removed def internal to xisearch and import it from mod_string spectr…

…um fundamental

spectrum_io/search_result/xisearch.py

@@ -92,57 +92,6 @@ def filter_xisearch_result(df: pd.DataFrame) -> pd.DataFrame:
 
         return df
 
-    @staticmethod
-    def add_mod_sequence(
-        xl: str,
-        seq_a: str,
-        seq_b: str,
-        mod_a: str,
-        mod_b: str,
-        crosslinker_position_a: int,
-        crosslinker_position_b: int,
-        mod_a_positions: Union[str, float],
-        mod_b_positions: Union[str, float],
-    ):
-        """
-        Function adds modification in peptide sequence for xl-prosit.
-        
-        :param xl: type of crosslinker used. Can be 'DSSO' or 'DSBU'.
-        :param seq_a: unmodified peptide a
-        :param seq_b: unmodified peptide b
-        :param mod_a: all modifications of pep a
-        :param mod_b: all modifications of pep b
-        :param crosslinker_position_a: crosslinker position of peptide a
-        :param crosslinker_position_b: crosslinker position of peptide b
-        :param mod_a_positions: position of all modifications of peptide a
-        :param mod_b_positions: position of all modifications of peptide b
-        :return: modified sequence a and b
-        """
-        # Check the crosslinker type and apply modification accordingly
-        if xl.lower() == "dsso":
-            modification = "K[UNIMOD:1896]"
-        elif xl.lower() == "dsbu":
-            modification = "K[UNIMOD:1884]"
-        else:
-            raise ValueError(f"Unknown crosslinker type provided: {xl}. Only 'DSSO' and 'DSBU' are supported.")
-
-        mod_a_positions = str(mod_a_positions)  # Ensure it's a string
-        mod_b_positions = str(mod_b_positions)  # Ensure it's a string
-
-        split_seq_a = [x for x in seq_a]
-        split_seq_b = [x for x in seq_b]
-        xisearch_to_internal(split_seq_a, mod_a, mod_a_positions)
-        xisearch_to_internal(split_seq_b, mod_b, mod_b_positions)
-
-
-
-        split_seq_a[int(crosslinker_position_a) - 1] = modification
-        split_seq_b[int(crosslinker_position_b) - 1] = modification
-        seq_mod_a = "".join(split_seq_a)
-        seq_mod_b = "".join(split_seq_b)
-
-        return seq_mod_a, seq_mod_b
-
     @staticmethod
     def update_columns_for_prosit(df: pd.DataFrame) -> pd.DataFrame:
         """
@@ -179,7 +128,7 @@ def update_columns_for_prosit(df: pd.DataFrame) -> pd.DataFrame:
         df["CROSSLINKER_POSITION_B"] = df["CROSSLINKER_POSITION_B"].astype("int")
 
         df[["MODIFIED_SEQUENCE_A", "MODIFIED_SEQUENCE_B"]] = df.apply(
-            lambda row: Xisearch.add_mod_sequence(
+            lambda row: xisearch_to_internal(
                 row["CROSSLINKER_TYPE"],
                 row["SEQUENCE_A"],
                 row["SEQUENCE_B"],