Merge pull request #467 from GavinHuttley/develop

API: PEP8 renaming of sequence attributes

src/cogent3/core/sequence.py

@@ -92,7 +92,7 @@ class SequenceI(object):
     # String methods delegated to self._seq -- remember to override if self._seq
     # isn't a string in your base class, but it's probably better to make
     # self._seq a property that contains the string.
-    LineWrap = None  # used for formatting FASTA strings
+    line_wrap = None  # used for formatting FASTA strings
 
     def __str__(self):
         """__str__ returns self._seq unmodified."""
@@ -1330,7 +1330,7 @@ class ArraySequenceBase(object):
     such as FASTA.
 
     A sequence Class has an alphabet (which can be overridden in instances
-    where necessary), a delimiter used for string conversions, a LineWrap
+    where necessary), a delimiter used for string conversions, a line_wrap
     for wrapping characters into lines for e.g. FASTA output.
 
     Note that a ArraySequence _must_ have an Alphabet, not a MolType,
@@ -1340,8 +1340,8 @@ class ArraySequenceBase(object):
 
     alphabet = None  # REPLACE IN SUBCLASSES
     moltype = None  # REPLACE IN SUBCLASSES
-    Delimiter = ""  # Used for string conversions
-    LineWrap = 80  # Wrap sequences at 80 characters by default.
+    delimiter = ""  # Used for string conversions
+    line_wrap = 80  # Wrap sequences at 80 characters by default.
 
     def __init__(self, data="", alphabet=None, name=None, info=None, check="ignored"):
         """Initializes sequence from data and alphabet.
@@ -1408,7 +1408,7 @@ def __str__(self):
         if hasattr(self.alphabet, "to_string"):
             return self.alphabet.to_string(self._data)
         else:
-            return self.Delimiter.join(map(str, self.alphabet.from_indices(self._data)))
+            return self.delimiter.join(map(str, self.alphabet.from_indices(self._data)))
 
     def __len__(self):
         """Returns length of data."""
@@ -1793,7 +1793,7 @@ class ArrayCodonSequence(ArraySequence):
 
     def __str__(self):
         """Joins triplets together as string."""
-        return self.Delimiter.join(map("".join, self.alphabet.from_indices(self._data)))
+        return self.delimiter.join(map("".join, self.alphabet.from_indices(self._data)))
 
     def _from_string(self, s):
         """Reads from a raw string, rather than a DnaSequence."""