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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2018, 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: Tobias Rausch <rausch@embl.de>
// Author: Anne-Katrin Emde <anne-katrin.emde@fu-berlin.de>
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_ALIGN_H_
#define SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_ALIGN_H_
namespace seqan {
///////////////////////////////////////////////////////////////////////////////////////////////////////
//Functions for Align<TSource,TSpec>
//project onto other sequence
template<typename TSource,typename TSpec,typename TValue, typename TId1, typename TPos1, typename TId2, typename TPos2,typename TMap>
void
_getOtherSequenceAndProject(Align<TSource,TSpec> & segment,
TValue seg_num,
TMap & seq_map,
TId1 ,
TPos1 node_i,
TId2 & seq_j_id,
TPos2 & node_j)
{
if(seg_num == 0)
{
seq_j_id = seq_map[getObjectId(source(row(segment, 1)))];
TPos1 view_clipped_end_pos = clippedEndPosition(row(segment,0)) - clippedBeginPosition(row(segment, 0));
if(node_i >= (TPos1)toSourcePosition(row(segment, 0), view_clipped_end_pos))
node_j = static_cast<TPos2>(-1);
else
node_j = toSourcePosition(row(segment, 1), toViewPosition(row(segment, 0), node_i));
}
else
{
seq_j_id = seq_map[getObjectId(source(row(segment, 0)))];
TPos1 view_clipped_end_pos = clippedEndPosition(row(segment, 1)) - clippedBeginPosition(row(segment, 1));
if(node_i >= (TPos1)toSourcePosition(row(segment, 1), view_clipped_end_pos))
node_j = static_cast<TPos2>(-1);
else
node_j = toSourcePosition(row(segment, 0), toViewPosition(row(segment, 1), node_i));
}
}
//unspektakul�re funktion, die die int ID zur�ckgibt (braucht man damit es f�r alle alignment typen geht)
//template<typename TSource,typename TSpec, typename TValue, typename TSeqMap>
//int
//_getSeqMapId(TSeqMap & seq_map,
// Align<TSource,TSpec> & segment,
// TValue seq_i)
//{
// return seq_map[getObjectId(source(row(segment,seq_i)))];
//}
//
//given seq and segment, get the sequenceId (seq_i) and its begin and end
//if seq = 0 get first sequence (that takes part in the segment match)
//if seq = 1 get second sequence
template<typename TAliSource,typename TAliSpec, typename TId, typename TPosition, typename TId2>
void
_getSeqBeginAndEnd(Align<TAliSource,TAliSpec> & segment,
std::map<const void * ,int> & seq_map,
TId & seq_i_id,
TPosition & begin_i,
TPosition & end_i,
TId2 seq)
{
seq_i_id = seq_map[getObjectId(source(row(segment,seq)))];
begin_i = clippedBeginPosition(row(segment, seq));
end_i = toSourcePosition(row(segment, seq), clippedEndPosition(row(segment, seq)) - begin_i);
}
////////////////////////////////////////////////////////////////////////////////////////
// 50000 _getRefinedMatchScore Functions
////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////
//TODO(singer): Remove this forward
template <typename T>
struct Row;
//for Align<TAliSource,TAliSpec>
//get score for alignment of length len starting at pos_i on first sequence
//and pos_j on second sequence
template<typename TScoreValue,typename TScoreSpec,typename TStringSet,typename TAliSource,typename TAliSpec,typename TValue>
TScoreValue
_getRefinedMatchScore(Score<TScoreValue,TScoreSpec> & score_type,
TStringSet &,
Align<TAliSource,TAliSpec> & segment,
TValue pos_i,
TValue pos_j,
TValue len,
TValue)
{
typedef Align<TAliSource,TAliSpec> TAlign;
typedef typename Row<TAlign>::Type TRow;
// typedef typename Iterator<TRow,GapsIterator<ArrayGaps> >::Type TIterator;
typedef typename Iterator<TRow, Rooted>::Type TIterator;
TIterator row0_it, row1_it;
row0_it = iter(row(segment,0),toViewPosition(row(segment,0),pos_i));
row1_it = iter(row(segment,1),toViewPosition(row(segment,1),pos_j));
len = toViewPosition(row(segment,0),pos_i + len) - toViewPosition(row(segment,0),pos_i);
TValue i = 0;
TScoreValue ret_score = 0;
while(i < len)
{
if(isGap(row1_it)||isGap(row0_it))
ret_score += scoreGapExtend(score_type);
else
ret_score += score(score_type,getValue(row0_it),getValue(row1_it));
++i;
++row0_it;
++row1_it;
}
return ret_score;
}
//get score for alignment starting at pos_i on first sequence
//and pos_j on second sequence, if len1!=len2 then the refinement
//process was stopped (the cut is not exact)
//template<typename TScore,typename TStringSet, typename TAliSource,typename TAliSpec,typename TValue>
//typename Value<TScore>::Type
//_getRefinedMatchScore(TScore & score_type,
// TStringSet &,
// Align<TAliSource,TAliSpec> & segment,
// TValue pos_i,
// TValue pos_j,
// TValue len1,
// TValue len2)
//{
// typedef Align<TAliSource,TAliSpec> TAlign;
// typedef typename Row<TAlign>::Type TRow;
// typedef typename Iterator<TRow>::Type TIterator;
// TIterator row0_it, row1_it;
// TValue len;
// row0_it = iter(row(segment,0),toViewPosition(row(segment,0),pos_i));
// row1_it = iter(row(segment,1),toViewPosition(row(segment,1),pos_j));
// len1 = toViewPosition(row(segment,0),pos_i + len1) - toViewPosition(row(segment,0),pos_i);
// len2 = toViewPosition(row(segment,1),pos_j + len2) - toViewPosition(row(segment,1),pos_j);
// len = (len1 < len2) ? len1 : len2;
// int i = 0;
// typename Value<TScore>::Type ret_score = 0;
//
// //calculate score for aligned region
// while(i < len)
// {
// ret_score += score(score_type,getValue(row0_it),getValue(row1_it));
// ++i;
// ++row0_it;
// ++row1_it;
// }
// //fill up with gaps if one sequence is longer than the other
// len = (len1 > len2) ? len1 : len2;
// ret_score += (len - i) * scoreGapExtend(score_type);
//
// return ret_score;
//}
} // namespace seqan
#endif // #ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_ALIGN_H_
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