Package csb :: Package bio :: Package hmm :: Class EmissionTable

Class EmissionTable

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

Represents a lookup table of emission probabilities. Provides dictionary-like access:

>>> state.emission[ProteinAlphabet.ALA]
emission probability for ALA

Instance Methods

__init__(self, emission=None, restrict=frozenset([STOP, GAP, INSERTION, ALA, ASX, CYS, ASP, GLU, PHE,...)
x.__init__(...) initializes x; see help(type(x)) for signature source code

append(self, residue, probability)
Append a new emission probability to the table.

source code

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

source code

update(self, residue, probability)
Update the emission probability of a given emission residue. 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, emission=None, restrict=`frozenset([`STOP`,` GAP`,` INSERTION`,` ALA`,` ASX`,` CYS`,` ASP`,` GLU`,` PHE`,...`)
(Constructor)

source code

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

Parameters:

emission (dict) - an initialization dictionary of emission probabilities
restrict (list) - a list of residue types allowed for this emission table. Defaults to the members of csb.bio.sequence.ProteinAlphabet

Overrides: object.__init__

(inherited documentation)

append(self, residue, probability)

source code

Append a new emission probability to the table.

Parameters:

residue (csb.core.EnumItem) - residue name (type) - a member of csb.bio.sequence.ProteinAlphabet
probability (float) - emission score

Raises:

EmissionExistsError - if residue is already defined

Overrides: core.DictionaryContainer.append

set(self, table)

source code

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

Parameters:

table (dict) - the new emission table

update(self, residue, probability)

source code

Update the emission probability of a given emission residue.

Parameters:

residue (csb.core.EnumItem) - name (type) of the residue to be updated
probability (float) - new emission score

Class EmissionTable

__init__(self, emission=None, restrict=frozenset([STOP, GAP, INSERTION, ALA, ASX, CYS, ASP, GLU, PHE,...) (Constructor)

append(self, residue, probability)

set(self, table)

update(self, residue, probability)

init(self, emission=None, restrict=`frozenset([`STOP`,` GAP`,` INSERTION`,` ALA`,` ASX`,` CYS`,` ASP`,` GLU`,` PHE`,...`)
(Constructor)