feat: detect nested ORFs (#501)

src/seq_analysis/orf.rs

@@ -93,16 +93,18 @@ pub struct Orf {
 
 /// The current algorithm state.
 struct State {
-    start_pos: [Option<usize>; 3],
+    start_pos: [Vec<usize>; 3],
     codon: VecDeque<u8>,
+    found: VecDeque<Orf>,
 }
 
 impl State {
     /// Create new state.
     pub fn new() -> Self {
         State {
-            start_pos: [None, None, None],
+            start_pos: [Vec::new(), Vec::new(), Vec::new()],
             codon: VecDeque::new(),
+            found: VecDeque::new(),
         }
     }
 }
@@ -126,9 +128,13 @@ where
     type Item = Orf;
 
     fn next(&mut self) -> Option<Orf> {
-        let mut result: Option<Orf> = None;
         let mut offset: usize;
 
+        // return any orfs already found
+        if !self.state.found.is_empty() {
+            return self.state.found.pop_front();
+        }
+
         for (index, nuc) in self.seq.by_ref() {
             // update the codon
             if self.state.codon.len() >= 3 {
@@ -137,28 +143,34 @@ where
             self.state.codon.push_back(*nuc.borrow());
             offset = (index + 1) % 3;
 
+            // check if entering orf
+            if self.finder.start_codons.contains(&self.state.codon) {
+                self.state.start_pos[offset].push(index);
+            }
             // inside orf
-            if self.state.start_pos[offset].is_some() {
+            if !self.state.start_pos[offset].is_empty() {
                 // check if leaving orf
                 if self.finder.stop_codons.contains(&self.state.codon) {
-                    // check if length is sufficient
-                    if index + 1 - self.state.start_pos[offset].unwrap() > self.finder.min_len {
-                        // build results
-                        result = Some(Orf {
-                            start: self.state.start_pos[offset].unwrap() - 2,
-                            end: index + 1,
-                            offset: offset as i8,
-                        });
+                    for start_pos in &self.state.start_pos[offset] {
+                        // check if length is sufficient
+                        if index + 1 - start_pos > self.finder.min_len {
+                            // build results
+                            self.state.found.push_back(Orf {
+                                start: start_pos - 2,
+                                end: index + 1,
+                                offset: offset as i8,
+                            });
+                        // if the first orf is too short, so are the others
+                        } else {
+                            break;
+                        }
                     }
                     // reinitialize
-                    self.state.start_pos[offset] = None;
+                    self.state.start_pos[offset] = Vec::new();
                 }
-            // check if entering orf
-            } else if self.finder.start_codons.contains(&self.state.codon) {
-                self.state.start_pos[offset] = Some(index);
             }
-            if result.is_some() {
-                return result;
+            if !self.state.found.is_empty() {
+                return self.state.found.pop_front();
             }
         }
         None
@@ -225,4 +237,28 @@ mod tests {
         ];
         assert_eq!(expected, finder.find_all(sequence).collect::<Vec<Orf>>());
     }
+
+    #[test]
+    fn test_three_nested_and_offset_orfs() {
+        let finder = basic_finder();
+        let sequence = b"ATGGGGATGGGGGGATGGAAAAATAAGTAG";
+        let expected = vec![
+            Orf {
+                start: 14,
+                end: 26,
+                offset: 2,
+            },
+            Orf {
+                start: 0,
+                end: 30,
+                offset: 0,
+            },
+            Orf {
+                start: 6,
+                end: 30,
+                offset: 0,
+            },
+        ];
+        assert_eq!(expected, finder.find_all(sequence).collect::<Vec<Orf>>());
+    }
 }