abstractification of conkit.io._parser.Parser class

CHANGELOG.rst

@@ -4,11 +4,11 @@ Changelog
 
 v0.8.3dev1
 ----------
-
-- ``_BandwidthCalc`` class renamed to ``BandwidthBase`` and turned into abstract class
-- ``LinearBW`` calculator added for linear bandwidth calculation in analysis
-- Distance definitions accept floating point values
 - ``requirements.txt`` file re-added for easier dependency installation
+- Distance definitions accept floating point values
+- ``LinearBW`` calculator added for linear bandwidth calculation in analysis
+- ``_BandwidthCalc`` class renamed to ``BandwidthBase``
+- Abstractified ``BandwidthBase``, and ``Parser`` with all subparser classes 
 - Bug fix
     - ``PconsParser`` class accepts negative ``raw_score`` values
     - ``SequenceFile.neff`` returns ``float`` instead of ``int``

conkit/io/_cache.py

@@ -100,13 +100,13 @@ def __repr__(self):
     def contact_file_parsers(self):
         """A dict of contact file parsers"""
         # Mask as dictionaries to not break existing code
-        return {c.id: c for c in self._parsers if c.group == "_ContactFileParser" or c.group == "_GenericStructureParser"}
+        return {c.id: c for c in self._parsers if c.group == "ContactFileParser" or c.group == "GenericStructureParser"}
 
     @property
     def sequence_file_parsers(self):
         """A dict of sequence file parsers"""
         # Mask as dictionaries to not break existing code
-        return {c.id: c for c in self._parsers if c.group == "_SequenceFileParser"}
+        return {c.id: c for c in self._parsers if c.group == "SequenceFileParser"}
 
     @property
     def file_parsers(self):

conkit/io/_parser.py

@@ -35,33 +35,31 @@
 __date__ = "04 Oct 2016"
 __version__ = "0.1"
 
+import abc
+
+ABC = abc.ABCMeta('ABC', (object,), {})
+
 from conkit.core.contact import Contact
 from conkit.core.contactmap import ContactMap
 from conkit.core.contactfile import ContactFile
 from conkit.core.sequence import Sequence
 from conkit.core.sequencefile import SequenceFile
 
 
-class _Parser(object):
-    """General purpose class for all parsers
-
-    Notes
-    -----
-    Do no instantiate this class directly
+class Parser(ABC):
+    """Abstract class for all parsers
 
     """
-    def __init__(self):
+    @abc.abstractmethod
+    def read(self):
         pass
 
+    @abc.abstractmethod
+    def write(self):
+        pass
 
-class _ContactFileParser(_Parser):
-    """General purpose class for all contact file parsers
-
-    """
-    def __init__(self):
-        super(_ContactFileParser, self).__init__()
-
-    def _reconstruct(self, hierarchy):
+    @classmethod
+    def _reconstruct(cls, hierarchy):
         """Wrapper to re-construct full hierarchy when parts are provided"""
         if isinstance(hierarchy, ContactFile):
             h = hierarchy
@@ -73,21 +71,19 @@ def _reconstruct(self, hierarchy):
             m = ContactMap('1')
             m.add(hierarchy)
             h.add(m)
+        elif isinstance(hierarchy, SequenceFile):
+            h = hierarchy
+        elif isinstance(hierarchy, Sequence):
+            h = SequenceFile('conkit')
+            h.add(hierarchy)
         return h 
 
 
-class _SequenceFileParser(_Parser):
-    """General purpose class for all sequence file parsers
-
-    """
-    def __init__(self):
-        super(_SequenceFileParser, self).__init__()
+class ContactFileParser(Parser):
+    """General purpose class for all contact file parsers"""
+    pass
+
 
-    def _reconstruct(self, hierarchy):
-        """Wrapper to re-construct full hierarchy when parts are provided"""
-        if isinstance(hierarchy, SequenceFile):
-            h = hierarchy
-        if isinstance(hierarchy, Sequence):
-            h = SequenceFile('conkit')
-            h.add(hierarchy)
-        return h
+class SequenceFileParser(Parser):
+    """General purpose class for all sequence file parsers"""
+    pass

conkit/io/a3m.py

@@ -44,12 +44,12 @@
 import os
 import re
 
-from conkit.io._parser import _SequenceFileParser
+from conkit.io._parser import SequenceFileParser
 from conkit.core.sequence import Sequence
 from conkit.core.sequencefile import SequenceFile
 
 
-class A3mParser(_SequenceFileParser):
+class A3mParser(SequenceFileParser):
     """Parser class for A3M sequence files
 
     """

conkit/io/bbcontacts.py

@@ -37,15 +37,15 @@
 
 import re
 
-from conkit.io._parser import _ContactFileParser
+from conkit.io._parser import ContactFileParser
 from conkit.core.contact import Contact
 from conkit.core.contactmap import ContactMap
 from conkit.core.contactfile import ContactFile
 
 RE_COMMENT = re.compile(r'^#+.*$')
 
 
-class BbcontactsParser(_ContactFileParser):
+class BbcontactsParser(ContactFileParser):
     """Class to parse a Bbcontacts contact file
     """
     def __init__(self):
@@ -112,8 +112,8 @@ def write(self, f_handle, hierarchy):
 
         Raises
         ------
-        RuntimeError
-           Not available
+        NotImplementedError
+           Write function not available
 
         """
-        raise RuntimeError('Not available')
+        raise NotImplementedError("Write function not available")

conkit/io/bclcontact.py

@@ -37,15 +37,15 @@
 
 import re
 
-from conkit.io._parser import _ContactFileParser
+from conkit.io._parser import ContactFileParser
 from conkit.core.contact import Contact
 from conkit.core.contactmap import ContactMap
 from conkit.core.contactfile import ContactFile
 
 RE_SPLIT = re.compile(r'\s+')
 
 
-class BCLContactParser(_ContactFileParser):
+class BCLContactParser(ContactFileParser):
     """Class to parse a BCL::Contact contact file
     """
     def __init__(self):
@@ -105,8 +105,9 @@ def write(self, f_handle, hierarchy):
 
         Raises
         ------
-        RuntimeError
-           Not available
+        NotImplementedError
+           Write function not available
 
         """
-        raise RuntimeError("Not available")
+        raise NotImplementedError("Write function not available")
+

conkit/io/casp.py

@@ -39,7 +39,7 @@
 import os
 import re
 
-from conkit.io._parser import _ContactFileParser
+from conkit.io._parser import ContactFileParser
 from conkit.core.contact import Contact
 from conkit.core.contactmap import ContactMap
 from conkit.core.contactfile import ContactFile
@@ -64,7 +64,7 @@
                                                      'res1_chain', 'res2_chain', 'res1_altseq', 'res2_altseq'])
 
 
-class CaspParser(_ContactFileParser):
+class CaspParser(ContactFileParser):
     """Parser class for CASP RR contact prediction file
 
     """

conkit/io/ccmpred.py

@@ -40,13 +40,13 @@
 import numpy as np
 import sys
 
-from conkit.io._parser import _ContactFileParser
+from conkit.io._parser import ContactFileParser
 from conkit.core.contact import Contact
 from conkit.core.contactmap import ContactMap
 from conkit.core.contactfile import ContactFile
 
 
-class CCMpredParser(_ContactFileParser):
+class CCMpredParser(ContactFileParser):
     """
     Class to parse a CCMpred contact matrix
 

conkit/io/comsat.py

@@ -38,15 +38,15 @@
 import os
 import re
 
-from conkit.io._parser import _ContactFileParser
+from conkit.io._parser import ContactFileParser
 from conkit.core.contact import Contact
 from conkit.core.contactmap import ContactMap
 from conkit.core.contactfile import ContactFile
 
 RE_SPLIT = re.compile(r'\s+')
 
 
-class ComsatParser(_ContactFileParser):
+class ComsatParser(ContactFileParser):
     """Class to parse a COMSAT contact file
     """
     def __init__(self):

conkit/io/epcmap.py

@@ -37,13 +37,13 @@
 
 import os
 
-from conkit.io._parser import _ContactFileParser
+from conkit.io._parser import ContactFileParser
 from conkit.core.contact import Contact
 from conkit.core.contactmap import ContactMap
 from conkit.core.contactfile import ContactFile
 
 
-class EPCMapParser(_ContactFileParser):
+class EPCMapParser(ContactFileParser):
     """Class to parse a EPC-Map contact prediction
     """
     def read(self, f_handle, f_id="epcmap"):

conkit/io/evfold.py

@@ -38,15 +38,15 @@
 import os
 import re
 
-from conkit.io._parser import _ContactFileParser
+from conkit.io._parser import ContactFileParser
 from conkit.core.contact import Contact
 from conkit.core.contactmap import ContactMap
 from conkit.core.contactfile import ContactFile
 
 RE_SPLIT = re.compile(r'\s+')
 
 
-class EVfoldParser(_ContactFileParser):
+class EVfoldParser(ContactFileParser):
     """Class to parse a EVfold contact file
     """
     def __init__(self):

conkit/io/fasta.py

@@ -37,12 +37,12 @@
 
 import os
 
-from conkit.io._parser import _SequenceFileParser
+from conkit.io._parser import SequenceFileParser
 from conkit.core.sequence import Sequence
 from conkit.core.sequencefile import SequenceFile
 
 
-class FastaParser(_SequenceFileParser):
+class FastaParser(SequenceFileParser):
     """Parser class for FASTA sequence files
     """
     def __init__(self):

conkit/io/freecontact.py

@@ -38,15 +38,15 @@
 import os
 import re
 
-from conkit.io._parser import _ContactFileParser
+from conkit.io._parser import ContactFileParser
 from conkit.core.contact import Contact
 from conkit.core.contactmap import ContactMap
 from conkit.core.contactfile import ContactFile
 
 RE_SPLIT = re.compile(r'\s+')
 
 
-class FreeContactParser(_ContactFileParser):
+class FreeContactParser(ContactFileParser):
     """Class to parse a FreeContact contact file
     """
     def __init__(self):

conkit/io/gremlin.py

@@ -38,7 +38,7 @@
 import os
 import re
 
-from conkit.io._parser import _ContactFileParser
+from conkit.io._parser import ContactFileParser
 from conkit.core.contact import Contact
 from conkit.core.contactmap import ContactMap
 from conkit.core.contactfile import ContactFile
@@ -49,7 +49,7 @@
 RE_SPLIT = re.compile(r'\s+')
 
 
-class GremlinParser(_ContactFileParser):
+class GremlinParser(ContactFileParser):
     """Parser class for GREMLIN contact prediction file
     """
     def __init__(self):

conkit/io/jones.py

@@ -37,12 +37,12 @@
 
 import os
 
-from conkit.io._parser import _SequenceFileParser
+from conkit.io._parser import SequenceFileParser
 from conkit.core.sequence import Sequence
 from conkit.core.sequencefile import SequenceFile
 
 
-class JonesParser(_SequenceFileParser):
+class JonesParser(SequenceFileParser):
     """Parser class for Jones sequence files
 
     This format is a "new" definition of sequence-only records.

conkit/io/membrain.py

@@ -39,7 +39,7 @@
 import os
 import re
 
-from conkit.io._parser import _ContactFileParser
+from conkit.io._parser import ContactFileParser
 from conkit.core.contact import Contact
 from conkit.core.contactmap import ContactMap
 from conkit.core.contactfile import ContactFile
@@ -48,7 +48,7 @@
 RE_SPLIT = re.compile(r'\s+')
 
 
-class MemBrainParser(_ContactFileParser):
+class MemBrainParser(ContactFileParser):
     """Class to parse a MemBrain contact file
     """
     def __init__(self):

conkit/io/pcons.py

@@ -43,7 +43,7 @@
 import os
 import re
 
-from conkit.io._parser import _ContactFileParser
+from conkit.io._parser import ContactFileParser
 from conkit.core.contact import Contact
 from conkit.core.contactmap import ContactMap
 from conkit.core.contactfile import ContactFile
@@ -60,7 +60,7 @@
 RE_SPLIT = re.compile(r'\s+')
 
 
-class PconsParser(_ContactFileParser):
+class PconsParser(ContactFileParser):
     """Class to parse a Pcons output
 
     This module can be used to parse all versions of the