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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: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
// Read support for the EMBL file format.
// ==========================================================================
#ifndef INCLUDE_SEQAN_SEQ_IO_READ_EMBL_H_
#define INCLUDE_SEQAN_SEQ_IO_READ_EMBL_H_
namespace seqan2 {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
struct Embl_;
typedef Tag<Embl_> Embl;
struct EmblHeader_;
typedef Tag<EmblHeader_> EmblHeader;
struct EmblSequence_;
typedef Tag<EmblSequence_> EmblSequence;
// ============================================================================
// Metafunctions
// ============================================================================
// --------------------------------------------------------------------------
// Metafunction MagicHeader
// --------------------------------------------------------------------------
template <typename T>
struct MagicHeader<Embl, T>
{
static char const VALUE[3];
};
template <typename T>
char const MagicHeader<Embl, T>::VALUE[3] = { 'I','D',' ' }; // typical Embl header
// --------------------------------------------------------------------------
// Metafunction FileExtensions
// --------------------------------------------------------------------------
template <typename T>
struct FileExtensions<Embl, T>
{
static char const * VALUE[1];
};
template <typename T>
char const * FileExtensions<Embl, T>::VALUE[1] =
{
".embl", // default output extension
};
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function splitEmblHeader()
// ----------------------------------------------------------------------------
/*!
* @fn readEmblHeader
* @headerfile <seqan/seq_io.h>
* @brief Split an EMBL header line.
*
* @signature void readEmblHeader(key, value, iter);
*
* @param[out] key A @link ContainerConcept @endlink object to write the key to.
* @param[out] value A @link ContainerConcept @endlink object to write the value to.
* @param[in] iter Input iterator.
*/
template <typename TKey, typename TValue, typename TFwdIterator>
inline SEQAN_FUNC_ENABLE_IF(Not<IsSameType<TFwdIterator, FormattedFile<Fastq, Input> > >, void)
readRecord(TKey & key, TValue & val, TFwdIterator & iter, EmblHeader)
{
clear(key);
clear(val);
skipUntil(iter, NotFunctor<IsWhitespace>());
readUntil(key, iter, IsWhitespace(), AssertFunctor<NotFunctor<CountDownFunctor<True, 2> >, ParseError>());
if (!atEnd(iter) && IsBlank()(value(iter)))
{
skipUntil(iter, NotFunctor<IsBlank>());
readUntil(val, iter, IsNewline());
}
skipLine(iter);
}
// ----------------------------------------------------------------------------
// Function nextIs()
// ----------------------------------------------------------------------------
// nextIs() for EMBL header records.
template <typename TFwdIterator>
inline bool
nextIs(TFwdIterator & iter, EmblHeader)
{
return !atEnd(iter) && !IsWhitespace()(value(iter));
}
// nextIs() for EMBL sequence records.
template <typename TFwdIterator>
inline bool
nextIs(TFwdIterator & iter, EmblSequence)
{
return !atEnd(iter) && IsWhitespace()(value(iter));
}
// ----------------------------------------------------------------------------
// Function readRecord()
// ----------------------------------------------------------------------------
// readRecord() for EMBL sequences records.
// Read all sequence, eat/ignore '//' line.
template <typename TSeqString, typename TFwdIterator>
inline SEQAN_FUNC_ENABLE_IF(Not<IsInputFile<TFwdIterator> >, void)
readRecord(TSeqString & seq, TFwdIterator & iter, EmblSequence)
{
typedef typename Value<TSeqString>::Type TSeqAlphabet;
typedef OrFunctor<OrFunctor<IsBlank, IsDigit>,
AssertFunctor<IsInAlphabet<TSeqAlphabet>, ParseError, Embl> > TSeqAsserter;
IsNewline isNewline;
TSeqAsserter asserter;
if (!atEnd(iter) && value(iter) == 'I')
skipLine(iter);
clear(seq);
for (; !atEnd(iter); skipLine(iter))
{
if (value(iter) == '/')
{
skipLine(iter);
break;
}
readUntil(seq, iter, isNewline, asserter);
}
}
// readRecord() for EMBL id/seq pairs.
template <typename TIdString, typename TSeqString, typename TFwdIterator>
inline SEQAN_FUNC_ENABLE_IF(Not<IsInputFile<TFwdIterator> >, void)
readRecord(TIdString & meta, TSeqString & seq, TFwdIterator & iter, Embl)
{
IsBlank isBlank;
IsWhitespace isWhite;
String<char, Array<2> > key;
// extract meta from "ID" line
clear(meta);
for (; !atEnd(iter) && !isBlank(value(iter)); skipLine(iter))
{
AssertFunctor<NotFunctor<CountDownFunctor<True, 2> >, ParseError, Embl> asserter;
clear(key);
readUntil(key, iter, isWhite, asserter);
if (!atEnd(iter) && isBlank(value(iter)) && key == "ID")
{
skipUntil(iter, NotFunctor<IsBlank>());
readUntil(meta, iter, IsNewline());
}
}
readRecord(seq, iter, EmblSequence());
}
template <typename TIdString, typename TSeqString, typename TQualString, typename TFwdIterator>
inline SEQAN_FUNC_ENABLE_IF(Not<IsInputFile<TFwdIterator> >, void)
readRecord(TIdString & meta, TSeqString & seq, TQualString & qual, TFwdIterator & iter, Embl)
{
clear(qual);
readRecord(meta, seq, iter, Embl());
}
} // namespace seqan2
#endif // #ifndef INCLUDE_SEQAN_SEQ_IO_READ_EMBL_H_
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