MCI_specification Class Reference

Constructor
def	__init__ (self, fname)
	init More...

Loading MCI Specification
def	__read_vertextypes_from_file__ (self, fhandle)
	Read vertex labels from input file assuming that the labels are given between a 'BEGIN-TYPES' tag and a 'END-TYPES' tag. More...
def	__read_oligomers_from_file__ (self, fhandle)
	Read oligomers from input file assuming that the sets are given between a 'BEGIN-OLIGOMERS' tag and a 'END-OLIGOMERS' tag. More...
def	__read_annotated_contacts_from_file__ (self, fhandle, unweighted)
	Read annotated contacts given in the input spec file Labels: F (Forbidden), E (Enforced), P (Possible, default) Weights: a floating point number in the interval [0,1], default: 1 Annotated contact havel both label (default, P) and weight (default, 0.5) More...
def	read_MCI_spec_from_input_file (self, unweighted)
	read_MCI_spec_from_input_file More...

Accessors / Modifiers
def	get_vertices (self)
	get_vertices More...
def	get_oligomers (self)
	Returns oligomers, which is object of the class MCI_oligomers. More...
def	get_pool_of_contacts_explored (self)
	Returns the set of pool of contacts from which algorithm chooses the contacts. More...
def	get_annotated_contacts (self)
	Returns annotated contacts, which is object of the class MCI_set_of_contacts. More...
def	set_annotated_contact (self, contact)
	Set contact label or weight if contact is already present then update weight and/or label else add the contact. More...
def	update_vertices (self, vertices)
	update_vertices More...
def	update_oligomers (self, key, oligomer)
	update_oligomers More...

Detailed Description

A class to specify the input of a connectivity inference problem.

This class specifies the input of a connectivity inference problem, as a set of vertices and oligomers. The oligomers are object instance of the class MCI_oligomers. xfc: make the labels and weights available from this class

Constructor & Destructor Documentation

__init__()

def __init__	(		self,
			fname
	)

init

Member Function Documentation

__read_annotated_contacts_from_file__()

def __read_annotated_contacts_from_file__	(		self,
			fhandle,
			unweighted
	)

Read annotated contacts given in the input spec file Labels: F (Forbidden), E (Enforced), P (Possible, default) Weights: a floating point number in the interval [0,1], default: 1 Annotated contact havel both label (default, P) and weight (default, 0.5)

__read_oligomers_from_file__()

def __read_oligomers_from_file__	(		self,
			fhandle
	)

Read oligomers from input file assuming that the sets are given between a 'BEGIN-OLIGOMERS' tag and a 'END-OLIGOMERS' tag.

Example: BEGIN-OLIGOMERS Csn1 Csn2 Csn3 Csn4 Csn6 Csn7 Csn8 Csn1 Csn3 Csn4 Csn5 Csn6 Csn7 Csn8 ... Csn4 Csn6 Csn7 Csn3 Csn8 END-OLIGOMERS

__read_vertextypes_from_file__()

def __read_vertextypes_from_file__	(		self,
			fhandle
	)

Read vertex labels from input file assuming that the labels are given between a 'BEGIN-TYPES' tag and a 'END-TYPES' tag.

Example: BEGIN-TYPES Csn1 Csn2 Csn3 Csn4 Csn5 Csn6 Csn7 Csn8 END-TYPES

get_annotated_contacts()

def get_annotated_contacts

(

self

)

Returns annotated contacts, which is object of the class MCI_set_of_contacts.

get_oligomers()

def get_oligomers

(

self

)

Returns oligomers, which is object of the class MCI_oligomers.

get_pool_of_contacts_explored()

def get_pool_of_contacts_explored

(

self

)

Returns the set of pool of contacts from which algorithm chooses the contacts.

get_vertices()

def get_vertices

(

self

)

get_vertices

read_MCI_spec_from_input_file()

def read_MCI_spec_from_input_file	(		self,
			unweighted
	)

read_MCI_spec_from_input_file

set_annotated_contact()

def set_annotated_contact	(		self,
			contact
	)

Set contact label or weight if contact is already present then update weight and/or label else add the contact.

update_oligomers()

def update_oligomers	(		self,
			key,
			oligomer
	)

update_oligomers

update_vertices()

def update_vertices	(		self,
			vertices
	)

update_vertices