Package csb :: Package bio :: Package hmm :: Class ProfileHMMSegment

Class ProfileHMMSegment

object --+    
         |    
ProfileHMM --+
             |
            ProfileHMMSegment

Known Subclasses:

EmissionProfileSegment

Represents a segment (fragment) of a ProfileHMM.

Instance Methods

__init__(self, hmm, start, end)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

Inherited from ProfileHMM: add_emission_pseudocounts, add_transition_pseudocounts, chain, convert_scores, emission_profile, emission_similarity, segment, serialize, structure, subregion, to_hmm

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

Static Methods
Inherited from `ProfileHMM`: `deserialize`

Properties
int	source_end End position of this segment in its source HMM
int	source_start Start position of this segment in its source HMM
Inherited from `ProfileHMM`: `alignment`, `all_layers`, `consensus`, `dssp`, `dssp_solvent`, `effective_matches`, `emission_pseudocounts`, `end`, `evd`, `family`, `has_structure`, `id`, `layers`, `length`, `logbase`, `name`, `pseudocounts`, `psipred`, `residues`, `scale`, `score_units`, `start`, `start_insertion`, `transition_pseudocounts`, `version` Inherited from `object`: `__class__`

Method Details

init(self, hmm, start, end)
(Constructor)

source code

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

Parameters:

hmm (ProfileHMM) - source HMM
start (int) - start layer of the segment (rank)
end (int) - end layer of the segment (rank)

Raises:

ValueError - when start or end positions are out of range

Overrides: object.__init__

(inherited documentation)

Property Details

source_end

End position of this segment in its source HMM

Get Method:: unreachable.source_end(self) - End position of this segment in its source HMM
Type:: int

source_start

Start position of this segment in its source HMM

Get Method:: unreachable.source_start(self) - Start position of this segment in its source HMM
Type:: int

Class ProfileHMMSegment

__init__(self, hmm, start, end) (Constructor)

source_end

source_start

init(self, hmm, start, end)
(Constructor)