Package csb :: Package bio :: Package hmm :: Class TransitionTable

Class TransitionTable

              object --+            
                       |            
    core.AbstractIndexer --+        
                           |        
core.BaseDictionaryContainer --+    
                               |    
        core.DictionaryContainer --+
                                   |
                                  TransitionTable

Represents a lookup table of transitions that are possible from within a given state.

Provides dictionary-like access, where dictionary keys are target states. These are members of the States enumeration, e.g.:

>>> state.transitions[States.Match]
transition info regarding transition from the current state to a Match state
>>> state.transitions[States.Match].predecessor
state
>>> state.transitions[States.Match].successor
the next match state

Instance Methods

__init__(self, transitions=None, restrict=frozenset([Deletion, End, Insertion, Match, Start]))
x.__init__(...) initializes x; see help(type(x)) for signature source code

append(self, transition)
Append a new transition to the table. source code

set(self, table)
Set the transition table using the dictionary provided in the argument.

source code

update(self, target_statekind, transition)
Update the information of a transition, which points to a target state of the specified States kind.

source code

Inherited from core.BaseDictionaryContainer: __bool__, __contains__, __getitem__, __iter__, __len__, __nonzero__, __repr__, keys

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

Inherited from core.BaseDictionaryContainer: length

Inherited from object: __class__

Method Details

init(self, transitions=None, restrict=`frozenset([`Deletion`,` End`,` Insertion`,` Match`,` Start`])`)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

transitions (dict) - an initialization dictionary of target State:Transition pairs
restrict (list) - a list of target states allowed for this transition table. Defaults to the States enum members

Overrides: object.__init__

(inherited documentation)

append(self, transition)

source code

Append a new transition to the table.

Parameters:

transition (Transition) - transition info

Raises:

TransitionExistsError - when a transition to the same target state already exists for the current state

Overrides: core.DictionaryContainer.append

set(self, table)

source code

Set the transition table using the dictionary provided in the argument.

Parameters:

table (dict) - the new transition table

update(self, target_statekind, transition)

source code

Update the information of a transition, which points to a target state of the specified States kind.

Parameters:

target_statekind (csb.core.EnumItem) - the key of the transition to be updated
transition (Transition) - new transition info object

Raises:

ValueError - if transition.successor.type differs from target_statekind

Class TransitionTable

__init__(self, transitions=None, restrict=frozenset([Deletion, End, Insertion, Match, Start])) (Constructor)

append(self, transition)

set(self, table)

update(self, target_statekind, transition)

init(self, transitions=None, restrict=`frozenset([`Deletion`,` End`,` Insertion`,` Match`,` Start`])`)
(Constructor)