parsimony.proto

syntax = "proto3";                                                                                                                                                                                              
package Parsimony;

message mut {
    int32 position = 1; // Position in the chromosome
    /* All nucleotides are encoded as integers (0:A, 1:C, 2:G, 3:T) */
    int32 ref_nuc = 2; // Reference nucleotide at this position
    int32 par_nuc = 3; // Nucleotide of parent at this position
    repeated int32 mut_nuc = 4; // Mutated nucleotide in this node at this position
    string chromosome = 5; // Chromosome string. Currently unused.
}

message mutation_list {
    repeated mut mutation = 1;
}

message condensed_node {
    string node_name = 1; // The node name as given in the newick tree
    repeated string condensed_leaves = 2; // A list of strings for the names of identical sequences all of which are represented by the node above
}

message node_metadata {
    repeated string clade_annotations = 1;
}

message data {
    string newick = 1; // Newick tree string. May contain distances, but note that these may be distinct from distances as calculated with UShER
    repeated mutation_list node_mutations = 2; // Mutations_list object for each node of this tree, in the order that nodes are encountered in a preorder traversal of the tree in the newick string
    repeated condensed_node condensed_nodes = 3; // A dictionary-like object mapping names in the newick tree to a larger set of identical nodes that have been collapsed into this single node
    repeated node_metadata metadata = 4; // Clade annotations on a per-node basis, in the order that nodes are encountered in a preorder traversal of the tree
}