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.