MG_preserves.cxx File Reference

#include "merge.hxx"
#include "MG_adapt_ali.hxx"
#include <aw_awar.hxx>
#include <aw_root.hxx>
#include <aw_msg.hxx>
#include <aw_select.hxx>
#include <arb_progress.h>
#include <arb_global_defs.h>
#include <arbdbt.h>
#include <set>
#include <string>

Include dependency graph for MG_preserves.cxx:

Go to the source code of this file.

Classes
struct	preserve_para
class	Candidate

Macros
#define	AWAR_REMAP_CANDIDATE   AWAR_MERGE_TMP "remap_candidates"
#define	AWAR_REMAP_ALIGNMENT   AWAR_MERGE_TMP "remap_alignment"
#define	AWAR_REMAP_SEL_REFERENCE   AWAR_MERGE_TMP "remap_reference"

Typedefs
typedef set< SmartPtr < Candidate > >	Candidates

Functions
static void	get_global_alignments (ConstStrArray &ali_names)
static void	init_alignments (preserve_para *para)
static void	clear_candidates (preserve_para *para)
static long	count_bases (const char *data, long len)
static long	count_bases (GBDATA *gb_data)
static bool	operator< (const SmartPtr< Candidate > &c1, const SmartPtr< Candidate > &c2)
static void	find_species_candidates (Candidates &candidates, const CharPtrArray &ali_names)
static void	find_SAI_candidates (Candidates &candidates, const CharPtrArray &ali_names)
static void	calculate_preserves_cb (AW_window *aww, preserve_para *para)
static void	read_references (ConstStrArray &refs, AW_root *aw_root)
static void	write_references (AW_root *aw_root, const CharPtrArray &ref_array)
static void	select_reference (AW_root *aw_root, const char *ref_to_select)
static char *	get_selected_reference (AW_root *aw_root)
static void	refresh_reference_list_cb (AW_root *aw_root, preserve_para *para)
static void	add_selected_cb (AW_window *aww, preserve_para *para)
static void	clear_references_cb (AW_window *aww)
static void	del_reference_cb (AW_window *aww)
static void	lower_reference_cb (AW_window *aww)
static void	raise_reference_cb (AW_window *aww)
static void	test_references_cb (AW_window *aww)
static void	init_preserve_awars (AW_root *aw_root)
AW_window *	MG_create_preserves_selection_window (AW_root *aw_root)

Macro Definition Documentation

#define AWAR_REMAP_CANDIDATE   AWAR_MERGE_TMP "remap_candidates"

Definition at line 33 of file MG_preserves.cxx.

Referenced by add_selected_cb(), init_preserve_awars(), and MG_create_preserves_selection_window().

#define AWAR_REMAP_ALIGNMENT   AWAR_MERGE_TMP "remap_alignment"

Definition at line 34 of file MG_preserves.cxx.

Referenced by calculate_preserves_cb(), init_preserve_awars(), and MG_create_preserves_selection_window().

#define AWAR_REMAP_SEL_REFERENCE   AWAR_MERGE_TMP "remap_reference"

Definition at line 35 of file MG_preserves.cxx.

Referenced by get_selected_reference(), init_preserve_awars(), MG_create_preserves_selection_window(), and select_reference().

Typedef Documentation

typedef set< SmartPtr<Candidate> > Candidates

Definition at line 167 of file MG_preserves.cxx.

Function Documentation

static void get_global_alignments ( ConstStrArray &  ali_names )

static

Definition at line 43 of file MG_preserves.cxx.

References GB_find_string(), GB_IGNORE_CASE, GBT_get_alignment_names(), GBT_get_presets(), GLOBAL_gb_dst, GLOBAL_gb_src, CharPtrArray::remove(), and SEARCH_GRANDCHILD.

Referenced by calculate_preserves_cb(), and init_alignments().

static void init_alignments ( preserve_para *  para )

static

Definition at line 55 of file MG_preserves.cxx.

References preserve_para::alignmentList, get_global_alignments(), and AW_selection_list::init_from_array().

Referenced by MG_create_preserves_selection_window().

static void clear_candidates ( preserve_para *  para )

static

Definition at line 62 of file MG_preserves.cxx.

References AW_selection_list::clear(), DISPLAY_NONE, AW_selection_list::insert_default(), NO_ALI_SELECTED, preserve_para::refCandidatesList, and AW_selection_list::update().

Referenced by calculate_preserves_cb(), and MG_create_preserves_selection_window().

static long count_bases ( const char *  data, long  len  )

static

Definition at line 71 of file MG_preserves.cxx.

References GAP::is_std_gap().

Referenced by Candidate::Candidate(), count_bases(), and SEC_region::update_base_count().

static long count_bases ( GBDATA *  gb_data )

static

Definition at line 83 of file MG_preserves.cxx.

References count_bases(), GB_BITS, GB_export_errorf(), GB_get_type_name(), GB_read_as_string(), GB_read_char_pntr(), GB_read_count(), GB_read_type(), and GB_STRING.

static bool operator< ( const SmartPtr< Candidate > &  c1, const SmartPtr< Candidate > &  c2  )

static

Definition at line 164 of file MG_preserves.cxx.

static void find_species_candidates ( Candidates &  candidates, const CharPtrArray &  ali_names  )

static

Definition at line 169 of file MG_preserves.cxx.

References arb_progress::aborted(), aw_message(), arb_progress::done(), GB_await_error(), GB_have_error(), GBS_free_hash(), GBS_global_string(), GBS_hash_elements(), GBS_read_hash(), GBT_create_species_hash(), GBT_first_species(), GBT_get_name_or_description(), GBT_next_species(), Candidate::get_score(), GLOBAL_gb_dst, GLOBAL_gb_src, Candidate::has_alignments(), and arb_progress::inc().

Referenced by calculate_preserves_cb().

static void find_SAI_candidates ( Candidates &  candidates, const CharPtrArray &  ali_names  )

static

Definition at line 205 of file MG_preserves.cxx.

References aw_message(), GB_await_error(), GB_have_error(), GBS_free_hash(), GBS_global_string(), GBS_hash_elements(), GBS_read_hash(), GBT_create_SAI_hash(), GBT_first_SAI(), GBT_get_name_or_description(), GBT_next_SAI(), Candidate::get_score(), GLOBAL_gb_dst, GLOBAL_gb_src, Candidate::has_alignments(), and arb_progress::inc().

Referenced by calculate_preserves_cb().

static void calculate_preserves_cb ( AW_window *  aww, preserve_para *  para  )

static

Definition at line 238 of file MG_preserves.cxx.

References AW_root::awar(), AWAR_REMAP_ALIGNMENT, clear_candidates(), find_SAI_candidates(), find_species_candidates(), get_global_alignments(), AW_window::get_root(), GLOBAL_gb_dst, GLOBAL_gb_src, AW_selection_list::insert(), ConstStrArray::put(), AW_awar::read_char_pntr(), preserve_para::refCandidatesList, and AW_selection_list::update().

Referenced by MG_create_preserves_selection_window().

static void read_references ( ConstStrArray &  refs, AW_root *  aw_root  )

static

Definition at line 283 of file MG_preserves.cxx.

References AW_root::awar(), AWAR_REMAP_SPECIES_LIST, GBT_splitNdestroy_string(), AW_awar::read_string(), and SPLIT_DROPEMPTY.

Referenced by add_selected_cb(), del_reference_cb(), lower_reference_cb(), raise_reference_cb(), and refresh_reference_list_cb().

static void write_references ( AW_root *  aw_root, const CharPtrArray &  ref_array  )

static

Definition at line 287 of file MG_preserves.cxx.

References AW_root::awar(), AWAR_REMAP_ENABLE, AWAR_REMAP_SPECIES_LIST, GBT_join_strings(), AW_awar::write_int(), and AW_awar::write_string().

Referenced by add_selected_cb(), del_reference_cb(), lower_reference_cb(), and raise_reference_cb().

static void select_reference ( AW_root *  aw_root, const char *  ref_to_select  )

static

Definition at line 293 of file MG_preserves.cxx.

References AW_root::awar(), AWAR_REMAP_SEL_REFERENCE, and AW_awar::write_string().

Referenced by add_selected_cb(), and del_reference_cb().

static char* get_selected_reference ( AW_root *  aw_root )

static

Definition at line 296 of file MG_preserves.cxx.

References AW_root::awar(), AWAR_REMAP_SEL_REFERENCE, and AW_awar::read_string().

Referenced by add_selected_cb(), del_reference_cb(), lower_reference_cb(), and raise_reference_cb().

static void refresh_reference_list_cb ( AW_root *  aw_root, preserve_para *  para  )

static

Definition at line 300 of file MG_preserves.cxx.

References AW_selection_list::init_from_array(), read_references(), and preserve_para::usedRefsList.

Referenced by MG_create_preserves_selection_window().

static void add_selected_cb ( AW_window *  aww, preserve_para *  para  )

static

Definition at line 306 of file MG_preserves.cxx.

References AW_root::awar(), AWAR_REMAP_CANDIDATE, AW_window::get_root(), get_selected_reference(), CharPtrArray::index_of(), CharPtrArray::move(), AW_selection_list::move_selection(), ConstStrArray::put_before(), read_references(), AW_awar::read_string(), preserve_para::refCandidatesList, select_reference(), and write_references().

Referenced by MG_create_preserves_selection_window().

static void clear_references_cb ( AW_window *  aww )

static

Definition at line 329 of file MG_preserves.cxx.

References AW_root::awar(), AWAR_REMAP_SPECIES_LIST, AW_window::get_root(), and AW_awar::write_string().

Referenced by MG_create_preserves_selection_window().

static void del_reference_cb ( AW_window *  aww )

static

Definition at line 334 of file MG_preserves.cxx.

References AW_window::get_root(), get_selected_reference(), CharPtrArray::index_of(), read_references(), CharPtrArray::safe_remove(), select_reference(), and write_references().

Referenced by MG_create_preserves_selection_window().

static void lower_reference_cb ( AW_window *  aww )

static

Definition at line 351 of file MG_preserves.cxx.

References AW_window::get_root(), get_selected_reference(), CharPtrArray::index_of(), CharPtrArray::move(), read_references(), and write_references().

Referenced by MG_create_preserves_selection_window().

static void raise_reference_cb ( AW_window *  aww )

static

Definition at line 366 of file MG_preserves.cxx.

References AW_window::get_root(), get_selected_reference(), CharPtrArray::index_of(), CharPtrArray::move(), read_references(), and write_references().

Referenced by MG_create_preserves_selection_window().

static void test_references_cb ( AW_window *  aww )

static

Definition at line 382 of file MG_preserves.cxx.

References AW_root::awar(), AWAR_REMAP_SPECIES_LIST, AW_window::get_root(), GLOBAL_gb_dst, GLOBAL_gb_src, and AW_awar::read_string().

Referenced by MG_create_preserves_selection_window().

static void init_preserve_awars ( AW_root *  aw_root )

static

Definition at line 392 of file MG_preserves.cxx.

References AWAR_REMAP_ALIGNMENT, AWAR_REMAP_CANDIDATE, AWAR_REMAP_SEL_REFERENCE, AW_root::awar_string(), and GLOBAL_gb_dst.

Referenced by MG_create_preserves_selection_window().

AW_window* MG_create_preserves_selection_window

(

AW_root *

aw_root

)

Definition at line 398 of file MG_preserves.cxx.

References AW_awar::add_callback(), add_selected_cb(), preserve_para::alignmentList, AW_POPDOWN(), AW_root::awar(), awar_list, AWAR_REMAP_ALIGNMENT, AWAR_REMAP_CANDIDATE, AWAR_REMAP_ENABLE, AWAR_REMAP_SEL_REFERENCE, AWAR_REMAP_SPECIES_LIST, calculate_preserves_cb(), clear_candidates(), clear_references_cb(), del_reference_cb(), GLOBAL_gb_dst, GLOBAL_gb_src, init_alignments(), init_preserve_awars(), lower_reference_cb(), makeHelpCallback(), raise_reference_cb(), preserve_para::refCandidatesList, refresh_reference_list_cb(), test_references_cb(), AW_awar::touch(), and preserve_para::usedRefsList.

Referenced by MG_create_merge_species_window().