ARB
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#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>
Go to the source code of this file.
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 [] |
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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().
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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().
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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.
References AW_awar::add_callback(), AW_root::awar_int(), AWAR_PRIMER_DESIGN_ALLOWED_MATCH_MIN_DIST, AWAR_PRIMER_DESIGN_APROX_MEM, AWAR_PRIMER_DESIGN_DIST_MAX, AWAR_PRIMER_DESIGN_DIST_MIN, AWAR_PRIMER_DESIGN_EXPAND_IUPAC, AWAR_PRIMER_DESIGN_GC_FACTOR, AWAR_PRIMER_DESIGN_GCRATIO_MAX, AWAR_PRIMER_DESIGN_GCRATIO_MIN, AWAR_PRIMER_DESIGN_LEFT_LENGTH, AWAR_PRIMER_DESIGN_LEFT_POS, AWAR_PRIMER_DESIGN_LENGTH_MAX, AWAR_PRIMER_DESIGN_LENGTH_MIN, AWAR_PRIMER_DESIGN_MAX_PAIRS, AWAR_PRIMER_DESIGN_RIGHT_LENGTH, AWAR_PRIMER_DESIGN_RIGHT_POS, AWAR_PRIMER_DESIGN_TEMP_FACTOR, AWAR_PRIMER_DESIGN_TEMPERATURE_MAX, AWAR_PRIMER_DESIGN_TEMPERATURE_MIN, AWAR_PRIMER_TARGET_STRING, AW_root::awar_string(), NULp, primer_design_event_check_primer_length(), and primer_design_event_update_memory().
Referenced by nt_create_all_awars().
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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().
Definition at line 158 of file primer_design.cxx.
References aw_message(), aw_question(), AW_root::awar(), AWAR_PRIMER_DESIGN_ALLOWED_MATCH_MIN_DIST, AWAR_PRIMER_DESIGN_DIST_MAX, AWAR_PRIMER_DESIGN_DIST_MIN, AWAR_PRIMER_DESIGN_EXPAND_IUPAC, AWAR_PRIMER_DESIGN_GC_FACTOR, AWAR_PRIMER_DESIGN_GCRATIO_MAX, AWAR_PRIMER_DESIGN_GCRATIO_MIN, AWAR_PRIMER_DESIGN_LEFT_LENGTH, AWAR_PRIMER_DESIGN_LEFT_POS, AWAR_PRIMER_DESIGN_LENGTH_MAX, AWAR_PRIMER_DESIGN_LENGTH_MIN, AWAR_PRIMER_DESIGN_MAX_PAIRS, AWAR_PRIMER_DESIGN_RIGHT_LENGTH, AWAR_PRIMER_DESIGN_RIGHT_POS, AWAR_PRIMER_DESIGN_TEMP_FACTOR, AWAR_PRIMER_DESIGN_TEMPERATURE_MAX, AWAR_PRIMER_DESIGN_TEMPERATURE_MIN, AWAR_SPECIES_NAME, AW_selection_list::clear(), create_primer_design_result_window(), error(), GB_await_error(), GB_get_usable_memory(), GB_read_count(), GB_read_string(), GBS_global_string(), GBS_static_string(), GBT_find_sequence(), GBT_find_species(), GBT_get_default_alignment(), PrimerDesign::get_error(), get_estimated_memory(), PrimerDesign::get_max_primer_length(), PrimerDesign::get_max_primer_pos(), PrimerDesign::get_result(), AW_window::get_root(), AW_selection_list::insert(), AW_selection_list::insert_default(), length, NULp, PD, pdrw, prd_assert, AW_awar::read_int(), AW_awar::read_string(), result, PrimerDesign::run(), s, ta, and AW_selection_list::update().
Referenced by create_primer_design_window().
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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().
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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().
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().
Definition at line 462 of file primer_design.cxx.
References aw_message(), AW_POPDOWN(), AW_ROOT_DEFAULT, AW_root::awar(), AWAR_PRIMER_DESIGN_ALLOWED_MATCH_MIN_DIST, AWAR_PRIMER_DESIGN_APROX_MEM, AWAR_PRIMER_DESIGN_DIST_MAX, AWAR_PRIMER_DESIGN_DIST_MIN, AWAR_PRIMER_DESIGN_EXPAND_IUPAC, AWAR_PRIMER_DESIGN_GC_FACTOR, AWAR_PRIMER_DESIGN_GCRATIO_MAX, AWAR_PRIMER_DESIGN_GCRATIO_MIN, AWAR_PRIMER_DESIGN_LEFT_LENGTH, AWAR_PRIMER_DESIGN_LEFT_POS, AWAR_PRIMER_DESIGN_LENGTH_MAX, AWAR_PRIMER_DESIGN_LENGTH_MIN, AWAR_PRIMER_DESIGN_MAX_PAIRS, AWAR_PRIMER_DESIGN_RIGHT_LENGTH, AWAR_PRIMER_DESIGN_RIGHT_POS, AWAR_PRIMER_DESIGN_TEMP_FACTOR, AWAR_PRIMER_DESIGN_TEMPERATURE_MAX, AWAR_PRIMER_DESIGN_TEMPERATURE_MIN, AWAR_SPECIES_NAME, AWT_insert_config_manager(), GBT_find_species(), GEN_is_genome_db(), makeHelpCallback(), NULp, primer_design_event_check_gc_factor(), primer_design_event_check_temp_factor(), primer_design_event_go(), primer_design_event_init(), AW_awar::read_string(), and ta.
Referenced by popup_new_main_window().
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Definition at line 36 of file primer_design.cxx.
Referenced by create_primer_design_result_window(), and primer_design_event_go().
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Definition at line 37 of file primer_design.cxx.
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Definition at line 441 of file primer_design.cxx.