bug fix

Author: mshahneh

modifinder/classes/Compound.py

@@ -116,6 +116,8 @@ def __init__(self, incoming_data=None, **kwargs):
         # attempt to initialize the class with the provided data
         if incoming_data is not None:
             convert.to_compound(incoming_data, use_object = self, **kwargs)
+        else:
+            self.update(**kwargs)
 
         # TODO: write setters for spectrum, structure to warn the user to update the dependent attributes
 

modifinder/classes/Spectrum.py

@@ -70,9 +70,10 @@ def __init__(self, incoming_data=None, normalize_peaks = True, **kwargs):
             return
 
         if incoming_data is not None:
-            convert.to_spectrum(incoming_data, self)
-
-        self.update(normalize_peaks = normalize_peaks, **kwargs)
+            kwargs['normalize_peaks'] = normalize_peaks
+            convert.to_spectrum(incoming_data, self, **kwargs)
+        else:
+            self.update(**kwargs)
 
     @property
     def adduct(self):
@@ -82,7 +83,13 @@ def adduct(self):
     def adduct(self, value):
         self._adduct = adduct_mapping.get(value, value)
         if self._adduct is not None:
-            self._adduct_mass = general_utils.get_adduct_mass(self._adduct)
+            try:
+                self._adduct_mass = general_utils.get_adduct_mass(self._adduct)
+            except Exception as e:
+                if not self.ignore_adduct_format:
+                    raise e
+                else:
+                    self._adduct_mass = None
         else:
             self._adduct_mass = 0
 
@@ -93,7 +100,7 @@ def adduct_mass(self):
     def update(self, peaks = None, peaks_json = None, mz=None, intensity=None, precursor_mz=None, precursor_charge=None, 
                _adduct = None, adduct=None, ms_level=None, instrument=None, ms_mass_analyzer=None, 
                ms_dissociation_method=None, spectrum_id=None, normalize_peaks = False, ratio_to_base_peak = None,
-               remove_large_peaks = False, keep_top_k=None, peak_fragments_map: dict = None, **kwargs):
+               remove_large_peaks = False, keep_top_k=None, peak_fragments_map: dict = None, ignore_adduct_format = False, **kwargs):
         """Update the Spectrum object with the given values.
 
         Args:
@@ -115,7 +122,10 @@ def update(self, peaks = None, peaks_json = None, mz=None, intensity=None, precu
             remove_large_peaks (bool): If True, remove all the peaks that are larger than the precursor m/z value.
             keep_top_k (int): If not None, only keep the top k peaks.
             peak_fragments_map (dict): A dictionary mapping peaks to fragments
+            ignore_adduct_format (bool): If True, if the adduct format is not recognized, it will not throw an error.
+            **kwargs: Additional keyword arguments.
         """
+        self.ignore_adduct_format = ignore_adduct_format
         if peaks_json is not None:
             peaks = json.loads(peaks_json)
         if peaks is not None:

modifinder/utilities/visualizer.py

@@ -597,13 +597,12 @@ def draw_alignment(spectrums, matches = None, output_type='png', normalize_peaks
             matches.append(match)
 
 
+    # if matches is one dimentional, convert it to two dimentional
+    if len(matches) > 0 and isinstance(matches[0], int):
+            matches = [matches]
+    
     if len(matches) > 0 and len(matches) != len(spectrums) - 1:
         raise ValueError("Number of matches should be equal to the number of spectrums - 1")
-    
-    # in case there is only one match, accept it as both a list of tuples or a list of lists
-    if len(matches) == 1:
-        if type(matches[0][0]) == int:
-            matches = [matches]
 
     flipped = False
     if "flipped" in kwargs: