Merge pull request #532 from GavinHuttley/develop

MAINT: various code and docstring tidies

LICENSE

@@ -1,4 +1,4 @@
-Copyright 2019 Gavin Huttley
+Copyright 2019-2020 Gavin Huttley
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 

setup.py

@@ -159,7 +159,7 @@ def CythonExtension(module_name, **kw):
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Intended Audience :: Science/Research",
-        "License :: OSI Approved :: GNU General Public License (GPL)",
+        "License :: OSI Approved :: BSD License",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "Topic :: Software Development :: Libraries :: Python Modules",
         "Operating System :: OS Independent",

src/cogent3/core/sequence.py

@@ -1092,22 +1092,19 @@ def annotate_matches_to(self, pattern, annot_type, name, allow_multiple=False):
 
 
 class ProteinSequence(Sequence):
-    """Holds the standard Protein sequence. MolType set in moltype module."""
+    """Holds the standard Protein sequence."""
 
     pass
 
 
 class ProteinWithStopSequence(Sequence):
-    """Holds the standard Protein sequence, allows for stop codon
-
-    MolType set in moltype module
-    """
+    """Holds the standard Protein sequence, allows for stop codon."""
 
     pass
 
 
 class NucleicAcidSequence(Sequence):
-    """base class for DNA and RNA sequences. Abstract."""
+    """Abstract base class for DNA and RNA sequences."""
 
     PROTEIN = None  # will set in moltype
     codon_alphabet = None  # will set in moltype
@@ -1279,6 +1276,8 @@ def strand_symmetry(self, motif_length=1):
 
 
 class DnaSequence(NucleicAcidSequence):
+    """Holds the standard DNA sequence."""
+
     def get_colour_scheme(self, colours):
         return {
             "A": colours.black,
@@ -1293,6 +1292,8 @@ def _seq_filter(self, seq):
 
 
 class RnaSequence(NucleicAcidSequence):
+    """Holds the standard RNA sequence."""
+
     def get_colour_scheme(self, colours):
         return {
             "A": colours.black,
@@ -1307,7 +1308,7 @@ def _seq_filter(self, seq):
 
 
 class ABSequence(Sequence):
-    """Used for two-state modeling; MolType set in moltypes."""
+    """Holds a two-state sequence, with characters of 'a', 'b'"""
 
     pass