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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: Tobias Rausch <rausch@embl.de>
// Author: Anne-Katrin Emde <anne-katrin.emde@fu-berlin.de>
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_FRAGMENT_H_
#define SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_FRAGMENT_H_
namespace seqan2 {
///////////////////////////////////////////////////////////////////////////////////////////////////////
//Functions for Fragments
//project onto other sequence for Graph<Alignment>
template<typename TFragSize, typename TFragSpec,typename TValue,typename TId1, typename TPos1, typename TId2, typename TPos2, typename TMap>
void
_getOtherSequenceAndProject(Fragment<TFragSize,TFragSpec> & segment,
TValue seg_num,
TMap &,
TId1 seq_i_id,
TPos1 pos_i,
TId2 & seq_j_id,
TPos2 & pos_j)
{
getProjectedPosition(segment,seg_num, seq_i_id, pos_i,seq_j_id,pos_j);
//if(seq_i_id == sequenceId(segment,0))
// seq_j_id = sequenceId(segment,1);
//else
// seq_j_id = sequenceId(segment,0);
}
//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 TFragSize, typename TFragSpec, typename TId, typename TPosition, typename TId2>
void
_getSeqBeginAndEnd(Fragment<TFragSize,TFragSpec> & segment,
std::map<const void * ,int> &,
TId & seq_i_id,
TPosition & begin_i,
TPosition & end_i,
TId2 seq)
{
seq_i_id = sequenceId(segment,seq);
if(seq==0)
begin_i = segment.begin1; // fragmentBegin(segment,seq_i_id);
else
begin_i = segment.begin2; // fragmentBegin(segment,seq_i_id);
end_i = begin_i + segment.len; //fragmentLength(segment,seq_i_id);
}
////////////////////////////////////////////////////////////////////////////////////////
// 50000 _getRefinedMatchScore Functions
////////////////////////////////////////////////////////////////////////////////////////
//get score for alignment starting at pos_i on one sequence (first sequence if i_am_first==true)
//and pos_j on other sequence (second sequence if i_am_first==true), if len1!=len2 then the refinement
//process was stopped (the cut is not exact)
//template<typename TScore,typename TStringSet,typename TFragId,typename TFragPos,typename TFragSize, typename TFragSpec,typename TValue>
//typename Value<TScore>::Type
//_getRefinedMatchScore(TScore & score_type,
// TStringSet & seqs,
// Fragment<TFragId,TFragPos,TFragSize,TFragSpec> & segment,
// TValue pos_i,
// TValue pos_j,
// TValue len1,
// TValue len2)
//{
// typename Infix<typename Value<TStringSet>::Type>::Type label0 = label(segment,seqs,sequenceId(segment,0));
// typename Infix<typename Value<TStringSet>::Type>::Type label1 = label(segment,seqs,sequenceId(segment,1));
// int i = 0;
// typename Value<TScore>::Type ret_score = 0;
// TValue len = (len1 < len2) ? len1 : len2;
// while(i < len)
// {
// ret_score += score(score_type,label0[i],label1[i]);
// ++i;
// }
// len = (len1 > len2) ? len1 : len2;
// ret_score += (len - i) * scoreGapExtend(score_type);
// return ret_score;
//}
//
//
///////////////////////////////////////////////////////////////////////////////////////////////
////die n�chsten beiden funktionen: f�r Fragmente und Score vom Typ Simple
////f�r den fall dass es keine mismatches innerhalb der segmente gibt und Score vom typ Simple ist
////TODO: m�sste f�r einen bestimmten TFragSpec sein (Exact oder noMismatches)
////get score for alignment starting at pos_i on one sequence (first sequence if i_am_first==true)
////and pos_j on other sequence (second sequence if i_am_first==true), if len1!=len2 then the refinement
////process was stopped (the cut is not exact)
//template<typename TScoreValue,typename TStringSet,typename TFragId,typename TFragPos,typename TFragSize, typename TFragSpec>
//TScoreValue
//_getRefinedMatchScore(Score<TScoreValue, Simple> & score_type,
// TStringSet & seqs,
// Fragment<TFragId,TFragPos,TFragSize,TFragSpec> & segment,
// TFragPos pos_i,
// TFragPos pos_j,
// TFragSize len1,
// TFragSize len2)
//{
// typename Infix<typename Value<TStringSet>::Type>::Type label0 = label(segment,seqs,sequenceId(segment,0));
// typename Infix<typename Value<TStringSet>::Type>::Type label1 = label(segment,seqs,sequenceId(segment,1));
// TScoreValue ret_score = 0;
// TFragSize len;
// if (len1 < len2) len = len1;
// else len = len2;
// if(len1 <= len2)
// {
// ret_score += len1 * scoreMatch(score_type);
// ret_score += (len2 - len1) * scoreGapExtend(score_type);
// }
// else{
// ret_score += len2 * scoreMatch(score_type);
// ret_score += (len1 - len2) * scoreGapExtend(score_type);
// }
// return ret_score;
//}
//get score for alignment of length len starting at pos_i on one sequence (first sequence if i_am_first==true)
//and pos_j on other sequence (second sequence if i_am_first==true)
template<typename TScoreValue,typename TScoreSpec,typename TStringSet,typename TFragment,typename TFragPos,typename TFragSize>
TScoreValue
_getRefinedMatchScore(Score<TScoreValue,TScoreSpec> & score_type,
TStringSet & seqs,
TFragment& segment,
TFragPos pos_i,
TFragPos pos_j,
TFragSize len,
TFragSize)
{
typedef typename Infix<typename Value<TStringSet>::Type>::Type TSegmentLabel;
TSegmentLabel label0 = label(segment,seqs, sequenceId(segment, 0));
TSegmentLabel label1 = label(segment,seqs, sequenceId(segment, 1));
typename Iterator<TSegmentLabel, Rooted>::Type label_it0 = begin(label0) + (pos_i - fragmentBegin(segment,sequenceId(segment,0)));
typename Iterator<TSegmentLabel, Rooted>::Type label_it1 = begin(label1) + (pos_j - fragmentBegin(segment,sequenceId(segment,1)));
int i = 0;
TScoreValue ret_score = 0;
while(i < (int) len)
{
ret_score += score(score_type,*label_it0,*label_it1);
++label_it0;
++label_it1;
++i;
}
return ret_score;
}
//get score for alignment of length len starting at pos_i on one sequence (first sequence if i_am_first==true)
//and pos_j on other sequence (second sequence if i_am_first==true)
template<typename TScoreValue,typename TStringSet,typename TFragPos,typename TFragSize, typename TSpec>
TScoreValue
_getRefinedMatchScore(Score<TScoreValue, Simple> & score_type,
TStringSet &,
Fragment<TFragSize,ExactFragment<TSpec> > &,
TFragPos,
TFragPos,
TFragSize len,
TFragSize)
{
return len*scoreMatch(score_type);
}
} // namespace
#endif // #ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_FRAGMENT_H_
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