resturctured project

src/bin/bin.rs

@@ -1,5 +1,4 @@
 extern crate clap;
-use std::collections::HashMap;
 
 use clap::{arg, Command};
 use bio::io::fasta;

src/suffix_node.rs

@@ -1,26 +1,11 @@
+pub mod node;
+
 use std::collections::HashMap;
 use std::fmt::{Display, Debug};
 use std::hash::Hash;
 use std::option::Option;
 use serde::{Serialize, Deserialize};
-
-pub trait SuffixNode<T> {
-    fn set_parent(&mut self, parent: usize);
-    fn get_parent(&self)->Option<&usize>;
-    fn get_child(&self, child:&T)->Option<&usize>;
-    fn get_child_mut(&mut self, child:&T)->Option<&mut usize>;
-    fn set_child(&mut self, edge:T, child:usize);
-    fn set_edge_length(&mut self, edge_length:usize);
-    fn get_end(&self)->usize;
-    fn get_edge_length(&self)-> usize;
-    fn get_string_id(&self)->Option<&usize>;
-    fn get_start(&self)->&usize;
-    fn set_string_id(&mut self, string_id:usize);
-    fn set_start(&mut self, new_start:usize);
-    fn has_children(&self)->bool;
-    fn get_children(&self)->&HashMap<T, usize>;
-    fn is_leaf(&self)->bool;
-}
+use crate::suffix_node::node::*;
 
 
 #[derive(Debug, PartialEq, Serialize, Deserialize)]

src/suffix_node/node.rs

@@ -0,0 +1,22 @@
+use std::collections::HashMap;
+
+pub type NodeID = usize;
+pub type StringID = usize;
+
+pub trait SuffixNode<T> {
+    fn set_parent(&mut self, parent: NodeID);
+    fn get_parent(&self)->Option<&NodeID>;
+    fn get_child(&self, child:&T)->Option<&NodeID>;
+    fn get_child_mut(&mut self, child:&T)->Option<&mut NodeID>;
+    fn set_child(&mut self, edge:T, child:NodeID);
+    fn set_edge_length(&mut self, edge_length:usize);
+    fn get_end(&self)->usize;
+    fn get_edge_length(&self)-> usize;
+    fn get_string_id(&self)->Option<&StringID>;
+    fn set_string_id(&mut self, string_id:StringID);
+    fn get_start(&self)->&usize;
+    fn set_start(&mut self, new_start:usize);
+    fn has_children(&self)->bool;
+    fn get_children(&self)->&HashMap<T, NodeID>;
+    fn is_leaf(&self)->bool;
+}

src/suffix_tree.rs

@@ -1,4 +1,8 @@
-use crate::suffix_node::{Node, SuffixNode};
+pub mod tree;
+
+use crate::suffix_tree::tree::*;
+use crate::suffix_node::node::*;
+use crate::suffix_node::*;
 use crate::tree_item::TreeItem;
 use crate::utils::Enode;
 use std::collections::{HashMap, HashSet, LinkedList};
@@ -8,23 +12,6 @@ use std::cmp;
 use std::option::Option;
 use serde::{Serialize, Deserialize};
 use itertools::Itertools;
-
-type NodeID = usize;
-type StringID = usize;
-
-pub trait SuffixTree<T>{
-    fn root(&self)->&NodeID;
-    fn is_leaf(&self, node_id: &NodeID)->bool;
-    fn get_node_child(&self, node_id: &NodeID, edge_label: &T)->Option<&NodeID>;
-    fn get_node_parent(&self, node_id: &NodeID)->Option<&NodeID>;
-    fn get_node_depth(&self, node_id: &NodeID)->usize;
-    fn get_suffix_link(&self, node_id: &NodeID) -> &usize;
-    fn get_node_label(&self, node_id: &NodeID)->&[T];
-    fn get_node_path_label(&self, node_id: &NodeID)->&[T];
-    fn get_node_path(&self, node_id: &NodeID)->LinkedList<NodeID>;
-    /// Checks if the input slice is a suffix of any of the strings present in the tree.
-    fn is_suffix(&self, s:&[T])->bool;
-    }
 
 
 /// A Generalized Truncated Suffix Tree implemented with a variation of Ukkonen's Algorithm.  

src/suffix_tree/tree.rs

@@ -0,0 +1,16 @@
+use crate::suffix_node::node::*;
+use std::collections::LinkedList;
+
+pub trait SuffixTree<T>{
+    fn root(&self)->&NodeID;
+    fn is_leaf(&self, node_id: &NodeID)->bool;
+    fn get_node_child(&self, node_id: &NodeID, edge_label: &T)->Option<&NodeID>;
+    fn get_node_parent(&self, node_id: &NodeID)->Option<&NodeID>;
+    fn get_node_depth(&self, node_id: &NodeID)->usize;
+    fn get_suffix_link(&self, node_id: &NodeID) -> &usize;
+    fn get_node_label(&self, node_id: &NodeID)->&[T];
+    fn get_node_path_label(&self, node_id: &NodeID)->&[T];
+    fn get_node_path(&self, node_id: &NodeID)->LinkedList<NodeID>;
+    /// Checks if the input slice is a suffix of any of the strings present in the tree.
+    fn is_suffix(&self, s:&[T])->bool;
+    }