MCI_set_of_contacts Class Reference

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

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

Comparing Solutions
	__eq__ (self, other)
	eq

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

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

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

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

Queries
	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).

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

Protein Neighborhood
	__fill_up_protein_to_neighbors_map__ (self)
	fill_up_protein_to_neighbors_map
	get_protein_to_neighbors_map (self)
	get_protein_to_neighbors_map

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__()

__init__	(		self,
			list_contacts )

init

Member Function Documentation

__add__()

__add__	(		self,
			contact )

add

__compute_false_positive_count__()

__compute_false_positive_count__	(		self,
			ref_set )

computing false positive count for a solution

__contains__()

__contains__	(		self,
			item )

contains

__eq__()

__eq__	(		self,
			other )

eq

__fill_up_protein_to_neighbors_map__()

__fill_up_protein_to_neighbors_map__

(

self

)

fill_up_protein_to_neighbors_map

__get_cost_due_to_weights__()

__get_cost_due_to_weights__

(

self

)

get_cost_due_to_weights

__get_cost_edge_size__()

__get_cost_edge_size__

(

self

)

get_cost_edge_size

__hash__()

__hash__

(

self

)

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

__iter__()

__iter__

(

self

)

iter

__len__()

__len__

(

self

)

len

__list_to_set_of_MCIcontact_instances__()

__list_to_set_of_MCIcontact_instances__	(		self,
			clist )

list_to_set_of_MCIcontact_instances

__repr__()

__repr__

(

self

)

functions for printing the object instance

__store_false_positive_count__()

__store_false_positive_count__	(		self,
			fpc )

store_false_positive_count

__str__()

__str__

(

self

)

str

__tuple_to_instance__()

__tuple_to_instance__	(		self,
			ctuple )

tuple_to_instance

get_contacts()

get_contacts

(

self

)

get_contacts

get_contacts_from_file()

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()

get_false_positive_count

(

self

)

get_false_positive_count

get_protein_to_neighbors_map()

get_protein_to_neighbors_map

(

self

)

get_protein_to_neighbors_map

get_solution_score()

get_solution_score

(

self

)

get_solution_score

is_valid_solution()

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()

pretty_print	(		self,
			msg )

pretty_print

pretty_print_one_sol()

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

xfc: fix this one

store_cost_components()

store_cost_components	(		self,
			nb_edges_cost,
			sum_weights_cost )

store_cost_components

store_solution_score()

store_solution_score	(		self,
			score )

Score of a solution.