Merge cfee351 into bd08234

src/alignment/poa.rs

@@ -195,7 +195,7 @@ impl Traceback {
         let mut i = self.last.index() + 1;
         let mut j = self.cols;
 
-        while i > 0 && j > 0 {
+        while i > 0 || j > 0 {
             // push operation and edge corresponding to (one of the) optimal
             // routes
             ops.push(self.matrix[i][j].op);
@@ -212,13 +212,14 @@ impl Traceback {
                     j -= 1;
                 }
                 AlignmentOperation::Match(None) => {
-                    break;
+                    i -= 1;
+                    j -= 1;
                 }
                 AlignmentOperation::Del(None) => {
-                    j -= 1;
+                    i -= 1;
                 }
                 AlignmentOperation::Ins(None) => {
-                    i -= 1;
+                    j -= 1;
                 }
             }
         }
@@ -432,11 +433,23 @@ impl<F: MatchFunc> Poa<F> {
     /// * `aln` - The alignment of the new sequence to the graph
     /// * `seq` - The sequence being incorporated
     pub fn add_alignment(&mut self, aln: &Alignment, seq: TextSlice) {
-        let mut prev: NodeIndex<usize> = NodeIndex::new(0);
+        let head = Topo::new(&self.graph).next(&self.graph).unwrap();
+        let mut prev: NodeIndex<usize> = NodeIndex::new(head.index());
         let mut i: usize = 0;
+        let mut edge_not_connected: bool = false;
         for op in aln.operations.iter() {
             match op {
                 AlignmentOperation::Match(None) => {
+                    let node: NodeIndex<usize> = NodeIndex::new(0);
+                    if (seq[i] != self.graph.raw_nodes()[head.index()].weight) && (seq[i] != b'X') {
+                        let node = self.graph.add_node(seq[i]);
+                        prev = node;
+                    }
+                    if edge_not_connected {
+                        self.graph.add_edge(prev, node, 1);
+                        prev = node;
+                        edge_not_connected = false;
+                    }
                     i += 1;
                 }
                 AlignmentOperation::Match(Some((_, p))) => {
@@ -452,15 +465,22 @@ impl<F: MatchFunc> Poa<F> {
                                 *self.graph.edge_weight_mut(edge).unwrap() += 1;
                             }
                             None => {
-                                // where the previous node was newly added
-                                self.graph.add_edge(prev, node, 1);
+                                if prev.index() != head.index() {
+                                    self.graph.add_edge(prev, node, 1);
+                                }
                             }
                         }
                         prev = NodeIndex::new(*p);
                     }
                     i += 1;
                 }
                 AlignmentOperation::Ins(None) => {
+                    let node = self.graph.add_node(seq[i]);
+                    if edge_not_connected {
+                        self.graph.add_edge(prev, node, 1);
+                    }
+                    prev = node;
+                    edge_not_connected = true;
                     i += 1;
                 }
                 AlignmentOperation::Ins(Some(_)) => {
@@ -479,6 +499,7 @@ impl<F: MatchFunc> Poa<F> {
 mod tests {
     use super::*;
     use crate::alignment::pairwise::Scoring;
+    use petgraph::dot::Dot;
     use petgraph::graph::NodeIndex;
 
     #[test]
@@ -587,4 +608,35 @@ mod tests {
             .add_to_graph();
         assert_eq!(aligner.alignment().score, 10);
     }
+    #[test]
+    fn test_edge_cases() {
+        // case 1
+        let scoring = Scoring::new(-1, 0, |a: u8, b: u8| if a == b { 1i32 } else { -1i32 });
+        let mut aligner = Aligner::new(scoring, b"BBA");
+        aligner.global(b"AAA").add_to_graph();
+        let g = aligner.graph().map(|_, n| (*n) as char, |_, e| *e);
+        let dot = format!("{:?}", Dot::new(&g));
+        assert_eq!(dot, "digraph {\n    0 [ label = \"'B'\" ]\n    1 [ label = \"'B'\" ]\n    2 [ label = \"'A'\" ]\n    3 [ label = \"'A'\" ]\n    4 [ label = \"'A'\" ]\n    0 -> 1 [ label = \"1\" ]\n    1 -> 2 [ label = \"1\" ]\n    3 -> 4 [ label = \"1\" ]\n    4 -> 2 [ label = \"1\" ]\n}\n");
+        // case 2
+        let scoring = Scoring::new(-1, 0, |a: u8, b: u8| if a == b { 1i32 } else { -1i32 });
+        let mut aligner = Aligner::new(scoring, b"AAA");
+        aligner.global(b"ABA").add_to_graph();
+        let g = aligner.graph().map(|_, n| (*n) as char, |_, e| *e);
+        let dot = format!("{:?}", Dot::new(&g));
+        assert_eq!(dot, "digraph {\n    0 [ label = \"'A'\" ]\n    1 [ label = \"'A'\" ]\n    2 [ label = \"'A'\" ]\n    3 [ label = \"'B'\" ]\n    0 -> 1 [ label = \"1\" ]\n    1 -> 2 [ label = \"1\" ]\n    0 -> 3 [ label = \"1\" ]\n    3 -> 2 [ label = \"1\" ]\n}\n");
+        // case 3
+        let scoring = Scoring::new(-1, 0, |a: u8, b: u8| if a == b { 1i32 } else { -1i32 });
+        let mut aligner = Aligner::new(scoring, b"BBBBBAAA");
+        aligner.global(b"AAA").add_to_graph();
+        let g = aligner.graph().map(|_, n| (*n) as char, |_, e| *e);
+        let dot = format!("{:?}", Dot::new(&g));
+        assert_eq!(dot, "digraph {\n    0 [ label = \"'B'\" ]\n    1 [ label = \"'B'\" ]\n    2 [ label = \"'B'\" ]\n    3 [ label = \"'B'\" ]\n    4 [ label = \"'B'\" ]\n    5 [ label = \"'A'\" ]\n    6 [ label = \"'A'\" ]\n    7 [ label = \"'A'\" ]\n    0 -> 1 [ label = \"1\" ]\n    1 -> 2 [ label = \"1\" ]\n    2 -> 3 [ label = \"1\" ]\n    3 -> 4 [ label = \"1\" ]\n    4 -> 5 [ label = \"1\" ]\n    5 -> 6 [ label = \"2\" ]\n    6 -> 7 [ label = \"2\" ]\n}\n");
+        // case 4
+        let scoring = Scoring::new(-1, 0, |a: u8, b: u8| if a == b { 1i32 } else { -1i32 });
+        let mut aligner = Aligner::new(scoring, b"AAA");
+        aligner.global(b"BBBBBAAA").add_to_graph();
+        let g = aligner.graph().map(|_, n| (*n) as char, |_, e| *e);
+        let dot = format!("{:?}", Dot::new(&g));
+        assert_eq!(dot, "digraph {\n    0 [ label = \"'A'\" ]\n    1 [ label = \"'A'\" ]\n    2 [ label = \"'A'\" ]\n    3 [ label = \"'B'\" ]\n    4 [ label = \"'B'\" ]\n    5 [ label = \"'B'\" ]\n    6 [ label = \"'B'\" ]\n    7 [ label = \"'B'\" ]\n    0 -> 1 [ label = \"2\" ]\n    1 -> 2 [ label = \"2\" ]\n    3 -> 4 [ label = \"1\" ]\n    4 -> 5 [ label = \"1\" ]\n    5 -> 6 [ label = \"1\" ]\n    6 -> 7 [ label = \"1\" ]\n    7 -> 0 [ label = \"1\" ]\n}\n");
+    }
 }