Generalize MS_Spectrum class to MsData

Author: rkjulian

docs/source/pymzml_spec.rst

@@ -30,8 +30,8 @@ Chromatogram
     :exclude-members: __repr__, __str__
 
 
-MS_Spectrum
+MsData
 -----------
 
-.. autoclass:: pymzml.spec.MS_Spectrum
+.. autoclass:: pymzml.msdata.MsData
     :members:

pymzml/chromatogram.py

@@ -35,11 +35,11 @@
 
 import re
 import numpy as np
-from .ms_spectrum import MS_Spectrum
+from .msdata import MsData
 from .obo import OboTranslator
 
 
-class Chromatogram(MS_Spectrum):
+class Chromatogram(MsData):
     """
     Class for Chromatogram access and handling.
     """

pymzml/ms_spectrum.py renamed to pymzml/msdata.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: latin-1 -*-
 """
-The MS_Spectrum class offers a base class for mass spectrometry data.
+The MsData class offers a base class for mass spectrometry data.
 It provides common functionality for both Spectrum and Chromatogram classes.
 """
 
@@ -42,9 +42,10 @@
 from .obo import OboTranslator
 
 
-class MS_Spectrum(object):
+class MsData(object):
     """
-    General spectrum class for data handling.
+    General base class for mass spectrometry data handling.
+    Provides common functionality for both Spectrum and Chromatogram classes.
     """
 
     def _read_accessions(self):

pymzml/spec.py

@@ -70,13 +70,14 @@
 ISOTOPE_AVERAGE_DIFFERENCE = 1.002
 
 # Import Chromatogram from chromatogram.py for backward compatibility
-# Import MS_Spectrum from ms_spectrum.py
-from .ms_spectrum import MS_Spectrum
+# Import MsData from msdata.py
+from .msdata import MsData
 
 
-class MS_Spectrum(object):
+class MS_Spectrum(MsData):
     """
     General spectrum class for data handling.
+    This class is kept for backward compatibility.
     """
 
     def _read_accessions(self):
@@ -396,7 +397,7 @@ def to_string(self, encoding="latin-1", method="xml"):
         return ElementTree.tostring(self.element, encoding=encoding, method=method)
 
 
-class Spectrum(MS_Spectrum):
+class Spectrum(MsData):
     """
     Spectrum class which inherits from class :py:attr:`pymzml.spec.MS_Spectrum`
 
@@ -1737,7 +1738,7 @@ def centroidedPeaks(self):
         return self.peaks("centroided")
 
 
-class Chromatogram(MS_Spectrum):
+class Chromatogram(MsData):
     """
     Class for Chromatogram access and handling.
     """