Package csb :: Package bio :: Package hmm :: Class State |
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# Class State

source code

    object --+
             |
            State

Describes a Hidden Markov Model state.

Instance Methods
__init__(self, type, emit=None) x.__init__(...) initializes x; see help(type(x)) for signature | source code
__repr__(self) repr(x) | source code
Inherited from `object`: `__delattr__`, `__format__`, `__getattribute__`, `__hash__`, `__new__`, `__reduce__`, `__reduce_ex__`, `__setattr__`, `__sizeof__`, `__str__`, `__subclasshook__`

Properties
EmissionTable | background Lookup table with background probabilities
EmissionTable | emission Lookup table with available emission probabilities
| rank
bool | silent Whether this state can emit something
TransitionTable | transitions Lookup table with available transitions to other states
enum item | type State type: one of the States
Inherited from `object`: `__class__`

Method Details

### __init__(self, type, emit=None) (Constructor) | source code
x.__init__(...) initializes x; see help(type(x)) for signature Parameters: `type` (csb.core.EnumItem) - one of the States enumeration values, e.g. States.Match `emit` (list) - a collection of emittable state names allowed for the state, e.g. the members of SequenceAlphabets.Protein. If not defined, the state will be created as a silent (unobservable). Raises: `ValueError` - if type is not a member of the States enum Overrides: object.__init__ (inherited documentation)

### __repr__(self) (Representation operator) | source code
repr(x) Overrides: object.__repr__ (inherited documentation)

Property Details

### background Lookup table with background probabilities Get Method: unreachable.background(self) - Lookup table with background probabilities Type: EmissionTable

### emission Lookup table with available emission probabilities Get Method: unreachable.emission(self) - Lookup table with available emission probabilities Type: EmissionTable

### rank Get Method: unreachable.rank(self) Set Method: unreachable.rank(self, value)

### silent Whether this state can emit something Get Method: unreachable.silent(self) - Whether this state can emit something Type: bool

### transitions Lookup table with available transitions to other states Get Method: unreachable.transitions(self) - Lookup table with available transitions to other states Type: TransitionTable

### type State type: one of the States Get Method: unreachable.type(self) - State type: one of the States Set Method: unreachable.type(self, value) Type: enum item