feature: add precursor stack manipulation tools to SpectrumLike and similar.

Author: mobiusklein

src/spectrum/bindata/encodings.rs

@@ -994,7 +994,7 @@ impl ArrayType {
             == (Self::NonStandardDataArray {
                 name: "".to_string().into(),
             })
-            .as_param_const()
+            .as_param(None)
             .curie()
             .unwrap()
         {

src/spectrum/chromatogram.rs

@@ -85,7 +85,7 @@ impl TimeInterval<Time> for Chromatogram {
 /// Analog of [`SpectrumLike`](crate::spectrum::SpectrumLike) for chromatograms or
 /// other measures over time.
 pub trait ChromatogramLike: ParamDescribed {
-    /// The method to access the spectrum description itself, which supplies
+    /// The method to access the chromatogram description itself, which supplies
     /// the data for most other methods on this trait.
     fn description(&self) -> &ChromatogramDescription;
 
@@ -98,7 +98,7 @@ pub trait ChromatogramLike: ParamDescribed {
         desc.precursor.first()
     }
 
-    /// Iterate over all precursors of the spectrum
+    /// Iterate over all precursors of the chromatogram
     fn precursor_iter(&self) -> impl Iterator<Item = &Precursor> {
         let desc = self.description();
         desc.precursor.iter()
@@ -110,12 +110,32 @@ pub trait ChromatogramLike: ParamDescribed {
         desc.precursor.first_mut()
     }
 
-    /// Iterate over all precursors of the spectrum mutably
+    /// Iterate over all precursors of the chromatogram mutably
     fn precursor_iter_mut(&mut self) -> impl Iterator<Item = &mut Precursor> {
         let desc = self.description_mut();
         desc.precursor.iter_mut()
     }
 
+    /// Add a precursor to the list of precursors for this chromatogram.
+    ///
+    /// Precursors beyond the first one correspond to lower exponentiated spectra, e.g. for an MS3 chromatogram
+    /// the first precursor is the MS2 product ion that was selected, and the second precursor corresponds
+    /// to the original MS1 ion that was chosen for MS2.
+    ///
+    /// Higher order precursors may be accessed with [`ChromatogramLike::precursor_iter`].
+    fn add_precursor(&mut self, precursor: Precursor) {
+        self.description_mut().precursor.push(precursor);
+    }
+
+    /// Remove the precursor entry at `index` in the precursor list.
+    ///
+    /// Care should be taken if you are attempting to re-order precursors.
+    /// It may be simpler to use [`ChromatogramLike::precursor_iter_mut`] to
+    /// re-arrange entries.
+    fn remove_precursor(&mut self, index: usize) -> Precursor {
+        self.description_mut().precursor.remove(index)
+    }
+
     #[inline]
     fn start_time(&self) -> Option<f64> {
         if let Ok(t) = self.time() {

src/spectrum/frame.rs

@@ -155,7 +155,10 @@ impl From<IonMobilityFrameDescription> for SpectrumDescription {
     }
 }
 
-/// A trait for providing a uniform delegated access to spectrum metadata
+/// A trait for providing a uniform delegated access to ion mobility frame metadata.
+///
+/// This is analogous to [`SpectrumLike`] but adapted for working with different underlying
+/// types.
 pub trait IonMobilityFrameLike<
     C: FeatureLike<MZ, IonMobility>,
     D: FeatureLike<Mass, IonMobility> + KnownCharge,
@@ -188,7 +191,7 @@ pub trait IonMobilityFrameLike<
         &mut self.description_mut().ion_mobility_unit
     }
 
-    /// Access the acquisition information for this spectrum.
+    /// Access the acquisition information for this frame.
     #[inline]
     fn acquisition(&self) -> &Acquisition {
         &self.description().acquisition
@@ -205,7 +208,7 @@ pub trait IonMobilityFrameLike<
         }
     }
 
-    /// Iterate over all precursors of the spectrum
+    /// Iterate over all precursors of the frame
     fn precursor_iter(&self) -> impl Iterator<Item = &Precursor> {
         let desc = self.description();
         desc.precursor.iter()
@@ -221,12 +224,33 @@ pub trait IonMobilityFrameLike<
         }
     }
 
-    /// Iterate over all precursors of the spectrum mutably
+    /// Iterate over all precursors of the frame mutably
     fn precursor_iter_mut(&mut self) -> impl Iterator<Item = &mut Precursor> {
         let desc = self.description_mut();
         desc.precursor.iter_mut()
     }
 
+    /// Add a precursor to the list of precursors for this frame.
+    ///
+    /// Precursors beyond the first one correspond to lower exponentiated spectra, e.g. for an MS3 frame
+    /// the first precursor is the MS2 product ion that was selected, and the second precursor corresponds
+    /// to the original MS1 ion that was chosen for MS2.
+    ///
+    /// Higher order precursors may be accessed with [`IonMobilityFrameLike::precursor_iter`].
+    fn add_precursor(&mut self, precursor: Precursor) {
+        self.description_mut().precursor.push(precursor);
+    }
+
+
+    /// Remove the precursor entry at `index` in the precursor list.
+    ///
+    /// Care should be taken if you are attempting to re-order precursors.
+    /// It may be simpler to use [`IonMobilityFrameLike::precursor_iter_mut`] to
+    /// re-arrange entries.
+    fn remove_precursor(&mut self, index: usize) -> Precursor {
+        self.description_mut().precursor.remove(index)
+    }
+
     /// A shortcut method to retrieve the scan start time of a spectrum
     #[inline]
     fn start_time(&self) -> f64 {

src/spectrum/scan_properties.rs

@@ -175,6 +175,15 @@ pub trait IonMobilityMeasure: ParamDescribed {
     fn has_ion_mobility(&self) -> bool {
         self.ion_mobility().is_some()
     }
+
+    fn ion_mobility_type(&self) -> Option<&Param> {
+        for u in ION_MOBILITY_SCAN_TERMS {
+            if let Some(v) = self.get_param_by_curie(&u) {
+                return Some(v);
+            }
+        }
+        None
+    }
 }
 
 pub(crate) const PRESET_SCAN_CONFIGURATION: CURIE = curie!(MS:1000616);

src/spectrum/spectrum_types.rs

@@ -82,6 +82,26 @@ pub trait SpectrumLike<
         desc.precursor.iter_mut()
     }
 
+    /// Add a precursor to the list of precursors for this spectrum.
+    ///
+    /// Precursors beyond the first one correspond to lower exponentiated spectra, e.g. for an MS3 spectrum
+    /// the first precursor is the MS2 product ion that was selected, and the second precursor corresponds
+    /// to the original MS1 ion that was chosen for MS2.
+    ///
+    /// Higher order precursors may be accessed with [`SpectrumLike::precursor_iter`].
+    fn add_precursor(&mut self, precursor: Precursor) {
+        self.description_mut().precursor.push(precursor);
+    }
+
+    /// Remove the precursor entry at `index` in the precursor list.
+    ///
+    /// Care should be taken if you are attempting to re-order precursors.
+    /// It may be simpler to use [`SpectrumLike::precursor_iter_mut`] to
+    /// re-arrange entries.
+    fn remove_precursor(&mut self, index: usize) -> Precursor {
+        self.description_mut().precursor.remove(index)
+    }
+
     /// A shortcut method to retrieve the scan start time of a spectrum
     #[inline]
     fn start_time(&self) -> f64 {