Made the MzSpecLibEncode trait more flexible

Author: douweschulte

mzannotate/src/mzspeclib/write.rs

@@ -4,9 +4,8 @@ use std::{
     num::NonZeroU32,
 };
 
-use itertools::Itertools;
 use mzcv::term;
-use mzdata::{mzpeaks::peak_set::PeakSetIter, params::Value, prelude::*};
+use mzdata::{params::Value, prelude::*};
 
 use crate::{
     mzspeclib::{Attribute, AttributeValue, Attributes, EntryType, Id, LibraryHeader},
@@ -203,7 +202,14 @@ impl<Writer: Write> MzSpecLibTextWriter<Writer, HeaderWritten> {
                     write!(&mut self.writer, "\t")?;
                 }
                 write!(&mut self.writer, "\t")?;
-                write!(&mut self.writer, "{}", p.aggregations().join(","))?;
+                let mut trailing = false;
+                for agg in p.aggregations() {
+                    if trailing {
+                        write!(&mut self.writer, ",")?;
+                    }
+                    write!(&mut self.writer, "{agg}")?;
+                    trailing = true;
+                }
             }
             writeln!(&mut self.writer)?;
         }
@@ -235,7 +241,9 @@ pub struct HeaderWritten;
 /// A single spectrum that can be encoded as an mzSpecLib file
 pub trait MzSpecLibEncode {
     /// The peak type
-    type Peak: MzSpecLibPeakEncode;
+    type Peak<'a>: MzSpecLibPeakEncode + 'a
+    where
+        Self: 'a;
     /// The key for this spectrum
     fn key(&self) -> Id;
     /// The attributes for this spectrum
@@ -249,7 +257,7 @@ pub trait MzSpecLibEncode {
         &self,
     ) -> impl Iterator<Item = (Id, Attributes, Self::InterpretationMemberIter)>;
     /// The peaks
-    fn peaks(&self) -> PeakSetIter<'_, Self::Peak>;
+    fn peaks(&self) -> impl Iterator<Item = Self::Peak<'_>>;
 }
 
 /// A peak that can be encoded for use in an mzSpecLib file
@@ -259,5 +267,5 @@ pub trait MzSpecLibPeakEncode: CentroidLike {
     /// The annotations
     fn annotations(&self) -> impl Iterator<Item = &Self::A>;
     /// The aggregations
-    fn aggregations(&self) -> impl Iterator<Item = &str>;
+    fn aggregations(&self) -> impl Iterator<Item = impl std::fmt::Display>;
 }

mzannotate/src/spectrum/peak.rs

@@ -1,3 +1,5 @@
+use std::fmt::Display;
+
 use mzcore::system::MassOverCharge;
 use mzdata::{
     mzpeaks::prelude::*,
@@ -212,7 +214,21 @@ impl<A: ToMzPAF> crate::mzspeclib::MzSpecLibPeakEncode for AnnotatedPeak<A> {
     }
 
     /// The aggregations
-    fn aggregations(&self) -> impl Iterator<Item = &str> {
+    fn aggregations(&self) -> impl Iterator<Item = impl Display> {
+        self.aggregations.iter().map(String::as_str)
+    }
+}
+
+impl<A: ToMzPAF> crate::mzspeclib::MzSpecLibPeakEncode for &AnnotatedPeak<A> {
+    type A = A;
+
+    /// The annotations
+    fn annotations(&self) -> impl Iterator<Item = &Self::A> {
+        self.annotations.iter()
+    }
+
+    /// The aggregations
+    fn aggregations(&self) -> impl Iterator<Item = impl Display> {
         self.aggregations.iter().map(String::as_str)
     }
 }

mzannotate/src/spectrum/spectrum.rs

@@ -3,11 +3,7 @@ use std::num::NonZeroU32;
 use mzcore::{chemistry::MassOutputMode, system::MassOverCharge};
 use mzcv::term;
 use mzdata::{
-    mzpeaks::{
-        MZPeakSetType,
-        peak_set::{PeakSetIter, PeakSetVec},
-        prelude::*,
-    },
+    mzpeaks::{MZPeakSetType, peak_set::PeakSetVec, prelude::*},
     params::{ParamDescribed, ParamLike, Unit, Value, ValueRef},
     prelude::{IonProperties, SpectrumLike},
     spectrum::{MultiLayerSpectrum, SignalContinuity, SpectrumDescription},
@@ -264,7 +260,10 @@ impl<Mode: MassOutputMode> From<AnnotatedSpectrum<Mode>> for MultiLayerSpectrum
 impl<Mode: MassOutputMode> crate::mzspeclib::MzSpecLibEncode for AnnotatedSpectrum<Mode> {
     type InterpretationMemberIter = Vec<(Id, Attributes)>;
     /// The peak type
-    type Peak = AnnotatedPeak<Fragment<Mode>>;
+    type Peak<'a>
+        = &'a AnnotatedPeak<Fragment<Mode>>
+    where
+        Mode: 'a;
 
     /// The key for this spectrum
     fn key(&self) -> Id {
@@ -327,7 +326,7 @@ impl<Mode: MassOutputMode> crate::mzspeclib::MzSpecLibEncode for AnnotatedSpectr
     }
 
     /// The peaks
-    fn peaks(&self) -> PeakSetIter<'_, Self::Peak> {
+    fn peaks(&self) -> impl Iterator<Item = Self::Peak<'_>> {
         self.peaks.iter()
     }
 }