Completed optimisation.

src/needle.rs

@@ -142,8 +142,10 @@ pub mod algo {
         ///
         /// The self parameter end gap cost is taken into account.
         pub fn initialise(&mut self) {
-            for i in (0..self.trace.len()).rev() {
-                for j in (0..self.trace[i].len()).rev() {
+            let trace_range = (0..self.trace.len()).rev();
+            for i in trace_range {
+                let trace_i_range = (0..self.trace[i].len()).rev();
+                for j in trace_i_range {
                     let val = self.trace[i][j];
                     let i_n = (i as i64) * self.end_gap;
                     let j_n = (j as i64) * self.end_gap;
@@ -219,9 +221,12 @@ pub mod algo {
             &self
         ) -> (Vec<(usize, usize)>, Vec<&Directions>) {
             // Here be the traceback
-            let mut coord = (self.x.len(), self.y.len());
-            let mut directions: Vec<&Directions> = Vec::new();
-            let mut indeces: Vec<(usize, usize)> = Vec::new();
+            let xlen = self.x.len();
+            let ylen = self.y.len();
+            let mut coord = (xlen, ylen);
+            let max_len = ylen.max(xlen);
+            let mut directions: Vec<&Directions> = Vec::with_capacity(max_len);
+            let mut indeces: Vec<(usize, usize)> = Vec::with_capacity(max_len);
             while coord != (0_usize, 0_usize) {
                 let (i, j) = coord;
                 let current_direction = &self.direction[i][j];
@@ -247,24 +252,26 @@ pub mod algo {
             indices: Vec<(usize, usize)>,
             directions: Vec<&Directions>,
         ) -> NeedlemanWunchAlignment {
-            let mut x: Vec<String> = Vec::with_capacity(directions.len());
-            let mut y: Vec<String> = Vec::with_capacity(directions.len());
+            let mut x: Vec<char> = Vec::with_capacity(directions.len());
+            let mut y: Vec<char> = Vec::with_capacity(directions.len());
+            let x_chars: Vec<char> = self.x.chars().collect();
+            let y_chars: Vec<char> = self.y.chars().collect();
             let indices: Vec<&(usize, usize)> = indices.iter().collect();
             for (index, direction) in directions.iter().enumerate() {
                 let (i, j) = (indices[index].0, indices[index].1);
-                let x_ch = self.x.chars().nth(i - 1).unwrap().to_string();
-                let y_ch = self.y.chars().nth(j - 1).unwrap().to_string();
+                let x_ch = x_chars[i - 1];
+                let y_ch = y_chars[j - 1];
                 match direction {
                     Directions::Diagonal => {
                         x.push(x_ch);
                         y.push(y_ch);
                     }
                     Directions::Up => {
-                        y.push("-".to_string());
+                        y.push('-');
                         x.push(x_ch);
                     }
                     Directions::Left => {
-                        x.push("-".to_string());
+                        x.push('-');
                         y.push(y_ch);
                     }
                     Directions::Unknown => {
@@ -274,10 +281,10 @@ pub mod algo {
             }
             x.reverse();
             y.reverse();
-            // let x: Vec<String> =
-            //     x.into_iter().map(|x_i| x_i.to_owned()).collect();
-            // let y: Vec<String> =
-            //     y.into_iter().map(|y_i| y_i.to_owned()).collect();
+            let x: Vec<String> =
+                x.into_iter().map(|x_i| x_i.to_string()).collect();
+            let y: Vec<String> =
+                y.into_iter().map(|y_i| y_i.to_string()).collect();
             NeedlemanWunchAlignment {
                 x: x.join(""),
                 y: y.join(""),
@@ -476,16 +483,21 @@ mod test_algo {
 
     #[test]
     fn test_long_output() {
-        for i in 1..500 {
-            let x: String = "MGLLCSRSRHHTEDTDENAQAAEIERRIEQEAKAEKHIRKLLLLGAGESGKSTIFKQASSDKRKIIKLLFQTGFDEGELKSYVPVIHANVYQTIKLLHDGTKEFAQNETDPAKYTLSSENMAIGEKLSEIGARLDYPRLTKDLAEGIETLWNDPAIQETCSRGNELQVPDCTKYLMENLKRLSDVNYIPTKEDVLYARVRTTGVVEIQFSPVGENKKSGEVYRLFDVGGQRNERRKWIHLFEGVTAVIFCAAISEYDQTLFEDEQKNRMMETKELFDWVLKQPCFEKTSIMLFLNKFDIFEKKVLDVPLNVCEWFRDYQPVSSGKQEIEHAYEFVKKKFEELYYQNTAPDRVDRVFKIYRTTALDQKLVKKTFKLVDETLRRRNLLEAGLL".to_string();
-            let y: String = "MGLLCSRSRHHTEDTDENTQAAEIERRIEQEAKAEKHIRKLLLLGAGESGKSTIFKQIKLLFQTGFDEGELKSYVPVIHANVYQTIKLLHDGTKEFAQNETDSAKYMLSSESIAIGEKLSEIGGRLDYPRLTKDIAEGIETLWKDPAIQETCARGNELQVPDCTKYLMENLKRLSDINYIPTKEDVLYARVRTTGVVEIQFSPVGENKKSGEVYRLFDVGGQRNERRKWIHLFEGVTAVIFCAAISEYDQTLFEDEQKNRMMETKELFDWVLKQPCFEKTSFMLFLNKFDIFEKKVLDVPLNVCEWFRDYQPVSSGKQEIEHAYEFVKKKFEELYYQNTAPDRVDRVFKIYRTTALDQKLVKKTFKLVDETLRRRNLLEA".to_string();
+        let x: String = "MGLLCSRSRHHTEDTDENAQAAEIERRIEQEAKAEKHIRKLLLLGAGESGKSTIFKQASSDKRKIIKLLFQTGFDEGELKSYVPVIHANVYQTIKLLHDGTKEFAQNETDPAKYTLSSENMAIGEKLSEIGARLDYPRLTKDLAEGIETLWNDPAIQETCSRGNELQVPDCTKYLMENLKRLSDVNYIPTKEDVLYARVRTTGVVEIQFSPVGENKKSGEVYRLFDVGGQRNERRKWIHLFEGVTAVIFCAAISEYDQTLFEDEQKNRMMETKELFDWVLKQPCFEKTSIMLFLNKFDIFEKKVLDVPLNVCEWFRDYQPVSSGKQEIEHAYEFVKKKFEELYYQNTAPDRVDRVFKIYRTTALDQKLVKKTFKLVDETLRRRNLLEAGLL".to_string();
+        let y: String = "MGLLCSRSRHHTEDTDENTQAAEIERRIEQEAKAEKHIRKLLLLGAGESGKSTIFKQIKLLFQTGFDEGELKSYVPVIHANVYQTIKLLHDGTKEFAQNETDSAKYMLSSESIAIGEKLSEIGGRLDYPRLTKDIAEGIETLWKDPAIQETCARGNELQVPDCTKYLMENLKRLSDINYIPTKEDVLYARVRTTGVVEIQFSPVGENKKSGEVYRLFDVGGQRNERRKWIHLFEGVTAVIFCAAISEYDQTLFEDEQKNRMMETKELFDWVLKQPCFEKTSFMLFLNKFDIFEKKVLDVPLNVCEWFRDYQPVSSGKQEIEHAYEFVKKKFEELYYQNTAPDRVDRVFKIYRTTALDQKLVKKTFKLVDETLRRRNLLEA".to_string();
+
+        let file: &Path = Path::new("data/blosum_62.txt");
+        let blosum = import_protein_substitution_matrix(file);
+        for i in 1..20 {
             let end_gap = -1 * i;
             let gap_score = end_gap;
-
-            let file: &Path = Path::new("data/blosum_62.txt");
-            let blosum = import_protein_substitution_matrix(file);
-            let mut alignment =
-                NeedlemanWunch::new(x, y, end_gap, gap_score, blosum);
+            let mut alignment = NeedlemanWunch::new(
+                x.clone(),
+                y.clone(),
+                end_gap,
+                gap_score,
+                blosum.clone(),
+            );
             alignment.set_traceback();
             let res = alignment.get_traceback();
             alignment.construct_alignment(res.0, res.1);