feat: modified visibility, clone for pysage connector

Cargo.toml

@@ -10,4 +10,4 @@ resolver = "2"
 [profile.release]
 lto = "fat"
 codegen-units = 1
-panic = "abort"
+panic = "abort"

crates/sage/src/database.rs

@@ -118,24 +118,24 @@ impl Builder {
 
 #[derive(Serialize, Clone, Debug)]
 pub struct Parameters {
-    bucket_size: usize,
+    pub bucket_size: usize,
     pub enzyme: EnzymeBuilder,
     pub fragment_min_mz: f32,
     pub fragment_max_mz: f32,
-    peptide_min_mass: f32,
-    peptide_max_mass: f32,
-    ion_kinds: Vec<Kind>,
-    min_ion_index: usize,
-    static_mods: HashMap<ModificationSpecificity, f32>,
-    variable_mods: HashMap<ModificationSpecificity, Vec<f32>>,
-    max_variable_mods: usize,
+    pub peptide_min_mass: f32,
+    pub peptide_max_mass: f32,
+    pub ion_kinds: Vec<Kind>,
+    pub min_ion_index: usize,
+    pub static_mods: HashMap<ModificationSpecificity, f32>,
+    pub variable_mods: HashMap<ModificationSpecificity, Vec<f32>>,
+    pub max_variable_mods: usize,
     pub decoy_tag: String,
     pub generate_decoys: bool,
     pub fasta: String,
 }
 
 impl Parameters {
-    fn digest(&self, fasta: &Fasta) -> Vec<Peptide> {
+    pub fn digest(&self, fasta: &Fasta) -> Vec<Peptide> {
         log::trace!("digesting fasta");
         let enzyme = self.enzyme.clone().into();
         // Generate all tryptic peptide sequences, including reversed (decoy)
@@ -335,7 +335,7 @@ pub struct IndexedDatabase {
     pub peptides: Vec<Peptide>,
     pub fragments: Vec<Theoretical>,
     pub ion_kinds: Vec<Kind>,
-    pub(crate) min_value: Vec<f32>,
+    pub min_value: Vec<f32>,
     /// Keep a list of potential (AA, mass) modifications for RT prediction
     pub potential_mods: Vec<(ModificationSpecificity, f32)>,
     pub bucket_size: usize,

crates/sage/src/enzyme.rs

@@ -89,6 +89,7 @@ pub struct EnzymeParameters {
     pub enyzme: Option<Enzyme>,
 }
 
+#[derive(Clone)]
 pub struct Enzyme {
     // Skip cleaving if the site is followed matching this AA
     pub skip_suffix: Option<char>,
@@ -150,7 +151,7 @@ impl Enzyme {
         }
     }
 
-    fn cleavage_sites(&self, sequence: &str) -> Vec<DigestSite> {
+    pub fn cleavage_sites(&self, sequence: &str) -> Vec<DigestSite> {
         let mut sites = Vec::new();
         let mut left = 0;
         for mat in self.regex.find_iter(sequence) {
@@ -180,7 +181,7 @@ impl Enzyme {
 }
 
 impl EnzymeParameters {
-    fn cleavage_sites(&self, sequence: &str) -> Vec<DigestSite> {
+    pub fn cleavage_sites(&self, sequence: &str) -> Vec<DigestSite> {
         match &self.enyzme {
             Some(enzyme) => enzyme.cleavage_sites(sequence),
             None => {

crates/sage/src/fasta.rs

@@ -2,6 +2,7 @@ use crate::enzyme::{Digest, EnzymeParameters};
 use rayon::prelude::*;
 use std::sync::Arc;
 
+#[derive(Clone)]
 pub struct Fasta {
     pub targets: Vec<(Arc<String>, String)>,
     decoy_tag: String,

crates/sage/src/fdr.rs

@@ -15,10 +15,10 @@ use std::hash::BuildHasher;
 
 #[derive(Copy, Clone, Debug)]
 pub struct Competition<Ix> {
-    forward: f32,
-    foward_ix: Option<Ix>,
-    reverse: f32,
-    reverse_ix: Option<Ix>,
+    pub forward: f32,
+    pub foward_ix: Option<Ix>,
+    pub reverse: f32,
+    pub reverse_ix: Option<Ix>,
 }
 
 struct Row<Ix> {

crates/sage/src/lfq.rs

@@ -79,10 +79,10 @@ pub struct PrecursorRange {
 /// storing fragment masses binned by precursor mass, store MS1 precursors
 /// binned by RT - This should enable rapid quantification as well
 pub struct FeatureMap {
-    ranges: Vec<PrecursorRange>,
-    min_rts: Vec<f32>,
-    bin_size: usize,
-    settings: LfqSettings,
+    pub ranges: Vec<PrecursorRange>,
+    pub min_rts: Vec<f32>,
+    pub bin_size: usize,
+    pub settings: LfqSettings,
 }
 
 pub fn build_feature_map(

crates/sage/src/mass.rs

@@ -96,6 +96,7 @@ pub const fn composition(aa: u8) -> Composition {
     }
 }
 
+#[derive(Clone, Debug)]
 pub struct Composition {
     pub carbon: u16,
     pub sulfur: u16,

crates/sage/src/spectrum.rs

@@ -36,6 +36,7 @@ pub struct Deisotoped {
     pub envelope: Option<usize>,
 }
 
+#[derive(Debug, Clone)]
 pub struct SpectrumProcessor {
     pub take_top_n: usize,
     pub max_fragment_mz: f32,

crates/sage/src/tmt.rs

@@ -289,6 +289,7 @@ const TMT18PLEX: [f32; 18] = [
 //     })
 // }
 
+#[derive(Clone)]
 pub struct TmtQuant {
     pub spec_id: String,
     pub file_id: usize,