GenomeBase – the genomes base module

This module have the class which every representation extends, if you are planning to create a new representation, you must take a inside look into this module.

class GenomeBase.G1DBase(size)

G1DBase Class - The base class for 1D chromosomes

Parameter:size – the 1D list size

New in version 0.6: Added te G1DBase class

append(value)

Appends an item to the end of the list

Example:

>>> genome.append(44)

Parameter:value – value to be added

clearList()

Remove all genes from Genome

copy(g)

Copy genome to ‘g’

Example:

>>> genome_origin.copy(genome_destination)

Parameter:g – the destination instance

getInternalList()

Returns the internal list of the genome

... note:: this method was created to solve performance issues :rtype: the internal list

getListSize()

Returns the list supposed size

Warning

this is different from what the len(obj) returns

remove(value)

Removes an item from the list

Example:

>>> genome.remove(44)

Parameter:value – value to be added

resumeString()

Returns a resumed string representation of the Genome

setInternalList(lst)

Assigns a list to the internal list of the chromosome

Parameter:lst – the list to assign the internal list of the chromosome

class GenomeBase.GTreeBase(root_node)

GTreeBase Class - The base class for the tree genomes

Parameter:root_node – the root node of the tree

New in version 0.6: Added te GTreeBase class

clone()

Clone this GenomeBase

Return type:the clone genome

Note

If you are planning to create a new chromosome representation, you must implement this method on your class.

copy(g, node=None, node_parent=None)

Copy the current contents GTreeBase to ‘g’

Parameter:g – the destination GTreeBase tree

Note

If you are planning to create a new chromosome representation, you must implement this method on your class.

getAllNodes()

Return a new list with all nodes

Return type:the list with all nodes

getHeight()

Return the tree height

Return type:the tree height

getNodeDepth(node)

Returns the depth of a node

Return type:the depth of the node, the depth of root node is 0

getNodeHeight(node)

Returns the height of a node

Note

If the node has no childs, the height will be 0.

Return type:the height of the node

getNodesCount(start_node=None)

Return the number of the nodes on the tree starting at the start_node, if start_node is None, then the method will count all the tree nodes.

Return type:the number of nodes

getRandomNode(node_type=0)

Returns a random node from the Tree

Parameter:node_type – 0 = Any, 1 = Leaf, 2 = Branch Return type:random node

getRoot()

Return the tree root node

Return type:the tree root node

getTraversalString(start_node=None, spc=0)

Returns a tree-formated string of the tree. This method is used by the __repr__ method of the tree

Return type:a string representing the tree

processNodes(cloning=False)

Creates a cache on the tree, this method must be called every time you change the shape of the tree. It updates the internal nodes list and the internal nodes properties such as depth and height.

setRoot(root)

Sets the root of the tree

Parameter:root – the tree root node

traversal(callback, start_node=None)

Traversal the tree, this method will call the user-defined callback function for each node on the tree

Parameters:

• callback – a function
• start_node – the start node to begin the traversal

class GenomeBase.GTreeNodeBase(parent, childs=None)

GTreeNodeBase Class - The base class for the node tree genomes

Parameters:

• parent – the parent node of the node
• childs – the childs of the node, must be a list of nodes

New in version 0.6: Added te GTreeNodeBase class

addChild(child)

Adds a child to the node

Parameter:child – the node to be added

clone()

Clone this GenomeBase

Return type:the clone genome

Note

If you are planning to create a new chromosome representation, you must implement this method on your class.

copy(g)

Copy the current contents GTreeNodeBase to ‘g’

Parameter:g – the destination node

Note

If you are planning to create a new chromosome representation, you must implement this method on your class.

getChild(index)

Returns the index-child of the node

Return type:child node

getChilds()

Return the childs of the node

Warning

use .getChilds()[:] if you’ll change the list itself, like using childs.reverse(), otherwise the original genome child order will be changed.

Return type:a list of nodes

getParent()

Get the parent node of the node

Return type:the parent node

isLeaf()

Return True if the node is a leaf

Return type:True or False

replaceChild(older, newer)

Replaces a child of the node

Parameters:

• older – the child to be replaces
• newer – the new child which replaces the older

setParent(parent)

Sets the parent of the node

Parameter:parent – the parent node

class GenomeBase.GenomeBase

GenomeBase Class - The base of all chromosome representation

clone()

Clone this GenomeBase

Return type:the clone genome

Note

If you are planning to create a new chromosome representation, you must implement this method on your class.

copy(g)

Copy the current GenomeBase to ‘g’

Parameter:g – the destination genome

Note

If you are planning to create a new chromosome representation, you must implement this method on your class.

crossover

This is the reproduction function slot, the crossover. You can change the default crossover method using:

genome.crossover.set(Crossovers.G1DListCrossoverUniform)

evaluate(**args)

Called to evaluate genome

Parameter:args – this parameters will be passes to the evaluator

evaluator

This is the evaluation function slot, you can add a function with the set method:

genome.evaluator.set(eval_func)

getFitnessScore()

Get the Fitness Score of the genome

Return type:genome fitness score

getParam(key, nvl=None)

Gets an internal parameter

Example:

>>> genome.getParam("rangemax")
100

Note

All the individuals of the population shares this parameters and uses the same instance of this dict.

Parameters:

• key – the key of param
• nvl – if the key doesn’t exist, the nvl will be returned

getRawScore()

Get the Raw Score of the genome

Return type:genome raw score

initializator

This is the initialization function of the genome, you can change the default initializator using the function slot:

genome.initializator.set(Initializators.G1DListInitializatorAllele)

In this example, the initializator Initializators.G1DListInitializatorAllele() will be used to create the initial population.

initialize(**args)

Called to initialize genome

Parameter:args – this parameters will be passed to the initializator

mutate(**args)

Called to mutate the genome

Parameter:args – this parameters will be passed to the mutator Return type:the number of mutations returned by mutation operator

mutator

This is the mutator function slot, you can change the default mutator using the slot set function:

genome.mutator.set(Mutators.G1DListMutatorSwap)

resetStats()

Clear score and fitness of genome

setParams(**args)

Set the internal params

Example:

>>> genome.setParams(rangemin=0, rangemax=100, gauss_mu=0, gauss_sigma=1)

Note

All the individuals of the population shares this parameters and uses the same instance of this dict.

Parameter:args – this params will saved in every chromosome for genetic op. use