ptreegen.distance_matrix.DistanceMatrix Class Reference

Basically a wrapper around a numpy array obejct representing the alignment distance matrix. More...

Public Member Functions
def	__init__
	Takes any "matrix-like" object and tries to convert it to a numpy array.
def	size
	A getter for the matrix size (number of columns/taxa).
def	distMatrix
	A getter for a copy of the whole distance matrix.
def	columnNames
	A getter for a list of column/taxa names.
def	getSeparation
	Returns a separation of value used in the Neigbor-joining algorithm.
def	getNearestNeigbors
	Finds the pair of nearest sequences.
def	getDistance
	Returns the distance from one sequence to another.
def	getIdx
	Finds the position of a sequence in the distance matrix.
def	getName
	Finds the name of a sequence based on its position in the matrix.
def	removeData
	Removes rows and columns for the specified sequences.
def	appendData
	Adds a row and a column for the specified sequence.

Private Attributes
	_distMatrix
	Distance matrix as a numpy array object.
	_columnNames
	List of column names (the identification strings of the sequences).

Detailed Description

Basically a wrapper around a numpy array obejct representing the alignment distance matrix.

Performs some other additional operations usefull for tree building.

Definition at line 13 of file distance_matrix.py.

Constructor & Destructor Documentation

def ptreegen.distance_matrix.DistanceMatrix.__init__	(		self,
			matrix,
			names = None
	)

Takes any "matrix-like" object and tries to convert it to a numpy array.

Parameters

matrix	a "matrix-like" object
names	optional parameter with column and row names (the taxa names)

Definition at line 21 of file distance_matrix.py.

    def __init__(self, matrix, names=None):
        self._distMatrix = np.array(matrix, float)
        assert len(self._distMatrix.shape) == 2
        assert self._distMatrix.shape[0] == self._distMatrix.shape[1]

        if not names:
            generated_names = []
            for i in range(self.size):
                generated_names.append("AUTOGEN_" + str(i+1))
            self._columnNames = list(generated_names)
        else:
            self._columnNames = list(names)

        assert len(self._columnNames) == len(self._distMatrix)