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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"
    def makeCalculator(self, *args, **kw):
        if args:
            discontinued('method', "makeCalculator(aligns)", '1.6')
            # and shadowing a quite different superclass method.
            self.setAlignment(*args)

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"
    def makeCalculator(self, *args, **kw):
        if args:
            discontinued('method', "makeCalculator(aligns)", '1.6')
            # and shadowing a quite different superclass method.
            self.setAlignment(*args)

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"
        """
 
        discontinued('method', "'getStatisticsAsDict' "
                "use 'getParamValueDict(['edge'])' is nearly equivalent", 
                '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"
        """
 
        discontinued('method', "'getStatisticsAsDict' "
                "use 'getParamValueDict(['edge'])' is nearly equivalent", 
                '1.6')

src/c/o/cogent-1.5.3/cogent/draw/rlg2mpl.py   cogent(Download)
import numpy
 
from cogent.util.warning import discontinued
 
__author__ = "Peter Maxwell"
        for (k,v) in kw.items():
            if k in ['wraps', 'border', 'withTrackLabelColumn']:
                discontinued('argument', "%s" % k, '1.6')
            else:
                kw2[k] = v

src/c/o/cogent-1.5.3/cogent/draw/dotplot.py   cogent(Download)
from matplotlib.patches import PathPatch
 
from cogent.util.warning import discontinued
from cogent.draw.linear import Display
from cogent.draw.rlg2mpl import Drawable, figureLayout
        # matplotlib is reasonably fast anyway, so:
        if join_gaps is not None:
            discontinued('argument', 'join_gaps', '1.6')
        ax = comparison_display(self.seq1d, self.seq2d, **kw)
        (fwd, rev) = self._calc_lines(window, None, min_gap)

src/p/y/pycogent-HEAD/cogent/draw/rlg2mpl.py   pycogent(Download)
import numpy
 
from cogent.util.warning import discontinued
 
__author__ = "Peter Maxwell"
        for (k,v) in kw.items():
            if k in ['wraps', 'border', 'withTrackLabelColumn']:
                discontinued('argument', "%s" % k, '1.6')
            else:
                kw2[k] = v

src/p/y/pycogent-HEAD/cogent/draw/dotplot.py   pycogent(Download)
from matplotlib.patches import PathPatch
 
from cogent.util.warning import discontinued
from cogent.draw.linear import Display
from cogent.draw.rlg2mpl import Drawable, figureLayout
        # matplotlib is reasonably fast anyway, so:
        if join_gaps is not None:
            discontinued('argument', 'join_gaps', '1.6')
        ax = comparison_display(self.seq1d, self.seq2d, **kw)
        (fwd, rev) = self._calc_lines(window, None, min_gap)

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
 
 

src/c/o/cogent-1.5.3/cogent/format/table.py   cogent(Download)
"""
import textwrap
from cogent.util.warning import discontinued
 
__author__ = "Gavin Huttley"

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