Small api fixes

snijderlab · Sep 20, 2024 · 4eccdc9 · 4eccdc9
1 parent 18f8f35
commit 4eccdc9
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Showing 5 changed files with 50 additions and 14 deletions.
diff --git a/rustyms-generate-imgt/src/combine.rs b/rustyms-generate-imgt/src/combine.rs
@@ -9,10 +9,7 @@ use rustyms::UnAmbiguous;
 use crate::imgt_gene::IMGTGene;
 use crate::structs::DataItem;
 
-use crate::shared::{
-    AnnotatedSequence, Annotation, Gene, Germline, Germlines,
-    Species,
-};
+use crate::shared::{AnnotatedSequence, Annotation, Gene, Germline, Germlines, Species};
 use crate::structs::SingleSeq;
 
 pub fn combine(

diff --git a/rustyms/src/glycan/monosaccharide.rs b/rustyms/src/glycan/monosaccharide.rs
@@ -13,13 +13,12 @@ include!("../shared/glycan_lists.rs");
 impl MonoSaccharide {
     /// Generate the composition used for searching on glycans
     pub(crate) fn search_composition(
-        mut composition: Vec<(Self, isize)>,
+        composition: &[(Self, isize)],
     ) -> Vec<(MolecularFormula, isize)> {
         // Sort on monosaccharide
-        composition.retain(|el| el.1 != 0);
         let mut composition = composition
-            .into_iter()
-            .map(|(m, n)| (m.formula(), n))
+            .iter()
+            .filter_map(|(m, n)| (*n != 0).then(|| (m.formula(), *n)))
             .collect_vec();
         composition.sort_unstable_by(|a, b| a.0.cmp(&b.0));
 

diff --git a/rustyms/src/mass_mode.rs b/rustyms/src/mass_mode.rs
@@ -17,3 +17,14 @@ pub enum MassMode {
     /// Only available with crate feature 'isotopes'.
     MostAbundant,
 }
+
+impl std::fmt::Display for MassMode {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        match self {
+            Self::Average => write!(f, "average weight"),
+            Self::Monoisotopic => write!(f, "monoisotopic mass"),
+            #[cfg(feature = "isotopes")]
+            Self::MostAbundant => write!(f, "most abundant mass"),
+        }
+    }
+}
diff --git a/rustyms/src/modification.rs b/rustyms/src/modification.rs
@@ -17,7 +17,7 @@ use crate::{
     peptide::Linked,
     placement_rule::PlacementRule,
     system::{Mass, OrderedMass},
-    AmbiguousLabel, AminoAcid, Chemical, DiagnosticIon, Fragment, LinearPeptide, Model,
+    AmbiguousLabel, AminoAcid, Chemical, DiagnosticIon, Fragment, LinearPeptide, MassMode, Model,
     MolecularFormula, Multi, NeutralLoss, SequenceElement, SequencePosition, Tolerance,
     WithinTolerance,
 };
@@ -586,12 +586,18 @@ impl SimpleModification {
     pub fn search(
         modification: &Self,
         tolerance: Tolerance<Mass>,
+        mass_mode: MassMode,
         custom_database: Option<&CustomDatabase>,
     ) -> ModificationSearchResult {
         match modification {
-            Self::Mass(mass) => ModificationSearchResult::Mass(
+            Self::Mass(mass)
+            | Self::Gno {
+                composition: GnoComposition::Weight(mass),
+                ..
+            } => ModificationSearchResult::Mass(
                 mass.into_inner(),
                 tolerance,
+                mass_mode,
                 [
                     Ontology::Unimod,
                     Ontology::Psimod,
@@ -606,7 +612,7 @@ impl SimpleModification {
                         .map(|(i, n, m)| (*o, *i, n, m))
                 })
                 .filter(|(_, _, _, m)| {
-                    tolerance.within(&mass.into_inner(), &m.formula().monoisotopic_mass())
+                    tolerance.within(&mass.into_inner(), &m.formula().mass(mass_mode))
                 })
                 .map(|(o, i, n, m)| (o, i, n.clone(), m.clone()))
                 .collect(),
@@ -630,8 +636,12 @@ impl SimpleModification {
                 .map(|(o, i, n, m)| (o, i, n.clone(), m.clone()))
                 .collect(),
             ),
-            Self::Glycan(glycan) => {
-                let search = MonoSaccharide::search_composition(glycan.clone());
+            Self::Glycan(glycan)
+            | Self::Gno {
+                composition: GnoComposition::Composition(glycan),
+                ..
+            } => {
+                let search = MonoSaccharide::search_composition(glycan);
                 ModificationSearchResult::Glycan(
                     glycan.clone(),
                     Ontology::Gnome
@@ -643,8 +653,14 @@ impl SimpleModification {
                                 ..
                             } = m
                             {
-                                MonoSaccharide::search_composition(structure.composition())
+                                MonoSaccharide::search_composition(&structure.composition())
                                     == *search
+                            } else if let Self::Gno {
+                                composition: GnoComposition::Composition(composition),
+                                ..
+                            } = m
+                            {
+                                MonoSaccharide::search_composition(composition) == *search
                             } else {
                                 false
                             }
@@ -709,6 +725,7 @@ pub enum ModificationSearchResult {
     Mass(
         Mass,
         Tolerance<Mass>,
+        MassMode,
         Vec<(Ontology, Option<usize>, String, SimpleModification)>,
     ),
     /// All modifications with the same formula

diff --git a/rustyms/src/shared/modification.rs b/rustyms/src/shared/modification.rs
@@ -188,3 +188,15 @@ pub enum GnoSubsumption {
     /// Indicates the topology, without reducing end ring and anomeric information
     Saccharide,
 }
+
+impl std::fmt::Display for GnoSubsumption {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        match self {
+            Self::AverageWeight => write!(f, "Average weight"),
+            Self::BaseComposition => write!(f, "Base composition (no isomeric information)"),
+            Self::Composition => write!(f, "Composition"),
+            Self::Topology => write!(f, "Topology (no linkage)"),
+            Self::Saccharide => write!(f, "Saccharide"),
+        }
+    }
+}