#include "SaiProbeVisualization.hxx"
#include "probe_match_parser.hxx"
#include <nds.h>
#include <items.h>
#include <awt_sel_boxes.hxx>
#include <awt_config_manager.hxx>
#include <aw_awars.hxx>
#include <aw_root.hxx>
#include <aw_preset.hxx>
#include <aw_msg.hxx>
#include <arbdbt.h>
#include <iostream>
#include <arb_global_defs.h>
#include <item_sel_list.h>
#include <gb_aci.h>

Include dependency graph for SaiProbeVisualization.cxx:

Macros
#define	PROBE_PREFIX_LENGTH 9

#define	PROBE_SUFFIX_LENGTH 9

#define	BUFSIZE 100

Functions
static const char *	getAwarName (int awarNo)

static void	colorDefChanged_callback (AW_root *awr, int awarNo)

static void	refreshCanvas (AW_root , AWT_canvas scr)

static void	createSaiProbeAwars (AW_root *aw_root)

static void	addCallBacks (AW_root awr, AWT_canvas scr)

static const char *	translateSAItoColors (AW_root awr, GBDATA gb_main, int start, int end, int speciesNo)

static int	calculateEndPosition (GBDATA *gb_main, int startPos, int speciesNo, int mode, int probeLen, GB_ERROR &error)

static void	paintBackgroundAndSAI (AW_device device, size_t probeRegionLen, AW_pos pbRgX1, AW_pos pbY, AW_pos pbMaxWidth, AW_pos pbMaxHeight, const char saiCols, int dispSai)

static void	paintProbeInfo (AW_device device, const char probe_info, AW_pos x, AW_pos y, AW_pos xoff, AW_pos yoff, AW_pos maxDescent, int textCOLOR)

static char *	GetDisplayInfo (AW_root root, GBDATA gb_main, const char speciesName, size_t displayWidth, const char default_tree_name)

void	transferProbeData (saiProbeData *spd)

static void	setup_saiColorDefs_config (AWT_config_definition &cdef)

static AW_window *	create_colorTranslationTable_window (AW_root *aw_root)

static AW_window *	createDisplayField_window (AW_root aw_root, GBDATA gb_main)

static AW_window *	createSaiColorWindow (AW_root aw_root, AW_gc_manager gc_manager)

AW_window *	createSaiProbeMatchWindow (AW_root awr, GBDATA gb_main)

Variables
static saiProbeData *	g_pbdata = NULp

static char *	saiValues = NULp

static bool	in_colorDefChanged_callback = false

static AWT_predefined_config	predefined_saiColorDefinitions []

Macro Definition Documentation

#define PROBE_PREFIX_LENGTH 9

Definition at line 32 of file SaiProbeVisualization.cxx.

Referenced by SAI_graphic::paint().

#define PROBE_SUFFIX_LENGTH 9

Definition at line 33 of file SaiProbeVisualization.cxx.

Referenced by calculateEndPosition().

#define BUFSIZE 100

Definition at line 40 of file SaiProbeVisualization.cxx.

Referenced by getAwarName().

Function Documentation

static const char* getAwarName ( int awarNo )

static

Definition at line 41 of file SaiProbeVisualization.cxx.

References AWAR_SPV_SAI_COLOR, and BUFSIZE.

Referenced by colorDefChanged_callback(), create_colorTranslationTable_window(), createSaiProbeAwars(), setup_saiColorDefs_config(), and translateSAItoColors().

static void colorDefChanged_callback	(	AW_root *	awr,
		int	awarNo
	)

static

Definition at line 101 of file SaiProbeVisualization.cxx.

References AW_root::awar(), AWAR_SPV_DISP_SAI, AW_root::awar_string(), getAwarName(), in_colorDefChanged_callback, AW_awar::read_string(), s, AW_awar::touch(), and AW_awar::write_string().

Referenced by createSaiProbeAwars().

static void refreshCanvas	(	AW_root *	,
		AWT_canvas *	scr
	)

static

Definition at line 141 of file SaiProbeVisualization.cxx.

References AWT_canvas::request_refresh().

Referenced by addCallBacks().

static void createSaiProbeAwars ( AW_root * aw_root )

static

Definition at line 147 of file SaiProbeVisualization.cxx.

References AW_awar::add_callback(), AW_ROOT_DEFAULT, AW_root::awar_int(), AWAR_SPV_DISP_SAI, AW_root::awar_string(), colorDefChanged_callback(), and getAwarName().

Referenced by createSaiProbeMatchWindow().

static void addCallBacks	(	AW_root *	awr,
		AWT_canvas *	scr
	)

static

Definition at line 157 of file SaiProbeVisualization.cxx.

References AW_awar::add_callback(), AW_root::awar(), AWAR_SPV_ACI_COMMAND, AWAR_SPV_DB_FIELD_NAME, AWAR_SPV_DB_FIELD_WIDTH, AWAR_SPV_DISP_SAI, AWAR_SPV_SAI_2_PROBE, AWAR_SPV_SELECTED_PROBE, and refreshCanvas().

Referenced by createSaiProbeMatchWindow().

static const char* translateSAItoColors	(	AW_root *	awr,
		GBDATA *	gb_main,
		int	start,
		int	end,
		int	speciesNo
	)

static

Definition at line 169 of file SaiProbeVisualization.cxx.

References alignment_name, ARB_alloc(), aw_message_if(), AW_root::awar(), AWAR_SPV_SAI_2_PROBE, error(), GB_await_error(), GB_end_transaction(), GB_entry(), GB_push_transaction(), GB_read_as_string(), GB_read_char_pntr(), GBT_find_SAI(), GBT_find_sequence(), GBT_find_species(), GBT_get_default_alignment(), getAwarName(), GAP::is_std_gap(), NULp, saiProbeData::probeSpecies, AW_awar::read_string(), SAI_CLR_COUNT, and start.

Referenced by SAI_graphic::paint().

static int calculateEndPosition	(	GBDATA *	gb_main,
		int	startPos,
		int	speciesNo,
		int	mode,
		int	probeLen,
		GB_ERROR &	error
	)

static

Definition at line 277 of file SaiProbeVisualization.cxx.

References alignment_name, GB_await_error(), GB_end_transaction(), GB_incur_error(), GB_push_transaction(), GB_read_char_pntr(), GBS_global_string(), GBT_find_sequence(), GBT_find_species(), GBT_get_default_alignment(), GAP::is_std_gap(), PROBE, PROBE_PREFIX, PROBE_SUFFIX, PROBE_SUFFIX_LENGTH, and saiProbeData::probeSpecies.

Referenced by SAI_graphic::paint().

static void paintBackgroundAndSAI	(	AW_device *	device,
		size_t	probeRegionLen,
		AW_pos	pbRgX1,
		AW_pos	pbY,
		AW_pos	pbMaxWidth,
		AW_pos	pbMaxHeight,
		const char *	saiCols,
		int	dispSai
	)

static

Definition at line 346 of file SaiProbeVisualization.cxx.

References AW_SCREEN, AW_device::box(), SAI_GC_0, SAI_GC_FOREGROUND, AW::FillStyle::SOLID, and AW_device::text().

Referenced by SAI_graphic::paint().

static void paintProbeInfo	(	AW_device *	device,
		const char *	probe_info,
		AW_pos	x,
		AW_pos	y,
		AW_pos	xoff,
		AW_pos	yoff,
		AW_pos	maxDescent,
		int	textCOLOR
	)

static

Definition at line 365 of file SaiProbeVisualization.cxx.

References AW_CLICK, AW_SCREEN, AW_device::line(), SAI_GC_PROBE, and AW_device::text().

Referenced by SAI_graphic::paint().

static char* GetDisplayInfo	(	AW_root *	root,
		GBDATA *	gb_main,
		const char *	speciesName,
		size_t	displayWidth,
		const char *	default_tree_name
	)

static

Definition at line 383 of file SaiProbeVisualization.cxx.

References ARB_strdup(), AWAR_SPV_ACI_COMMAND, AWAR_SPV_DB_FIELD_NAME, AW_root::awar_string(), error(), GB_await_error(), GB_command_interpreter_in_env(), GB_FIND, GB_have_error(), GB_read_as_string(), GB_search(), GBS_global_string(), GBT_expect_species(), NO_FIELD_SELECTED, NULp, AW_awar::read_char_pntr(), AW_awar::read_string(), sai_assert, and ta.

Referenced by SAI_graphic::paint().

void transferProbeData ( saiProbeData * spd )

Definition at line 622 of file SaiProbeVisualization.cxx.

Referenced by popupSaiProbeMatchWindow(), and probe_match_event().

static void setup_saiColorDefs_config ( AWT_config_definition & cdef )

static

Definition at line 659 of file SaiProbeVisualization.cxx.

References AWT_config_definition::add(), and getAwarName().

Referenced by create_colorTranslationTable_window().

static AW_window* create_colorTranslationTable_window ( AW_root * aw_root )

static

Definition at line 666 of file SaiProbeVisualization.cxx.

References AW_POPDOWN(), AW_ROOT_DEFAULT, AWAR_SPV_DISP_SAI, AWT_insert_config_manager(), getAwarName(), makeHelpCallback(), NULp, SAI_CLR_COUNT, and setup_saiColorDefs_config().

Referenced by createSaiProbeMatchWindow().

static AW_window* createDisplayField_window	(	AW_root *	aw_root,
		GBDATA *	gb_main
	)

static

Definition at line 703 of file SaiProbeVisualization.cxx.

References AW_POPDOWN(), AWAR_SPV_ACI_COMMAND, AWAR_SPV_DB_FIELD_NAME, AWAR_SPV_DB_FIELD_WIDTH, create_itemfield_selection_button(), FIELD_FILTER_NDS, makeHelpCallback(), NDS_popup_select_srtaci_window(), NULp, and SPECIES_get_selector().

Referenced by createSaiProbeMatchWindow().

static AW_window* createSaiColorWindow	(	AW_root *	aw_root,
		AW_gc_manager *	gc_manager
	)

static

Definition at line 739 of file SaiProbeVisualization.cxx.

References AW_create_gc_window_named().

Referenced by createSaiProbeMatchWindow().

AW_window* createSaiProbeMatchWindow	(	AW_root *	awr,
		GBDATA *	gb_main
	)

Variable Documentation

saiProbeData* g_pbdata = NULp

static

Definition at line 35 of file SaiProbeVisualization.cxx.

char* saiValues = NULp

static

Definition at line 36 of file SaiProbeVisualization.cxx.

bool in_colorDefChanged_callback = false

static

Definition at line 38 of file SaiProbeVisualization.cxx.

Referenced by colorDefChanged_callback().

AWT_predefined_config predefined_saiColorDefinitions[]

static

Initial value:

= {
    {
        "*binary",
        "Use with SAIs containing binary columns\ne.g. \'markerline\'",
        "0='-.0=';1='';2='';3='';4='';5='';6='';7='';8='';9='1x'"
    },
    {
        "*column_weights_09",
        "Use with SAIs containing column weights (0-9)\ne.g. MAX_FREQUENCY",
        "0='0';1='1';2='2';3='3';4='4';5='5';6='6';7='7';8='8';9='9'"
    },
    {
        "*column_weights_0Z_posvar",
        "Use with SAIs containing column weights (0-9,A-Z)\ne.g. POS_VAR_BY_PARSIMONY",
        "0='012';1='345';2='678';3='9AB';4='CDE';5='FGH';6='IJK';7='LMN';8='OPQ';9='RST'"
    },
    {
        "*sequence_data",
        "Use with SAIs containing nucleotide sequence data",
        "0='-.';1='';2='';3='A';4='';5='C';6='';7='G';8='';9='TU'"
    },
    {
        "*helix",
        "Use with SAI:HELIX",
        "0='';1='';2='';3='<[';4='';5='';6='>]';7='';8='';9=''"
    },
    { NULp, NULp, NULp }
}

Definition at line 630 of file SaiProbeVisualization.cxx.

Macros

Functions

Variables

Macro Definition Documentation

Function Documentation

Variable Documentation