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

source code

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