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moved fasta and aligned_buffer stuff to ivy_mike

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1 parent 1c345aa commit e0c6b83b0aecc45e0b96b4a91d4164601d1159d1 @sim82 committed Sep 13, 2012
Showing with 59 additions and 1,150 deletions.
  1. +14 −14 align_pvec_vec.h
  2. +0 −388 aligned_buffer.h
  3. +0 −708 fasta.h
  4. +4 −4 fasta_random_sample2.cpp
  5. +2 −2 fasta_to_phy.cpp
  6. +1 −1 ivy_mike
  7. +11 −7 papara.cpp
  8. +27 −26 stepwise_align.h
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@@ -25,16 +25,16 @@
#include <vector>
#include <algorithm>
-#include "aligned_buffer.h"
+#include "ivymike/aligned_buffer.h"
#include "vec_unit.h"
template<typename score_t, size_t W>
class align_pvec_score{
- aligned_buffer<score_t> m_a_prof;
- aligned_buffer<score_t> m_cgap_prof;
+ ivy_mike::aligned_buffer<score_t> m_a_prof;
+ ivy_mike::aligned_buffer<score_t> m_cgap_prof;
- mutable aligned_buffer<score_t> m_s;
- mutable aligned_buffer<score_t> m_out_score;
+ mutable ivy_mike::aligned_buffer<score_t> m_s;
+ mutable ivy_mike::aligned_buffer<score_t> m_out_score;
const score_t m_mismatch_score;
@@ -78,14 +78,14 @@ class align_pvec_score{
}
}
public:
- align_pvec_score( const aligned_buffer<score_t> &a_prof, const aligned_buffer<score_t> &a_aux_prof, score_t mismatch_score, score_t match_cgap, score_t gap_open, score_t gap_extend )
+ align_pvec_score( const ivy_mike::aligned_buffer<score_t> &a_prof, const ivy_mike::aligned_buffer<score_t> &a_aux_prof, score_t mismatch_score, score_t match_cgap, score_t gap_open, score_t gap_extend )
: m_mismatch_score(mismatch_score),m_match_cgap(match_cgap), m_gap_open(gap_open), m_gap_extend( gap_extend )
{
m_a_prof = a_prof;
m_cgap_prof.reserve( a_aux_prof.size());
- for( typename aligned_buffer<score_t>::const_iterator it = a_aux_prof.begin(); it != a_aux_prof.end(); ++it ) {
+ for( typename ivy_mike::aligned_buffer<score_t>::const_iterator it = a_aux_prof.begin(); it != a_aux_prof.end(); ++it ) {
m_cgap_prof.push_back( map_cgap(*it));
}
@@ -204,15 +204,15 @@ class align_pvec_score{
template<size_t W>
class align_pvec_gapp_score{
- typedef int32_t pstate_t;
- typedef float score_t;
+ typedef int32_t pstate_t;
+ typedef float score_t;
- aligned_buffer<pstate_t> m_a_prof;
- aligned_buffer<score_t> m_gapp_prof;
+ ivy_mike::aligned_buffer<pstate_t> m_a_prof;
+ ivy_mike::aligned_buffer<score_t> m_gapp_prof;
- mutable aligned_buffer<score_t> m_s;
- mutable aligned_buffer<score_t> m_out_score;
+ mutable ivy_mike::aligned_buffer<score_t> m_s;
+ mutable ivy_mike::aligned_buffer<score_t> m_out_score;
const score_t m_mismatch_score;
@@ -231,7 +231,7 @@ class align_pvec_gapp_score{
// }
// }
public:
- align_pvec_gapp_score( const aligned_buffer<pstate_t> &a_prof, const aligned_buffer<score_t> &a_gapp_prof, score_t mismatch_score, score_t match_cgap, score_t gap_open, score_t gap_extend )
+ align_pvec_gapp_score( const ivy_mike::aligned_buffer<pstate_t> &a_prof, const ivy_mike::aligned_buffer<score_t> &a_gapp_prof, score_t mismatch_score, score_t match_cgap, score_t gap_open, score_t gap_extend )
: m_mismatch_score(mismatch_score),m_match_cgap(match_cgap), m_gap_open(gap_open), m_gap_extend( gap_extend )
{
m_a_prof = a_prof;
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