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< softbase >	softbaselist
typedef softbaselist::iterator	softbaseiter
typedef softbaselist::const_iterator	const_softbaseiter

Functions
static void	drop_dots (softbaselist &softbases, int excessive_positions)
static MG_remap *	MG_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

Definition at line 606 of file MG_adapt_ali.cxx.

References MG_remap::add_reference(), ARB_strdup(), aw_message(), GB_read_as_string(), GB_read_char_pntr(), GB_read_type(), GB_STRING, GBS_global_string(), GBT_find_SAI(), GBT_find_sequence(), GBT_find_species(), NULp, and warning().

Referenced by MG_remaps::MG_remaps().

static GB_ERROR adaptCopiedAlignment ( const MG_remap &  remap, GBDATA *  source_species, GBDATA *  destination_species, const char *  alignment_name  )

static

Definition at line 690 of file MG_adapt_ali.cxx.

References error(), GB_await_error(), GB_read_string(), GB_write_string(), GBS_checksum(), GBS_global_string(), GBT_find_sequence(), GBT_get_name_or_description(), NULp, and MG_remap::remap().

Referenced by MG_adaptAllCopiedAlignments().

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 725 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.