From 26bca34353f8cfc6e74d6433d58eff532a94d001 Mon Sep 17 00:00:00 2001
From: tibvdm <tibovandemoortele@hotmail.com>
Date: Fri, 23 Aug 2024 11:21:39 +0200
Subject: [PATCH] improve checks

---
 sa-index/src/sa_searcher.rs | 70 +++++++++++++++++++------------------
 sa-mappings/src/proteins.rs |  2 ++
 2 files changed, 38 insertions(+), 34 deletions(-)

diff --git a/sa-index/src/sa_searcher.rs b/sa-index/src/sa_searcher.rs
index f23c7e9..34be8c0 100644
--- a/sa-index/src/sa_searcher.rs
+++ b/sa-index/src/sa_searcher.rs
@@ -1,5 +1,5 @@
 use std::{cmp::min, ops::Deref};
-use sa_mappings::proteins::{Protein, Proteins, SEPARATION_CHARACTER, TERMINATION_CHARACTER};
+use sa_mappings::proteins::{Protein, Proteins, SEPARATION_CHARACTER};
 
 use crate::{
     sa_searcher::BoundSearch::{Maximum, Minimum},
@@ -341,40 +341,41 @@ impl Searcher {
                 while sa_index < max_bound {
                     let suffix = self.sa.get(sa_index) as usize;
 
-                    // filter away matches where I was wrongfully equalized to L, and check the
-                    // unmatched prefix when I and L equalized, we only need to
-                    // check the prefix, not the whole match, when the prefix is 0, we don't need to
-                    // check at all
-                    if suffix >= skip
-                        && ((skip == 0
-                            || Self::check_prefix(
-                                current_search_string_prefix,
-                                &self.proteins.input_string[suffix - skip..suffix],
-                                equate_il
-                            ))
-                            && Self::check_suffix(
-                                skip,
-                                il_locations_current_suffix,
-                                current_search_string_suffix,
-                                &self.proteins.input_string[suffix..suffix + search_string.len() - skip],
-                                equate_il
-                            ))
-                    {
-                        if tryptic && (
-                            (suffix - skip == 0)
-                                || self.proteins.input_string[suffix - skip - 1] == b'R'
-                                || self.proteins.input_string[suffix - skip - 1] == b'K'
-                                || self.proteins.input_string[suffix - skip - 1] == SEPARATION_CHARACTER
-                            ) && (
-                                self.proteins.input_string[suffix - skip + search_string.len() + 1] != b'P'
-                                    || self.proteins.input_string[suffix - skip + search_string.len() + 1] == SEPARATION_CHARACTER
-                                    || self.proteins.input_string[suffix - skip + search_string.len() + 1] == TERMINATION_CHARACTER
-                            )
-                        {
-                            sa_index += 1;
-                            continue;
-                        }
+                    // If the suffix is smaller than the skip factor, we can't check the prefix
+                    let checkable_suffix = suffix >= skip;
+
+                    // Check for trypticity if a tryptic search is performed
+                    let is_tryptic = tryptic && (
+                        self.proteins.input_string[suffix - skip - 1] == b'R' ||
+                            self.proteins.input_string[suffix - skip - 1] == b'K' ||
+                            self.proteins.input_string[suffix - skip - 1] == SEPARATION_CHARACTER
+                    ) && self.proteins.input_string[suffix - skip + search_string.len()] != b'P';
 
+                    if !is_tryptic {
+                        sa_index += 1;
+                        continue;
+                    }
+
+                    // If the skip factor is 0, the entire search string should match.
+                    let completely_matched = checkable_suffix && skip == 0;
+
+                    // If the skip factor is not 0, the prefix should match the prefix of the search string.
+                    let prefix_matched = completely_matched || Self::check_prefix(
+                        current_search_string_prefix,
+                        &self.proteins.input_string[suffix - skip..suffix],
+                        equate_il
+                    );
+
+                    // If the prefix is matched, we can check the suffix.
+                    let suffix_matched = prefix_matched && Self::check_suffix(
+                        skip,
+                        il_locations_current_suffix,
+                        current_search_string_suffix,
+                        &self.proteins.input_string[suffix..suffix + search_string.len() - skip],
+                        equate_il
+                    );
+
+                    if suffix_matched {
                         matching_suffixes.push((suffix - skip) as i64);
 
                         // return if max number of matches is reached
@@ -382,6 +383,7 @@ impl Searcher {
                             return SearchAllSuffixesResult::MaxMatches(matching_suffixes);
                         }
                     }
+
                     sa_index += 1;
                 }
             }
diff --git a/sa-mappings/src/proteins.rs b/sa-mappings/src/proteins.rs
index f2b24cc..a9d4071 100644
--- a/sa-mappings/src/proteins.rs
+++ b/sa-mappings/src/proteins.rs
@@ -65,6 +65,8 @@ impl Proteins {
         // because of the encoded functional annotations
         let mut lines = ByteLines::new(BufReader::new(file));
 
+        input_string.push(SEPARATION_CHARACTER.into());
+
         while let Some(Ok(line)) = lines.next() {
             let mut fields = line.split(|b| *b == b'\t');