LoD_Comparison_Database.py

Meow

class Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.LoD_Comparison_Database.LoD_Comparison_Database

This is a database that holds all the entries of CNA_Entry objects.

LoD_Similarity_Analysis(dir_1, dir_2)

This def will obtain the max similarity percentage from the compararison of two clusters, name_1 and name_2.

Parameters

  • name_1 (int) – The name of the first cluster you would like to look for an entry in the CNA_Database.

  • name_2 (int) – The name of the second cluster you would like to look for an entry in the CNA_Database.

Returns

The result from the IDCM. This will be True if this cluster pair is in the database, False if not.

Rtypes

bool

add(dir_1, dir_2, result)

This def will obtain the CNA Information for the comparison of name_1 and name_2, and add it to the CNA_Database

Parameters

  • name_1 (int) – The name of the first cluster to compare against.

  • name_2 (int) – The name of the second cluster to compare against.

  • result (bool) – The result of the comparison of the IDCM. True if they are structurally similar by the IDCM, False if not.

are_all_entries_false(all_collections)

This method checks if all entries in the database are false. This method performs this after clusters have been removed from the population or offspring_pool due to violating the IDCM predatino operator. At this point, all entries should be false.

Parameters

all_collections (list of Organisms.GA.Collections.Collections) – This is a list of the population and the offspring pool.

check_for_issues(population)

This method check to make sure there are no issue with the LoD Database after the natural selection process

Parameters

population (Organisms.GA.Population.Population) – This is the population

get_cluster_names(order=False)

Will provide a list of all the names of all the clusters in the Collection

Parameters

order (bool) – This tag will tell this method whether the user would like the list of names given in order.

Returns

List of the names of all the clusters in the Population

get_entry(dir_1, dir_2)

This def will return the CNA results from the comparison of two clusters.

Parameters

  • name_1 (int) – the name of the first cluster you want to compare with.

  • name_2 (int) – the name of the second cluster you want to compare with.

Returns

The CNA_Entry that contains all the CNA information about the comparison of these two clusters.

Rtypes

CNA_Entry

is_cluster_pair_in_the_database(dir_1, dir_2)

Determine if a CNA entry exists for two clusters in the database

Parameters

  • name_1 (int) – The name of the first cluster you would like to look for an entry in the CNA_Database.

  • name_2 (int) – The name of the second cluster you would like to look for an entry in the CNA_Database.

Returns

True if this cluster pair is in the database, False if not.

Rtypes

bool

keys()

give the names of the clusters in the database

Returns

The list of the names of the clusters in the database.

Return type

list of ints

make_database_table()

This method prints a table of the database.

remove(dir_to_remove)

Remove all entries that exists in the database that are associated with a particular cluster.

Parameters

name_to_remove (int) – The name of the cluster you would like to remove from the CNA_Database.

reset()

Reset the LoD database with a new database

which_clusters_in_LoD_comparison_database_are_similar()

This method will return a dict of all the similar clusters in the LoD database, where pairs of clusters have been deemed structurally similar by the IDCM.

Returns

A dictionary of all the clusters that have been deemed structurally similar to each other. The format of this dictionary is {name_1: [name_2, name_3, …, names of all the clusters that name_1 is structurally similar to by the IDCM], …}.

Rtypes

dict.

class Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.LoD_Comparison_Database.Tree

This is a Tree designed for the CNA_Database to hold references of CNA_Entry.