Added known misbehaving alignment

rustyms/src/align/bad_alignments.rs

@@ -0,0 +1,34 @@
+#![allow(clippy::missing_panics_doc)]
+
+use crate::{
+    align::{align, matrix, AlignType},
+    LinearPeptide, SimpleLinear, Tolerance,
+};
+
+#[test]
+fn overextended_rotation() {
+    test_alignment("IVQEVS", "LEVQVES", "1i1I2=2r1=");
+}
+
+fn test_alignment(peptide_one: &str, peptide_two: &str, path: &str) {
+    let first_peptide = LinearPeptide::pro_forma(peptide_one, None)
+        .unwrap()
+        .into_simple_linear()
+        .unwrap();
+    let second_peptide = LinearPeptide::pro_forma(peptide_two, None)
+        .unwrap()
+        .into_simple_linear()
+        .unwrap();
+    let alignment = align::<4, SimpleLinear, SimpleLinear>(
+        &first_peptide,
+        &second_peptide,
+        matrix::BLOSUM62,
+        Tolerance::new_ppm(10.0),
+        AlignType::GLOBAL,
+    );
+    assert_eq!(
+        alignment.short(),
+        path,
+        "Alignment of {peptide_one} vs {peptide_two} did not go to plan"
+    );
+}

rustyms/src/align/mod.rs

@@ -28,6 +28,8 @@
 
 mod align_type;
 mod alignment;
+#[cfg(test)]
+mod bad_alignments;
 mod diagonal_array;
 mod mass_alignment;
 mod piece;

rustyms/src/glycan/positioned_structure.rs

@@ -26,7 +26,11 @@ pub struct PositionedGlycanStructure {
 }
 
 impl Chemical for PositionedGlycanStructure {
-    fn formula_inner(&self, sequence_index: SequencePosition, peptide_index: usize) -> MolecularFormula {
+    fn formula_inner(
+        &self,
+        sequence_index: SequencePosition,
+        peptide_index: usize,
+    ) -> MolecularFormula {
         self.sugar.formula_inner(sequence_index, peptide_index)
             + self
                 .branches
@@ -72,7 +76,8 @@ impl PositionedGlycanStructure {
                         .flat_map(move |(f, bonds)| {
                             full_formula.iter().map(move |full| {
                                 Fragment::new(
-                                    full - self.formula_inner(SequencePosition::default(), peptide_index)
+                                    full - self
+                                        .formula_inner(SequencePosition::default(), peptide_index)
                                         + f,
                                     Charge::zero(),
                                     peptidoform_index,