Implement stage 2, no more generics for the mapping

Author: tibvdm

sa-index/src/peptide_search.rs

@@ -5,7 +5,6 @@ use serde::Serialize;
 use crate::{
     array::SuffixArrayBackend,
     sa_searcher::{SearchAllSuffixesResult, Searcher},
-    suffix_to_protein_index::SuffixToProteinMappingBackend,
 };
 
 #[derive(Debug, Serialize)]
@@ -51,8 +50,8 @@ impl From<ProteinRef<'_>> for ProteinInfo {
 /// The second argument is a list of all matching proteins for the peptide
 /// Returns None if the peptides does not have any matches, or if the peptide is shorter than the
 /// sparseness factor k used in the index
-pub fn search_proteins_for_peptide<'a, SA: SuffixArrayBackend, STPM: SuffixToProteinMappingBackend>(
-    searcher: &'a Searcher<SA, STPM>,
+pub fn search_proteins_for_peptide<'a, SA: SuffixArrayBackend>(
+    searcher: &'a Searcher<SA>,
     peptide: &str,
     cutoff: usize,
     equate_il: bool,
@@ -77,8 +76,8 @@ pub fn search_proteins_for_peptide<'a, SA: SuffixArrayBackend, STPM: SuffixToPro
     Some((cutoff_used, proteins))
 }
 
-pub fn search_peptide<SA: SuffixArrayBackend, STPM: SuffixToProteinMappingBackend>(
-    searcher: &Searcher<SA, STPM>,
+pub fn search_peptide<SA: SuffixArrayBackend>(
+    searcher: &Searcher<SA>,
     peptide: &str,
     cutoff: usize,
     equate_il: bool,
@@ -108,8 +107,8 @@ pub fn search_peptide<SA: SuffixArrayBackend, STPM: SuffixToProteinMappingBacken
 /// # Returns
 ///
 /// Returns an `OutputData<SearchOnlyResult>` object with the search results for the peptides
-pub fn search_all_peptides<SA: SuffixArrayBackend, STPM: SuffixToProteinMappingBackend>(
-    searcher: &Searcher<SA, STPM>,
+pub fn search_all_peptides<SA: SuffixArrayBackend>(
+    searcher: &Searcher<SA>,
     peptides: &Vec<String>,
     cutoff: usize,
     equate_il: bool,

sa-index/src/sa_searcher.rs

@@ -6,9 +6,7 @@ use text_compression::{ProteinText, ProteinTextBackend, ProteinTextSlice};
 use crate::{
     KmerTable, Nullable, array::SuffixArrayBackend,
     sa_searcher::BoundSearch::{Maximum, Minimum},
-    suffix_to_protein_index::{
-        SuffixToProteinMappingBackend, SuffixToProteinMapping,
-    },
+    suffix_to_protein_index::{SuffixToProteinMapping, SuffixToProteinMappingBackend},
 };
 
 
@@ -76,18 +74,18 @@ impl PartialEq for SearchAllSuffixesResult {
 ///   taxonomic analysis provided by Unipept
 /// * `function_aggregator` - Object used to retrieve the functional annotations and to calculate
 ///   the functional analysis provided by Unipept
-pub struct Searcher<SA: SuffixArrayBackend, STPM: SuffixToProteinMappingBackend = SuffixToProteinMapping> {
+pub struct Searcher<SA: SuffixArrayBackend> {
     pub sa: SA,
     pub proteins: Proteins,
-    pub suffix_index_to_protein: STPM,
+    pub suffix_index_to_protein: SuffixToProteinMapping,
     pub kmer_table: Option<KmerTable>,
     /// Total nanoseconds spent inside `search_bounds()` across all queries (since last drain).
     pub search_bounds_ns: AtomicU64,
     /// Total nanoseconds spent iterating matches in `search_matching_suffixes()` (since last drain).
     pub match_iter_ns: AtomicU64,
 }
 
-impl<SA: SuffixArrayBackend, STPM: SuffixToProteinMappingBackend> Searcher<SA, STPM> {
+impl<SA: SuffixArrayBackend> Searcher<SA> {
     /// Creates a new Searcher object
     ///
     /// # Arguments
@@ -104,7 +102,7 @@ impl<SA: SuffixArrayBackend, STPM: SuffixToProteinMappingBackend> Searcher<SA, S
     /// # Returns
     ///
     /// Returns a new Searcher object
-    pub fn new(sa: SA, proteins: Proteins, suffix_index_to_protein: STPM) -> Self {
+    pub fn new(sa: SA, proteins: Proteins, suffix_index_to_protein: SuffixToProteinMapping) -> Self {
         Self {
             sa,
             proteins,