#include "primer_design.hxx"
#include "PRD_Design.hxx"
#include "PRD_SequenceIterator.hxx"
#include <GEN.hxx>
#include <awt_sel_boxes.hxx>
#include <awt_config_manager.hxx>
#include <aw_awars.hxx>
#include <aw_msg.hxx>
#include <arb_progress.h>
#include <aw_root.hxx>
#include <aw_question.hxx>
#include <aw_select.hxx>
#include <arbdbt.h>
#include <adGene.h>
#include <string>
#include <cmath>

Include dependency graph for primer_design.cxx:

Functions
static double	get_estimated_memory (AW_root *root)

static void	primer_design_event_update_memory (AW_root *root)

static void	primer_design_event_check_primer_length (AW_root *root, bool max_changed)

void	create_primer_design_variables (AW_root *aw_root, AW_default aw_def, AW_default global)

static void	create_primer_design_result_window (AW_window *aww)

static void	primer_design_event_go (AW_window aww, GBDATA gb_main)

static void	primer_design_event_check_temp_factor (AW_window *aww)

static void	primer_design_event_check_gc_factor (AW_window *aww)

static void	primer_design_event_init (AW_window aww, GBDATA gb_main, bool from_gene)

AW_window *	create_primer_design_window (AW_root root, GBDATA gb_main)

Variables
static AW_window_simple *	pdrw = NULp

static AW_selection_list *	resultList = NULp

static AWT_config_mapping_def	primer_design_config_mapping []

Function Documentation

static double get_estimated_memory ( AW_root * root )

static

Definition at line 39 of file primer_design.cxx.

References AW_root::awar(), AWAR_PRIMER_DESIGN_LEFT_LENGTH, AWAR_PRIMER_DESIGN_LENGTH_MAX, AWAR_PRIMER_DESIGN_RIGHT_LENGTH, length, and AW_awar::read_int().

Referenced by primer_design_event_go(), and primer_design_event_update_memory().

static void primer_design_event_update_memory ( AW_root * root )

static

Definition at line 46 of file primer_design.cxx.

References AW_root::awar(), AWAR_PRIMER_DESIGN_APROX_MEM, GBS_global_string(), get_estimated_memory(), NULp, and AW_awar::write_string().

Referenced by create_primer_design_variables().

static void primer_design_event_check_primer_length	(	AW_root *	root,
		bool	max_changed
	)

static

Definition at line 68 of file primer_design.cxx.

References AW_root::awar(), AWAR_PRIMER_DESIGN_LENGTH_MAX, AWAR_PRIMER_DESIGN_LENGTH_MIN, prd_assert, AW_awar::read_int(), and AW_awar::write_int().

Referenced by create_primer_design_variables().

void create_primer_design_variables	(	AW_root *	aw_root,
		AW_default	aw_def,
		AW_default	global
	)

Definition at line 94 of file primer_design.cxx.

Referenced by nt_create_all_awars().

static void create_primer_design_result_window ( AW_window * aww )

static

Definition at line 119 of file primer_design.cxx.

References AW_POPDOWN(), AWAR_PRIMER_TARGET_STRING, awt_clear_selection_list_cb(), create_load_box_for_selection_lists(), create_print_box_for_selection_lists(), create_save_box_for_selection_lists(), AW_window::get_root(), StorableSelectionList::get_typedsellist(), makeHelpCallback(), and pdrw.

Referenced by primer_design_event_go().

static void primer_design_event_go	(	AW_window *	aww,
		GBDATA *	gb_main
	)

static

Definition at line 158 of file primer_design.cxx.

Referenced by create_primer_design_window().

static void primer_design_event_check_temp_factor ( AW_window * aww )

static

Definition at line 268 of file primer_design.cxx.

References AW_root::awar(), AWAR_PRIMER_DESIGN_GC_FACTOR, AWAR_PRIMER_DESIGN_TEMP_FACTOR, AW_window::get_root(), AW_awar::read_int(), and AW_awar::write_int().

Referenced by create_primer_design_window().

static void primer_design_event_check_gc_factor ( AW_window * aww )

static

Definition at line 278 of file primer_design.cxx.

References AW_root::awar(), AWAR_PRIMER_DESIGN_GC_FACTOR, AWAR_PRIMER_DESIGN_TEMP_FACTOR, AW_window::get_root(), AW_awar::read_int(), and AW_awar::write_int().

Referenced by create_primer_design_window().

static void primer_design_event_init	(	AW_window *	aww,
		GBDATA *	gb_main,
		bool	from_gene
	)

static

Definition at line 288 of file primer_design.cxx.

References aw_message(), AW_root::awar(), AWAR_GENE_NAME, AWAR_ORGANISM_NAME, AWAR_PRIMER_DESIGN_DIST_MAX, AWAR_PRIMER_DESIGN_DIST_MIN, AWAR_PRIMER_DESIGN_LEFT_LENGTH, AWAR_PRIMER_DESIGN_LEFT_POS, AWAR_PRIMER_DESIGN_RIGHT_LENGTH, AWAR_PRIMER_DESIGN_RIGHT_POS, AWAR_SPECIES_NAME, SequenceIterator::BACKWARD, SequenceIterator::EOS, error(), SequenceIterator::FORWARD, GB_await_error(), GB_export_errorf(), GB_read_string(), GBS_global_string(), GBT_find_sequence(), GBT_find_species(), GBT_get_default_alignment(), GBT_read_gene_sequence_and_length(), GEN_find_gene(), GEN_free_position(), GEN_is_genome_db(), GEN_read_position(), AW_window::get_root(), SequenceIterator::IGNORE, GEN_position::joinable, length, SequenceIterator::nextBase(), NULp, SequenceIterator::pos, prd_assert, AW_awar::read_int(), AW_awar::read_string(), SequenceIterator::restart(), GEN_position::start_pos, ta, AW_awar::write_int(), and AW_awar::write_string().

Referenced by create_primer_design_window().

AW_window* create_primer_design_window	(	AW_root *	root,
		GBDATA *	gb_main
	)

Definition at line 462 of file primer_design.cxx.

Referenced by popup_new_main_window().

Variable Documentation

AW_window_simple* pdrw = NULp

static

Definition at line 36 of file primer_design.cxx.

Referenced by create_primer_design_result_window(), and primer_design_event_go().

AW_selection_list* resultList = NULp

static

Definition at line 37 of file primer_design.cxx.

AWT_config_mapping_def primer_design_config_mapping[]

static

Initial value:

= {
    { AWAR_PRIMER_DESIGN_LEFT_POS,               "lpos" },
    { AWAR_PRIMER_DESIGN_LEFT_LENGTH,            "llen" },
    { AWAR_PRIMER_DESIGN_RIGHT_POS,              "rpos" },
    { AWAR_PRIMER_DESIGN_RIGHT_LENGTH,           "rlen" },
    { AWAR_PRIMER_DESIGN_LENGTH_MIN,             "lenmin" },
    { AWAR_PRIMER_DESIGN_LENGTH_MAX,             "lenmax" },
    { AWAR_PRIMER_DESIGN_DIST_MIN,               "distmin" },
    { AWAR_PRIMER_DESIGN_DIST_MAX,               "distmax" },
    { AWAR_PRIMER_DESIGN_GCRATIO_MIN,            "gcmin" },
    { AWAR_PRIMER_DESIGN_GCRATIO_MAX,            "gcmax" },
    { AWAR_PRIMER_DESIGN_TEMPERATURE_MIN,        "tempmin" },
    { AWAR_PRIMER_DESIGN_TEMPERATURE_MAX,        "tempmax" },
    { AWAR_PRIMER_DESIGN_ALLOWED_MATCH_MIN_DIST, "minmatchdist" },
    { AWAR_PRIMER_DESIGN_EXPAND_IUPAC,           "iupac" },
    { AWAR_PRIMER_DESIGN_MAX_PAIRS,              "maxpairs" },
    { AWAR_PRIMER_DESIGN_GC_FACTOR,              "gcfactor" },
    { AWAR_PRIMER_DESIGN_TEMP_FACTOR,            "temp_factor" },
    { NULp, NULp }
}

Definition at line 441 of file primer_design.cxx.

Functions

Variables

Function Documentation

Variable Documentation