Biobase.Taxonomy.Utils

Functions for processing of taxonomy data.

Datatypes

module Biobase.Taxonomy.Types

Processing

compareSubTrees :: [Gr SimpleTaxon Double] -> (Int, Gr CompareTaxon Double)

Extract a subtree correpsonding to input node paths to root. Only nodes in level number distance to root are included. Used in Ids2TreeCompare tool.

extractTaxonomySubTreebyLevel :: [Node] -> Gr SimpleTaxon Double -> Maybe Int -> Gr SimpleTaxon Double

Extract a subtree corresponding to input node paths to root. Only nodes in level number distance to root are included. Used in Ids2Tree tool.

extractTaxonomySubTreebyLevelNew :: [Node] -> Gr SimpleTaxon Double -> Maybe Int -> Gr SimpleTaxon Double

Extract a subtree corresponding to input node paths to root. Only nodes in level number distance to root are included. Used in Ids2Tree tool.

extractTaxonomySubTreebyRank :: [Node] -> Gr SimpleTaxon Double -> Maybe Rank -> Gr SimpleTaxon Double

Extract a subtree corresponding to input node paths to root. If a Rank is provided, all node that are less or equal are omitted

safeNodePath :: Maybe Node -> Gr SimpleTaxon Double -> Maybe Node -> Either String Path

Returns path between 2 maybe nodes. Used in TreeDistance tool.

getParentbyRank :: Node -> Gr SimpleTaxon Double -> Maybe Rank -> Maybe (Node, SimpleTaxon)

Extract parent node with specified Rank