module Biobase.Taxonomy.Import
-- | NCBI taxonomy dump nodes and names in the input directory path are
-- parsed and a SimpleTaxon tree is generated.
readTaxonomy :: String -> IO (Either ParseError (Gr SimpleTaxon Double))
-- | NCBI taxonomy dump nodes and names in the input directory path are
-- parsed and a SimpleTaxon tree with scientific names for each node is
-- generated.
readNamedTaxonomy :: String -> IO (Either ParseError (Gr SimpleTaxon Double))
-- | NCBI taxonomy dump nodes and names in the input directory path are
-- parsed and a SimpleTaxon tree is generated.
parseTaxonomy :: String -> Either ParseError (Gr SimpleTaxon Double)
-- | parse NCBITaxCitations from input string
parseNCBITaxCitations :: String -> Either ParseError [TaxCitation]
-- | parse NCBITaxCitations from input filePath
readNCBITaxCitations :: String -> IO (Either ParseError [TaxCitation])
-- | parse NCBITaxDelNodes from input string
parseNCBITaxDelNodes :: String -> Either ParseError [TaxDelNode]
-- | parse NCBITaxDelNodes from input filePath
readNCBITaxDelNodes :: String -> IO (Either ParseError [TaxDelNode])
-- | parse NCBITaxDivisons from input string
parseNCBITaxDivisions :: String -> Either ParseError [TaxDivision]
-- | parse NCBITaxDivisons from input filePath
readNCBITaxDivisions :: String -> IO (Either ParseError [TaxDivision])
-- | parse NCBITaxGenCodes from input string
parseNCBITaxGenCodes :: String -> Either ParseError [TaxGenCode]
-- | parse NCBITaxGenCodes from input filePath
readNCBITaxGenCodes :: String -> IO (Either ParseError [TaxGenCode])
-- | parse NCBITaxMergedNodes from input string
parseNCBITaxMergedNodes :: String -> Either ParseError [TaxMergedNode]
-- | parse NCBITaxMergedNodes from input filePath
readNCBITaxMergedNodes :: String -> IO (Either ParseError [TaxMergedNode])
-- | parse NCBITaxNames from input string
parseNCBITaxNames :: String -> Either ParseError [TaxName]
-- | parse NCBITaxNames from input filePath
readNCBITaxNames :: String -> IO (Either ParseError [TaxName])
-- | parse NCBITaxNames from input string
parseNCBITaxNodes :: String -> Either ParseError TaxNode
-- | parse NCBITaxCitations from input filePath
readNCBITaxNodes :: String -> IO (Either ParseError [TaxNode])
-- | parse NCBISimpleTaxNames from input string
parseNCBISimpleTaxons :: String -> Either ParseError SimpleTaxon
-- | parse NCBITaxCitations from input filePath
readNCBISimpleTaxons :: String -> IO (Either ParseError [SimpleTaxon])
-- | Parse the input as NCBITax datatype
readNCBITaxonomyDatabase :: String -> IO (Either [String] NCBITaxDump)
-- | Functions for processing of taxonomy data.
module Biobase.Taxonomy.Utils
-- | Extract a subtree correpsonding to input node paths to root. Only
-- nodes in level number distance to root are included. Used in
-- Ids2TreeCompare tool.
compareSubTrees :: [Gr SimpleTaxon Double] -> (Int, Gr CompareTaxon 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.
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. If a Rank
-- is provided, all node that are less or equal are omitted
extractTaxonomySubTreebyRank :: [Node] -> Gr SimpleTaxon Double -> Maybe Rank -> Gr SimpleTaxon Double
-- | Returns path between 2 maybe nodes. Used in TreeDistance tool.
safeNodePath :: Maybe Node -> Gr SimpleTaxon Double -> Maybe Node -> Either String Path
-- | Extract parent node with specified Rank
getParentbyRank :: Node -> Gr SimpleTaxon Double -> Maybe Rank -> Maybe (Node, SimpleTaxon)
-- | Functions for visualization of taxonomy data.
module Biobase.Taxonomy.Visualization
-- | Draw tree comparison graph in dot format. Used in Ids2TreeCompare
-- tool.
drawTaxonomyComparison :: Bool -> (Int, Gr CompareTaxon Double) -> String
-- | Draw graph in dot format. Used in Ids2Tree tool.
drawTaxonomy :: Bool -> Gr SimpleTaxon Double -> String
-- | Write tree representation either as dot or json to provided file path
writeTree :: String -> String -> Bool -> Gr SimpleTaxon Double -> IO ()
-- | Write tree representation as dot to provided file path. Graphviz tools
-- like dot can be applied to the written .dot file to generate e.g.
-- svg-format images.
writeDotTree :: String -> Bool -> Gr SimpleTaxon Double -> IO ()
-- | Write tree representation as json to provided file path. You can
-- visualize the result for example with 3Djs.
writeJsonTree :: String -> Gr SimpleTaxon Double -> IO ()
-- | Functions for parsing, processing and visualization of taxonomy data.
module Biobase.Taxonomy