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src/p/y/pycogent-HEAD/cogent/align/pairwise.py   pycogent(Download)
from cogent.align.traceback import map_traceback
from cogent.util import parallel
from cogent.util.warning import discontinued, deprecated
 
 
    def getLocalViterbiScoreAndAlignment(self, posterior_probs=False, **kw):
        deprecated('method', 'getLocalViterbiScoreAndAlignment', 
                'getViterbiScoreAndAlignment(local=True)', '1.7', stack_level=3)
        kw['posterior_probs'] = posterior_probs
        return self.getViterbiScoreAndAlignment(local=True, **kw)

src/c/o/cogent-1.5.3/cogent/evolve/likelihood_function.py   cogent(Download)
from cogent.recalculation.definition import ParameterController
 
from cogent.util.warning import discontinued, deprecated
 
__author__ = "Peter Maxwell"
    def setpar(self, param_name, value, edge=None, **scope):
        deprecated('method', 'setpar','setParamRule', '1.6')
        return self.setParamRule(param_name, edge=edge, value=value, is_constant=True, **scope)
 
    def testfunction(self):
        deprecated('method', 'testfunction','getLogLikelihood', '1.6')

src/p/y/pycogent-HEAD/cogent/evolve/likelihood_function.py   pycogent(Download)
from cogent.recalculation.definition import ParameterController
 
from cogent.util.warning import discontinued, deprecated
 
__author__ = "Peter Maxwell"
    def setpar(self, param_name, value, edge=None, **scope):
        deprecated('method', 'setpar','setParamRule', '1.6')
        return self.setParamRule(param_name, edge=edge, value=value, is_constant=True, **scope)
 
    def testfunction(self):
        deprecated('method', 'testfunction','getLogLikelihood', '1.6')

src/c/o/cogent-1.5.3/cogent/evolve/parameter_controller.py   cogent(Download)
 
from cogent.align.pairwise import AlignableSeq
from cogent.util.warning import discontinued, deprecated
 
__author__ = "Peter Maxwell"
        if 'is_const' in kwargs:
            is_constant = kwargs.pop('is_const')
            deprecated('argument', 'is_const', 'is_constant', 1.6)
 
        counts = self.model.countMotifs(align,
    def setMotifProbs(self, motif_probs, locus=None, bin=None, is_constant=None, 
                is_independent=None, auto=False, **kwargs):
        if 'is_const' in kwargs:
            is_constant = kwargs.pop('is_const')
            deprecated('argument', 'is_const', 'is_constant', 1.6)
        if 'is_const' in scope_info:
            is_constant = scope_info.pop('is_const')
            deprecated('argument', 'is_const', 'is_constant', 1.6)
 
        par_name = str(par_name)

src/p/y/pycogent-HEAD/cogent/evolve/parameter_controller.py   pycogent(Download)
 
from cogent.align.pairwise import AlignableSeq
from cogent.util.warning import discontinued, deprecated
 
__author__ = "Peter Maxwell"
        if 'is_const' in kwargs:
            is_constant = kwargs.pop('is_const')
            deprecated('argument', 'is_const', 'is_constant', 1.6)
 
        counts = self.model.countMotifs(align,
    def setMotifProbs(self, motif_probs, locus=None, bin=None, is_constant=None, 
                is_independent=None, auto=False, **kwargs):
        if 'is_const' in kwargs:
            is_constant = kwargs.pop('is_const')
            deprecated('argument', 'is_const', 'is_constant', 1.6)
        if 'is_const' in scope_info:
            is_constant = scope_info.pop('is_const')
            deprecated('argument', 'is_const', 'is_constant', 1.6)
 
        par_name = str(par_name)

src/c/o/cogent-1.5.3/cogent/app/raxml.py   cogent(Download)
from cogent.core.alignment import Alignment
from cogent.core.moltype import DNA, RNA, PROTEIN
from cogent.util.warning import deprecated
from random import choice, randint
from os import walk
class Raxml(CommandLineApplication):
    """RAxML application controller"""
 
    deprecated('class',
               'cogent.app.raxml.Raxml',

src/c/o/cogent-1.5.3/cogent/app/muscle.py   cogent(Download)
from cogent.core.tree import PhyloNode
from cogent.parse.fasta import MinimalFastaParser
from cogent.util.warning import deprecated
 
__author__ = "Rob Knight"
class Muscle(CommandLineApplication):
    """Muscle application controller"""
 
    deprecated('class',
               'cogent.app.muscle.Muscle',

src/p/y/pycogent-HEAD/cogent/app/raxml.py   pycogent(Download)
from cogent.core.alignment import Alignment
from cogent.core.moltype import DNA, RNA, PROTEIN
from cogent.util.warning import deprecated
from random import choice, randint
from os import walk
class Raxml(CommandLineApplication):
    """RAxML application controller"""
 
    deprecated('class',
               'cogent.app.raxml.Raxml',

src/p/y/pycogent-HEAD/cogent/app/muscle.py   pycogent(Download)
from cogent.core.tree import PhyloNode
from cogent.parse.fasta import MinimalFastaParser
from cogent.util.warning import deprecated
 
__author__ = "Rob Knight"
class Muscle(CommandLineApplication):
    """Muscle application controller"""
 
    deprecated('class',
               'cogent.app.muscle.Muscle',

src/c/o/cogent-1.5.3/cogent/evolve/discrete_markov.py   cogent(Download)
import numpy
 
from cogent.util.warning import deprecated
from cogent.recalculation.definition import (NonParamDefn, CalcDefn, 
    EvaluatedCell, PartitionDefn, ConstCell, ConstDefn,
def DiscreteSubstitutionModel(*args, **kw):
    deprecated("class",
        "cogent.evolve.discrete_markov.DiscreteSubstitutionModel",
        "cogent.evolve.substitution_model.DiscreteSubstitutionModel",
        '1.6')

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