MP_noclass.cxx File Reference

#include "MultiProbe.hxx"
#include "mp_proto.hxx"
#include "MP_externs.hxx"
#include "MP_probe.hxx"
#include <aw_select.hxx>
#include <aw_msg.hxx>
#include <arb_progress.h>
#include <aw_root.hxx>
#include <TreeCallbacks.hxx>
#include <client.h>
#include <AP_TreeColors.hxx>
#include <ctime>

Include dependency graph for MP_noclass.cxx:

Go to the source code of this file.

Functions
int	get_random (int min, int max)
long	k_chosenFrom_n (int k, int n)
static void	refresh_without_dbsync (AWT_canvas *scr)
void	MP_close_main (AW_window *aww)
static char *	MP_get_probes (const char *str)
void	MP_gen_quality (AW_root *awr)
void	MP_modify_selected (AW_root *awr)
void	MP_gen_singleprobe (AW_root *awr)
static void	init_system3_tab ()
void	MP_popup_result_window (AW_window *)
bool	MP_aborted (int gen_cnt, double avg_fit, double min_fit, double max_fit, arb_progress &progress)
void	MP_compute (AW_window *, GBDATA *gb_main)
static bool	MP_is_probe (char *seq)
void	MP_new_sequence (AW_window *aww)
void	MP_cache_sonden (AW_window *)
void	MP_cache_sonden2 (AW_root *)
void	MP_show_probes_in_tree_move (AW_window *aww, bool backward, AW_selection_list *resultProbesList)
void	MP_show_probes_in_tree (AW_window *)
void	MP_mark_probes_in_tree (AW_window *aww)
void	MP_Comment (AW_window *, const char *new_comment)
void	MP_selected_chosen (AW_root *aw_root)
void	MP_group_all_except_marked (AW_window *)
void	MP_normal_colors_in_tree (AW_window *)
void	MP_delete_selected (UNFIXED, AW_selection_list *sellist)
char *	MP_get_comment (int which, const char *str)
void	MP_result_combination_chosen (AW_root *aw_root)
int	MP_init_local_com_struct (mp_gl_struct &mp_pd_gl)

Variables
int **	system3_tab = NULp
static int	system3_tab_size = 0
unsigned char **	hamming_tab = NULp
bool	new_pt_server = true

Function Documentation

int get_random	(	int	min,
		int	max
	)

Definition at line 43 of file MP_noclass.cxx.

References GB_random(), min, and mp_assert.

Referenced by Generation::create_next_generation(), probe_combi_statistic::crossover_Probes(), Generation::init_valuation(), probe_combi_statistic::mutate_Probe(), and probe_combi_statistic::ok_for_next_gen().

long k_chosenFrom_n	(	int	k,
		int	n
	)

Definition at line 34 of file MP_noclass.cxx.

Referenced by ProbeValuation::evolution(), and ProbeValuation::ProbeValuation().

static void refresh_without_dbsync ( AWT_canvas *  scr )

static

Definition at line 48 of file MP_noclass.cxx.

References AWT_graphic::exports, AWT_canvas::gb_main, AWT_graphic_exports::get_modifying_flag_ref(), AWT_canvas::gfx, AWT_canvas::instant_refresh(), and AWT_graphic::notify_synchronized().

Referenced by MP_close_main(), MP_mark_probes_in_tree(), MP_normal_colors_in_tree(), and MP_show_probes_in_tree().

void MP_close_main

(

AW_window *

aww

)

Definition at line 54 of file MP_noclass.cxx.

References AW_POPDOWN(), AWT_TREE, AWT_canvas::gb_main, MP_Main::get_canvas(), MP_Main::get_mp_window(), MP_Main::get_p_eval(), MP_Window::get_result_window(), MP_Main::get_stc(), mp_main, new_pt_server, NULp, refresh_without_dbsync(), MP_Main::set_p_eval(), MP_Main::set_stc(), ta, and AP_tree::uncolorize().

Referenced by MP_Window::MP_Window().

static char* MP_get_probes ( const char *  str )

static

Definition at line 75 of file MP_noclass.cxx.

References ARB_strdup(), and result.

Referenced by MP_Comment(), MP_compute(), MP_gen_quality(), MP_gen_singleprobe(), MP_is_probe(), MP_mark_probes_in_tree(), MP_modify_selected(), MP_selected_chosen(), and MP_show_probes_in_tree().

void MP_gen_quality

(

AW_root *

awr

)

Definition at line 88 of file MP_noclass.cxx.

References AW_root::awar(), AW_selection_list::delete_value(), AW_selection_list::insert(), AW_selection_list::insert_default(), MP_AWAR_SELECTEDPROBES, MP_get_comment(), MP_get_probes(), mp_gl_awars, awar_vars::probe_quality, AW_awar::read_string(), selected_list, awar_vars::singlemismatches, AW_selection_list::sort(), AW_selection_list::update(), and AW_awar::write_string().

Referenced by MP_Main::~MP_Main().

void MP_modify_selected

(

AW_root *

awr

)

Definition at line 123 of file MP_noclass.cxx.

References ARB_strdup(), AW_root::awar(), AW_selection_list::clear(), List< Type >::get_first(), AW_scalar::get_string(), AW_selection_list_iterator::get_value(), AW_selection_list::insert(), List< Type >::insert_as_last(), AW_selection_list::insert_default(), MP_AWAR_SELECTEDPROBES, MP_get_comment(), MP_get_probes(), mp_gl_awars, awar_vars::no_of_mismatches, remembered_mismatches, List< Type >::remove_first(), selected_list, AW_selection_list::sort(), AW_selection_list::update(), and AW_awar::write_string().

Referenced by MP_Main::~MP_Main().

void MP_gen_singleprobe

(

AW_root *

awr

)

Definition at line 173 of file MP_noclass.cxx.

References AW_root::awar(), AW_selection_list::delete_value(), awar_vars::ecolipos, AW_selection_list::insert(), AW_selection_list::insert_default(), MP_AWAR_SELECTEDPROBES, MP_get_probes(), mp_gl_awars, awar_vars::probe_quality, AW_awar::read_string(), selected_list, awar_vars::singlemismatches, AW_selection_list::sort(), AW_selection_list::update(), and AW_awar::write_string().

Referenced by MP_Main::~MP_Main().

static void init_system3_tab ( )

static

Definition at line 195 of file MP_noclass.cxx.

References hamming_tab, mp_gl_awars, awar_vars::no_of_probes, system3_tab, and system3_tab_size.

Referenced by MP_compute(), and MP_popup_result_window().

void MP_popup_result_window

(

AW_window *

)

Definition at line 273 of file MP_noclass.cxx.

References MP_Window::create_result_window(), MP_Main::get_aw_root(), MP_Main::get_mp_window(), init_system3_tab(), and mp_main.

Referenced by MP_Window::MP_Window().

bool MP_aborted	(	int	gen_cnt,
		double	avg_fit,
		double	min_fit,
		double	max_fit,
		arb_progress &	progress
	)

Definition at line 278 of file MP_noclass.cxx.

References arb_progress::aborted(), and arb_progress::subtitle().

Referenced by Generation::calcFitness(), and ProbeValuation::evolution().

void MP_compute	(	AW_window *	,
		GBDATA *	gb_main
	)

Definition at line 291 of file MP_noclass.cxx.

References AW_window::activate(), aw_message(), AW_selection_list::clear(), MP_Window::create_result_window(), MP_Main::destroy_probe_eval(), MP_Main::get_aw_root(), MP_Main::get_mp_window(), MP_Main::get_stc(), AW_scalar::get_string(), AW_selection_list_iterator::get_value(), init_system3_tab(), ProbeValuation::init_valuation(), AW_selection_list::insert_default(), MP_get_comment(), MP_get_probes(), mp_gl_awars, mp_main, MP_Main::new_probe_eval(), new_pt_server, awar_vars::no_of_probes, NULp, pt_server_different, result_probes_list, selected_list, MO_Liste::set_gb_main(), MP_Main::set_stc(), AW_selection_list::size(), and AW_selection_list::update().

Referenced by MP_Window::MP_Window().

static bool MP_is_probe ( char *  seq )

static

Definition at line 360 of file MP_noclass.cxx.

References MP_get_probes(), MP_probe_tab, result, and s.

Referenced by MP_new_sequence().

void MP_new_sequence

(

AW_window *

aww

)

Definition at line 381 of file MP_noclass.cxx.

References aw_message(), AW_root::awar(), GBS_global_string(), GBS_global_string_copy(), AW_window::get_root(), AW_selection_list::insert(), MP_AWAR_SELECTEDPROBES, MP_AWAR_SEQIN, mp_gl_awars, MP_is_probe(), awar_vars::probe_quality, AW_awar::read_string(), selected_list, seq, awar_vars::singlemismatches, AW_selection_list::sort(), AW_selection_list::update(), and AW_awar::write_string().

Referenced by MP_Window::MP_Window().

void MP_cache_sonden

(

AW_window *

)

Definition at line 401 of file MP_noclass.cxx.

References new_pt_server.

Referenced by MP_Window::MP_Window().

void MP_cache_sonden2

(

AW_root *

)

Definition at line 402 of file MP_noclass.cxx.

References new_pt_server.

Referenced by MP_Window::MP_Window().

void MP_show_probes_in_tree_move	(	AW_window *	aww,
		bool	backward,
		AW_selection_list *	resultProbesList
	)

Definition at line 404 of file MP_noclass.cxx.

References AW_selection_list::move_selection(), and MP_show_probes_in_tree().

Referenced by MP_Window::create_result_window().

void MP_show_probes_in_tree

(

AW_window *

)

Definition at line 409 of file MP_noclass.cxx.

References ARB_strdup(), ST_Container::Auswahlliste, aw_message(), AW_root::awar(), AWT_TREE, ST_Container::Bakterienliste, AWT_canvas::gb_main, Sondentopf::gen_color_hash(), MP_Main::get_aw_root(), MP_Main::get_canvas(), Sondentopf::get_color_hash(), MP_Main::get_stc(), MAXMISMATCHES, MAXPROBECOMBIS, MAXSONDENHASHSIZE, MP_AWAR_RESULTPROBES, MP_get_comment(), MP_get_probes(), mp_gl_awars, mp_main, new_pt_server, awar_vars::no_of_probes, NULp, awar_vars::outside_mismatches_difference, pt_server_different, Sondentopf::put_Sonde(), AW_awar::read_string(), refresh_without_dbsync(), MP_Main::set_stc(), ST_Container::sondentopf, and ta.

Referenced by MP_Window::create_result_window(), and MP_show_probes_in_tree_move().

void MP_mark_probes_in_tree

(

AW_window *

aww

)

Definition at line 507 of file MP_noclass.cxx.

References ARB_strdup(), ST_Container::Auswahlliste, aw_message(), AW_root::awar(), AWT_GC_BLACK, ST_Container::Bakterienliste, AWT_canvas::gb_main, GB_pop_transaction(), GB_push_transaction(), GB_write_flag(), GBS_read_hash(), GBT_first_species(), GBT_get_name_or_description(), GBT_next_species(), Sondentopf::gen_color_hash(), MP_Main::get_aw_root(), MP_Main::get_canvas(), Sondentopf::get_color_hash(), MP_Main::get_stc(), MAXMISMATCHES, MAXPROBECOMBIS, MAXSONDENHASHSIZE, MP_AWAR_RESULTPROBES, MP_get_comment(), MP_get_probes(), mp_gl_awars, mp_main, MP_normal_colors_in_tree(), new_pt_server, awar_vars::no_of_probes, NULp, awar_vars::outside_mismatches_difference, pt_server_different, Sondentopf::put_Sonde(), AW_awar::read_string(), refresh_without_dbsync(), MP_Main::set_stc(), ST_Container::sondentopf, and ta.

Referenced by MP_Window::create_result_window().

void MP_Comment	(	AW_window *	,
		const char *	new_comment
	)

Definition at line 615 of file MP_noclass.cxx.

References AW_root::awar(), AW_selection_list::delete_value(), GBS_global_string_copy(), MP_Main::get_aw_root(), AW_selection_list::insert(), AW_selection_list::move_selection(), MP_AWAR_AUTOADVANCE, MP_AWAR_RESULTPROBES, MP_AWAR_RESULTPROBESCOMMENT, MP_get_comment(), MP_get_probes(), mp_main, NULp, AW_awar::read_int(), AW_awar::read_string(), result_probes_list, SEPARATOR, AW_selection_list::update(), and AW_awar::write_string().

Referenced by MP_Window::create_result_window().

void MP_selected_chosen

(

AW_root *

aw_root

)

Definition at line 665 of file MP_noclass.cxx.

References aw_message(), AW_root::awar(), AW_root::awar_string(), MP_AWAR_ECOLIPOS, MP_AWAR_QUALITY, MP_AWAR_SELECTEDPROBES, MP_AWAR_SEQIN, MP_AWAR_SINGLEMISMATCHES, MP_get_comment(), MP_get_probes(), AW_awar::read_char_pntr(), AW_awar::write_int(), and AW_awar::write_string().

Referenced by MP_Window::MP_Window().

void MP_group_all_except_marked

(

AW_window *

)

Definition at line 696 of file MP_noclass.cxx.

References MP_Main::get_canvas(), mp_main, NT_expand_marked_cb(), and NULp.

Referenced by MP_Window::create_result_window().

void MP_normal_colors_in_tree

(

AW_window *

)

Definition at line 701 of file MP_noclass.cxx.

References AWT_TREE, AWT_canvas::gb_main, MP_Main::get_canvas(), AWT_graphic_tree::get_root_node(), mp_main, refresh_without_dbsync(), ta, and AP_tree::uncolorize().

Referenced by MP_Window::create_result_window(), and MP_mark_probes_in_tree().

void MP_delete_selected	(	UNFIXED	,
		AW_selection_list *	sellist
	)

Definition at line 715 of file MP_noclass.cxx.

References AW_selection_list::default_is_selected(), AW_selection_list::delete_element_at(), AW_selection_list::get_index_of_selected(), AW_selection_list::select_element_at(), and AW_selection_list::update().

Referenced by MP_Window::create_result_window(), MP_collect_probes(), and MP_Window::MP_Window().

char* MP_get_comment	(	int	which,
		const char *	str
	)

Definition at line 725 of file MP_noclass.cxx.

References ARB_strpartdup(), mp_assert, NULp, and result.

Referenced by ProbeValuation::init_valuation(), MP_Comment(), MP_compute(), MP_gen_quality(), MP_mark_probes_in_tree(), MP_modify_selected(), MP_result_combination_chosen(), MP_selected_chosen(), and MP_show_probes_in_tree().

void MP_result_combination_chosen

(

AW_root *

aw_root

)

Definition at line 749 of file MP_noclass.cxx.

References AW_root::awar(), MP_AWAR_RESULTPROBES, MP_AWAR_RESULTPROBESCOMMENT, MP_get_comment(), AW_awar::read_char_pntr(), and AW_awar::write_string().

Referenced by MP_Window::create_result_window().

int MP_init_local_com_struct

(

mp_gl_struct &

mp_pd_gl

)

Definition at line 764 of file MP_noclass.cxx.

References aisc_create(), mp_gl_struct::com, GB_getenvUSER(), mp_gl_struct::link, mp_gl_struct::locs, and NULp.

Referenced by MO_Liste::get_all_species(), and Sonde::get_matching_species().

Variable Documentation

int** system3_tab = NULp

Definition at line 28 of file MP_noclass.cxx.

Referenced by probe_combi_statistic::calc_index_system3(), and init_system3_tab().

int system3_tab_size = 0

static

Definition at line 29 of file MP_noclass.cxx.

Referenced by init_system3_tab().

unsigned char** hamming_tab = NULp

Definition at line 31 of file MP_noclass.cxx.

Referenced by init_system3_tab().

bool new_pt_server = true

Definition at line 32 of file MP_noclass.cxx.

Referenced by ProbeValuation::init_valuation(), MP_cache_sonden(), MP_cache_sonden2(), MP_close_main(), MP_compute(), MP_mark_probes_in_tree(), MP_show_probes_in_tree(), and MP_Main::~MP_Main().