#include "graph_aligner_gui.hxx"
#include "ed4_defs.hxx"
#include <fast_aligner.hxx>
#include <aw_awars.hxx>
#include <aw_global_awars.hxx>
#include <aw_msg.hxx>
#include <aw_root.hxx>
#include <awt_sel_boxes.hxx>
#include <awt_config_manager.hxx>
#include <servercntrl.h>
#include <PT_com.h>
#include <client.h>
#include <arbdbt.h>
#include <arb_strbuf.h>
#include <arb_misc.h>
#include <arb_file.h>
#include <sys/types.h>
#include <sys/wait.h>
#include <unistd.h>
#include <string>
#include <sstream>
#include <iostream>
#include <vector>

Include dependency graph for graph_aligner_gui.cxx:

Classes
struct	sina_arb_interface_def

Macros
#define	ga_assert(cond) arb_assert(cond)

#define	GA_AWAR_ROOT "sina/"

#define	GA_AWAR_TEMP "tmp/" GA_AWAR_ROOT

#define	GA_AWAR_CMD GA_AWAR_ROOT "cmd"

#define	GA_AWAR_TGT GA_AWAR_ROOT "target"

#define	GA_AWAR_SAI GA_AWAR_ROOT "sai"

#define	GA_AWAR_ALIGNMENT GA_AWAR_ROOT "alignment"

#define	GA_AWAR_PROTECTION GA_AWAR_ROOT "protection"

#define	GA_AWAR_TURN_CHECK GA_AWAR_ROOT "turncheck"

#define	GA_AWAR_REALIGN GA_AWAR_ROOT "realign"

#define	GA_AWAR_MATCH_SCORE GA_AWAR_ROOT "match_score"

#define	GA_AWAR_MISMATCH_SCORE GA_AWAR_ROOT "mismatch_score"

#define	GA_AWAR_GAP_PEN GA_AWAR_ROOT "gap_pen"

#define	GA_AWAR_GAP_EXT GA_AWAR_ROOT "gap_ext"

#define	GA_AWAR_ADVANCED GA_AWAR_ROOT "advanced"

#define	GA_AWAR_FS_MIN GA_AWAR_ROOT "fs_min"

#define	GA_AWAR_FS_MAX GA_AWAR_ROOT "fs_max"

#define	GA_AWAR_FS_MSC GA_AWAR_ROOT "fs_msc"

#define	GA_AWAR_MIN_FULL GA_AWAR_ROOT "min_full"

#define	GA_AWAR_FULL_MINLEN GA_AWAR_ROOT "full_minlen"

#define	GA_AWAR_OVERHANG GA_AWAR_ROOT "overhang"

#define	GA_AWAR_THREADS GA_AWAR_ROOT "threads"

#define	GA_AWAR_QSIZE GA_AWAR_ROOT "qsize"

#define	GA_AWAR_KMER_LEN GA_AWAR_ROOT "kmer_len"

#define	GA_AWAR_KMER_MM GA_AWAR_ROOT "kmer_mm"

#define	GA_AWAR_MIN_LEN GA_AWAR_ROOT "min_len"

#define	GA_AWAR_WEIGHT GA_AWAR_ROOT "weight"

#define	GA_AWAR_INSERT GA_AWAR_ROOT "insert"

#define	GA_AWAR_LOWERCASE GA_AWAR_ROOT "lowercase"

#define	GA_AWAR_AUTOFILTER GA_AWAR_ROOT "autofilter"

#define	GA_AWAR_KMER_NOREL GA_AWAR_ROOT "kmer_norel"

#define	GA_AWAR_KMER_NOFAST GA_AWAR_ROOT "kmer_nofast"

#define	GA_AWAR_SHOW_DIST GA_AWAR_ROOT "show_dist"

#define	GA_AWAR_SHOW_DIFF GA_AWAR_ROOT "show_diff"

#define	GA_AWAR_COLOR GA_AWAR_ROOT "color"

#define	GA_AWAR_GENE_START GA_AWAR_ROOT "gene_start"

#define	GA_AWAR_GENE_END GA_AWAR_ROOT "gene_end"

#define	GA_AWAR_FS_COVER_GENE GA_AWAR_ROOT "fs_cover_gene"

#define	GA_AWAR_USED_RELS GA_AWAR_ROOT "write_used_rels"

#define	GA_AWAR_CALC_IDENTITY GA_AWAR_ROOT "calc_idty"

#define	GA_AWAR_NOWARN_START GA_AWAR_ROOT "nowarn_start"

#define	GA_AWAR_REFDB_MODE GA_AWAR_ROOT "refdb_mode"

#define	GA_AWAR_REFDB GA_AWAR_ROOT "refdb"

#define	GA_AWAR_REFDB_SELECT GA_AWAR_TEMP "refdb"

Enumerations
enum	RefDbMode { REF_EXPLICIT, REF_LAST_SAVE, REF_CURRENT }

enum	SinaArbInterfaceVersion { ARB_5_99, ARB_7_1 }

Functions
static void	refDbModeChanged_cb (AW_root *root)

static void	newRefDbSelected_cb (AW_root *root)

void	create_sina_variables (AW_root *root, AW_default db1)

static const char *	get_interface_id (SinaArbInterfaceVersion version)

static GB_ERROR	detect_sina_version (AW_root *awr)

AW_active	sina_mask (AW_root *awr)

const char *	stream2static (const std::stringstream &str)

const char *	empty_as_none (const char *sainame)

static void	sina_start (AW_window window, const AlignDataAccess data_access)

static char *	filter_posvar_SAI_for_ali (GBDATA gb_extended, const char ali_name)

static void	accept_selected_ref_db (AW_window aww, const char const *awar_filename)

static AW_window *	create_ref_db_selection_window (AW_root *aw_root)

static void	sina_select_ref_db (AW_window *aww)

static void	sina_cmd_changed_cb (AW_root *awr)

static AW_window_simple *	new_sina_simple (AW_root root, const AlignDataAccess alignData, bool adv)

void	show_sina_window (UNFIXED, const AlignDataAccess *alignData)

Variables
const SinaArbInterfaceVersion	NO_INTERFACE = SinaArbInterfaceVersion(-1)

static sina_arb_interface_def	supported_sina_versions []

static SinaArbInterfaceVersion	used_sina_interface = NO_INTERFACE

static AWT_config_mapping_def	sina_config_mapping []

static SinaArbInterfaceVersion	gui_sina_interface = NO_INTERFACE

Macro Definition Documentation

#define ga_assert ( cond ) arb_assert(cond)

Definition at line 47 of file graph_aligner_gui.cxx.

Referenced by awt_create_filter_awars(), awt_create_select_filter(), awt_create_select_filter_window_aw_cb(), ColumnStat::ColumnStat(), WeightedFilter::create_aliview(), WeightedFilter::create_weights(), and sina_start().

#define GA_AWAR_ROOT "sina/"

Definition at line 49 of file graph_aligner_gui.cxx.

#define GA_AWAR_TEMP "tmp/" GA_AWAR_ROOT

Definition at line 50 of file graph_aligner_gui.cxx.

#define GA_AWAR_CMD GA_AWAR_ROOT "cmd"

Definition at line 52 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), detect_sina_version(), new_sina_simple(), and sina_start().

#define GA_AWAR_TGT GA_AWAR_ROOT "target"

Definition at line 53 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_SAI GA_AWAR_ROOT "sai"

Definition at line 54 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_ALIGNMENT GA_AWAR_ROOT "alignment"

Definition at line 55 of file graph_aligner_gui.cxx.

#define GA_AWAR_PROTECTION GA_AWAR_ROOT "protection"

Definition at line 56 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_TURN_CHECK GA_AWAR_ROOT "turncheck"

Definition at line 57 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_REALIGN GA_AWAR_ROOT "realign"

Definition at line 58 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_MATCH_SCORE GA_AWAR_ROOT "match_score"

Definition at line 59 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_MISMATCH_SCORE GA_AWAR_ROOT "mismatch_score"

Definition at line 60 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_GAP_PEN GA_AWAR_ROOT "gap_pen"

Definition at line 61 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_GAP_EXT GA_AWAR_ROOT "gap_ext"

Definition at line 62 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_ADVANCED GA_AWAR_ROOT "advanced"

Definition at line 63 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and show_sina_window().

#define GA_AWAR_FS_MIN GA_AWAR_ROOT "fs_min"

Definition at line 64 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_FS_MAX GA_AWAR_ROOT "fs_max"

Definition at line 65 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_FS_MSC GA_AWAR_ROOT "fs_msc"

Definition at line 66 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_MIN_FULL GA_AWAR_ROOT "min_full"

Definition at line 67 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_FULL_MINLEN GA_AWAR_ROOT "full_minlen"

Definition at line 68 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_OVERHANG GA_AWAR_ROOT "overhang"

Definition at line 69 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_THREADS GA_AWAR_ROOT "threads"

Definition at line 70 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables().

#define GA_AWAR_QSIZE GA_AWAR_ROOT "qsize"

Definition at line 71 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables().

#define GA_AWAR_KMER_LEN GA_AWAR_ROOT "kmer_len"

Definition at line 72 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_KMER_MM GA_AWAR_ROOT "kmer_mm"

Definition at line 73 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_MIN_LEN GA_AWAR_ROOT "min_len"

Definition at line 74 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_WEIGHT GA_AWAR_ROOT "weight"

Definition at line 75 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_INSERT GA_AWAR_ROOT "insert"

Definition at line 76 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_LOWERCASE GA_AWAR_ROOT "lowercase"

Definition at line 77 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_AUTOFILTER GA_AWAR_ROOT "autofilter"

Definition at line 78 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_KMER_NOREL GA_AWAR_ROOT "kmer_norel"

Definition at line 79 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_KMER_NOFAST GA_AWAR_ROOT "kmer_nofast"

Definition at line 80 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_SHOW_DIST GA_AWAR_ROOT "show_dist"

Definition at line 81 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_SHOW_DIFF GA_AWAR_ROOT "show_diff"

Definition at line 82 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_COLOR GA_AWAR_ROOT "color"

Definition at line 83 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_GENE_START GA_AWAR_ROOT "gene_start"

Definition at line 84 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_GENE_END GA_AWAR_ROOT "gene_end"

Definition at line 85 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_FS_COVER_GENE GA_AWAR_ROOT "fs_cover_gene"

Definition at line 86 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_USED_RELS GA_AWAR_ROOT "write_used_rels"

Definition at line 87 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_CALC_IDENTITY GA_AWAR_ROOT "calc_idty"

Definition at line 88 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_NOWARN_START GA_AWAR_ROOT "nowarn_start"

Definition at line 89 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_REFDB_MODE GA_AWAR_ROOT "refdb_mode"

Definition at line 90 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), newRefDbSelected_cb(), refDbModeChanged_cb(), and show_sina_window().

#define GA_AWAR_REFDB GA_AWAR_ROOT "refdb"

Definition at line 91 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), newRefDbSelected_cb(), refDbModeChanged_cb(), and sina_start().

#define GA_AWAR_REFDB_SELECT GA_AWAR_TEMP "refdb"

Definition at line 92 of file graph_aligner_gui.cxx.

Referenced by accept_selected_ref_db(), create_sina_variables(), newRefDbSelected_cb(), and refDbModeChanged_cb().

Enumeration Type Documentation

enum RefDbMode

Enumerator
REF_EXPLICIT
REF_LAST_SAVE
REF_CURRENT

Definition at line 94 of file graph_aligner_gui.cxx.

enum SinaArbInterfaceVersion

Enumerator
ARB_5_99
ARB_7_1

Definition at line 194 of file graph_aligner_gui.cxx.

Function Documentation

static void refDbModeChanged_cb ( AW_root * root )

static

Definition at line 100 of file graph_aligner_gui.cxx.

References aw_message(), AW_root::awar(), AWAR_SAVED_DB_PATH, GA_AWAR_REFDB, GA_AWAR_REFDB_MODE, GA_AWAR_REFDB_SELECT, GB_is_readablefile(), AW_awar::read_char_pntr(), AW_awar::read_int(), REF_CURRENT, REF_EXPLICIT, and REF_LAST_SAVE.

Referenced by create_sina_variables().

static void newRefDbSelected_cb ( AW_root * root )

static

Definition at line 133 of file graph_aligner_gui.cxx.

References AW_root::awar(), GA_AWAR_REFDB, GA_AWAR_REFDB_MODE, GA_AWAR_REFDB_SELECT, GB_is_readablefile(), AW_awar::read_char_pntr(), REF_CURRENT, REF_EXPLICIT, AW_awar::write_int(), and AW_awar::write_string().

Referenced by create_sina_variables().

void create_sina_variables	(	AW_root *	root,
		AW_default	db1
	)

Definition at line 145 of file graph_aligner_gui.cxx.

References AW_awar::add_callback(), AW_root::awar_float(), AW_root::awar_int(), AWAR_PT_SERVER, AW_root::awar_string(), GA_AWAR_ADVANCED, GA_AWAR_AUTOFILTER, GA_AWAR_CALC_IDENTITY, GA_AWAR_CMD, GA_AWAR_COLOR, GA_AWAR_FS_COVER_GENE, GA_AWAR_FS_MAX, GA_AWAR_FS_MIN, GA_AWAR_FS_MSC, GA_AWAR_FULL_MINLEN, GA_AWAR_GAP_EXT, GA_AWAR_GAP_PEN, GA_AWAR_GENE_END, GA_AWAR_GENE_START, GA_AWAR_INSERT, GA_AWAR_KMER_LEN, GA_AWAR_KMER_MM, GA_AWAR_KMER_NOFAST, GA_AWAR_KMER_NOREL, GA_AWAR_LOWERCASE, GA_AWAR_MATCH_SCORE, GA_AWAR_MIN_FULL, GA_AWAR_MIN_LEN, GA_AWAR_MISMATCH_SCORE, GA_AWAR_NOWARN_START, GA_AWAR_OVERHANG, GA_AWAR_PROTECTION, GA_AWAR_QSIZE, GA_AWAR_REALIGN, GA_AWAR_REFDB, GA_AWAR_REFDB_MODE, GA_AWAR_REFDB_SELECT, GA_AWAR_SAI, GA_AWAR_SHOW_DIFF, GA_AWAR_SHOW_DIST, GA_AWAR_TGT, GA_AWAR_THREADS, GA_AWAR_TURN_CHECK, GA_AWAR_USED_RELS, GA_AWAR_WEIGHT, newRefDbSelected_cb(), REF_CURRENT, and refDbModeChanged_cb().

Referenced by ed4_create_all_awars().

static const char* get_interface_id ( SinaArbInterfaceVersion version )

static

Definition at line 214 of file graph_aligner_gui.cxx.

References sina_arb_interface_def::id, NO_INTERFACE, and sina_arb_interface_def::version.

Referenced by sina_cmd_changed_cb().

static GB_ERROR detect_sina_version ( AW_root * awr )

static

Definition at line 226 of file graph_aligner_gui.cxx.

References ARB_executable(), ARB_path_contains_unwanted_chars(), ARB_warn_about_unwanted_chars(), AW_root::awar(), EXIT_FAILURE, EXIT_SUCCESS, GA_AWAR_CMD, GB_getenv(), GBS_global_string(), GBS_global_string_copy(), sina_arb_interface_def::id, NO_INTERFACE, NULp, AW_awar::read_char_pntr(), string(), used_sina_interface, and sina_arb_interface_def::version.

Referenced by sina_cmd_changed_cb(), and sina_mask().

AW_active sina_mask ( AW_root * awr )

Definition at line 284 of file graph_aligner_gui.cxx.

References AWM_ALL, AWM_DISABLED, and detect_sina_version().

Referenced by ED4_root::generate_window().

const char* stream2static ( const std::stringstream & str )

inline

Definition at line 294 of file graph_aligner_gui.cxx.

References GBS_static_string().

Referenced by sina_start().

const char* empty_as_none ( const char * sainame )

inline

Definition at line 298 of file graph_aligner_gui.cxx.

Referenced by sina_start().

static void sina_start	(	AW_window *	window,
		const AlignDataAccess *	data_access
	)

static

Definition at line 304 of file graph_aligner_gui.cxx.

References AISC_MAGIC_NUMBER, AlignDataAccess::alignment_name, ARB_5_99, ARB_7_1, arb_look_and_start_server(), aw_message(), aw_message_if(), AW_root::awar(), AWAR_PT_SERVER, AWAR_SPECIES_NAME, GBS_strstruct::cat(), GBS_strstruct::cat_sQuoted(), empty_as_none(), ga_assert, GA_AWAR_AUTOFILTER, GA_AWAR_CALC_IDENTITY, GA_AWAR_CMD, GA_AWAR_COLOR, GA_AWAR_FS_COVER_GENE, GA_AWAR_FS_MAX, GA_AWAR_FS_MIN, GA_AWAR_FS_MSC, GA_AWAR_FULL_MINLEN, GA_AWAR_GAP_EXT, GA_AWAR_GAP_PEN, GA_AWAR_GENE_END, GA_AWAR_GENE_START, GA_AWAR_INSERT, GA_AWAR_KMER_LEN, GA_AWAR_KMER_MM, GA_AWAR_KMER_NOFAST, GA_AWAR_KMER_NOREL, GA_AWAR_LOWERCASE, GA_AWAR_MATCH_SCORE, GA_AWAR_MIN_FULL, GA_AWAR_MIN_LEN, GA_AWAR_MISMATCH_SCORE, GA_AWAR_NOWARN_START, GA_AWAR_OVERHANG, GA_AWAR_PROTECTION, GA_AWAR_REALIGN, GA_AWAR_REFDB, GA_AWAR_SAI, GA_AWAR_SHOW_DIFF, GA_AWAR_SHOW_DIST, GA_AWAR_TGT, GA_AWAR_TURN_CHECK, GA_AWAR_USED_RELS, GA_AWAR_WEIGHT, GB_await_error(), GB_begin_transaction(), GB_commit_transaction(), GB_find(), GB_fopen_tempfile(), gb_main, AlignDataAccess::gb_main, GB_read_char_pntr(), GB_remove_on_exit(), GB_unique_filename(), GB_xcmd(), GBS_global_string(), GBS_read_arb_tcp(), GBT_first_marked_species(), GBT_next_marked_species(), GBS_strstruct::get_data(), AlignDataAccess::get_first_selected_species, AlignDataAccess::get_next_selected_species, AW_window::get_root(), NULp, GBS_strstruct::putfloat(), GBS_strstruct::putlong(), AW_awar::read_char_pntr(), AW_awar::read_float(), AW_awar::read_int(), AW_awar::read_string(), SEARCH_CHILD, stream2static(), used_sina_interface, and XCMD_ASYNC_WAITKEY.

Referenced by new_sina_simple().

static char* filter_posvar_SAI_for_ali	(	GBDATA *	gb_extended,
		const char *	ali_name
	)

static

Definition at line 490 of file graph_aligner_gui.cxx.

References GB_FIND, GB_find(), GB_read_char_pntr(), GB_read_string(), GB_search(), GBS_global_string_copy(), NULp, result, SEARCH_CHILD, and type.

Referenced by new_sina_simple().

static void accept_selected_ref_db	(	AW_window *	aww,
		const char const	awar_filename
	)

static

Definition at line 546 of file graph_aligner_gui.cxx.

References AW_root::awar(), GA_AWAR_REFDB_SELECT, GB_is_readablefile(), AW_window::get_root(), AW_window::hide(), AW_awar::read_string(), and AW_awar::write_string().

Referenced by create_ref_db_selection_window().

static AW_window* create_ref_db_selection_window ( AW_root * aw_root )

static

Definition at line 559 of file graph_aligner_gui.cxx.

References accept_selected_ref_db(), awt_create_load_box(), and NULp.

Referenced by sina_select_ref_db().

static void sina_select_ref_db ( AW_window * aww )

static

Definition at line 569 of file graph_aligner_gui.cxx.

References AW_window::activate(), create_ref_db_selection_window(), and AW_window::get_root().

Referenced by new_sina_simple().

static void sina_cmd_changed_cb ( AW_root * awr )

static

Definition at line 583 of file graph_aligner_gui.cxx.

References aw_message(), detect_sina_version(), GBS_global_string(), get_interface_id(), gui_sina_interface, and used_sina_interface.

Referenced by new_sina_simple().

static AW_window_simple* new_sina_simple	(	AW_root *	root,
		const AlignDataAccess *	alignData,
		bool	adv
	)

static

Definition at line 598 of file graph_aligner_gui.cxx.

References AW_awar::add_callback(), AlignDataAccess::alignment_name, ARB_5_99, ARB_7_1, AW_POPDOWN(), AW_ROOT_DEFAULT, AW_root::awar(), AWAR_PT_SERVER, AWAR_SPECIES_NAME, awt_create_PTSERVER_selection_button(), awt_create_SAI_selection_button(), AWT_insert_config_manager(), filter_posvar_SAI_for_ali(), GA_AWAR_ADVANCED, GA_AWAR_AUTOFILTER, GA_AWAR_CALC_IDENTITY, GA_AWAR_CMD, GA_AWAR_COLOR, GA_AWAR_FS_COVER_GENE, GA_AWAR_FS_MAX, GA_AWAR_FS_MIN, GA_AWAR_FS_MSC, GA_AWAR_FULL_MINLEN, GA_AWAR_GAP_EXT, GA_AWAR_GAP_PEN, GA_AWAR_GENE_END, GA_AWAR_GENE_START, GA_AWAR_INSERT, GA_AWAR_KMER_LEN, GA_AWAR_KMER_MM, GA_AWAR_KMER_NOFAST, GA_AWAR_KMER_NOREL, GA_AWAR_LOWERCASE, GA_AWAR_MATCH_SCORE, GA_AWAR_MIN_FULL, GA_AWAR_MIN_LEN, GA_AWAR_MISMATCH_SCORE, GA_AWAR_NOWARN_START, GA_AWAR_OVERHANG, GA_AWAR_PROTECTION, GA_AWAR_REALIGN, GA_AWAR_REFDB, GA_AWAR_REFDB_MODE, GA_AWAR_SAI, GA_AWAR_SHOW_DIFF, GA_AWAR_SHOW_DIST, GA_AWAR_TGT, GA_AWAR_TURN_CHECK, GA_AWAR_USED_RELS, GA_AWAR_WEIGHT, AlignDataAccess::gb_main, gui_sina_interface, makeHelpCallback(), NO_INTERFACE, NULp, REF_CURRENT, REF_EXPLICIT, REF_LAST_SAVE, show_sina_window(), sina_cmd_changed_cb(), sina_select_ref_db(), sina_start(), and used_sina_interface.

Referenced by show_sina_window().

void show_sina_window	(	UNFIXED	,
		const AlignDataAccess *	alignData
	)

Definition at line 856 of file graph_aligner_gui.cxx.

References AW_root::awar(), GA_AWAR_ADVANCED, GA_AWAR_REFDB_MODE, new_sina_simple(), NULp, AW_awar::read_int(), REF_EXPLICIT, AW_root::SINGLETON, and AW_awar::touch().

Referenced by ED4_root::generate_window(), and new_sina_simple().

Variable Documentation

const SinaArbInterfaceVersion NO_INTERFACE = SinaArbInterfaceVersion(-1)

Definition at line 198 of file graph_aligner_gui.cxx.

Referenced by detect_sina_version(), get_interface_id(), and new_sina_simple().

sina_arb_interface_def supported_sina_versions[]

static

Initial value:

= {
    
    { ARB_7_1, "ARB7.1" },   
    { ARB_5_99, "ARB5.99" }, 
    { NO_INTERFACE, "<none>" }, 
}

Definition at line 205 of file graph_aligner_gui.cxx.

SinaArbInterfaceVersion used_sina_interface = NO_INTERFACE

static

Definition at line 224 of file graph_aligner_gui.cxx.

Referenced by detect_sina_version(), new_sina_simple(), sina_cmd_changed_cb(), and sina_start().

AWT_config_mapping_def sina_config_mapping[]

static

Definition at line 505 of file graph_aligner_gui.cxx.

SinaArbInterfaceVersion gui_sina_interface = NO_INTERFACE

static

Definition at line 581 of file graph_aligner_gui.cxx.

Referenced by new_sina_simple(), and sina_cmd_changed_cb().

Classes

Macros

Enumerations

Functions

Variables

Macro Definition Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation