ptreegen.computation.Computation Class Reference

Parses user specified options and delegetes appropriate actions to other modules. More...

Public Member Functions
def	__init__
	Constructor initializes the object variables and calls other modules to do so.
def	parseOptions
	Parses the options passed to the constructor.
def	checkAlignment
	Checks the input alignment for duplicate taxa id strings.
def	computeTree
	Method that delegates tree computation to the appropriate module.
def	update
	Method that can be used to update the results, if the Computation class changes.
def	computeDistanceMatrix
	Computes the distance matrix from the alignment.
def	cleanAlignment
	Method responsible for the correct alignment cleaning.
def	showResults

Public Attributes
	algorithm
	The methodology used to build the tree as one of those in ptreegen::enums.
	gapPenalty
	Cost of gaps when they are included in the distance computation.
	includeGaps
	Specifies if columns with gaps should be left in the alignment or deleted.
	removePoor
	Specifies if poorly conserved regions should be removed from the alignment.
	gapCutoff
	If at least x% in column are not gaps, then the column is left in the alignment.
	pairCutoff
	If at least x% of pairs in column are identical, then the column is left in the alignment.
	seqType
	The type of the input sequence as one of ptreegen::enums.
	distFunction
	Pointer to function used to compute distances between a two sequences.
	parsIterCnt
	options
	Reference to the dictionary like object.
	alignment
	Reference to an object representing the multiple sequence alignment.
	distanceMatrix
	The distance matrix for the alignment.
	tree
	The generated tree.
	visualization

Detailed Description

Parses user specified options and delegetes appropriate actions to other modules.

Also serves as a data storage of computed results.

Definition at line 24 of file computation.py.

Constructor & Destructor Documentation

def ptreegen.computation.Computation.__init__	(		self,
			options
	)

Constructor initializes the object variables and calls other modules to do so.

Parameters

options

computation options in the form of a dictionary-like object

Definition at line 31 of file computation.py.

    def __init__(self, options):
        self.algorithm = None
        self.gapPenalty = None
        self.includeGaps = None
        self.removePoor = None
        self.gapCutoff = None
        self.pairCutoff = None
        self.seqType = None
        self.distFunction = None
        self.parsIterCnt = None
        self.options = options
        self.parseOptions(self.options)
        self.alignment = self.cleanAlignment(self.alignment)
        self.checkAlignment()
        self.distanceMatrix = None
        self.tree = self.computeTree()
        self.visualization = visualization.Visualization(self.tree, self.options)