treetime/treeanc.py
def _store_compressed_sequence_to_node(self, node):
        """
        make a compressed representation of a pair of sequences only counting
        the number of times a particular pair of states (e.g. (A,T)) is observed
        the the aligned sequences of parent and child.

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

         node : PhyloTree.Clade
            Tree node. **Note** because the method operates
            on the sequences on both sides of a branch, sequence reconstruction
            must be performed prior to calling this method.

        """
        seq_pairs, multiplicity = self.gtr.compress_sequence_pair(node.up.cseq,
                                              node.cseq,
                                              pattern_multiplicity = self.multiplicity,
                                              ignore_gaps = self.ignore_gaps)
        node.compressed_sequence = {'pair':seq_pairs, 'multiplicity':multiplicity}
def _store_compressed_sequence_to_node(self, node):
        """
        make a compressed representation of a pair of sequences only counting
        the number of times a particular pair of states (e.g. (A,T)) is observed
        the the aligned sequences of parent and child.

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

         node : PhyloTree.Clade
            Tree node. **Note** because the method operates
            on the sequences on both sides of a branch, sequence reconstruction
            must be performed prior to calling this method.

        """
        seq_pairs, multiplicity = self.gtr.compress_sequence_pair(node.up.cseq,
                                              node.cseq,
                                              pattern_multiplicity = self.multiplicity,
                                              ignore_gaps = self.ignore_gaps)
        node.compressed_sequence = {'pair':seq_pairs, 'multiplicity':multiplicity}
def _store_compressed_sequence_to_node ( self , node ) : seq_pairs , multiplicity = self . gtr . compress_sequence_pair ( node . up . cseq , node . cseq , pattern_multiplicity = self . multiplicity , ignore_gaps = self . ignore_gaps ) node . compressed_sequence = { 'pair' : seq_pairs , 'multiplicity' : multiplicity }
make a compressed representation of a pair of sequences only counting
        the number of times a particular pair of states (e.g. (A,T)) is observed
        the the aligned sequences of parent and child.

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

         node : PhyloTree.Clade
            Tree node. **Note** because the method operates
            on the sequences on both sides of a branch, sequence reconstruction
            must be performed prior to calling this method.
make a compressed representation of a pair of sequences only counting the number of times a particular pair of states ( e . g . ( A T )) is observed the the aligned sequences of parent and child .