AP_seq_dna.cxx File Reference

#include "AP_seq_dna.hxx"
#include <arb_mem.h>
#include <AP_pro_a_nucs.hxx>
#include <AP_filter.hxx>
#include <ARB_Tree.hxx>

Include dependency graph for AP_seq_dna.cxx:

Go to the source code of this file.

Classes
struct	count_unweighted
struct	count_weighted
struct	count_nothing
struct	count_mutpsite
class	CombinableSeq

Macros
#define	NEVER_COMBINE_ASYNC

Functions
bool	hasGap (char c)
bool	isGap (char c)
bool	notHasGap (char c)
bool	notIsGap (char c)
template<class COUNT , class SITE >
static long	do_combine (size_t sequence_len, const char *__restrict p1, const char *__restrict p2, char *__restrict p, COUNT count, SITE site)
template<class COUNT >
static long	do_countMutations (size_t sequence_len, const char *__restrict p1, const char *__restrict p2, COUNT count)

Macro Definition Documentation

#define NEVER_COMBINE_ASYNC

Definition at line 203 of file AP_seq_dna.cxx.

Function Documentation

bool hasGap ( char  c )

inline

Definition at line 9 of file AP_seq_dna.cxx.

References AP_GAP.

Referenced by notHasGap().

bool isGap ( char  c )

inline

Definition at line 10 of file AP_seq_dna.cxx.

References AP_GAP.

Referenced by notIsGap().

bool notHasGap ( char  c )

inline

Definition at line 12 of file AP_seq_dna.cxx.

References hasGap().

bool notIsGap ( char  c )

inline

Definition at line 13 of file AP_seq_dna.cxx.

References isGap().

template<class COUNT , class SITE >

static long do_combine ( size_t  sequence_len, const char *__restrict  p1, const char *__restrict  p2, char *__restrict  p, COUNT  count, SITE  site  )

static

BELOW CODE CAREFULLY DESIGNED TO ALLOW VECTORIZATION

If you mess with it, use "-fopt-info" or "-ftree-vectorizer-verbose=n". Make sure you still see "LOOP VECTORIZED" in the output!

Definition at line 127 of file AP_seq_dna.cxx.

template<class COUNT >

static long do_countMutations ( size_t  sequence_len, const char *__restrict  p1, const char *__restrict  p2, COUNT  count  )

static

Definition at line 149 of file AP_seq_dna.cxx.