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Classes | Typedefs | Functions | Variables
MG_adapt_ali.cxx File Reference
#include "merge.hxx"
#include "MG_adapt_ali.hxx"
#include <aw_msg.hxx>
#include <arbdbt.h>
#include <arb_strbuf.h>
#include <arb_global_defs.h>
#include <cmath>
#include <list>
Include dependency graph for MG_adapt_ali.cxx:

Go to the source code of this file.

Classes

struct  softbase
 
class  MG_remap
 

Typedefs

typedef std::list< softbasesoftbaselist
 
typedef softbaselist::iterator softbaseiter
 
typedef
softbaselist::const_iterator 
const_softbaseiter
 

Functions

static void drop_dots (softbaselist &softbases, int excessive_positions)
 
static MG_remapMG_create_remap (GBDATA *gb_left, GBDATA *gb_right, const char *reference_species_names, const char *alignment_name)
 
static GB_ERROR adaptCopiedAlignment (const MG_remap &remap, GBDATA *source_species, GBDATA *destination_species, const char *alignment_name)
 
GB_ERROR MG_adaptAllCopiedAlignments (const MG_remaps &remaps, GBDATA *source_species, GBDATA *destination_species)
 

Variables

const int NO_POSITION = -1
 
const int LEFT_BORDER = -2
 
const int RIGHT_BORDER = -3
 

Typedef Documentation

typedef std::list<softbase> softbaselist

Definition at line 52 of file MG_adapt_ali.cxx.

typedef softbaselist::iterator softbaseiter

Definition at line 53 of file MG_adapt_ali.cxx.

typedef softbaselist::const_iterator const_softbaseiter

Definition at line 54 of file MG_adapt_ali.cxx.

Function Documentation

static void drop_dots ( softbaselist softbases,
int  excessive_positions 
)
static

Definition at line 321 of file MG_adapt_ali.cxx.

static MG_remap* MG_create_remap ( GBDATA gb_left,
GBDATA gb_right,
const char reference_species_names,
const char alignment_name 
)
static
static GB_ERROR adaptCopiedAlignment ( const MG_remap remap,
GBDATA source_species,
GBDATA destination_species,
const char alignment_name 
)
static
GB_ERROR MG_adaptAllCopiedAlignments ( const MG_remaps remaps,
GBDATA source_species,
GBDATA destination_species 
)

if the 'adapt alignment' toggle is checked in 'merge species' window (i.e. if remaps.doesRemap), then this function does adapt all alignment data in 'destination_species', where source- and destination-data are identical (i.e. have just been copied before).

Definition at line 718 of file MG_adapt_ali.cxx.

References adaptCopiedAlignment(), MG_remaps::alignment_name(), MG_remaps::doesRemap(), error(), NULp, MG_remaps::remap(), and MG_remaps::size().

Referenced by MG_transfer_one_species(), transfer_single_field(), and AdaptedAlignmentTransporter::transport().

Variable Documentation

const int NO_POSITION = -1

Definition at line 30 of file MG_adapt_ali.cxx.

const int LEFT_BORDER = -2

Definition at line 31 of file MG_adapt_ali.cxx.

Referenced by MG_remap::remap().

const int RIGHT_BORDER = -3

Definition at line 32 of file MG_adapt_ali.cxx.