From be2f56d0bdd5e3a38d4435ef9ca5597d1b11205d Mon Sep 17 00:00:00 2001
From: theGreatHerrLebert <davidteschner@googlemail.com>
Date: Thu, 25 Jul 2024 13:50:45 +0200
Subject: [PATCH] adding hyper score to cmd arguments

---
 crates/sage-cli/src/input.rs | 21 +++++++++++++++++++++
 crates/sage-cli/src/main.rs  |  4 ++--
 crates/sage/src/scoring.rs   | 18 +-----------------
 tests/config.json            |  3 ++-
 4 files changed, 26 insertions(+), 20 deletions(-)

diff --git a/crates/sage-cli/src/input.rs b/crates/sage-cli/src/input.rs
index 50624357..2ddb43bc 100644
--- a/crates/sage-cli/src/input.rs
+++ b/crates/sage-cli/src/input.rs
@@ -1,6 +1,7 @@
 use anyhow::{ensure, Context};
 use clap::ArgMatches;
 use sage_cloudpath::{tdf::BrukerSpectrumProcessor, CloudPath};
+use sage_core::scoring::ScoreType;
 use sage_core::{
     database::{Builder, Parameters},
     lfq::LfqSettings,
@@ -41,6 +42,9 @@ pub struct Search {
 
     #[serde(skip_serializing)]
     pub annotate_matches: bool,
+
+    #[serde(skip_serializing)]
+    pub score_type: ScoreType,
 }
 
 #[derive(Deserialize)]
@@ -68,6 +72,7 @@ pub struct Input {
 
     annotate_matches: Option<bool>,
     write_pin: Option<bool>,
+    score_type: Option<String>,
 }
 
 #[derive(Serialize, Deserialize, Debug)]
@@ -287,6 +292,21 @@ impl Input {
             None => CloudPath::Local(std::env::current_dir()?),
         };
 
+        let score_type = match self.score_type {
+            Some(s) => {
+                // check if s in ["sage_hyperscore", "openms_hyperscore"]
+                match s.to_lowercase().as_str() {
+                    "sage_hyperscore" => ScoreType::SageHyperScore,
+                    "openms_hyperscore" => ScoreType::OpenMSHyperScore,
+                    _ => {
+                        log::warn!("Invalid score type: {}. Supported values are: 'sage_hyperscore', 'openms_hyperscore', defaulting to sage_hyperscore", s);
+                        ScoreType::SageHyperScore
+                    }
+                }
+            }
+            None => ScoreType::SageHyperScore,
+        };
+
         Ok(Search {
             version: clap::crate_version!().into(),
             database,
@@ -311,6 +331,7 @@ impl Input {
             output_paths: Vec::new(),
             write_pin: self.write_pin.unwrap_or(false),
             bruker_spectrum_processor: self.bruker_spectrum_processor.unwrap_or_default(),
+            score_type,
         })
     }
 }
diff --git a/crates/sage-cli/src/main.rs b/crates/sage-cli/src/main.rs
index d4bfef08..9b9f2b51 100644
--- a/crates/sage-cli/src/main.rs
+++ b/crates/sage-cli/src/main.rs
@@ -6,7 +6,7 @@ use rayon::prelude::*;
 use sage_cloudpath::CloudPath;
 use sage_core::database::IndexedDatabase;
 use sage_core::mass::Tolerance;
-use sage_core::scoring::{Feature, Scorer, ScoreType};
+use sage_core::scoring::{Feature, Scorer};
 use sage_core::spectrum::{ProcessedSpectrum, SpectrumProcessor};
 use sage_core::tmt::TmtQuant;
 use std::time::Instant;
@@ -272,7 +272,7 @@ impl Runner {
             report_psms: self.parameters.report_psms,
             wide_window: self.parameters.wide_window,
             annotate_matches: self.parameters.annotate_matches,
-            score_type: ScoreType::SageHyperScore,
+            score_type: self.parameters.score_type,
         };
 
         //Collect all results into a single container
diff --git a/crates/sage/src/scoring.rs b/crates/sage/src/scoring.rs
index e30e1d72..13a698c3 100644
--- a/crates/sage/src/scoring.rs
+++ b/crates/sage/src/scoring.rs
@@ -8,28 +8,12 @@ use serde::Serialize;
 use std::ops::AddAssign;
 use std::sync::atomic::{AtomicUsize, Ordering};
 
-#[derive(Copy, Clone, Debug, Serialize)]
+#[derive(Copy, Clone, Debug)]
 pub enum ScoreType {
     SageHyperScore,
     OpenMSHyperScore,
 }
 
-impl ScoreType {
-    pub fn from_str(s: &str) -> Self {
-        match s {
-            "sage_hyperscore" => ScoreType::SageHyperScore,
-            "openms_hyperscore" => ScoreType::OpenMSHyperScore,
-            _ => panic!("unknown score type."),
-        }
-    }
-    pub fn to_str(&self) -> &str {
-        match self {
-            ScoreType::SageHyperScore => "SageHyperscore",
-            ScoreType::OpenMSHyperScore => "OpenMSHyperscore",
-        }
-    }
-}
-
 /// Structure to hold temporary scores
 #[derive(Copy, Clone, Default, Debug)]
 struct Score {
diff --git a/tests/config.json b/tests/config.json
index e935013c..939575f1 100644
--- a/tests/config.json
+++ b/tests/config.json
@@ -37,5 +37,6 @@
     ],
     "mzml_paths": [
         "tests/LQSRPAAPPAPGPGQLTLR.mzML"
-    ]
+    ],
+    "score_type": "sage_hyperscore"
 }
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