ARB
Classes | Macros | Typedefs | Functions
TranslateRealign.cxx File Reference
#include <TranslateRealign.h>
#include <Translate.hxx>
#include <AP_codon_table.hxx>
#include <AP_pro_a_nucs.hxx>
#include <aw_question.hxx>
#include <arb_progress.h>
#include <arb_global_defs.h>
#include <arbdbt.h>
#include <arb_defs.h>
#include <string>
Include dependency graph for TranslateRealign.cxx:

Go to the source code of this file.

Classes

class  BufferPtr< T >
 
class  SizedBufferPtr< T >
 
class  Distributor
 
class  FailedAt
 
class  RealignAttempt
 
class  Realigner
 
struct  Data
 

Macros

#define ali_assert(cond)   arb_assert(cond)
 

Typedefs

typedef SizedBufferPtr< const
char
SizedReadBuffer
 
typedef SizedBufferPtr< charSizedWriteBuffer
 

Functions

bool legal_ORF_pos (int p)
 
GB_ERROR ALI_translate_marked (GBDATA *gb_main, bool use_entries, bool save_entries, int selected_startpos, bool translate_all, const char *ali_source, const char *ali_dest)
 
bool isGap (char c)
 
static GB_ERROR distribute_xdata (SizedReadBuffer &dna, size_t xcount, char *xtarget_, bool gap_before, bool gap_after, const TransTables &allowed, TransTables &remaining)
 
charunalign (const char *data, size_t len, size_t &compressed_len)
 
GB_ERROR ALI_realign_marked (GBDATA *gb_main, const char *ali_source, const char *ali_dest, size_t &neededLength, bool unmark_succeeded, bool cutoff_dna)
 

Macro Definition Documentation

#define ali_assert (   cond)    arb_assert(cond)

Typedef Documentation

Definition at line 73 of file TranslateRealign.cxx.

Definition at line 74 of file TranslateRealign.cxx.

Function Documentation

bool legal_ORF_pos ( int  p)
inline

Definition at line 79 of file TranslateRealign.cxx.

Referenced by ALI_translate_marked().

GB_ERROR ALI_translate_marked ( GBDATA gb_main,
bool  use_entries,
bool  save_entries,
int  selected_startpos,
bool  translate_all,
const char ali_source,
const char ali_dest 
)
bool isGap ( char  c)
inline
static GB_ERROR distribute_xdata ( SizedReadBuffer dna,
size_t  xcount,
char xtarget_,
bool  gap_before,
bool  gap_after,
const TransTables allowed,
TransTables remaining 
)
static

distributes 'dna' to marked X-positions

Parameters
xtargetdestination buffer (target positions are marked with '!')
xcountnumber of X's encountered
gap_beforetrue if resulting realignment has a gap or the start of alignment before the X-positions
gap_afteranalog to 'gap_before'
allowedallowed translation tables
remainingremaining allowed translation tables (with those tables disabled for which no distribution possible)
Returns
error if dna distribution wasn't possible

Definition at line 508 of file TranslateRealign.cxx.

References ali_assert, BufferPtr< T >::copy(), error(), FALLTHROUGH, BufferPtr< T >::get(), Distributor::get_score(), BufferPtr< T >::inc(), TransTables::is_subset_of(), isGap(), SizedBufferPtr< T >::length(), Distributor::mayFailTranslation(), NULp, BufferPtr< T >::offset(), BufferPtr< T >::put(), Distributor::size(), tree_defaults::SPREAD, Distributor::translates_to_Xs(), and SizedBufferPtr< T >::valid().

char* unalign ( const char data,
size_t  len,
size_t &  compressed_len 
)
inline

Definition at line 817 of file TranslateRealign.cxx.

References isGap().

Referenced by Realigner::realign_seq().

GB_ERROR ALI_realign_marked ( GBDATA gb_main,
const char ali_source,
const char ali_dest,
size_t &  neededLength,
bool  unmark_succeeded,
bool  cutoff_dna 
)