Implement suggested changes

Author: RalfG

ms2rescore/config_parser.py

@@ -89,7 +89,12 @@ def _validate_processes(config: Dict) -> Dict:
 
 def _validate_regular_expressions(config: Dict) -> Dict:
     """Validate regular expressions in configuration."""
-    for field in ["psm_id_pattern", "spectrum_id_pattern"]:
+    for field in [
+        "psm_id_pattern",
+        "spectrum_id_pattern",
+        "psm_id_rt_pattern",
+        "psm_id_im_pattern",
+    ]:
         if config["ms2rescore"][field]:
 
             # Check if valid regex

ms2rescore/parse_psms.py

@@ -62,7 +62,7 @@ def parse_psms(config: Dict, psm_list: Union[PSMList, None]) -> PSMList:
         )
         new_ids = [_match_psm_ids(old_id, pattern) for old_id in psm_list["spectrum_id"]]
 
-        # Validate that n unique IDs remains the same
+        # Validate that the number of unique IDs remains the same
         if len(set(new_ids)) != len(set(psm_list["spectrum_id"])):
             example_old_id = psm_list["spectrum_id"][0]
             example_new_id = new_ids[0]

ms2rescore/parse_spectra.py

@@ -205,7 +205,7 @@ def _get_precursor_values(
             if spectrum_id_pattern:
                 precursors = _apply_spectrum_id_pattern(precursors, spectrum_id_pattern)
 
-            # Ensure all PSMs have a precursor values
+            # Ensure all PSMs have precursor values
             for psm in psm_list_run:
                 if psm.spectrum_id not in precursors:
                     raise MS2RescoreConfigurationError(