From 1ca82659c187c1f89238042802614b9387aa7f28 Mon Sep 17 00:00:00 2001
From: zhouxiexuan <zhouxiexuan@qq.com>
Date: Tue, 19 Dec 2023 16:25:01 +0100
Subject: [PATCH] peptdeep upgraded

---
 alphaviz/contrib/reader_utils.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/alphaviz/contrib/reader_utils.py b/alphaviz/contrib/reader_utils.py
index 05e05d1..9740ad6 100644
--- a/alphaviz/contrib/reader_utils.py
+++ b/alphaviz/contrib/reader_utils.py
@@ -18,8 +18,8 @@
 
 from alpharaw.ms_data_base import ms_reader_provider
 
-from peptdeep.psm_frag_reader.library_frag_reader import (
-    SpectronautMSMSReader
+from alphabase.spectral_library.reader import (
+    LibraryReaderBase
 )
 from peptdeep.psm_frag_reader.maxquant_frag_reader import (
     MaxQuantMSMSReader
@@ -140,9 +140,8 @@ def _get_psm_reader(
                 max_frag_charge=max_frag_charge
             )
         elif psm_type.lower() in ['swath','spectroanut']:
-            reader = SpectronautMSMSReader(
-                frag_types=frag_types,
-                max_frag_charge=max_frag_charge
+            reader = LibraryReaderBase(
+                charged_frag_types=frag_types,
             )
     else:
         reader = psm_reader_provider.get_reader(psm_type)