treetime/treeanc.py
def set_gtr(self, in_gtr, **kwargs):
        """
        Create new GTR model if needed, and set the model as an attribute of the
        TreeAnc class

        Parameters
        -----------

         in_gtr : str, GTR
            The gtr model to be assigned. If string is passed,
            it is taken as the name of a standard GTR model, and is
            attempted to be created through :code:`GTR.standard()` interface. If a
            GTR instance is passed, it is set directly .

         **kwargs
            Keyword arguments to construct the GTR model. If none are passed, defaults
            are assumed.

        """
        if isinstance(in_gtr, str):
            self._gtr = GTR.standard(model=in_gtr, **kwargs)
            self._gtr.logger = self.logger

        elif isinstance(in_gtr, GTR) or isinstance(in_gtr, GTR_site_specific):
            self._gtr = in_gtr
            self._gtr.logger=self.logger
        else:
            self.logger("TreeAnc.gtr_setter: can't interpret GTR model", 1, warn=True)
            raise TypeError("Cannot set GTR model in TreeAnc class: GTR or "
                "string expected")

        if self._gtr.ambiguous is None:
            self.fill_overhangs=False
def set_gtr(self, in_gtr, **kwargs):
        """
        Create new GTR model if needed, and set the model as an attribute of the
        TreeAnc class

        Parameters
        -----------

         in_gtr : str, GTR
            The gtr model to be assigned. If string is passed,
            it is taken as the name of a standard GTR model, and is
            attempted to be created through :code:`GTR.standard()` interface. If a
            GTR instance is passed, it is set directly .

         **kwargs
            Keyword arguments to construct the GTR model. If none are passed, defaults
            are assumed.

        """
        if isinstance(in_gtr, str):
            self._gtr = GTR.standard(model=in_gtr, **kwargs)
            self._gtr.logger = self.logger

        elif isinstance(in_gtr, GTR) or isinstance(in_gtr, GTR_site_specific):
            self._gtr = in_gtr
            self._gtr.logger=self.logger
        else:
            self.logger("TreeAnc.gtr_setter: can't interpret GTR model", 1, warn=True)
            raise TypeError("Cannot set GTR model in TreeAnc class: GTR or "
                "string expected")

        if self._gtr.ambiguous is None:
            self.fill_overhangs=False
def set_gtr ( self , in_gtr , * * kwargs ) : if isinstance ( in_gtr , str ) : self . _gtr = GTR . standard ( model = in_gtr , * * kwargs ) self . _gtr . logger = self . logger elif isinstance ( in_gtr , GTR ) or isinstance ( in_gtr , GTR_site_specific ) : self . _gtr = in_gtr self . _gtr . logger = self . logger else : self . logger ( "TreeAnc.gtr_setter: can't interpret GTR model" , 1 , warn = True ) raise TypeError ( "Cannot set GTR model in TreeAnc class: GTR or " "string expected" ) if self . _gtr . ambiguous is None : self . fill_overhangs = False
Create new GTR model if needed, and set the model as an attribute of the
        TreeAnc class

        Parameters
        -----------

         in_gtr : str, GTR
            The gtr model to be assigned. If string is passed,
            it is taken as the name of a standard GTR model, and is
            attempted to be created through :code:`GTR.standard()` interface. If a
            GTR instance is passed, it is set directly .

         **kwargs
            Keyword arguments to construct the GTR model. If none are passed, defaults
            are assumed.
Create new GTR model if needed and set the model as an attribute of the TreeAnc class