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A Hier instance is a container for
the set of taxonomic ranks used in the classification.
Its constructor is not designed to be called directly;
that constructor is used only in the initialization of
the Txny instance.
# - - - - - c l a s s H i e r - - - - -
class Hier:
"""Represents the set of ranks used in the classification.
Exports:
Hier ( rankSetNode ):
[ rankSetNode is a RANK_SET_N Element ->
return a new Hier instance made from rankSetNode ]
.txKeyLen:
[ number of characters in a taxonomic key with this
hierarchy ]
.canParentHaveChild ( p, c ):
[ p and c are Rank instances ->
if there exists a non-optional rank m in self.__rankList
such that p.depth < m.depth < c.depth ->
return 0
else -> return 1 ]
.genusRank():
[ if self has a genus rank ->
return that rank as a Rank instance
else -> return None ]
.subgenusRank():
[ if self has a subgenus rank ->
return that rank as a Rank instance
else -> return None ]
.speciesRank():
[ if self has a species rank ->
return that rank as a Rank instance
else -> return None ]
.formRank():
[ if self has a form rank ->
return that rank as a Rank instance
else -> return None ]
.lookupRankCode ( rankCode ):
[ rankCode is a string ->
if there is a rank in self whose .code equals rankCode ->
return the corresponding Rank instance
else -> raise KeyError ]
.__getitem__ ( self, n ):
[ n is an integer ->
if n is the rank depth of a rank in self ->
return that rank
else -> raise IndexError ]
.__iter__ ( self ):
[ return an iterator that yields the ranks in self
from highest to deepest ]
.__len__ ( self ):
[ return the number of ranks in self ]
State/Invariants:
.__rankList:
[ a list of the Rank instances in self from highest to deepest ]
.__rankCodeMap:
[ a dictionary whose values are the Rank instances in self,
and for each value the key is its .code attribute ]
"""
This is the constructor for the Hier
class. It takes as an argument a Element node representing the rankSet element.
# - - - H i e r . _ _ i n i t _ _ - - -
def __init__ ( self, rankSetNode ):
"""Constructor.
[ rankSetNode is a RANK_SET_N Element ->
return a new Hier instance made from rankSetNode ]
"""
#-- 1 --
# [ self.__rankList := a list of Rank instances made from the
# RANK_N children of rankSetNode, in the same order ]
self.__rankList = [
Rank(self, rankNode)
for rankNode in rankSetNode.findall(rnc.RANK_N) ]
#-- 2 --
# [ self.txKeyLen := sum of all child rank .keyLen attributes
# self.__rankCodeMap := entries mapping R.code |-> R for
# R the set of all ranks in self ]
self.txKeyLen = 0
self.__rankCodeMap = {}
for rank in self.__rankList:
self.txKeyLen += rank.keyLen
self.__rankCodeMap[rank.code] = rank