MCI_set_of_contacts Class Reference

Constructor
def	__init__ (self, list_contacts)
	init More...
def	__tuple_to_instance__ (self, ctuple)
	tuple_to_instance More...
def	__list_to_set_of_MCIcontact_instances__ (self, clist)
	list_to_set_of_MCIcontact_instances More...

Emulating a Container
def	__iter__ (self)
	iter More...
def	__len__ (self)
	len More...
def	__contains__ (self, item)
	contains More...
def	__add__ (self, contact)
	add More...
def	__hash__ (self)
	This function enables the object instance to be used as a key. More...

Comparing Solutions
def	__eq__ (self, other)
	eq More...

Printing
def	__repr__ (self)
	functions for printing the object instance More...
def	__str__ (self)
	str More...
def	pretty_print_one_sol (self, cost, sol_number=None, trees=True)
	xfc: fix this one More...
def	pretty_print (self, msg)
	pretty_print More...

Loading Reference Contacts
def	get_contacts_from_file (self, afile)
	This function could, for instance, read reference contacts. More...

Accessors / Modifiers
def	get_contacts (self)
	get_contacts More...
def	get_solution_score (self)
	get_solution_score More...
def	store_solution_score (self, score)
	Score of a solution. More...

False Positive Count
def	__compute_false_positive_count__ (self, ref_set)
	computing false positive count for a solution More...
def	__store_false_positive_count__ (self, fpc)
	store_false_positive_count More...
def	get_false_positive_count (self)
	get_false_positive_count More...

Queries
def	is_valid_solution (self, oligomers, V=None)
	function that returns true if the solution is valid wrt oligomers A solution is a pair (cost, list of contacts) or a triple (cost, list of contacts, time). More...

Cost Management
def	__get_cost_edge_size__ (self)
	get_cost_edge_size More...
def	__get_cost_due_to_weights__ (self)
	get_cost_due_to_weights More...
def	store_cost_components (self, nb_edges_cost, sum_weights_cost)
	store_cost_components More...

Protein Neighborhood
def	__fill_up_protein_to_neighbors_map__ (self)
	fill_up_protein_to_neighbors_map More...
def	get_protein_to_neighbors_map (self)
	get_protein_to_neighbors_map More...

Detailed Description

A class to specify a set of contacts.

A class to specify a set of contacts, either from a solution of a Connectivity inference problem, or from a reference set of contacts.
A set of contacts has a canonical representation which is merely the lexico ordering of its contacts.
For a set of contacts from a solution, this class can also store the two more attributes:
** score of a solution – sum over scores of all the contacts in the solution (requires whole solution set)
** false positive count – number of contacts in the solution not matching the reference set.

Constructor & Destructor Documentation

__init__()

def __init__	(		self,
			list_contacts
	)

init

Member Function Documentation

__add__()

def __add__	(		self,
			contact
	)

add

__compute_false_positive_count__()

def __compute_false_positive_count__	(		self,
			ref_set
	)

computing false positive count for a solution

__contains__()

def __contains__	(		self,
			item
	)

contains

__eq__()

def __eq__	(		self,
			other
	)

eq

__fill_up_protein_to_neighbors_map__()

def __fill_up_protein_to_neighbors_map__

(

self

)

fill_up_protein_to_neighbors_map

__get_cost_due_to_weights__()

def __get_cost_due_to_weights__

(

self

)

get_cost_due_to_weights

__get_cost_edge_size__()

def __get_cost_edge_size__

(

self

)

get_cost_edge_size

__hash__()

def __hash__

(

self

)

This function enables the object instance to be used as a key.

__iter__()

def __iter__

(

self

)

iter

__len__()

def __len__

(

self

)

len

__list_to_set_of_MCIcontact_instances__()

def __list_to_set_of_MCIcontact_instances__	(		self,
			clist
	)

list_to_set_of_MCIcontact_instances

__repr__()

def __repr__

(

self

)

functions for printing the object instance

__store_false_positive_count__()

def __store_false_positive_count__	(		self,
			fpc
	)

store_false_positive_count

__str__()

def __str__

(

self

)

str

__tuple_to_instance__()

def __tuple_to_instance__	(		self,
			ctuple
	)

tuple_to_instance

get_contacts()

def get_contacts

(

self

)

get_contacts

get_contacts_from_file()

def get_contacts_from_file	(		self,
			afile
	)

This function could, for instance, read reference contacts.

Note that reference contacts are not always at disposal.

get_false_positive_count()

def get_false_positive_count

(

self

)

get_false_positive_count

get_protein_to_neighbors_map()

def get_protein_to_neighbors_map

(

self

)

get_protein_to_neighbors_map

get_solution_score()

def get_solution_score

(

self

)

get_solution_score

is_valid_solution()

def is_valid_solution	(		self,
			oligomers,
			V = None
	)

function that returns true if the solution is valid wrt oligomers A solution is a pair (cost, list of contacts) or a triple (cost, list of contacts, time).

A solution is valid if for each oligomer, the subgraph induced by that oligomer over the list of contacts is connected.

pretty_print()

def pretty_print	(		self,
			msg
	)

pretty_print

pretty_print_one_sol()

def pretty_print_one_sol	(		self,
			cost,
			sol_number = None,
			trees = True
	)

xfc: fix this one

store_cost_components()

def store_cost_components	(		self,
			nb_edges_cost,
			sum_weights_cost
	)

store_cost_components

store_solution_score()

def store_solution_score	(		self,
			score
	)

Score of a solution.