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Each taxon in the tree is represented by one Taxon instance.
# - - - - - c l a s s T a x o n - - - - -
class Taxon:
"""Represents one taxonomic grouping of organisms.
Exports:
Taxon ( txny, parentTaxon, taxonNode ):
[ (txny is the containing Txny instance) and
(parentTaxon is the parent Taxon instance, or None for
root) and
(taxonNode is a TAXON_N Element) ->
return a new Taxon instance pointing back to txny, with
parent=parentTaxon, representing taxonNode and its
descendants ]
.txny: [ as passed to constructor, read-only ]
.parent: [ parentTaxon passed to constructor, read-only ]
.abbr:
[ if self has a standard abbreviation ->
that abbrevation
else -> None ]
.rank: [ self's taxonomic rank as a Rank instance ]
.sci: [ self's scientific name ]
.txKey:
[ self's taxonomic key, a string of digits that orders
taxa in phylogenetic order ]
.contains ( other ):
[ other is a Taxon instance in self.txny ->
if self is an ancestor of other ->
return 1
else -> return 0 ]
.nearestAncestor ( other ):
[ other is a Taxon ->
return the Taxon representing the nearest ancestor
of self and other ]
.__cmp__ ( self, other ):
[ other is a Taxon ->
if self precedes other ->
return a negative number
else if self is the same as other ->
return 0
else -> return a positive number ]
.__getitem__ ( n ):
[ n is an integer ->
if 0 <= n < (number of self's children) ->
return self's nth child, counting from 0
else -> raise KeyError ]
.__iter__ ( self ):
[ return an iterator that generates self's children
in taxonomic order ]
.__len__ ( self ):
[ return number of self's child taxa ]
.__str__ ( self ):
[ return a string representation of self ]
.eng: [ self's English name, normalized ]
.engComma: [ self's English name, inverted ]
.tex: [ self's English name with TeX markup ]
.texComma: [ same as .tex, but inverted ]
.engHtml(cssClass=None):
[ if cssClass is None ->
return self's English name as HTML with italics marked up
using the deprecated 'i' element
else ->
return self's English name as HTML with italics marked up
using a span element with class=cssClass ]
.engHtmlComma(cssClass=None):
[ like .engHtml but "Generic[, Specific]" ]
.engHtmlSubelt(node, cssClass=None):
[ (node is an et.Element) ->
if cssClass is None ->
node := node with self's English name added, italics
marked up using the deprecated 'i' element
if cssClass is a string ->
node := node with self's English name added, italics
marked up using a span element with class=cssClass ]
.engHtmlSubeltComma(node, cssClass=None):
[ same as .engHtmlSubelt but with the name inverted ]
The internal state includes a list of self's child taxa, if any.
State/Invariant:
.__rawEng:
[ English name from file, inverted, with underbars to
indicate italics ]
.__childList:
[ a list of the direct child taxa of self, in phylogenetic
order, if any, as Taxon instances ]
"""
The private .__childList attribute will
hold pointers to self's children, if any.
The argument is another Taxon. The method
returns True if and only if the other taxon is
contained in self, False
otherwise.
The logic is straightforward: if the nearest common
ancestor of self and the other
taxon is self, then self contains the other taxon.
# - - - T a x o n . c o n t a i n s - - -
def contains ( self, other ):
"""Does self contain other?
"""
#-- 1 --
# [ ancestor := nearest ancestor of self and other ]
ancestor = self.nearestAncestor(other)
#-- 2 --
return (self is ancestor)