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The AHA Model
Revision: 12809
Reference implementation 04 (HEDG02_04)
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The AHA Model
Revision: 12809
Reference implementation 04 (HEDG02_04)
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The Genome objects of the AHA Model. More...
Go to the source code of this file.
Data Types | |
| type | the_genome::gene |
| This describes an individual gene object. See the genome structure for as general description and gene for details. More... | |
| type | the_genome::chromosome |
| This type describes the chromosome object. Chromosome consists of an array of alleles and a descriptive string label. See "the genome structure" for as general description and "chromosome" for details. More... | |
| type | the_genome::individual_genome |
| This type describes parameters of the individual agent's genome The genome is an array of allocatable the_genome::chromosome objects, different kinds of agents may have different genomes with different number of chromosomes. See "the genome structure" for as general description and "genome" for details. More... | |
Modules | |
| module | the_genome |
| Definition the genetic architecture of the agent. | |
Functions/Subroutines | |
| elemental subroutine | the_genome::chromosome_sort_rank_id (this) |
Sort GENE objects within the CHROMOSOME by their rank_id. The two subroutines qsort and qs_partition_rank_id are a variant of the recursive quick-sort algorithm adapted for sorting integer components of the the CHROMOSOME object. More... | |
| recursive pure subroutine | qsort (A) |
qsort and qs_partition_ are the two parts of the recursive sort algorithm qsort is the recursive frontend. Sorts genes within the chromosome by components of the array of alleles. More... | |
| pure subroutine | qs_partition_rank_id (A, marker) |
qsort and qs_partition_ are the two parts of the recursive sort algorithm qs_partition_rank_id is a pivot backend, here it sorts genes within the chromosome object by integer rank_id components of the genes. More... | |
| subroutine | the_genome::allele_init_random (this) |
| Initialises allele with a random integer. Note that we do not set the labels for the alleles here during the random initialisation. More... | |
| elemental subroutine | the_genome::allele_create_zero (this) |
| Create allele with zero value. We don't set labels for alleles here. More... | |
| subroutine | the_genome::allele_label_init_random (this) |
| The (pair of) alleles here are assigned random string labels Not sure if that is necessary for any application though. More... | |
| elemental subroutine | the_genome::allele_label_set (this, label) |
| Set labels for the alleles. The subroutine parameter is array of labels. More... | |
| elemental character(len=label_length) function | the_genome::allele_label_get (this) |
| Get the i-th allele label. More... | |
| elemental subroutine | the_genome::allele_value_set (this, set_value, nr) |
| Set a single value of the allele additive component. More... | |
| pure subroutine | the_genome::alleles_value_vector_set (this, values) |
| Set values of the alleles as a vector, i.e. sets the whole gene values. More... | |
| elemental integer function | the_genome::allele_value_get (this, nr) |
| Get the value of the allele. More... | |
| pure subroutine | the_genome::allele_values_vector_get (this, values) |
| Get the vector of all values of the alleles, i.e. gets the gene values. More... | |
| elemental subroutine | the_genome::allele_rank_id_set (this, value_id) |
| subroutine | the_genome::allele_mutate_random (this, prob) |
| Introduce a random point mutation to a random allele component. More... | |
| subroutine | the_genome::allele_mutate_random_batch (this, prob) |
| Introduce a random mutation of the whole set of additive allele components. More... | |
| subroutine | the_genome::chromosome_init_allocate_random (this, length, label) |
| This subroutine initialises the chromosome with, and allocates, random alleles, sets one of them randomly dominant and optionally defines the chromosome label. More... | |
| subroutine | the_genome::chromosome_create_allocate_zero (this, length, label) |
| Init a new chromosome, zero, non-random. More... | |
| elemental subroutine | the_genome::chromosome_recalculate_rank_ids (this) |
| This subroutine recalculates rank_id indices for consecutive gene objects within the chromosome. This may be necessary after reordering by random relocation mutation. More... | |
| subroutine | the_genome::chromosome_mutate_relocate_swap_random (this, prob) |
| Mutate within the same chromosome, relocate a gene (unit of alleles) to a different random position within the same chromosome, the misplaced gene moves to the relocated gene position, so they are just swap. More... | |
| subroutine | the_genome::chromosome_mutate_relocate_shift_random (this, prob) |
Mutate within the same chromosome, relocate a gene (unit of alleles) to a different random position within the same chromosome, shifting all other genes within the chromosome down one position. This works as follows: first, we randomly determine the gene to relocate, assign it a new random rank_id. Then re-sort the chromosome according to the new ranks with qsort with the qs_partition_rank_id backend. More... | |
| subroutine | the_genome::genome_init_random (this, label) |
| Initialise the genome at random, and set sex as determined by the sex determination locus. More... | |
| subroutine | the_genome::genome_create_zero (this) |
| Create a new empty genome, and set sex as determined by the sex determination locus. Genome values are from parents using inherit functions. More... | |
| subroutine | the_genome::genome_label_set (this, label) |
| Label genome. If label is not provided, make a random string. More... | |
| elemental character(len=label_length) function | the_genome::genome_label_get (this) |
| Accessor function to get the genome label. The label is a kind of a (random) text string name of the genome and the individual agent. More... | |
| subroutine | the_genome::genome_sex_determine_init (this) |
| Sex determination initialisation subroutine. More... | |
| elemental logical function | the_genome::genome_get_sex_is_male (this) |
| Get the logical sex ID of the genome object component. More... | |
| elemental logical function | the_genome::genome_get_sex_is_female (this) |
| Get the logical sex ID of the genome object component. More... | |
| elemental character(len=label_length) function | the_genome::genome_get_sex_label (this) |
| Get the descriptive sex label: male or female. More... | |
| elemental subroutine | the_genome::genome_individual_set_alive (this) |
| Set the individual to be alive, normally this function is used after init or birth. More... | |
| elemental subroutine | the_genome::genome_individual_set_dead (this) |
| Set the individual to be dead. Note that this function does not deallocate the individual agent object, this may be a separate destructor function. More... | |
| elemental logical function | the_genome::genome_individual_check_alive (this) |
| Check if the individual is alive. More... | |
| elemental logical function | the_genome::genome_individual_check_dead (this) |
Check if the individual is dead (the opposite of is_alive). More... | |
| subroutine | the_genome::genome_individual_recombine_homol_full_rand_alleles (this, mother, father, exchange_ratio) |
Internal genetic recombination backend, exchange individual alleles between homologous chromosomes in mother and father genomes to form the this (offspring) genome. Fully random recombination. More... | |
| subroutine | the_genome::genome_individual_recombine_homol_part_rand_alleles (this, mother, father, exchange_ratio) |
Internal genetic recombination backend, exchange individual alleles between homologous chromosomes in mother and father genomes to form the this (offspring) genome. Partially random recombination, identical across the homologous chromosomes. More... | |
| subroutine | the_genome::genome_individual_crossover_homol_fix (this, mother, father, pattern_matrix) |
Internal fixed genetic crossover backend, exchange blocks of alleles between homologous chromosomes in mother and father genomes to form the this (offspring) genome. More... | |
| subroutine | the_genome::genome_mutate_wrapper (this, p_point, p_set, p_swap, p_shift) |
| Perform a probabilistic random mutation(s) on the individual genome. This is a high level wrapper to build mutations from various components. More... | |
Neuronal response functions | |
There are two separate functions that produce a trait value from the genotype. The procedure | |
| subroutine | the_genome::trait_init_genotype_gamma2gene (this, this_trait, g_p_matrix, init_val, gerror_cv, label) |
| Initialise an individual trait of the agent that depends on the genotype. This can be any trait upwards in the class hierarchy. More... | |
| subroutine | the_genome::trait_set_genotype_gamma2gene (this, this_trait, g_p_matrix, init_val, gerror_cv) |
| Set an individual trait of the agent that depends on the genotype. This can be any trait upwards in the class hierarchy. More... | |
The genotype to phenotype functions based on fixed linear | |
transformation. | |
| subroutine | the_genome::trait_init_linear_sum_additive_comps_2genes_r (this, this_trait, g_p_matrix, phenotype_min, phenotype_max, label) |
| Initialise an individual trait of the agent that depends on the genotype. This can be any trait upwards in the class hierarchy. More... | |
| subroutine | the_genome::trait_set_linear_sum_additive_comps_2genes_r (this, this_trait, g_p_matrix, phenotype_min, phenotype_max) |
| Set an individual trait of the agent that depends on the genotype. This can be any trait upwards in the class hierarchy. More... | |
Variables | |
| character(len= *), parameter, private | the_genome::modname = "(THE_GENOME)" |
| recursive pure subroutine chromosome_sort_rank_id::qsort | ( | type(gene), dimension(:), intent(inout) | A | ) |
qsort and qs_partition_ are the two parts of the recursive sort algorithm qsort is the recursive frontend. Sorts genes within the chromosome by components of the array of alleles.
| [in,out] | a | [inout] input array to be sorted. It has the same type as the individual component objects of the array-object that we are going to sort. |
Definition at line 334 of file m_genome.f90.
| pure subroutine chromosome_sort_rank_id::qs_partition_rank_id | ( | type(gene), dimension(:), intent(inout) | A, |
| integer, intent(out) | marker | ||
| ) |
qsort and qs_partition_ are the two parts of the recursive sort algorithm qs_partition_rank_id is a pivot backend, here it sorts genes within the chromosome object by integer rank_id components of the genes.
| [in,out] | a | [inout] input array to be sorted. |
| [out] | marker | internal pivot marker. |
x, has the same type as the sorted object component.Definition at line 355 of file m_genome.f90.
1.9.1