ptreegen.parsimony.SmallParsimony Class Reference

Represents a solution to the small parsimony problem (tree is known and we are intersted in the parsimony score of the tree). More...

Public Member Functions
def	__init__
	Constructor takes tree and a corresponding alignment as input and saves references to them as SmallParsimony::_tree and SmallParsimony::_alignment.
def	cost
	A getter for the cost value.

Private Member Functions
def	_solve
	Iteraterates over each column of the alignment and computes the parsimony score for each.
def	_assign
	Recursive method implementing the Fitch's algorithm.

Private Attributes
	_tree
	Refernce to the tree being scored.
	_alignment
	Refernce to the coresponding alignment.
	_sequencesDict
	Associates sequence id string with a sequence instance.
	_treeCharacterDict
	A dictionary that stores the character sets asigned to each node everytime the SmallParsimony::_assign() method is executed for each column of the alignment.
	_cost
	Variable to store the intermediate results.

Detailed Description

Represents a solution to the small parsimony problem (tree is known and we are intersted in the parsimony score of the tree).

It implements the Fitch's algorithm to score the tree, therefore the input tree should be a rooted binary tree, even though this implementation is extended to work with any type of tree.

See Also

LargeParsimony

Definition at line 26 of file parsimony.py.

Constructor & Destructor Documentation

def ptreegen.parsimony.SmallParsimony.__init__	(		self,
			tree,
			alignment
	)

Constructor takes tree and a corresponding alignment as input and saves references to them as SmallParsimony::_tree and SmallParsimony::_alignment.

Parameters

tree	the tree to be scored
alignment	alignment corresponding to the input tree

Definition at line 35 of file parsimony.py.

    def __init__(self, tree, alignment):
        self._tree = tree
        self._alignment = alignment
        self._sequencesDict = {x.id : x.seq for x in list(alignment)}
        leaf_names = set(tree.get_leaf_names())
        if len(self._sequencesDict) != len(leaf_names):
            raise RuntimeError("Number of sequnces in alignment:\n" + repr(alignment)
                               + "\ndoes not match the number of leaves in tree:\n" + repr(tree))
        for seq_id in self._sequencesDict:
            if seq_id not in leaf_names:
                raise RuntimeError("Sequence ID (" + seq_id
                                   + ") does not match any leaf in tree:\n" + repr(tree))

        self._treeCharacterDict = dict()
        self._cost = float('inf')