treetime/treeanc.py
def expanded_sequence(self, node, include_additional_constant_sites=False):
        """
        Expand a nodes compressed sequence into the real sequence

        Parameters
        ----------
        node : PhyloTree.Clade
           Tree node

        Returns
        -------
        seq : np.array
           Sequence as np.array of chars
        """
        if include_additional_constant_sites:
            L = self.seq_len
        else:
            L = self.seq_len - self.additional_constant_sites

        return node.cseq[self.full_to_reduced_sequence_map[:L]]
def expanded_sequence(self, node, include_additional_constant_sites=False):
        """
        Expand a nodes compressed sequence into the real sequence

        Parameters
        ----------
        node : PhyloTree.Clade
           Tree node

        Returns
        -------
        seq : np.array
           Sequence as np.array of chars
        """
        if include_additional_constant_sites:
            L = self.seq_len
        else:
            L = self.seq_len - self.additional_constant_sites

        return node.cseq[self.full_to_reduced_sequence_map[:L]]
Expand a nodes compressed sequence into the real sequence

        Parameters
        ----------
        node : PhyloTree.Clade
           Tree node

        Returns
        -------
        seq : np.array
           Sequence as np.array of chars