;
//////////////////////////////////////////////////////////////////////////////
/*!
* @typedef DnaString
* @headerfile <seqan/sequence.h>
* @brief An AllocString with Dna alphabet.
*
* @signature typedef String<Dna> CharString;
*/
typedef String<Dna, Alloc<void> > DnaString;
//____________________________________________________________________________
/*!
* @typedef DnaIterator
* @headerfile <seqan/sequence.h>
* @brief A rooted iterator over a Dna.
*
* @signature typedef Iterator<DnaString, Rooted>::Type DnaIterator;
*/
typedef Iterator<DnaString, Rooted>::Type DnaIterator;
//////////////////////////////////////////////////////////////////////////////
/*!
* @typedef Dna5String
* @headerfile <seqan/sequence.h>
* @brief An AllocString with Dna5 alphabet.
*
* @signature typedef String<Dna5> CharString;
*/
typedef String<Dna5, Alloc<void> > Dna5String;
//////////////////////////////////////////////////////////////////////////////
/*!
* @typedef DnaQString
* @headerfile <seqan/sequence.h>
* @brief An AllocString with DnaQ alphabet.
*
* @signature typedef String<DnaQ> CharString;
*/
typedef String<DnaQ, Alloc<void> > DnaQString;
//////////////////////////////////////////////////////////////////////////////
/*!
* @typedef Dna5QString
* @headerfile <seqan/sequence.h>
* @brief An AllocString with Dna5Q alphabet.
*
* @signature typedef String<Dna5Q> CharString;
*/
typedef String<Dna5Q, Alloc<void> > Dna5QString;
//____________________________________________________________________________
/*!
* @typedef Dna5Iterator
* @headerfile <seqan/sequence.h>
* @brief A rooted iterator over a Dna5.
*
* @signature typedef Iterator<Dna5String, Rooted>::Type Dna5Iterator;
*/
typedef Iterator<Dna5String, Rooted>::Type Dna5Iterator;
//////////////////////////////////////////////////////////////////////////////
/*!
* @typedef RnaString
* @headerfile <seqan/sequence.h>
* @brief An AllocString with Rna alphabet.
*
* @signature typedef String<Rna> CharString;
*/
typedef String<Rna, Alloc<void> > RnaString;
//____________________________________________________________________________
/*!
* @typedef RnaIterator
* @headerfile <seqan/sequence.h>
* @brief A rooted iterator over a Rna.
*
* @signature typedef Iterator<RnaString, Rooted>::Type RnaIterator;
*/
typedef Iterator<RnaString, Rooted>::Type RnaIterator;
//////////////////////////////////////////////////////////////////////////////
/*!
* @typedef Rna5String
* @headerfile <seqan/sequence.h>
* @brief An AllocString with Rna5 alphabet.
*
* @signature typedef String<Rna5> CharString;
*/
typedef String<Rna5, Alloc<void> > Rna5String;
//____________________________________________________________________________
/*!
* @typedef Rna5Iterator
* @headerfile <seqan/sequence.h>
* @brief A rooted iterator over a Rna5.
*
* @signature typedef Iterator<Rna5String, Rooted>::Type Rna5Iterator;
*/
typedef Iterator<Rna5String, Rooted>::Type Rna5Iterator;
//////////////////////////////////////////////////////////////////////////////
/*!
* @typedef IupacString
* @headerfile <seqan/sequence.h>
* @brief An AllocString with Iupac alphabet.
*
* @signature typedef String<Iupac> CharString;
*/
typedef String<Iupac, Alloc<void> > IupacString;
//____________________________________________________________________________
/*!
* @typedef IupacIterator
* @headerfile <seqan/sequence.h>
* @brief A rooted iterator over a Iupac.
*
* @signature typedef Iterator<IupacString, Rooted>::Type IupacIterator;
*/
typedef Iterator<IupacString, Rooted>::Type IupacIterator;
//////////////////////////////////////////////////////////////////////////////
/*!
* @typedef Peptide
* @headerfile <seqan/sequence.h>
* @brief An AllocString with AminoAcid alphabet.
*
* @signature typedef String<AminoAcid> Peptide;
*/
typedef String<AminoAcid, Alloc<void> > Peptide;
//____________________________________________________________________________
/*!
* @typedef PeptideIterator
* @headerfile <seqan/sequence.h>
* @brief A rooted iterator over a Peptide.
*
* @signature typedef Iterator<Peptide, Rooted>::Type PeptideIterator;
*/
typedef Iterator<Peptide, Rooted>::Type PeptideIterator;
//////////////////////////////////////////////////////////////////////////////
} //namespace seqan2
#endif //#ifndef SEQAN_HEADER_...
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