Fix links reordering

Author: Keats

src/formats/json.rs

@@ -66,7 +66,6 @@ where
     } else {
         Ok(TaxRank::Unspecified)
     }
-
 }
 
 fn serialize_tax_rank<S>(x: &TaxRank, s: S) -> Result<S::Ok, S::Error>
@@ -191,17 +190,7 @@ fn load_node_link_json(tax_json: &Value) -> TaxonomyResult<GeneralTaxonomy> {
         // content
         let fixed_source = idx_mapping_after_sorting[&link.source];
         let fixed_target = idx_mapping_after_sorting[&link.target];
-
         parent_ids[fixed_source] = fixed_target;
-        // parent should always be higher than child in the tree and since we might
-        // have moved things around we need to ensure it stays the case
-        if fixed_target > fixed_source {
-            parent_ids[fixed_target] = fixed_source;
-        } else {
-            parent_ids[fixed_source] = fixed_target;
-        }
-        parent_ids[idx_mapping_after_sorting[&link.source]] =
-            idx_mapping_after_sorting[&link.target];
     }
 
     GeneralTaxonomy::from_arrays(

src/lib.rs

@@ -11,10 +11,9 @@ mod taxonomy;
 
 pub use crate::taxonomy::Taxonomy;
 pub use base::GeneralTaxonomy;
+pub use errors::{Error, ErrorKind};
 pub use formats::json;
 pub use formats::ncbi;
 pub use formats::newick;
 pub use formats::phyloxml;
 pub use rank::TaxRank;
-pub use errors::{Error, ErrorKind};
-

src/taxonomy.rs

@@ -17,7 +17,6 @@ pub trait Taxonomy<'t> {
     /// This method must return the node itself as the first entry in the list
     /// and the root node as the last entry in the list.
     fn lineage(&'t self, tax_id: &'t str) -> TaxonomyResult<Vec<&'t str>> {
-        // make a vec of parents of id1
         let mut parents = Vec::new();
         let mut last_parent = tax_id;
         parents.push(tax_id);