NetworkEvolutionLib::MainWindow Class Reference

#include <GenerateGAInputs.h>

Public Slots

void go ()
void updateScene (int, int, void **, double *, int ***)

Signals

void terminate ()

Public Member Functions

 MainWindow ()
 ~MainWindow ()
QSize sizeHint () const
 MainWindow ()
 ~MainWindow ()
QSize sizeHint () const

Static Public Member Functions

static int MainCallback (int, int, void **, double *, int ***)

Data Fields

QProcess proc

Private Slots

void clear ()
void save ()
void run ()
void reset ()
void fitnessSelected (const QString &)
void useMassAction (bool use)
void useEnzyme (bool use)
void useProtein (bool use)
void useGRN (bool use)
void setMassActionProb (double value)
void setEnzymeProb (double value)
void setProteinProb (double value)
void setGRNProb (double value)
void setUniUni (double value)
void setUniBi (double value)
void setBiUni (double value)
void setBiBi (double value)
void setNoReactant (double value)
void setNoProduct (double value)
void set_ma_min_constant (double value)
void set_ma_max_constant (double value)
void set_ma_mutate_constants (double value)
void set_ma_mutate_remove_reaction (double value)
void set_ma_mutate_add_reaction (double value)
void set_enzyme_min_kcat (double value)
void set_enzyme_min_log_keq (double value)
void set_enzyme_min_alpha (double value)
void set_enzyme_min_h (double value)
void set_enzyme_min_s_half (double value)
void set_enzyme_min_p_half (double value)
void set_enzyme_max_kcat (double value)
void set_enzyme_max_log_keq (double value)
void set_enzyme_max_alpha (double value)
void set_enzyme_max_h (double value)
void set_enzyme_max_s_half (double value)
void set_enzyme_max_p_half (double value)
void set_enzyme_mutate_enzyme (double value)
void set_enzyme_mutate_k_cat (double value)
void set_enzyme_mutate_k_eq (double value)
void set_enzyme_mutate_alpha (double value)
void set_enzyme_mutate_h (double value)
void set_enzyme_mutate_s_half (double value)
void set_enzyme_mutate_p_half (double value)
void set_enzyme_mutate_remove (double value)
void set_enzyme_mutate_add (double value)
void set_prot_min_ka (double value)
void set_prot_min_vmax (double value)
void set_prot_min_total (double value)
void set_prot_max_ka (double value)
void set_prot_max_vmax (double value)
void set_prot_max_total (double value)
void set_prot_mutate_rewire (double value)
void set_prot_mutate_parameter (double value)
void set_prot_mutate_total (double value)
void set_prot_mutate_addremove (double value)
void set_grn_init_inflow (double value)
void set_grn_init_cost_per_protein (double value)
void set_grn_min_complex_size (int value)
void set_grn_max_complex_size (int value)
void set_grn_min_Ka (double value)
void set_grn_min_Vmax (double value)
void set_grn_min_degradation (double value)
void set_grn_max_Ka (double value)
void set_grn_max_Vmax (double value)
void set_grn_max_degradation (double value)
void set_grn_mutate_Ka (double value)
void set_grn_mutate_Vmax (double value)
void set_grn_mutate_complex (double value)
void set_grn_mutate_add_gene (double value)
void set_grn_mutate_remove_gene (double value)
void setCodeFile (const QString &file)
void setLogFile (const QString &file)
void setSeed (const QString &s)
void setRuns (int i)
void setGenerations (int i)
void setPopSz (int i)
void setInitPopSz (int i)
void set_min_species (int value)
void set_min_reactions (int value)
void set_max_species (int value)
void set_max_reactions (int value)
void set_crossover_rate (double value)
void set_init_iv (double value)
void set_mutate_iv (double value)
void set_lineageTracking (bool value)
void setCompileCommand (const QString &s)
void setBestNetworkFitness1 (bool value)
void setBestNetworkScript1 (bool value)
void setBestNetworkSize1 (bool value)
void setBestNetworkLineage1 (bool value)
void setAllFitness1 (bool value)
void setAllNetworkLineage1 (bool value)
void setBestNetworkFitness2 (bool value)
void setBestNetworkScript2 (bool value)
void setBestNetworkSize2 (bool value)
void setBestNetworkLineage2 (bool value)
void setAllFitness2 (bool value)
void setAllNetworkLineage2 (bool value)
void showSeed (bool value)
void setMaxFitness (double value)
void setSelectionFunc (const QString &s)

Private Member Functions

QWidget * setupNetworkOptions ()
void setupMassActionNetwork (QTreeWidget *)
void setupEnzymeNetwork (QTreeWidget *)
void setupProteinNetwork (QTreeWidget *)
void setupGeneticNetwork (QTreeWidget *)
QWidget * setupGAOptions ()
QWidget * setupEditor ()
QString init ()
QString mainFunction ()
QString callbackFunction ()
QComboBox * comboBox ()
void insertTextItem (double, double, int, int, int, int)

Private Attributes

QComboBox * fitnessComboBox
Tinkercell::CodeEditor * codeEditor
double uni_uni
double uni_bi
double bi_uni
double bi_bi
double no_reactant
double no_product
double ma_min_constant
double ma_max_constant
double ma_mutate_constants
double ma_mutate_remove_reaction
double ma_mutate_add_reaction
double prot_min_ka
double prot_min_vmax
double prot_min_total
double prot_max_ka
double prot_max_vmax
double prot_max_total
double prot_mutate_rewire
double prot_mutate_parameter
double prot_mutate_total
double prot_mutate_addremove
double enzyme_min_kcat
double enzyme_min_log_keq
double enzyme_min_alpha
double enzyme_min_h
double enzyme_min_s_half
double enzyme_min_p_half
double enzyme_max_kcat
double enzyme_max_log_keq
double enzyme_max_alpha
double enzyme_max_h
double enzyme_max_s_half
double enzyme_max_p_half
double enzyme_mutate_enzyme
double enzyme_mutate_k_cat
double enzyme_mutate_k_eq
double enzyme_mutate_alpha
double enzyme_mutate_h
double enzyme_mutate_s_half
double enzyme_mutate_p_half
double enzyme_mutate_remove
double enzyme_mutate_add
double grn_init_inflow
double grn_init_cost_per_protein
int grn_min_complex_size
int grn_max_complex_size
double grn_min_Ka
double grn_min_Vmax
double grn_min_degradation
double grn_max_Ka
double grn_max_Vmax
double grn_max_degradation
double grn_mutate_Ka
double grn_mutate_Vmax
double grn_mutate_complex
double grn_mutate_add_gene
double grn_mutate_remove_gene
int species_min
int species_max
int reactions_min
int reactions_max
double crossover_rate
double init_iv
double mutate_iv
bool lineageTracking
double mass_action_prob
double enzyme_prob
double protein_net_prob
double grn_prob
QString codeFile
QString logFile
int runs
int generations
int popSz
int initPopSz
QString seeds
QString compileCommand
int bestNetworkFitness1
int bestNetworkScript1
int bestNetworkSize1
int bestNetworkLineage1
int allFitness1
int allNetworkLineage1
int bestNetworkFitness2
int bestNetworkScript2
int bestNetworkSize2
int bestNetworkLineage2
int allFitness2
int allNetworkLineage2
int seeds2
double max_fitness
QStringList selectionFunctions
QString selectionFunction
QGraphicsScene * scene
QList< QPointF > previousGen
QList< QPointF > nextGen

Detailed Description

Definition at line 41 of file GenerateGAInputs.h.

Constructor & Destructor Documentation

NetworkEvolutionLib::MainWindow::MainWindow (  ) 

Definition at line 33 of file GenerateGAInputs.cpp.

References clear(), close(), reset(), run(), save(), selectionFunctions, setupEditor(), setupGAOptions(), and setupNetworkOptions().

NetworkEvolutionLib::MainWindow::~MainWindow (  ) 

Definition at line 149 of file GenerateGAInputs.cpp.

References allFitness1, allFitness2, allNetworkLineage1, allNetworkLineage2, bestNetworkFitness1, bestNetworkFitness2, bestNetworkLineage1, bestNetworkLineage2, bestNetworkScript1, bestNetworkScript2, bestNetworkSize1, bestNetworkSize2, bi_bi, bi_uni, codeFile, compileCommand, crossover_rate, enzyme_max_alpha, enzyme_max_h, enzyme_max_kcat, enzyme_max_log_keq, enzyme_max_p_half, enzyme_max_s_half, enzyme_min_alpha, enzyme_min_h, enzyme_min_kcat, enzyme_min_log_keq, enzyme_min_p_half, enzyme_min_s_half, enzyme_mutate_add, enzyme_mutate_enzyme, enzyme_mutate_h, enzyme_mutate_k_cat, enzyme_mutate_k_eq, enzyme_mutate_p_half, enzyme_mutate_remove, enzyme_mutate_s_half, enzyme_prob, generations, grn_init_cost_per_protein, grn_init_inflow, grn_max_complex_size, grn_max_degradation, grn_max_Ka, grn_max_Vmax, grn_min_complex_size, grn_min_degradation, grn_min_Ka, grn_min_Vmax, grn_mutate_add_gene, grn_mutate_complex, grn_mutate_Ka, grn_mutate_remove_gene, grn_mutate_Vmax, grn_prob, init_iv, initPopSz, lineageTracking, logFile, ma_max_constant, ma_min_constant, ma_mutate_add_reaction, ma_mutate_constants, ma_mutate_remove_reaction, mass_action_prob, max_fitness, mutate_iv, no_product, no_reactant, popSz, prot_max_ka, prot_max_total, prot_max_vmax, prot_min_ka, prot_min_total, prot_min_vmax, prot_mutate_addremove, prot_mutate_parameter, prot_mutate_rewire, prot_mutate_total, protein_net_prob, reactions_max, reactions_min, runs, seeds2, selectionFunction, species_max, species_min, uni_bi, and uni_uni.

NetworkEvolutionLib::MainWindow::MainWindow (  ) 
NetworkEvolutionLib::MainWindow::~MainWindow (  ) 

Member Function Documentation

QString NetworkEvolutionLib::MainWindow::callbackFunction (  )  [private]

Definition at line 1338 of file GenerateGAInputs.cpp.

References max_fitness.

void NetworkEvolutionLib::MainWindow::clear (  )  [private, slot]

Definition at line 1684 of file GenerateGAInputs.cpp.

References codeEditor.

Referenced by fitnessSelected(), and MainWindow().

QComboBox * NetworkEvolutionLib::MainWindow::comboBox (  )  [private]

Definition at line 1644 of file GenerateGAInputs.cpp.

Referenced by setupEditor(), and setupGAOptions().

void NetworkEvolutionLib::MainWindow::fitnessSelected ( const QString &  s  )  [private, slot]

Definition at line 1666 of file GenerateGAInputs.cpp.

References clear(), codeEditor, and fitnessComboBox.

Referenced by setupEditor().

void NetworkEvolutionLib::MainWindow::go (  )  [slot]

Definition at line 220 of file RunEvolution.cpp.

References File, and updateScene().

Referenced by main().

QString NetworkEvolutionLib::MainWindow::init (  )  [private]

Definition at line 1197 of file GenerateGAInputs.cpp.

References allFitness1, allFitness2, allNetworkLineage1, allNetworkLineage2, bestNetworkFitness1, bestNetworkFitness2, bestNetworkLineage1, bestNetworkLineage2, bestNetworkScript1, bestNetworkScript2, bestNetworkSize1, bestNetworkSize2, bi_bi, bi_uni, crossover_rate, enzyme_max_alpha, enzyme_max_h, enzyme_max_kcat, enzyme_max_log_keq, enzyme_max_p_half, enzyme_max_s_half, enzyme_min_alpha, enzyme_min_h, enzyme_min_kcat, enzyme_min_log_keq, enzyme_min_p_half, enzyme_min_s_half, enzyme_mutate_add, enzyme_mutate_alpha, enzyme_mutate_enzyme, enzyme_mutate_h, enzyme_mutate_k_cat, enzyme_mutate_k_eq, enzyme_mutate_p_half, enzyme_mutate_remove, enzyme_mutate_s_half, enzyme_prob, grn_init_cost_per_protein, grn_init_inflow, grn_max_complex_size, grn_max_degradation, grn_max_Ka, grn_max_Vmax, grn_min_complex_size, grn_min_degradation, grn_min_Ka, grn_min_Vmax, grn_mutate_add_gene, grn_mutate_complex, grn_mutate_Ka, grn_mutate_remove_gene, grn_mutate_Vmax, grn_prob, init_iv, lineageTracking, logFile, ma_max_constant, ma_min_constant, ma_mutate_add_reaction, ma_mutate_constants, ma_mutate_remove_reaction, mass_action_prob, mutate_iv, no_product, no_reactant, prot_max_ka, prot_max_total, prot_max_vmax, prot_min_ka, prot_min_total, prot_min_vmax, prot_mutate_addremove, prot_mutate_parameter, prot_mutate_rewire, prot_mutate_total, protein_net_prob, reactions_max, reactions_min, seeds, seeds2, selectionFunction, species_max, species_min, uni_bi, and uni_uni.

Referenced by run().

void NetworkEvolutionLib::MainWindow::insertTextItem ( double  fitness,
double  max,
int  iteration,
int  index,
int  parent1,
int  parent2 
) [private]

Definition at line 135 of file RunEvolution.cpp.

References cos(), h, mtrand(), nextGen, previousGen, scene, sin(), x, and y.

static int NetworkEvolutionLib::MainWindow::MainCallback ( int  ,
int  ,
void **  ,
double *  ,
int ***   
) [static]
QString NetworkEvolutionLib::MainWindow::mainFunction (  )  [private]

Definition at line 1356 of file GenerateGAInputs.cpp.

References generations, initPopSz, popSz, and runs.

void NetworkEvolutionLib::MainWindow::reset (  )  [private, slot]

Definition at line 1438 of file GenerateGAInputs.cpp.

References allFitness1, allFitness2, allNetworkLineage1, allNetworkLineage2, bestNetworkFitness1, bestNetworkFitness2, bestNetworkLineage1, bestNetworkLineage2, bestNetworkScript1, bestNetworkScript2, bestNetworkSize1, bestNetworkSize2, bi_bi, bi_uni, codeFile, compileCommand, crossover_rate, enzyme_max_alpha, enzyme_max_h, enzyme_max_kcat, enzyme_max_log_keq, enzyme_max_p_half, enzyme_max_s_half, enzyme_min_alpha, enzyme_min_h, enzyme_min_kcat, enzyme_min_log_keq, enzyme_min_p_half, enzyme_min_s_half, enzyme_mutate_add, enzyme_mutate_alpha, enzyme_mutate_enzyme, enzyme_mutate_h, enzyme_mutate_k_cat, enzyme_mutate_k_eq, enzyme_mutate_p_half, enzyme_mutate_remove, enzyme_mutate_s_half, enzyme_prob, generations, grn_init_cost_per_protein, grn_init_inflow, grn_max_complex_size, grn_max_degradation, grn_max_Ka, grn_max_Vmax, grn_min_complex_size, grn_min_degradation, grn_min_Ka, grn_min_Vmax, grn_mutate_add_gene, grn_mutate_complex, grn_mutate_Ka, grn_mutate_remove_gene, grn_mutate_Vmax, grn_prob, init_iv, initPopSz, lineageTracking, logFile, ma_max_constant, ma_min_constant, ma_mutate_add_reaction, ma_mutate_constants, ma_mutate_remove_reaction, mass_action_prob, max_fitness, mutate_iv, no_product, no_reactant, popSz, prot_max_ka, prot_max_total, prot_max_vmax, prot_min_ka, prot_min_total, prot_min_vmax, prot_mutate_addremove, prot_mutate_parameter, prot_mutate_rewire, prot_mutate_total, protein_net_prob, reactions_max, reactions_min, runs, seeds2, selectionFunction, selectionFunctions, species_max, species_min, uni_bi, and uni_uni.

Referenced by MainWindow().

void NetworkEvolutionLib::MainWindow::run (  )  [private, slot]

Definition at line 1379 of file GenerateGAInputs.cpp.

References codeEditor, compileCommand, generations, init(), initPopSz, popSz, proc, and system().

Referenced by MainWindow().

void NetworkEvolutionLib::MainWindow::save (  )  [private, slot]

Definition at line 1690 of file GenerateGAInputs.cpp.

References codeEditor, and fitnessComboBox.

Referenced by MainWindow().

void NetworkEvolutionLib::MainWindow::set_crossover_rate ( double  value  )  [inline, private, slot]

Definition at line 227 of file GenerateGAInputs.h.

References crossover_rate.

Referenced by setupNetworkOptions().

void NetworkEvolutionLib::MainWindow::set_enzyme_max_alpha ( double  value  )  [inline, private, slot]

Definition at line 166 of file GenerateGAInputs.h.

References enzyme_max_alpha.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_max_h ( double  value  )  [inline, private, slot]

Definition at line 167 of file GenerateGAInputs.h.

References enzyme_max_h.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_max_kcat ( double  value  )  [inline, private, slot]

Definition at line 164 of file GenerateGAInputs.h.

References enzyme_max_kcat.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_max_log_keq ( double  value  )  [inline, private, slot]

Definition at line 165 of file GenerateGAInputs.h.

References enzyme_max_log_keq.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_max_p_half ( double  value  )  [inline, private, slot]

Definition at line 169 of file GenerateGAInputs.h.

References enzyme_max_p_half.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_max_s_half ( double  value  )  [inline, private, slot]

Definition at line 168 of file GenerateGAInputs.h.

References enzyme_max_s_half.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_min_alpha ( double  value  )  [inline, private, slot]

Definition at line 159 of file GenerateGAInputs.h.

References enzyme_min_alpha.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_min_h ( double  value  )  [inline, private, slot]

Definition at line 160 of file GenerateGAInputs.h.

References enzyme_min_h.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_min_kcat ( double  value  )  [inline, private, slot]

Definition at line 157 of file GenerateGAInputs.h.

References enzyme_min_kcat.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_min_log_keq ( double  value  )  [inline, private, slot]

Definition at line 158 of file GenerateGAInputs.h.

References enzyme_min_log_keq.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_min_p_half ( double  value  )  [inline, private, slot]

Definition at line 162 of file GenerateGAInputs.h.

References enzyme_min_p_half.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_min_s_half ( double  value  )  [inline, private, slot]

Definition at line 161 of file GenerateGAInputs.h.

References enzyme_min_s_half.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_mutate_add ( double  value  )  [inline, private, slot]

Definition at line 179 of file GenerateGAInputs.h.

References enzyme_mutate_add.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_mutate_alpha ( double  value  )  [inline, private, slot]

Definition at line 174 of file GenerateGAInputs.h.

References enzyme_mutate_alpha.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_mutate_enzyme ( double  value  )  [inline, private, slot]

Definition at line 171 of file GenerateGAInputs.h.

References enzyme_mutate_enzyme.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_mutate_h ( double  value  )  [inline, private, slot]

Definition at line 175 of file GenerateGAInputs.h.

References enzyme_mutate_h.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_mutate_k_cat ( double  value  )  [inline, private, slot]

Definition at line 172 of file GenerateGAInputs.h.

References enzyme_mutate_k_cat.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_mutate_k_eq ( double  value  )  [inline, private, slot]

Definition at line 173 of file GenerateGAInputs.h.

References enzyme_mutate_k_eq.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_mutate_p_half ( double  value  )  [inline, private, slot]

Definition at line 177 of file GenerateGAInputs.h.

References enzyme_mutate_p_half.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_mutate_remove ( double  value  )  [inline, private, slot]

Definition at line 178 of file GenerateGAInputs.h.

References enzyme_mutate_remove.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_enzyme_mutate_s_half ( double  value  )  [inline, private, slot]

Definition at line 176 of file GenerateGAInputs.h.

References enzyme_mutate_s_half.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::set_grn_init_cost_per_protein ( double  value  )  [inline, private, slot]

Definition at line 194 of file GenerateGAInputs.h.

References grn_init_cost_per_protein.

Referenced by setupGeneticNetwork().

void NetworkEvolutionLib::MainWindow::set_grn_init_inflow ( double  value  )  [inline, private, slot]

Definition at line 193 of file GenerateGAInputs.h.

References grn_init_inflow.

Referenced by setupGeneticNetwork().

void NetworkEvolutionLib::MainWindow::set_grn_max_complex_size ( int  value  )  [inline, private, slot]

Definition at line 196 of file GenerateGAInputs.h.

References grn_max_complex_size.

Referenced by setupGeneticNetwork().

void NetworkEvolutionLib::MainWindow::set_grn_max_degradation ( double  value  )  [inline, private, slot]

Definition at line 203 of file GenerateGAInputs.h.

References grn_max_degradation.

Referenced by setupGeneticNetwork().

void NetworkEvolutionLib::MainWindow::set_grn_max_Ka ( double  value  )  [inline, private, slot]

Definition at line 201 of file GenerateGAInputs.h.

References grn_max_Ka.

Referenced by setupGeneticNetwork().

void NetworkEvolutionLib::MainWindow::set_grn_max_Vmax ( double  value  )  [inline, private, slot]

Definition at line 202 of file GenerateGAInputs.h.

References grn_max_Vmax.

Referenced by setupGeneticNetwork().

void NetworkEvolutionLib::MainWindow::set_grn_min_complex_size ( int  value  )  [inline, private, slot]

Definition at line 195 of file GenerateGAInputs.h.

References grn_min_complex_size.

Referenced by setupGeneticNetwork().

void NetworkEvolutionLib::MainWindow::set_grn_min_degradation ( double  value  )  [inline, private, slot]

Definition at line 200 of file GenerateGAInputs.h.

References grn_min_degradation.

Referenced by setupGeneticNetwork().

void NetworkEvolutionLib::MainWindow::set_grn_min_Ka ( double  value  )  [inline, private, slot]

Definition at line 198 of file GenerateGAInputs.h.

References grn_min_Ka.

Referenced by setupGeneticNetwork().

void NetworkEvolutionLib::MainWindow::set_grn_min_Vmax ( double  value  )  [inline, private, slot]

Definition at line 199 of file GenerateGAInputs.h.

References grn_min_Vmax.

Referenced by setupGeneticNetwork().

void NetworkEvolutionLib::MainWindow::set_grn_mutate_add_gene ( double  value  )  [inline, private, slot]

Definition at line 208 of file GenerateGAInputs.h.

References grn_mutate_add_gene.

Referenced by setupGeneticNetwork().

void NetworkEvolutionLib::MainWindow::set_grn_mutate_complex ( double  value  )  [inline, private, slot]

Definition at line 207 of file GenerateGAInputs.h.

References grn_mutate_complex.

Referenced by setupGeneticNetwork().

void NetworkEvolutionLib::MainWindow::set_grn_mutate_Ka ( double  value  )  [inline, private, slot]

Definition at line 205 of file GenerateGAInputs.h.

References grn_mutate_Ka.

Referenced by setupGeneticNetwork().

void NetworkEvolutionLib::MainWindow::set_grn_mutate_remove_gene ( double  value  )  [inline, private, slot]

Definition at line 209 of file GenerateGAInputs.h.

References grn_mutate_remove_gene.

Referenced by setupGeneticNetwork().

void NetworkEvolutionLib::MainWindow::set_grn_mutate_Vmax ( double  value  )  [inline, private, slot]

Definition at line 206 of file GenerateGAInputs.h.

References grn_mutate_Vmax.

Referenced by setupGeneticNetwork().

void NetworkEvolutionLib::MainWindow::set_init_iv ( double  value  )  [inline, private, slot]

Definition at line 228 of file GenerateGAInputs.h.

References init_iv.

Referenced by setupNetworkOptions().

void NetworkEvolutionLib::MainWindow::set_lineageTracking ( bool  value  )  [inline, private, slot]

Definition at line 230 of file GenerateGAInputs.h.

References lineageTracking.

Referenced by setupNetworkOptions().

void NetworkEvolutionLib::MainWindow::set_ma_max_constant ( double  value  )  [inline, private, slot]

Definition at line 152 of file GenerateGAInputs.h.

References ma_max_constant.

Referenced by setupMassActionNetwork().

void NetworkEvolutionLib::MainWindow::set_ma_min_constant ( double  value  )  [inline, private, slot]

Definition at line 151 of file GenerateGAInputs.h.

References ma_min_constant.

Referenced by setupMassActionNetwork().

void NetworkEvolutionLib::MainWindow::set_ma_mutate_add_reaction ( double  value  )  [inline, private, slot]

Definition at line 155 of file GenerateGAInputs.h.

References ma_mutate_add_reaction.

Referenced by setupMassActionNetwork().

void NetworkEvolutionLib::MainWindow::set_ma_mutate_constants ( double  value  )  [inline, private, slot]

Definition at line 153 of file GenerateGAInputs.h.

References ma_mutate_constants.

Referenced by setupMassActionNetwork().

void NetworkEvolutionLib::MainWindow::set_ma_mutate_remove_reaction ( double  value  )  [inline, private, slot]

Definition at line 154 of file GenerateGAInputs.h.

References ma_mutate_remove_reaction.

Referenced by setupMassActionNetwork().

void NetworkEvolutionLib::MainWindow::set_max_reactions ( int  value  )  [inline, private, slot]

Definition at line 226 of file GenerateGAInputs.h.

References reactions_max.

Referenced by setupNetworkOptions().

void NetworkEvolutionLib::MainWindow::set_max_species ( int  value  )  [inline, private, slot]

Definition at line 225 of file GenerateGAInputs.h.

References species_max.

Referenced by setupNetworkOptions().

void NetworkEvolutionLib::MainWindow::set_min_reactions ( int  value  )  [inline, private, slot]

Definition at line 224 of file GenerateGAInputs.h.

References reactions_min.

Referenced by setupNetworkOptions().

void NetworkEvolutionLib::MainWindow::set_min_species ( int  value  )  [inline, private, slot]

Definition at line 223 of file GenerateGAInputs.h.

References species_min.

Referenced by setupNetworkOptions().

void NetworkEvolutionLib::MainWindow::set_mutate_iv ( double  value  )  [inline, private, slot]

Definition at line 229 of file GenerateGAInputs.h.

References mutate_iv.

Referenced by setupNetworkOptions().

void NetworkEvolutionLib::MainWindow::set_prot_max_ka ( double  value  )  [inline, private, slot]

Definition at line 184 of file GenerateGAInputs.h.

References prot_max_ka.

Referenced by setupProteinNetwork().

void NetworkEvolutionLib::MainWindow::set_prot_max_total ( double  value  )  [inline, private, slot]

Definition at line 186 of file GenerateGAInputs.h.

References prot_max_total.

Referenced by setupProteinNetwork().

void NetworkEvolutionLib::MainWindow::set_prot_max_vmax ( double  value  )  [inline, private, slot]

Definition at line 185 of file GenerateGAInputs.h.

References prot_max_vmax.

Referenced by setupProteinNetwork().

void NetworkEvolutionLib::MainWindow::set_prot_min_ka ( double  value  )  [inline, private, slot]

Definition at line 181 of file GenerateGAInputs.h.

References prot_min_ka.

Referenced by setupProteinNetwork().

void NetworkEvolutionLib::MainWindow::set_prot_min_total ( double  value  )  [inline, private, slot]

Definition at line 183 of file GenerateGAInputs.h.

References prot_min_total.

Referenced by setupProteinNetwork().

void NetworkEvolutionLib::MainWindow::set_prot_min_vmax ( double  value  )  [inline, private, slot]

Definition at line 182 of file GenerateGAInputs.h.

References prot_min_vmax.

Referenced by setupProteinNetwork().

void NetworkEvolutionLib::MainWindow::set_prot_mutate_addremove ( double  value  )  [inline, private, slot]

Definition at line 191 of file GenerateGAInputs.h.

References prot_mutate_addremove.

Referenced by setupProteinNetwork().

void NetworkEvolutionLib::MainWindow::set_prot_mutate_parameter ( double  value  )  [inline, private, slot]

Definition at line 189 of file GenerateGAInputs.h.

References prot_mutate_parameter.

Referenced by setupProteinNetwork().

void NetworkEvolutionLib::MainWindow::set_prot_mutate_rewire ( double  value  )  [inline, private, slot]

Definition at line 188 of file GenerateGAInputs.h.

References prot_mutate_rewire.

Referenced by setupProteinNetwork().

void NetworkEvolutionLib::MainWindow::set_prot_mutate_total ( double  value  )  [inline, private, slot]

Definition at line 190 of file GenerateGAInputs.h.

References prot_mutate_total.

Referenced by setupProteinNetwork().

void NetworkEvolutionLib::MainWindow::setAllFitness1 ( bool  value  )  [inline, private, slot]

Definition at line 238 of file GenerateGAInputs.h.

References allFitness1.

Referenced by setupGAOptions().

void NetworkEvolutionLib::MainWindow::setAllFitness2 ( bool  value  )  [inline, private, slot]

Definition at line 245 of file GenerateGAInputs.h.

References allFitness2.

Referenced by setupGAOptions().

void NetworkEvolutionLib::MainWindow::setAllNetworkLineage1 ( bool  value  )  [inline, private, slot]

Definition at line 239 of file GenerateGAInputs.h.

References allNetworkLineage1.

Referenced by setupGAOptions().

void NetworkEvolutionLib::MainWindow::setAllNetworkLineage2 ( bool  value  )  [inline, private, slot]

Definition at line 246 of file GenerateGAInputs.h.

References allNetworkLineage2.

Referenced by setupGAOptions().

void NetworkEvolutionLib::MainWindow::setBestNetworkFitness1 ( bool  value  )  [inline, private, slot]

Definition at line 234 of file GenerateGAInputs.h.

References bestNetworkFitness1.

Referenced by setupGAOptions().

void NetworkEvolutionLib::MainWindow::setBestNetworkFitness2 ( bool  value  )  [inline, private, slot]

Definition at line 241 of file GenerateGAInputs.h.

References bestNetworkFitness2.

Referenced by setupGAOptions().

void NetworkEvolutionLib::MainWindow::setBestNetworkLineage1 ( bool  value  )  [inline, private, slot]

Definition at line 237 of file GenerateGAInputs.h.

References bestNetworkLineage1.

Referenced by setupGAOptions().

void NetworkEvolutionLib::MainWindow::setBestNetworkLineage2 ( bool  value  )  [inline, private, slot]

Definition at line 244 of file GenerateGAInputs.h.

References bestNetworkLineage2.

Referenced by setupGAOptions().

void NetworkEvolutionLib::MainWindow::setBestNetworkScript1 ( bool  value  )  [inline, private, slot]

Definition at line 235 of file GenerateGAInputs.h.

References bestNetworkScript1.

Referenced by setupGAOptions().

void NetworkEvolutionLib::MainWindow::setBestNetworkScript2 ( bool  value  )  [inline, private, slot]

Definition at line 242 of file GenerateGAInputs.h.

References bestNetworkScript2.

Referenced by setupGAOptions().

void NetworkEvolutionLib::MainWindow::setBestNetworkSize1 ( bool  value  )  [inline, private, slot]

Definition at line 236 of file GenerateGAInputs.h.

References bestNetworkSize1.

Referenced by setupGAOptions().

void NetworkEvolutionLib::MainWindow::setBestNetworkSize2 ( bool  value  )  [inline, private, slot]

Definition at line 243 of file GenerateGAInputs.h.

References bestNetworkSize2.

Referenced by setupGAOptions().

void NetworkEvolutionLib::MainWindow::setBiBi ( double  value  )  [inline, private, slot]

Definition at line 147 of file GenerateGAInputs.h.

References bi_bi.

Referenced by setupMassActionNetwork().

void NetworkEvolutionLib::MainWindow::setBiUni ( double  value  )  [inline, private, slot]

Definition at line 146 of file GenerateGAInputs.h.

References bi_uni.

Referenced by setupMassActionNetwork().

void NetworkEvolutionLib::MainWindow::setCodeFile ( const QString &  file  )  [inline, private, slot]

Definition at line 211 of file GenerateGAInputs.h.

References codeFile, and compileCommand.

Referenced by setupGAOptions().

void NetworkEvolutionLib::MainWindow::setCompileCommand ( const QString &  s  )  [inline, private, slot]

Definition at line 232 of file GenerateGAInputs.h.

References compileCommand.

void NetworkEvolutionLib::MainWindow::setEnzymeProb ( double  value  )  [inline, private, slot]

Definition at line 140 of file GenerateGAInputs.h.

References enzyme_prob.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::setGenerations ( int  i  )  [inline, private, slot]

Definition at line 219 of file GenerateGAInputs.h.

References generations.

Referenced by setupGAOptions().

void NetworkEvolutionLib::MainWindow::setGRNProb ( double  value  )  [inline, private, slot]

Definition at line 142 of file GenerateGAInputs.h.

References grn_prob.

Referenced by setupGeneticNetwork().

void NetworkEvolutionLib::MainWindow::setInitPopSz ( int  i  )  [inline, private, slot]

Definition at line 221 of file GenerateGAInputs.h.

References initPopSz.

Referenced by setupGAOptions().

void NetworkEvolutionLib::MainWindow::setLogFile ( const QString &  file  )  [inline, private, slot]

Definition at line 216 of file GenerateGAInputs.h.

References logFile.

Referenced by setupGAOptions().

void NetworkEvolutionLib::MainWindow::setMassActionProb ( double  value  )  [inline, private, slot]

Definition at line 139 of file GenerateGAInputs.h.

References mass_action_prob.

Referenced by setupMassActionNetwork().

void NetworkEvolutionLib::MainWindow::setMaxFitness ( double  value  )  [inline, private, slot]

Definition at line 249 of file GenerateGAInputs.h.

References max_fitness.

void NetworkEvolutionLib::MainWindow::setNoProduct ( double  value  )  [inline, private, slot]

Definition at line 149 of file GenerateGAInputs.h.

References no_product.

Referenced by setupMassActionNetwork().

void NetworkEvolutionLib::MainWindow::setNoReactant ( double  value  )  [inline, private, slot]

Definition at line 148 of file GenerateGAInputs.h.

References no_reactant.

Referenced by setupMassActionNetwork().

void NetworkEvolutionLib::MainWindow::setPopSz ( int  i  )  [inline, private, slot]

Definition at line 220 of file GenerateGAInputs.h.

References popSz.

Referenced by setupGAOptions().

void NetworkEvolutionLib::MainWindow::setProteinProb ( double  value  )  [inline, private, slot]

Definition at line 141 of file GenerateGAInputs.h.

References protein_net_prob.

Referenced by setupProteinNetwork().

void NetworkEvolutionLib::MainWindow::setRuns ( int  i  )  [inline, private, slot]

Definition at line 218 of file GenerateGAInputs.h.

References runs.

void NetworkEvolutionLib::MainWindow::setSeed ( const QString &  s  )  [inline, private, slot]

Definition at line 217 of file GenerateGAInputs.h.

References seeds.

Referenced by setupGAOptions().

void NetworkEvolutionLib::MainWindow::setSelectionFunc ( const QString &  s  )  [inline, private, slot]

Definition at line 250 of file GenerateGAInputs.h.

References selectionFunction.

Referenced by setupGAOptions().

void NetworkEvolutionLib::MainWindow::setUniBi ( double  value  )  [inline, private, slot]

Definition at line 145 of file GenerateGAInputs.h.

References uni_bi.

Referenced by setupMassActionNetwork().

void NetworkEvolutionLib::MainWindow::setUniUni ( double  value  )  [inline, private, slot]

Definition at line 144 of file GenerateGAInputs.h.

References uni_uni.

Referenced by setupMassActionNetwork().

QWidget * NetworkEvolutionLib::MainWindow::setupEditor (  )  [private]

Definition at line 1171 of file GenerateGAInputs.cpp.

References codeEditor, comboBox(), fitnessComboBox, and fitnessSelected().

Referenced by MainWindow().

void NetworkEvolutionLib::MainWindow::setupEnzymeNetwork ( QTreeWidget *  treeWidget  )  [private]

Definition at line 391 of file GenerateGAInputs.cpp.

References enzyme_max_alpha, enzyme_max_h, enzyme_max_kcat, enzyme_max_log_keq, enzyme_max_p_half, enzyme_max_s_half, enzyme_min_alpha, enzyme_min_h, enzyme_min_kcat, enzyme_min_log_keq, enzyme_min_p_half, enzyme_min_s_half, enzyme_mutate_add, enzyme_mutate_alpha, enzyme_mutate_enzyme, enzyme_mutate_h, enzyme_mutate_k_cat, enzyme_mutate_k_eq, enzyme_mutate_p_half, enzyme_mutate_remove, enzyme_mutate_s_half, enzyme_prob, set_enzyme_max_alpha(), set_enzyme_max_h(), set_enzyme_max_kcat(), set_enzyme_max_log_keq(), set_enzyme_max_p_half(), set_enzyme_max_s_half(), set_enzyme_min_alpha(), set_enzyme_min_h(), set_enzyme_min_kcat(), set_enzyme_min_log_keq(), set_enzyme_min_p_half(), set_enzyme_min_s_half(), set_enzyme_mutate_add(), set_enzyme_mutate_alpha(), set_enzyme_mutate_enzyme(), set_enzyme_mutate_h(), set_enzyme_mutate_k_cat(), set_enzyme_mutate_k_eq(), set_enzyme_mutate_p_half(), set_enzyme_mutate_remove(), set_enzyme_mutate_s_half(), setEnzymeProb(), and useEnzyme().

Referenced by setupNetworkOptions().

QWidget * NetworkEvolutionLib::MainWindow::setupGAOptions (  )  [private]

Definition at line 970 of file GenerateGAInputs.cpp.

References allFitness1, allFitness2, allNetworkLineage1, allNetworkLineage2, bestNetworkFitness1, bestNetworkFitness2, bestNetworkLineage1, bestNetworkLineage2, bestNetworkScript1, bestNetworkScript2, bestNetworkSize1, bestNetworkSize2, codeFile, comboBox(), generations, initPopSz, log(), log2(), logFile, popSz, seeds2, selectionFunctions, setAllFitness1(), setAllFitness2(), setAllNetworkLineage1(), setAllNetworkLineage2(), setBestNetworkFitness1(), setBestNetworkFitness2(), setBestNetworkLineage1(), setBestNetworkLineage2(), setBestNetworkScript1(), setBestNetworkScript2(), setBestNetworkSize1(), setBestNetworkSize2(), setCodeFile(), setGenerations(), setInitPopSz(), setLogFile(), setPopSz(), setSeed(), setSelectionFunc(), and showSeed().

Referenced by MainWindow().

void NetworkEvolutionLib::MainWindow::setupGeneticNetwork ( QTreeWidget *  treeWidget  )  [private]

Definition at line 717 of file GenerateGAInputs.cpp.

References grn_init_cost_per_protein, grn_init_inflow, grn_max_complex_size, grn_max_degradation, grn_max_Ka, grn_max_Vmax, grn_min_complex_size, grn_min_degradation, grn_min_Ka, grn_min_Vmax, grn_mutate_add_gene, grn_mutate_complex, grn_mutate_Ka, grn_mutate_remove_gene, grn_mutate_Vmax, grn_prob, set_grn_init_cost_per_protein(), set_grn_init_inflow(), set_grn_max_complex_size(), set_grn_max_degradation(), set_grn_max_Ka(), set_grn_max_Vmax(), set_grn_min_complex_size(), set_grn_min_degradation(), set_grn_min_Ka(), set_grn_min_Vmax(), set_grn_mutate_add_gene(), set_grn_mutate_complex(), set_grn_mutate_Ka(), set_grn_mutate_remove_gene(), set_grn_mutate_Vmax(), setGRNProb(), and useGRN().

Referenced by setupNetworkOptions().

void NetworkEvolutionLib::MainWindow::setupMassActionNetwork ( QTreeWidget *  treeWidget  )  [private]

Definition at line 259 of file GenerateGAInputs.cpp.

References bi_bi, bi_uni, ma_max_constant, ma_min_constant, ma_mutate_add_reaction, ma_mutate_constants, ma_mutate_remove_reaction, mass_action_prob, no_product, no_reactant, set_ma_max_constant(), set_ma_min_constant(), set_ma_mutate_add_reaction(), set_ma_mutate_constants(), set_ma_mutate_remove_reaction(), setBiBi(), setBiUni(), setMassActionProb(), setNoProduct(), setNoReactant(), setUniBi(), setUniUni(), uni_bi, uni_uni, and useMassAction().

Referenced by setupNetworkOptions().

QWidget * NetworkEvolutionLib::MainWindow::setupNetworkOptions (  )  [private]

Definition at line 877 of file GenerateGAInputs.cpp.

References crossover_rate, init_iv, lineageTracking, mutate_iv, reactions_max, reactions_min, set_crossover_rate(), set_init_iv(), set_lineageTracking(), set_max_reactions(), set_max_species(), set_min_reactions(), set_min_species(), set_mutate_iv(), setupEnzymeNetwork(), setupGeneticNetwork(), setupMassActionNetwork(), setupProteinNetwork(), species_max, and species_min.

Referenced by MainWindow().

void NetworkEvolutionLib::MainWindow::setupProteinNetwork ( QTreeWidget *  treeWidget  )  [private]

Definition at line 603 of file GenerateGAInputs.cpp.

References prot_max_ka, prot_max_total, prot_max_vmax, prot_min_ka, prot_min_total, prot_min_vmax, prot_mutate_addremove, prot_mutate_parameter, prot_mutate_rewire, prot_mutate_total, protein_net_prob, set_prot_max_ka(), set_prot_max_total(), set_prot_max_vmax(), set_prot_min_ka(), set_prot_min_total(), set_prot_min_vmax(), set_prot_mutate_addremove(), set_prot_mutate_parameter(), set_prot_mutate_rewire(), set_prot_mutate_total(), setProteinProb(), and useProtein().

Referenced by setupNetworkOptions().

void NetworkEvolutionLib::MainWindow::showSeed ( bool  value  )  [inline, private, slot]

Definition at line 248 of file GenerateGAInputs.h.

References seeds.

Referenced by setupGAOptions().

QSize NetworkEvolutionLib::MainWindow::sizeHint (  )  const
QSize NetworkEvolutionLib::MainWindow::sizeHint (  )  const

Definition at line 1192 of file GenerateGAInputs.cpp.

void NetworkEvolutionLib::MainWindow::terminate (  )  [signal]

Definition at line 359 of file moc_GenerateGAInputs.cxx.

void NetworkEvolutionLib::MainWindow::updateScene ( int  ,
int  ,
void **  ,
double *  ,
int ***   
) [slot]

Referenced by go().

void NetworkEvolutionLib::MainWindow::useEnzyme ( bool  use  )  [inline, private, slot]

Definition at line 135 of file GenerateGAInputs.h.

References enzyme_prob.

Referenced by setupEnzymeNetwork().

void NetworkEvolutionLib::MainWindow::useGRN ( bool  use  )  [inline, private, slot]

Definition at line 137 of file GenerateGAInputs.h.

References grn_prob.

Referenced by setupGeneticNetwork().

void NetworkEvolutionLib::MainWindow::useMassAction ( bool  use  )  [inline, private, slot]

Definition at line 134 of file GenerateGAInputs.h.

References mass_action_prob.

Referenced by setupMassActionNetwork().

void NetworkEvolutionLib::MainWindow::useProtein ( bool  use  )  [inline, private, slot]

Definition at line 136 of file GenerateGAInputs.h.

References protein_net_prob.

Referenced by setupProteinNetwork().

Field Documentation

int NetworkEvolutionLib::MainWindow::allFitness1 [private]

Definition at line 110 of file GenerateGAInputs.h.

Referenced by init(), reset(), setAllFitness1(), setupGAOptions(), and ~MainWindow().

int NetworkEvolutionLib::MainWindow::allFitness2 [private]

Definition at line 114 of file GenerateGAInputs.h.

Referenced by init(), reset(), setAllFitness2(), setupGAOptions(), and ~MainWindow().

int NetworkEvolutionLib::MainWindow::allNetworkLineage1 [private]

Definition at line 110 of file GenerateGAInputs.h.

Referenced by init(), reset(), setAllNetworkLineage1(), setupGAOptions(), and ~MainWindow().

int NetworkEvolutionLib::MainWindow::allNetworkLineage2 [private]

Definition at line 114 of file GenerateGAInputs.h.

Referenced by init(), reset(), setAllNetworkLineage2(), setupGAOptions(), and ~MainWindow().

int NetworkEvolutionLib::MainWindow::bestNetworkFitness1 [private]

Definition at line 110 of file GenerateGAInputs.h.

Referenced by init(), reset(), setBestNetworkFitness1(), setupGAOptions(), and ~MainWindow().

int NetworkEvolutionLib::MainWindow::bestNetworkFitness2 [private]

Definition at line 114 of file GenerateGAInputs.h.

Referenced by init(), reset(), setBestNetworkFitness2(), setupGAOptions(), and ~MainWindow().

int NetworkEvolutionLib::MainWindow::bestNetworkLineage1 [private]

Definition at line 110 of file GenerateGAInputs.h.

Referenced by init(), reset(), setBestNetworkLineage1(), setupGAOptions(), and ~MainWindow().

int NetworkEvolutionLib::MainWindow::bestNetworkLineage2 [private]

Definition at line 114 of file GenerateGAInputs.h.

Referenced by init(), reset(), setBestNetworkLineage2(), setupGAOptions(), and ~MainWindow().

int NetworkEvolutionLib::MainWindow::bestNetworkScript1 [private]

Definition at line 110 of file GenerateGAInputs.h.

Referenced by init(), reset(), setBestNetworkScript1(), setupGAOptions(), and ~MainWindow().

int NetworkEvolutionLib::MainWindow::bestNetworkScript2 [private]

Definition at line 114 of file GenerateGAInputs.h.

Referenced by init(), reset(), setBestNetworkScript2(), setupGAOptions(), and ~MainWindow().

int NetworkEvolutionLib::MainWindow::bestNetworkSize1 [private]

Definition at line 110 of file GenerateGAInputs.h.

Referenced by init(), reset(), setBestNetworkSize1(), setupGAOptions(), and ~MainWindow().

int NetworkEvolutionLib::MainWindow::bestNetworkSize2 [private]

Definition at line 114 of file GenerateGAInputs.h.

Referenced by init(), reset(), setBestNetworkSize2(), setupGAOptions(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::bi_bi [private]

Definition at line 70 of file GenerateGAInputs.h.

Referenced by init(), reset(), setBiBi(), setupMassActionNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::bi_uni [private]

Definition at line 70 of file GenerateGAInputs.h.

Referenced by init(), reset(), setBiUni(), setupMassActionNetwork(), and ~MainWindow().

Tinkercell::CodeEditor* NetworkEvolutionLib::MainWindow::codeEditor [private]

Definition at line 54 of file GenerateGAInputs.h.

Referenced by clear(), fitnessSelected(), run(), save(), and setupEditor().

QString NetworkEvolutionLib::MainWindow::codeFile [private]

Definition at line 105 of file GenerateGAInputs.h.

Referenced by reset(), setCodeFile(), setupGAOptions(), and ~MainWindow().

QString NetworkEvolutionLib::MainWindow::compileCommand [private]

Definition at line 108 of file GenerateGAInputs.h.

Referenced by reset(), run(), setCodeFile(), setCompileCommand(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::crossover_rate [private]

Definition at line 98 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_crossover_rate(), setupNetworkOptions(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_max_alpha [private]

Definition at line 79 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_max_alpha(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_max_h [private]

Definition at line 79 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_max_h(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_max_kcat [private]

Definition at line 79 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_max_kcat(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_max_log_keq [private]

Definition at line 79 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_max_log_keq(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_max_p_half [private]

Definition at line 79 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_max_p_half(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_max_s_half [private]

Definition at line 79 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_max_s_half(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_min_alpha [private]

Definition at line 78 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_min_alpha(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_min_h [private]

Definition at line 78 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_min_h(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_min_kcat [private]

Definition at line 78 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_min_kcat(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_min_log_keq [private]

Definition at line 78 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_min_log_keq(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_min_p_half [private]

Definition at line 78 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_min_p_half(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_min_s_half [private]

Definition at line 78 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_min_s_half(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_mutate_add [private]

Definition at line 80 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_mutate_add(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_mutate_alpha [private]

Definition at line 80 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_mutate_alpha(), and setupEnzymeNetwork().

double NetworkEvolutionLib::MainWindow::enzyme_mutate_enzyme [private]

Definition at line 80 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_mutate_enzyme(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_mutate_h [private]

Definition at line 80 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_mutate_h(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_mutate_k_cat [private]

Definition at line 80 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_mutate_k_cat(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_mutate_k_eq [private]

Definition at line 80 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_mutate_k_eq(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_mutate_p_half [private]

Definition at line 80 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_mutate_p_half(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_mutate_remove [private]

Definition at line 80 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_mutate_remove(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_mutate_s_half [private]

Definition at line 80 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_enzyme_mutate_s_half(), setupEnzymeNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::enzyme_prob [private]

Definition at line 103 of file GenerateGAInputs.h.

Referenced by init(), reset(), setEnzymeProb(), setupEnzymeNetwork(), useEnzyme(), and ~MainWindow().

QComboBox* NetworkEvolutionLib::MainWindow::fitnessComboBox [private]

Definition at line 53 of file GenerateGAInputs.h.

Referenced by fitnessSelected(), save(), and setupEditor().

int NetworkEvolutionLib::MainWindow::generations [private]

Definition at line 106 of file GenerateGAInputs.h.

Referenced by mainFunction(), reset(), run(), setGenerations(), setupGAOptions(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::grn_init_cost_per_protein [private]

Definition at line 90 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_grn_init_cost_per_protein(), setupGeneticNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::grn_init_inflow [private]

Definition at line 90 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_grn_init_inflow(), setupGeneticNetwork(), and ~MainWindow().

int NetworkEvolutionLib::MainWindow::grn_max_complex_size [private]

Definition at line 92 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_grn_max_complex_size(), setupGeneticNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::grn_max_degradation [private]

Definition at line 94 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_grn_max_degradation(), setupGeneticNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::grn_max_Ka [private]

Definition at line 94 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_grn_max_Ka(), setupGeneticNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::grn_max_Vmax [private]

Definition at line 94 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_grn_max_Vmax(), setupGeneticNetwork(), and ~MainWindow().

int NetworkEvolutionLib::MainWindow::grn_min_complex_size [private]

Definition at line 91 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_grn_min_complex_size(), setupGeneticNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::grn_min_degradation [private]

Definition at line 93 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_grn_min_degradation(), setupGeneticNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::grn_min_Ka [private]

Definition at line 93 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_grn_min_Ka(), setupGeneticNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::grn_min_Vmax [private]

Definition at line 93 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_grn_min_Vmax(), setupGeneticNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::grn_mutate_add_gene [private]

Definition at line 95 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_grn_mutate_add_gene(), setupGeneticNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::grn_mutate_complex [private]

Definition at line 95 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_grn_mutate_complex(), setupGeneticNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::grn_mutate_Ka [private]

Definition at line 95 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_grn_mutate_Ka(), setupGeneticNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::grn_mutate_remove_gene [private]

Definition at line 95 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_grn_mutate_remove_gene(), setupGeneticNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::grn_mutate_Vmax [private]

Definition at line 95 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_grn_mutate_Vmax(), setupGeneticNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::grn_prob [private]

Definition at line 103 of file GenerateGAInputs.h.

Referenced by init(), reset(), setGRNProb(), setupGeneticNetwork(), useGRN(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::init_iv [private]

Definition at line 99 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_init_iv(), setupNetworkOptions(), and ~MainWindow().

int NetworkEvolutionLib::MainWindow::initPopSz [private]

Definition at line 106 of file GenerateGAInputs.h.

Referenced by mainFunction(), reset(), run(), setInitPopSz(), setupGAOptions(), and ~MainWindow().

bool NetworkEvolutionLib::MainWindow::lineageTracking [private]

Definition at line 101 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_lineageTracking(), setupNetworkOptions(), and ~MainWindow().

QString NetworkEvolutionLib::MainWindow::logFile [private]

Definition at line 105 of file GenerateGAInputs.h.

Referenced by init(), reset(), setLogFile(), setupGAOptions(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::ma_max_constant [private]

Definition at line 71 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_ma_max_constant(), setupMassActionNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::ma_min_constant [private]

Definition at line 71 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_ma_min_constant(), setupMassActionNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::ma_mutate_add_reaction [private]

Definition at line 72 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_ma_mutate_add_reaction(), setupMassActionNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::ma_mutate_constants [private]

Definition at line 72 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_ma_mutate_constants(), setupMassActionNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::ma_mutate_remove_reaction [private]

Definition at line 72 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_ma_mutate_remove_reaction(), setupMassActionNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::mass_action_prob [private]

Definition at line 103 of file GenerateGAInputs.h.

Referenced by init(), reset(), setMassActionProb(), setupMassActionNetwork(), useMassAction(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::max_fitness [private]

Definition at line 118 of file GenerateGAInputs.h.

Referenced by callbackFunction(), reset(), setMaxFitness(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::mutate_iv [private]

Definition at line 100 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_mutate_iv(), setupNetworkOptions(), and ~MainWindow().

QList<QPointF> NetworkEvolutionLib::MainWindow::nextGen [private]

Definition at line 65 of file RunEvolution.h.

Referenced by insertTextItem().

double NetworkEvolutionLib::MainWindow::no_product [private]

Definition at line 70 of file GenerateGAInputs.h.

Referenced by init(), reset(), setNoProduct(), setupMassActionNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::no_reactant [private]

Definition at line 70 of file GenerateGAInputs.h.

Referenced by init(), reset(), setNoReactant(), setupMassActionNetwork(), and ~MainWindow().

int NetworkEvolutionLib::MainWindow::popSz [private]

Definition at line 106 of file GenerateGAInputs.h.

Referenced by mainFunction(), reset(), run(), setPopSz(), setupGAOptions(), and ~MainWindow().

QList<QPointF> NetworkEvolutionLib::MainWindow::previousGen [private]

Definition at line 65 of file RunEvolution.h.

Referenced by insertTextItem().

QProcess NetworkEvolutionLib::MainWindow::proc

Definition at line 48 of file GenerateGAInputs.h.

Referenced by main(), and run().

double NetworkEvolutionLib::MainWindow::prot_max_ka [private]

Definition at line 75 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_prot_max_ka(), setupProteinNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::prot_max_total [private]

Definition at line 75 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_prot_max_total(), setupProteinNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::prot_max_vmax [private]

Definition at line 75 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_prot_max_vmax(), setupProteinNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::prot_min_ka [private]

Definition at line 74 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_prot_min_ka(), setupProteinNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::prot_min_total [private]

Definition at line 74 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_prot_min_total(), setupProteinNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::prot_min_vmax [private]

Definition at line 74 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_prot_min_vmax(), setupProteinNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::prot_mutate_addremove [private]

Definition at line 76 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_prot_mutate_addremove(), setupProteinNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::prot_mutate_parameter [private]

Definition at line 76 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_prot_mutate_parameter(), setupProteinNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::prot_mutate_rewire [private]

Definition at line 76 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_prot_mutate_rewire(), setupProteinNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::prot_mutate_total [private]

Definition at line 76 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_prot_mutate_total(), setupProteinNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::protein_net_prob [private]

Definition at line 103 of file GenerateGAInputs.h.

Referenced by init(), reset(), setProteinProb(), setupProteinNetwork(), useProtein(), and ~MainWindow().

int NetworkEvolutionLib::MainWindow::reactions_max [private]

Definition at line 97 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_max_reactions(), setupNetworkOptions(), and ~MainWindow().

int NetworkEvolutionLib::MainWindow::reactions_min [private]

Definition at line 97 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_min_reactions(), setupNetworkOptions(), and ~MainWindow().

int NetworkEvolutionLib::MainWindow::runs [private]

Definition at line 106 of file GenerateGAInputs.h.

Referenced by mainFunction(), reset(), setRuns(), and ~MainWindow().

QGraphicsScene* NetworkEvolutionLib::MainWindow::scene [private]

Definition at line 64 of file RunEvolution.h.

Referenced by insertTextItem().

QString NetworkEvolutionLib::MainWindow::seeds [private]

Definition at line 107 of file GenerateGAInputs.h.

Referenced by init(), setSeed(), and showSeed().

int NetworkEvolutionLib::MainWindow::seeds2 [private]

Definition at line 114 of file GenerateGAInputs.h.

Referenced by init(), reset(), setupGAOptions(), and ~MainWindow().

QString NetworkEvolutionLib::MainWindow::selectionFunction [private]

Definition at line 121 of file GenerateGAInputs.h.

Referenced by init(), reset(), setSelectionFunc(), and ~MainWindow().

QStringList NetworkEvolutionLib::MainWindow::selectionFunctions [private]

Definition at line 120 of file GenerateGAInputs.h.

Referenced by MainWindow(), reset(), and setupGAOptions().

int NetworkEvolutionLib::MainWindow::species_max [private]

Definition at line 97 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_max_species(), setupNetworkOptions(), and ~MainWindow().

int NetworkEvolutionLib::MainWindow::species_min [private]

Definition at line 97 of file GenerateGAInputs.h.

Referenced by init(), reset(), set_min_species(), setupNetworkOptions(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::uni_bi [private]

Definition at line 70 of file GenerateGAInputs.h.

Referenced by init(), reset(), setUniBi(), setupMassActionNetwork(), and ~MainWindow().

double NetworkEvolutionLib::MainWindow::uni_uni [private]

Definition at line 70 of file GenerateGAInputs.h.

Referenced by init(), reset(), setUniUni(), setupMassActionNetwork(), and ~MainWindow().

The documentation for this class was generated from the following files:
Generated on Tue Nov 3 23:17:14 2009 for Network Evolution Library by  doxygen 1.6.1