Safe Haskell | None |
---|---|
Language | Haskell2010 |
This module contains data structures for taxonomy data
Synopsis
- data SimpleTaxon = SimpleTaxon {}
- data CompareTaxon = CompareTaxon {
- compareScientificName :: Text
- compareRank :: Rank
- inTree :: [Int]
- data Taxon = Taxon {}
- data TaxonName = TaxonName {}
- data Lineage = Lineage {}
- data LineageTaxon = LineageTaxon {}
- data NCBITaxDump = NCBITaxDump {
- taxCitations :: [TaxCitation]
- taxDelNodes :: [TaxDelNode]
- taxDivisions :: [TaxDivision]
- taxGenCodes :: [TaxGenCode]
- taxMergedNodes :: [TaxMergedNode]
- taxNames :: [TaxName]
- taxNodes :: [TaxNode]
- data TaxCitation = TaxCitation {}
- data TaxDelNode = TaxDelNode {}
- data TaxDivision = TaxDivision {}
- data TaxGenCode = TaxGenCode {}
- data TaxMergedNode = TaxMergedNode {}
- data TaxName = TaxName {
- nameTaxId :: Int
- nameTxt :: Text
- uniqueName :: ByteString
- nameClass :: ByteString
- data Rank
- = Norank
- | Form
- | Variety
- | Infraspecies
- | Subspecies
- | Speciessubgroup
- | Species
- | Speciesgroup
- | Superspecies
- | Series
- | Section
- | Subgenus
- | Genus
- | Subtribe
- | Tribe
- | Supertribe
- | Subfamily
- | Family
- | Superfamily
- | Parvorder
- | Infraorder
- | Suborder
- | Order
- | Superorder
- | Magnorder
- | Cohort
- | Legion
- | Parvclass
- | Infraclass
- | Subclass
- | Class
- | Superclass
- | Microphylum
- | Infraphylum
- | Subphylum
- | Phylum
- | Superphylum
- | Infrakingdom
- | Subkingdom
- | Kingdom
- | Superkingdom
- | Domain
- readsRank :: String -> [(Rank, String)]
- data TaxNode = TaxNode {}
- data SimpleGene2Accession = SimpleGene2Accession {}
- data Gene2Accession = Gene2Accession {
- taxIdEntry :: Int
- geneID :: Int
- status :: ByteString
- rnaNucleotideAccessionVersion :: ByteString
- rnaNucleotideGi :: ByteString
- proteinAccessionVersion :: ByteString
- proteinGi :: ByteString
- genomicNucleotideAccessionVersion :: ByteString
- genomicNucleotideGi :: ByteString
- startPositionOnTheGenomicAccession :: ByteString
- endPositionOnTheGenomicAccession :: ByteString
- orientation :: ByteString
- assembly :: ByteString
- maturePeptideAccessionVersion :: ByteString
- maturePeptideGi :: ByteString
- simpleTaxonJSONValue :: Gr SimpleTaxon Double -> Node -> Value
Documentation
data SimpleTaxon Source #
SimpleTaxon only contains the most relevant fields of a taxonomy entry. For all annotaded fields use the Taxon datatype and its associated functions
SimpleTaxon | |
|
Instances
Eq SimpleTaxon Source # | |
Defined in Biobase.Taxonomy.Types (==) :: SimpleTaxon -> SimpleTaxon -> Bool # (/=) :: SimpleTaxon -> SimpleTaxon -> Bool # | |
Read SimpleTaxon Source # | |
Defined in Biobase.Taxonomy.Types readsPrec :: Int -> ReadS SimpleTaxon # readList :: ReadS [SimpleTaxon] # readPrec :: ReadPrec SimpleTaxon # readListPrec :: ReadPrec [SimpleTaxon] # | |
Show SimpleTaxon Source # | |
Defined in Biobase.Taxonomy.Types showsPrec :: Int -> SimpleTaxon -> ShowS # show :: SimpleTaxon -> String # showList :: [SimpleTaxon] -> ShowS # | |
ToJSON (Gr SimpleTaxon Double) Source # | |
Defined in Biobase.Taxonomy.Types toJSON :: Gr SimpleTaxon Double -> Value # toEncoding :: Gr SimpleTaxon Double -> Encoding # toJSONList :: [Gr SimpleTaxon Double] -> Value # toEncodingList :: [Gr SimpleTaxon Double] -> Encoding # |
data CompareTaxon Source #
Datastructure for tree comparisons
CompareTaxon | |
|
Instances
Eq CompareTaxon Source # | |
Defined in Biobase.Taxonomy.Types (==) :: CompareTaxon -> CompareTaxon -> Bool # (/=) :: CompareTaxon -> CompareTaxon -> Bool # | |
Read CompareTaxon Source # | |
Defined in Biobase.Taxonomy.Types readsPrec :: Int -> ReadS CompareTaxon # readList :: ReadS [CompareTaxon] # | |
Show CompareTaxon Source # | |
Defined in Biobase.Taxonomy.Types showsPrec :: Int -> CompareTaxon -> ShowS # show :: CompareTaxon -> String # showList :: [CompareTaxon] -> ShowS # |
Data structure for Entrez taxonomy fetch result
Taxon | |
|
Instances
Lineage Taxons denote all parent Taxonomy nodes of a node retrieved by Entrez fetch
data LineageTaxon Source #
Lineage Taxons denote all parent Taxonomy nodes of a node retrieved by Entrez fetch
Instances
Eq LineageTaxon Source # | |
Defined in Biobase.Taxonomy.Types (==) :: LineageTaxon -> LineageTaxon -> Bool # (/=) :: LineageTaxon -> LineageTaxon -> Bool # | |
Show LineageTaxon Source # | |
Defined in Biobase.Taxonomy.Types showsPrec :: Int -> LineageTaxon -> ShowS # show :: LineageTaxon -> String # showList :: [LineageTaxon] -> ShowS # |
data NCBITaxDump Source #
NCBI Taxonomy database dump hierachichal data structure as defined in ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_readme.txt
NCBITaxDump | |
|
Instances
Eq NCBITaxDump Source # | |
Defined in Biobase.Taxonomy.Types (==) :: NCBITaxDump -> NCBITaxDump -> Bool # (/=) :: NCBITaxDump -> NCBITaxDump -> Bool # | |
Read NCBITaxDump Source # | |
Defined in Biobase.Taxonomy.Types readsPrec :: Int -> ReadS NCBITaxDump # readList :: ReadS [NCBITaxDump] # readPrec :: ReadPrec NCBITaxDump # readListPrec :: ReadPrec [NCBITaxDump] # | |
Show NCBITaxDump Source # | |
Defined in Biobase.Taxonomy.Types showsPrec :: Int -> NCBITaxDump -> ShowS # show :: NCBITaxDump -> String # showList :: [NCBITaxDump] -> ShowS # |
data TaxCitation Source #
Datastructure for entries of Taxonomy database dump citations file
Instances
Eq TaxCitation Source # | |
Defined in Biobase.Taxonomy.Types (==) :: TaxCitation -> TaxCitation -> Bool # (/=) :: TaxCitation -> TaxCitation -> Bool # | |
Read TaxCitation Source # | |
Defined in Biobase.Taxonomy.Types readsPrec :: Int -> ReadS TaxCitation # readList :: ReadS [TaxCitation] # readPrec :: ReadPrec TaxCitation # readListPrec :: ReadPrec [TaxCitation] # | |
Show TaxCitation Source # | |
Defined in Biobase.Taxonomy.Types showsPrec :: Int -> TaxCitation -> ShowS # show :: TaxCitation -> String # showList :: [TaxCitation] -> ShowS # |
data TaxDelNode Source #
Datastructure for entries of Taxonomy database dump deleted nodes file
Instances
Eq TaxDelNode Source # | |
Defined in Biobase.Taxonomy.Types (==) :: TaxDelNode -> TaxDelNode -> Bool # (/=) :: TaxDelNode -> TaxDelNode -> Bool # | |
Read TaxDelNode Source # | |
Defined in Biobase.Taxonomy.Types readsPrec :: Int -> ReadS TaxDelNode # readList :: ReadS [TaxDelNode] # readPrec :: ReadPrec TaxDelNode # readListPrec :: ReadPrec [TaxDelNode] # | |
Show TaxDelNode Source # | |
Defined in Biobase.Taxonomy.Types showsPrec :: Int -> TaxDelNode -> ShowS # show :: TaxDelNode -> String # showList :: [TaxDelNode] -> ShowS # |
data TaxDivision Source #
Datastructure for entries of Taxonomy database dump division file
Instances
Eq TaxDivision Source # | |
Defined in Biobase.Taxonomy.Types (==) :: TaxDivision -> TaxDivision -> Bool # (/=) :: TaxDivision -> TaxDivision -> Bool # | |
Read TaxDivision Source # | |
Defined in Biobase.Taxonomy.Types readsPrec :: Int -> ReadS TaxDivision # readList :: ReadS [TaxDivision] # readPrec :: ReadPrec TaxDivision # readListPrec :: ReadPrec [TaxDivision] # | |
Show TaxDivision Source # | |
Defined in Biobase.Taxonomy.Types showsPrec :: Int -> TaxDivision -> ShowS # show :: TaxDivision -> String # showList :: [TaxDivision] -> ShowS # |
data TaxGenCode Source #
Datastructure for entries of Taxonomy database dump gencode file
TaxGenCode | |
|
Instances
Eq TaxGenCode Source # | |
Defined in Biobase.Taxonomy.Types (==) :: TaxGenCode -> TaxGenCode -> Bool # (/=) :: TaxGenCode -> TaxGenCode -> Bool # | |
Read TaxGenCode Source # | |
Defined in Biobase.Taxonomy.Types readsPrec :: Int -> ReadS TaxGenCode # readList :: ReadS [TaxGenCode] # readPrec :: ReadPrec TaxGenCode # readListPrec :: ReadPrec [TaxGenCode] # | |
Show TaxGenCode Source # | |
Defined in Biobase.Taxonomy.Types showsPrec :: Int -> TaxGenCode -> ShowS # show :: TaxGenCode -> String # showList :: [TaxGenCode] -> ShowS # |
data TaxMergedNode Source #
Datastructure for entries of Taxonomy database dump mergednodes file
Instances
Eq TaxMergedNode Source # | |
Defined in Biobase.Taxonomy.Types (==) :: TaxMergedNode -> TaxMergedNode -> Bool # (/=) :: TaxMergedNode -> TaxMergedNode -> Bool # | |
Read TaxMergedNode Source # | |
Defined in Biobase.Taxonomy.Types readsPrec :: Int -> ReadS TaxMergedNode # readList :: ReadS [TaxMergedNode] # | |
Show TaxMergedNode Source # | |
Defined in Biobase.Taxonomy.Types showsPrec :: Int -> TaxMergedNode -> ShowS # show :: TaxMergedNode -> String # showList :: [TaxMergedNode] -> ShowS # |
Datastructure for entries of Taxonomy database dump names file
TaxName | |
|
Taxonomic ranks: NCBI uses the uncommon Speciessubgroup
Datastructure for entries of Taxonomy database dump nodes file
TaxNode | |
|
data SimpleGene2Accession Source #
Simple Gene2Accession table
Instances
Eq SimpleGene2Accession Source # | |
Defined in Biobase.Taxonomy.Types (==) :: SimpleGene2Accession -> SimpleGene2Accession -> Bool # (/=) :: SimpleGene2Accession -> SimpleGene2Accession -> Bool # | |
Read SimpleGene2Accession Source # | |
Defined in Biobase.Taxonomy.Types | |
Show SimpleGene2Accession Source # | |
Defined in Biobase.Taxonomy.Types showsPrec :: Int -> SimpleGene2Accession -> ShowS # show :: SimpleGene2Accession -> String # showList :: [SimpleGene2Accession] -> ShowS # |
data Gene2Accession Source #
Datastructure for Gene2Accession table
Instances
Eq Gene2Accession Source # | |
Defined in Biobase.Taxonomy.Types (==) :: Gene2Accession -> Gene2Accession -> Bool # (/=) :: Gene2Accession -> Gene2Accession -> Bool # | |
Read Gene2Accession Source # | |
Defined in Biobase.Taxonomy.Types readsPrec :: Int -> ReadS Gene2Accession # readList :: ReadS [Gene2Accession] # | |
Show Gene2Accession Source # | |
Defined in Biobase.Taxonomy.Types showsPrec :: Int -> Gene2Accession -> ShowS # show :: Gene2Accession -> String # showList :: [Gene2Accession] -> ShowS # |
simpleTaxonJSONValue :: Gr SimpleTaxon Double -> Node -> Value Source #