Package csb :: Package apps :: Module buildhmm :: Class ProfileBuilder

Class ProfileBuilder

object --+
         |
        ProfileBuilder

Known Subclasses:

Nested Classes
	__metaclass__ Metaclass for defining Abstract Base Classes (ABCs).

Instance Methods

__init__(self, query, target_id, database, tk_root, tk_config, pseudo=True, ss=True, cpu=1)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

build_alignment(self)

source code

calibrate_hmm(self)

source code

configure_input(self)

source code

make_hmm(self)

source code

run(self)

source code

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

Static Methods

create(query, target_id, database, tk_root, tk_config, pseudo=True, ss=True, cpu=1)

source code

Class Variables
	EMISSION_PSEUDO = `'-pcm 4 -pca 2.5 -pcb 0.5 -pcc 1.0'`
	TRANSITION_PSEUDO = `'-gapb 1.0 -gapd 0.15 -gape 1.0 -gapf 0.6 ...`
	__abstractmethods__ = `frozenset(['configure_input'])`

Properties
	target_id
Inherited from `object`: `__class__`

Method Details

init(self, query, target_id, database, tk_root, tk_config, pseudo=True, ss=True, cpu=1)
(Constructor)

source code

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

Overrides: object.__init__: (inherited documentation)

Class Variable Details

TRANSITION_PSEUDO

Value:

'-gapb 1.0 -gapd 0.15 -gape 1.0 -gapf 0.6 -gapg 0.6 -gapi 0.6'

Property Details

target_id

Get Method:: unreachable.target_id(self)

Class ProfileBuilder

__init__(self, query, target_id, database, tk_root, tk_config, pseudo=True, ss=True, cpu=1) (Constructor)

TRANSITION_PSEUDO

target_id

init(self, query, target_id, database, tk_root, tk_config, pseudo=True, ss=True, cpu=1)
(Constructor)