#include "SoTl.hxx"#include "mpdefs.h"#include <aw_awar.hxx>#include <aw_base.hxx>#include <arb_string.h>
Go to the source code of this file.
Classes | |
| struct | awar_vars |
| class | MP_Main |
| class | MP_Window |
| class | Bakt_Info |
| class | Hit |
| class | Sondentopf |
| class | Sonde |
| struct | ST_Container |
| class | MO_Liste |
| class | Bitvector |
Macros | |
| #define | mp_assert(x) arb_assert(x) |
| #define | MP_AWAR_SEQIN "tmp/mp/seqin" |
| #define | MP_AWAR_SELECTEDPROBES "mp/selectedprobes" |
| #define | MP_AWAR_PROBELIST "mp/probelist" |
| #define | MP_AWAR_WEIGHTEDMISMATCHES "mp/weightedmismatches" |
| #define | MP_AWAR_COMPLEMENT "mp/complement" |
| #define | MP_AWAR_MISMATCHES "mp/mismatches" |
| #define | MP_AWAR_PTSERVER AWAR_PT_SERVER |
| #define | MP_AWAR_LOADLIST "mp/loadlist" |
| #define | MP_AWAR_RESULTPROBES "mp/resultprobes" |
| #define | MP_AWAR_RESULTPROBESCOMMENT "mp/resultprobescomment" |
| #define | MP_AWAR_NOOFPROBES "mp/noofprobes" |
| #define | MP_AWAR_QUALITY "mp/quality" |
| #define | MP_AWAR_SINGLEMISMATCHES "mp/singlemismatches" |
| #define | MP_AWAR_OUTSIDEMISMATCHES "mp/outsidemismatches" |
| #define | MP_AWAR_QUALITYBORDER1 "mp/qualityborder1" |
| #define | MP_AWAR_GREYZONE "mp/greyzone" |
| #define | MP_AWAR_EMPHASIS "mp/emphasis" |
| #define | MP_AWAR_ECOLIPOS "mp/ecolipos" |
| #define | MP_AWAR_AUTOADVANCE "mp/auto_advance" |
| #define | QUALITYDEFAULT 3 |
| #define | MAXPROBECOMBIS 6 |
| #define | MAXMISMATCHES 6 |
| #define | FITNESSSCALEFACTOR 10 |
| #define | MULTROULETTEFACTOR 10 |
| #define | MAXINITPOPULATION 50 |
| #define | MAXPOPULATION MAXINITPOPULATION |
| #define | CROSSOVER_WS 60 |
| #define | MUTATION_WS 33 |
| #define | SIGMATRUNCATION_CONST 2 |
| #define | C_MULT 1.4 |
| #define | LIST(TYP) ((List<Sonde>*) TYP) |
| #define | MAXSONDENHASHSIZE 1000 |
Functions | |
| long | k_chosenFrom_n (int k, int n) |
| int | get_random (int min, int max) |
| void | MP_compute (AW_window *, GBDATA *gb_main) |
Variables | |
| AW_selection_list * | selected_list |
| char | MP_probe_tab [256] |
| AW_selection_list * | result_probes_list |
| int | remembered_mismatches |
| int | anz_elem_marked |
| int | anz_elem_unmarked |
| unsigned char ** | hamming_tab |
| int ** | system3_tab |
| bool | pt_server_different |
| bool | new_pt_server |
| MP_Main * | mp_main |
| awar_vars | mp_gl_awars |
Macro Definition Documentation
| #define mp_assert | ( | x | ) | arb_assert(x) |
Definition at line 30 of file MultiProbe.hxx.
Referenced by MO_Liste::set_gb_main().
| #define MP_AWAR_SEQIN "tmp/mp/seqin" |
Definition at line 44 of file MultiProbe.hxx.
Referenced by MP_new_sequence(), MP_selected_chosen(), and MP_Window::MP_Window().
| #define MP_AWAR_SELECTEDPROBES "mp/selectedprobes" |
Definition at line 45 of file MultiProbe.hxx.
Referenced by MP_gen_quality(), MP_gen_singleprobe(), MP_modify_selected(), MP_new_sequence(), MP_selected_chosen(), and MP_Window::MP_Window().
| #define MP_AWAR_PROBELIST "mp/probelist" |
Definition at line 46 of file MultiProbe.hxx.
Referenced by MP_Window::MP_Window().
| #define MP_AWAR_WEIGHTEDMISMATCHES "mp/weightedmismatches" |
Definition at line 47 of file MultiProbe.hxx.
Referenced by MP_Window::MP_Window().
| #define MP_AWAR_COMPLEMENT "mp/complement" |
Definition at line 48 of file MultiProbe.hxx.
Referenced by MP_Window::MP_Window().
| #define MP_AWAR_MISMATCHES "mp/mismatches" |
Definition at line 49 of file MultiProbe.hxx.
Referenced by MP_Main::~MP_Main().
| #define MP_AWAR_PTSERVER AWAR_PT_SERVER |
Definition at line 50 of file MultiProbe.hxx.
Referenced by MP_Window::MP_Window().
| #define MP_AWAR_LOADLIST "mp/loadlist" |
Definition at line 51 of file MultiProbe.hxx.
| #define MP_AWAR_RESULTPROBES "mp/resultprobes" |
Definition at line 52 of file MultiProbe.hxx.
Referenced by MP_Window::create_result_window(), MP_Comment(), MP_mark_probes_in_tree(), MP_result_combination_chosen(), and MP_show_probes_in_tree().
| #define MP_AWAR_RESULTPROBESCOMMENT "mp/resultprobescomment" |
Definition at line 53 of file MultiProbe.hxx.
Referenced by MP_Window::create_result_window(), MP_Comment(), and MP_result_combination_chosen().
| #define MP_AWAR_NOOFPROBES "mp/noofprobes" |
Definition at line 54 of file MultiProbe.hxx.
Referenced by MP_Window::MP_Window().
| #define MP_AWAR_QUALITY "mp/quality" |
Definition at line 55 of file MultiProbe.hxx.
Referenced by MP_selected_chosen(), MP_Window::MP_Window(), and MP_Main::~MP_Main().
| #define MP_AWAR_SINGLEMISMATCHES "mp/singlemismatches" |
Definition at line 56 of file MultiProbe.hxx.
Referenced by MP_selected_chosen(), and MP_Main::~MP_Main().
| #define MP_AWAR_OUTSIDEMISMATCHES "mp/outsidemismatches" |
Definition at line 57 of file MultiProbe.hxx.
Referenced by MP_Window::MP_Window().
| #define MP_AWAR_QUALITYBORDER1 "mp/qualityborder1" |
Definition at line 58 of file MultiProbe.hxx.
Referenced by MP_Window::MP_Window().
| #define MP_AWAR_GREYZONE "mp/greyzone" |
Definition at line 59 of file MultiProbe.hxx.
Referenced by MP_Window::MP_Window().
| #define MP_AWAR_EMPHASIS "mp/emphasis" |
Definition at line 60 of file MultiProbe.hxx.
| #define MP_AWAR_ECOLIPOS "mp/ecolipos" |
Definition at line 61 of file MultiProbe.hxx.
Referenced by MP_selected_chosen().
| #define MP_AWAR_AUTOADVANCE "mp/auto_advance" |
Definition at line 62 of file MultiProbe.hxx.
Referenced by MP_Window::create_result_window(), and MP_Comment().
| #define QUALITYDEFAULT 3 |
Definition at line 64 of file MultiProbe.hxx.
| #define MAXPROBECOMBIS 6 |
Definition at line 65 of file MultiProbe.hxx.
Referenced by MP_mark_probes_in_tree(), MP_show_probes_in_tree(), and MP_Window::MP_Window().
| #define MAXMISMATCHES 6 |
Definition at line 66 of file MultiProbe.hxx.
Referenced by GenerationDuplicates::GenerationDuplicates(), MP_mark_probes_in_tree(), and MP_show_probes_in_tree().
| #define FITNESSSCALEFACTOR 10 |
Definition at line 67 of file MultiProbe.hxx.
Referenced by probe_combi_statistic::calc_fitness().
| #define MULTROULETTEFACTOR 10 |
Definition at line 70 of file MultiProbe.hxx.
Referenced by Generation::init_roulette_wheel(), probe_combi_statistic::ok_for_next_gen(), and probe_combi_statistic::sub_expected_children().
| #define MAXINITPOPULATION 50 |
Definition at line 71 of file MultiProbe.hxx.
Referenced by ProbeValuation::evolution(), Generation::init_valuation(), ProbeValuation::init_valuation(), and ProbeValuation::ProbeValuation().
| #define MAXPOPULATION MAXINITPOPULATION |
Definition at line 72 of file MultiProbe.hxx.
Referenced by Generation::create_next_generation(), ProbeValuation::evolution(), and Generation::insert().
| #define CROSSOVER_WS 60 |
Definition at line 73 of file MultiProbe.hxx.
Referenced by Generation::create_next_generation().
| #define MUTATION_WS 33 |
Definition at line 74 of file MultiProbe.hxx.
Referenced by probe_combi_statistic::mutate_Probe().
| #define SIGMATRUNCATION_CONST 2 |
Definition at line 75 of file MultiProbe.hxx.
Referenced by probe_combi_statistic::sigma_truncation().
| #define C_MULT 1.4 |
Definition at line 76 of file MultiProbe.hxx.
Definition at line 82 of file MultiProbe.hxx.
Referenced by Sondentopf::fill_Stat_Arrays(), Sondentopf::gen_color_hash(), Sondentopf::gen_Mergefeld(), Sondentopf::put_Sonde(), and Sondentopf::~Sondentopf().
| #define MAXSONDENHASHSIZE 1000 |
Definition at line 84 of file MultiProbe.hxx.
Referenced by ProbeValuation::init_valuation(), MP_mark_probes_in_tree(), and MP_show_probes_in_tree().
Function Documentation
Definition at line 34 of file MP_noclass.cxx.
Referenced by ProbeValuation::evolution(), and ProbeValuation::ProbeValuation().
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().
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().
Variable Documentation
| AW_selection_list* selected_list |
Definition at line 32 of file MP_Window.cxx.
Referenced by ProbeValuation::init_valuation(), MP_compute(), MP_gen_quality(), MP_gen_singleprobe(), MP_modify_selected(), and MP_new_sequence().
| char MP_probe_tab[256] |
Definition at line 25 of file MP_main.cxx.
Referenced by MP_is_probe().
| AW_selection_list* result_probes_list |
Definition at line 33 of file MP_Window.cxx.
Referenced by ProbeValuation::insert_in_result_list(), MP_Comment(), and MP_compute().
| int remembered_mismatches |
Definition at line 26 of file MP_main.cxx.
Referenced by MP_modify_selected().
| int anz_elem_marked |
Definition at line 27 of file MP_main.cxx.
Referenced by MO_Liste::fill_marked_bakts().
| int anz_elem_unmarked |
Definition at line 28 of file MP_main.cxx.
Referenced by ST_Container::ST_Container().
| unsigned char** hamming_tab |
Definition at line 31 of file MP_noclass.cxx.
Referenced by init_system3_tab().
| int** system3_tab |
Definition at line 28 of file MP_noclass.cxx.
Referenced by probe_combi_statistic::calc_index_system3(), and init_system3_tab().
| bool pt_server_different |
Definition at line 29 of file MP_main.cxx.
Referenced by MO_Liste::get_all_species(), ProbeValuation::init_valuation(), MP_compute(), MP_mark_probes_in_tree(), MP_show_probes_in_tree(), and ST_Container::ST_Container().
| bool new_pt_server |
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().
| MP_Main* mp_main |
Definition at line 24 of file MP_main.cxx.
Referenced by probe_combi_statistic::calc_fitness(), Generation::check_for_results(), Generation::gen_determ_combis(), Generation::Generation(), Generation::init_valuation(), ProbeValuation::init_valuation(), MP_close_main(), MP_Comment(), MP_compute(), MP_group_all_except_marked(), MP_mark_probes_in_tree(), MP_normal_colors_in_tree(), MP_popup_result_window(), MP_show_probes_in_tree(), probe_combi_statistic::mutate_Probe(), and Sondentopf::put_Sonde().
| awar_vars mp_gl_awars |
Definition at line 23 of file MP_main.cxx.
Referenced by ST_Container::cache_Sonde(), probe_combi_statistic::calc_fitness(), probe_combi_statistic::calc_index_system3(), Generation::calcFitness(), probe_combi_statistic::check_duplicates(), probe_combi_statistic::crossover_Probes(), ProbeValuation::evolution(), Sondentopf::fill_Stat_Arrays(), Sondentopf::gen_color_hash(), Generation::gen_determ_combis(), Sonde::gen_Hitliste(), Sondentopf::gen_Mergefeld(), Hit::Hit(), init_system3_tab(), Generation::init_valuation(), GenerationDuplicates::insert(), ProbeValuation::insert_in_result_list(), MP_compute(), MP_gen_quality(), MP_gen_singleprobe(), MP_mark_probes_in_tree(), MP_modify_selected(), MP_new_sequence(), MP_show_probes_in_tree(), probe_combi_statistic::mutate_Probe(), probe_combi_statistic::print(), probe_combi_statistic::probe_combi_statistic(), probe_tabs::probe_tabs(), ProbeValuation::ProbeValuation(), and ST_Container::ST_Container().
