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src
lib
align
domain_aln.hpp
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/*
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* domain_aln.hpp
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*
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* Created on: Sep 11, 2013
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* Author: ckeme_01
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*/
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#ifndef DOMAIN_ALN_HPP_
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#define DOMAIN_ALN_HPP_
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//C++ header
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#include <algorithm>
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#include <map>
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#include <stack>
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#include <utility>
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#include <vector>
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//MDAT header
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#include "
Library.hpp
"
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#include "../Sequence/ProteinSequenceSet.hpp"
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#include "../Annotation/DomainArchitecture.hpp"
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#include "../utils/MatrixStack.hpp"
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#include "../utils/ThreadPool.hpp"
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#include "
consistency_aln.hpp
"
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namespace
MDAT
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{
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struct
Opt_DA
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{
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Opt_DA
() :
match
(0),
mismatch
(0),
matches
(),
terminal_gop
(0),
terminal_gep
(0),
gop
(0),
gep
(0), l_prop(0), scale(0), dmpm_f(
""
)
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{}
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int
match
;
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int
mismatch
;
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MDAT::Matrix<short>
matches
;
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int
terminal_gop
;
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int
terminal_gep
;
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int
gop
;
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int
gep
;
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int
l_prop;
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int
scale;
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std::string dmpm_f;
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};
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void
rads_align_archi
(
const
Opt_DA
&opts,
const
DomainArchitecture
&doms1,
const
DomainArchitecture
&doms2,
MatrixStack
<3,std::pair<int, char> > &matrices);
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void
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rads_traceback_archi(
Library<DomainArchitectureSet >
&lib,
const
DomainArchitecture
&arch1,
const
DomainArchitecture
&arch2,
const
MatrixStack
<3,std::pair<int, char> > &matrices);
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Matrix<float>
*
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all_rads_pair_align_archi
(
Library<DomainArchitectureSet >
&lib,
const
ProteinSequenceSet<Default>
&seqSet,
const
Opt_DA
&opts);
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Matrix<float>
*
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all_rads_pair_align_archi
(
Library<DomainArchitectureSet >
&lib,
const
ProteinSequenceSet<Default>
&seqSet,
const
Opt_DA
&opts,
unsigned
int
n_threads);
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void
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refine
(
DomainArchitectureSet
&
set
);
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}
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#endif
/* DOMAIN_ALN_HPP_ */
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