Crate nwr

Structs

NamedMatrix

A named matrix for storing pairwise distances/scores with sequence names

ScoringMatrix

Taxon

Functions

add_comment

Adds key-value comments to a node

add_comment_kv

Adds key-value comments to a node

batch_exec

Helper function to handle batch execution of SQL statements

check_monophyly

connect_txdb

Connect taxonomy.sqlite in this dir

cosine_similarity

dot_product

Computes the dot product of two vectors a and b.

euclidean_distance

Computes the Euclidean distance between two vectors a and b.

find_rank

format_subtree

format_tree

Writes the tree with indentations

get_all_descendent

All direct or indirect descendents of the Node. The ID given as argument is included in the results.

get_ancestor

Retrieve the ancestor

get_comment_k

Retrieves value from comments of a node

get_descendent

All direct descendents of the Node, not a recursive fetchall

get_id_comment

Get hash of id-comment

get_lineage

All Nodes to the root (with ID 1)

get_name_id

Get hash of name-id

get_names

Get node names

get_tax_id

Names to Taxonomy IDs

get_taxon

IDs to Nodes

insert_parent

Insert a node in the middle of the desired node and its parent

jaccard_intersection

Computes the Jaccard intersection of two vectors a and b. The Jaccard intersection is the sum of the minimum values of corresponding elements.

jaccard_union

Computes the Jaccard union of two vectors a and b. The Jaccard union is the sum of the maximum values of corresponding elements.

match_names

match_positions

match_restrict

mean

Computes the mean (average) of a vector a.

norm_l2

Computes the L2 norm (Euclidean norm) of a vector a.

norm_l2_sq

Computes the squared L2 norm of a vector a.

nwr_path

nwr working path

order_tree_an

Sort the children of each node by alphanumeric order of labels

order_tree_list

Sort the children of each node by a list of names

order_tree_nd

Sort the children of each node by number of descendants

pearson_correlation

Computes the Pearson correlation coefficient between two vectors a and b.

read_newick

sum

Computes the sum of all elements in a vector a.

swap_parent

Swap parent-child link of a node

term_to_tax_id

Convert terms to Taxonomy IDs Accepted forms: ID; “scientific name”; scientific_name

weighted_jaccard_similarity