Package csb :: Package bio :: Package hmm :: Class HMMLayer

Class HMMLayer

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

Provides a dictionary-like catalog of the available states at this layer. Lookup keys are members of the States enumeration, e.g.:

>>> profile.layers[i][States.Deletion]
the deletion state at layer number i

Instance Methods

__init__(self, rank, residue, states=None)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

append(self, state)
Append a new state to the catalog. source code

update(self, state_kind, state)
Update the sate of the specified kind under the current layer.

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
int	effective_deletions Number of effective deletions at this layer
int	effective_insertions Number of effective insertions at this layer
int	effective_matches Number of effective matches at this layer
int	rank Layer's position
Residue	residue Representative residue
Inherited from `core.BaseDictionaryContainer`: `length` Inherited from `object`: `__class__`

Method Details

init(self, rank, residue, states=None)
(Constructor)

source code

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

Parameters:

rank (int) - layer's number
residue (ProteinResidue) - a representative ProteinResidue that is associated with this layer
states (dict) - initialization dictionary of States.Item:State pairs

Overrides: object.__init__

(inherited documentation)

append(self, state)

source code

Append a new state to the catalog.

Parameters:

state (State) - the new state

Raises:

StateExistsError - when a state of the same type is already defined

Overrides: core.DictionaryContainer.append

update(self, state_kind, state)

source code

Update the sate of the specified kind under the current layer.

Parameters:

state_kind (csb.core.EnumItem) - state type (key) - a member of States
state (State) - the new state info

Raises:

ValueError - if state.type differs from state_kind

Property Details

effective_deletions

Number of effective deletions at this layer

Get Method:: unreachable.effective_deletions(self) - Number of effective deletions at this layer
Set Method:: unreachable.effective_deletions(self, value)
Type:: int

effective_insertions

Number of effective insertions at this layer

Get Method:: unreachable.effective_insertions(self) - Number of effective insertions at this layer
Set Method:: unreachable.effective_insertions(self, value)
Type:: int

effective_matches

Number of effective matches at this layer

Get Method:: unreachable.effective_matches(self) - Number of effective matches at this layer
Set Method:: unreachable.effective_matches(self, value)
Type:: int

rank

Layer's position

Get Method:: unreachable.rank(self) - Layer's position
Set Method:: unreachable.rank(self, value)
Type:: int

residue

Representative residue

Get Method:: unreachable.residue(self) - Representative residue
Set Method:: unreachable.residue(self, residue)
Type:: Residue

Class HMMLayer

__init__(self, rank, residue, states=None) (Constructor)

append(self, state)

update(self, state_kind, state)

effective_deletions

effective_insertions

effective_matches

rank

residue

init(self, rank, residue, states=None)
(Constructor)