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// ==========================================================================
// parse_lm
// ==========================================================================
// 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>
// ==========================================================================
// SEQAN_NO_GENERATED_FORWARDS
#ifndef INCLUDE_SEQAN_PARSE_LM_PARSE_STELLAR_GFF_H_
#define INCLUDE_SEQAN_PARSE_LM_PARSE_STELLAR_GFF_H_
namespace seqan2 {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
struct StellarGff_;
typedef Tag<StellarGff_> StellarGff;
// ============================================================================
// Metafunctions
// ============================================================================
// ----------------------------------------------------------------------------
// Metafunction Value
// ----------------------------------------------------------------------------
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function readRecord()
// ----------------------------------------------------------------------------
template <typename TLocalMatchStore, typename TForwardIter>
inline void
readRecord(TLocalMatchStore & store,
TForwardIter & iter,
StellarGff const & /*tag*/)
{
typedef typename TLocalMatchStore::TPosition TPosition;
// Read line.
CharString buffer;
char subjectStrand = 'X';
CharString subjectName;
CharString queryName;
TPosition subjectBeginPos = 0;
TPosition subjectEndPos = 0;
TPosition queryBeginPos = 0;
TPosition queryEndPos = 0;
// Field: SUBJECT
readUntil(subjectName, iter, IsTab());
// Skip TAB.
skipOne(iter, IsTab());
// Field: SOURCE
skipUntil(iter, IsTab());
// Skip TAB.
skipOne(iter, IsTab());
// Field: TYPE
skipUntil(iter, IsTab());
// Skip TAB.
skipOne(iter, IsTab());
// Field: START
clear(buffer);
readUntil(buffer, iter, NotFunctor<IsDigit>());
subjectBeginPos = lexicalCast<TPosition>(buffer) - 1;
// Skip TAB.
skipOne(iter, IsTab());
// Field: END
clear(buffer);
readUntil(buffer, iter, NotFunctor<IsDigit>());
subjectEndPos = lexicalCast<TPosition>(buffer);
// Skip TAB.
skipOne(iter, IsTab());
// Field: SCORE
skipUntil(iter, IsTab());
// Skip TAB.
skipOne(iter, IsTab());
// Field: STRAND
clear(buffer);
readOne(subjectStrand, iter, OrFunctor<EqualsChar<'+'>, EqualsChar<'-'> >());
// Skip TAB.
skipOne(iter, IsTab());
// Field: FRAME
skipOne(iter);
// Skip TAB.
skipOne(iter, IsTab());
// The GROUP field contains the information about the query.
// query sequence
readUntil(queryName, iter, EqualsChar<';'>());
// Skip semicolon.
skipOne(iter, EqualsChar<';'>());
// "seq2Range="
clear(buffer);
readUntil(buffer, iter, EqualsChar<'='>());
if (buffer != "seq2Range")
{
throw ParseError("Format error; Expected 'seq2Range'");
return; // FORMAT ERROR, should probably be a constant
}
// Skip '='
skipOne(iter, EqualsChar<'='>());
// query begin pos
clear(buffer);
readUntil(buffer, iter, NotFunctor<IsDigit>());
queryBeginPos = lexicalCast<TPosition>(buffer) - 1;
// skip comma
skipOne(iter, EqualsChar<','>());
// query end pos
clear(buffer);
readUntil(buffer, iter, NotFunctor<IsDigit>());
queryEndPos = lexicalCast<TPosition>(buffer);
// Skip semicolon.
skipOne(iter, EqualsChar<';'>());
// Skip "eValue=*;"
clear(buffer);
readUntil(buffer, iter, EqualsChar<'='>());
if (buffer != "eValue")
{
throw ParseError("Format error; Expected 'eValue'");
return; // FORMAT ERROR, should probably be a constant
}
// Skip '='
skipOne(iter, EqualsChar<'='>());
// Skip until semicolon.
skipUntil(iter, EqualsChar<';'>());
// And skip the semicolon.
skipOne(iter, EqualsChar<';'>());
// Skip "cigar".
clear(buffer);
readUntil(buffer, iter, EqualsChar<'='>());
if (buffer != "cigar")
{
throw ParseError("Format error; Expected 'cigar'");
return; // FORMAT ERROR, should probably be a constant
}
// Skip '='
skipOne(iter, EqualsChar<'='>());
// Read cigar string.
clear(buffer);
readUntil(buffer, iter, EqualsChar<';'>());
// Skip semicolon.
skipOne(iter, EqualsChar<';'>());
// ignore rest of the field, skip to next line
skipLine(iter);
// Finally, append the local match.
if (subjectStrand == '-')
std::swap(subjectBeginPos, subjectEndPos);
appendLocalMatch(store, subjectName, subjectBeginPos, subjectEndPos, queryName, queryBeginPos, queryEndPos, buffer);
}
} // namespace seqan2
#endif // INCLUDE_SEQAN_PARSE_LM_PARSE_STELLAR_GFF_H_
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