ARB
Classes | Macros | Functions | Variables
MultiProbe.hxx File Reference
#include "SoTl.hxx"
#include "mpdefs.h"
#include <aw_awar.hxx>
#include <aw_base.hxx>
#include <arb_string.h>
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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_listselected_list
 
char MP_probe_tab [256]
 
AW_selection_listresult_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_Mainmp_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"
#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"
#define MP_AWAR_RESULTPROBESCOMMENT   "mp/resultprobescomment"
#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
#define MAXMISMATCHES   6
#define FITNESSSCALEFACTOR   10

Definition at line 67 of file MultiProbe.hxx.

Referenced by probe_combi_statistic::calc_fitness().

#define MULTROULETTEFACTOR   10
#define MAXINITPOPULATION   50
#define MAXPOPULATION   MAXINITPOPULATION
#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.

#define LIST (   TYP)    ((List<Sonde>*) TYP)
#define MAXSONDENHASHSIZE   1000

Function Documentation

long k_chosenFrom_n ( int  k,
int  n 
)

Definition at line 35 of file MP_noclass.cxx.

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

int get_random ( int  min,
int  max 
)
void MP_compute ( AW_window ,
GBDATA gb_main 
)

Variable Documentation

AW_selection_list* selected_list
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 35 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 32 of file MP_noclass.cxx.

Referenced by init_system3_tab().

int** system3_tab

Definition at line 29 of file MP_noclass.cxx.

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

bool pt_server_different
bool new_pt_server
MP_Main* mp_main
awar_vars mp_gl_awars