Refactoring Data Types (Draft) about phylo-rs HOT 4 CLOSED

Yep, this can be done. I have pushed some changes to this branch with new implementations of the rooted tree and rooted node trait. Some of the method implementations for each are pending, and more can be added. It also might be a good idea to move methods like SPR, NNI etc to tree instead of PhyloTree as these are not specific to phylogenetic trees....

from phylo-rs.

For future reference

NodeID : Hash + Clone + Drop

Node {

• getid(&self) -> NodeID
• setid (&mut self, NodeID)
• addchild(&mut self, Node)
• setparent(&mut self,Node)
• getparent(&mut self, Node);
• getchildren(&mut self) -> impl Iterator
• isleaf(&self) -> boolean
• removechild(&mut self, NodeID)
  }

from phylo-rs.

I have updated the trait bounds for nodeid on the node trait.

from phylo-rs.

It would also make sense to put similar trait bounds on the associated-type taxa as there are for NodeID. Specifically, it would also need to implement Display and Debug as well.

Building on that, the trait bounds of a rooted tree would be as follows:

Tree{

• get_node(&self, NodeID)->Node;
• set_node(&mut self, Node);
• add_child(&mut self, parent_id, Node);
• set_edge(&mut self,parent_id, child_id);
• get_root(&self)->NodeID;
• remove_node(&mut self, NodeID);
• contains_node(&self, NodeID)->bool;
• delete_edge(&mut self, parent_id, child_id);
• clean(&mut self);
  }

from phylo-rs.