remove tryptic check for testing purpose

unipept · Aug 23, 2024 · 1791652 · 1791652
1 parent 8fca836
commit 1791652
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Showing 2 changed files with 14 additions and 17 deletions.
diff --git a/sa-index/src/sa_searcher.rs b/sa-index/src/sa_searcher.rs
@@ -308,12 +308,10 @@ impl Searcher {
         equate_il: bool,
         tryptic_search: bool
     ) -> SearchAllSuffixesResult {
-        eprintln!("trypic_search: {}", tryptic_search);
-
         // If we perform a tryptic search, the last character of the search string should be R or K
-        // if tryptic_search && search_string[search_string.len() - 1] != b'R' && search_string[search_string.len() - 1] != b'K' {
-        //     return SearchAllSuffixesResult::NoMatches;
-        // }
+        if tryptic_search && search_string[search_string.len() - 1] != b'R' && search_string[search_string.len() - 1] != b'K' {
+            return SearchAllSuffixesResult::NoMatches;
+        }
 
         let mut matching_suffixes: Vec<i64> = vec![];
         let mut il_locations = vec![];
@@ -345,16 +343,17 @@ impl Searcher {
 
                     // If the suffix is smaller than the skip factor, we can't check the prefix
                     if suffix >= skip
-                        // && (
-                        //     // Skip this check if we are not performing a tryptic search
-                        //     !tryptic_search
-                        //     // Check if the match is 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() + 1] != b'P')
-                        // )
+                        && (
+                            // Skip this check if we are not performing a tryptic search
+                            !tryptic_search
+                            // Check if the match is tryptic
+                            || ((
+                                (suffix == skip) ||
+                                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')
+                        )
                         && ((
                             // If the skip factor is 0, the entire search string should match.
                             skip == 0

diff --git a/sa-mappings/src/proteins.rs b/sa-mappings/src/proteins.rs
@@ -65,8 +65,6 @@ 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');