ptreegen.visualization.Visualization Class Reference

Similar to the ptreegen::computation::Computation class. More...

Public Member Functions
def	__init__
	Besides member initialization, it handles initial styling of the tree.
def	parseOptions
	Parses options selected by the user and prepares the necessary workflow.
def	saveNewick
	Creates a file in the same directory as the input alignment and saves the tree in the Newick format.
def	savePNG
	Creates a file in the same directory as the input alignment and saves the tree as a PNG image.
def	saveSVG
	Creates a file in the same directory as the input alignment and saves the tree as an SVG image.
def	showGUI
	Shows the tree in a windowed viewer app.
def	printToStdout
	Prints the tree topology to stdout.
def	show
	Executes the workflow specified by the Visualization::_formatingMethods member.

Private Attributes
	_tree
	reference to the tree being displayed
	_options
	set of options (same set as in the case of the ptreegen::computation::Computation class)
	_formatingMethods
	A list of function pointers that represents the workflow of operations.
	_storageDir
	the output directory
	_filePrefix
	prefix for the output files
	_style
	Instance representing the rendered style of the tree.

Detailed Description

Similar to the ptreegen::computation::Computation class.

It manages the visual components of the computation process and displays results to the user.

Definition at line 18 of file visualization.py.

Constructor & Destructor Documentation

def ptreegen.visualization.Visualization.__init__	(		self,
			tree,
			options
	)

Besides member initialization, it handles initial styling of the tree.

Parameters

tree	input phylogenetic tree that will be processed
options	set of options (same set as in the case of the ptreegen::computation::Computation class)

Definition at line 27 of file visualization.py.

    def __init__(self, tree, options):
        self._tree = tree
        self._options = options
        self._formatingMethods = []
        self._storageDir = None
        self._filePrefix = None
        self._style = TreeStyle()
        self._style.show_leaf_name = True
        self._style.show_branch_length = False
        self._style.scale = 80
        self._style.branch_vertical_margin = 15
        self._style.rotation = 90
        self._style.arc_start = -180
        self._style.arc_span = 180

        self.parseOptions(options)