Author: bugman
Date: Fri Jan 30 17:31:48 2015
New Revision: 27397
URL: http://svn.gna.org/viewcvs/relax?rev=27397&view=rev
Log:
Fixes for the sequence alignment objects for the relax data store.
The Sequence_alignments(RelaxListType) and Alignment(Element) classes were not
being set up
correctly. The container names and descriptions were missing.
Modified:
trunk/data_store/seq_align.py
Modified: trunk/data_store/seq_align.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/data_store/seq_align.py?rev=27397&r1=27396&r2=27397&view=diff
==============================================================================
--- trunk/data_store/seq_align.py (original)
+++ trunk/data_store/seq_align.py Fri Jan 30 17:31:48 2015
@@ -30,6 +30,17 @@
class Sequence_alignments(RelaxListType):
"""The structure for holding all sequence alignments."""
+
+ def __init__(self):
+ """Initialise some class variables."""
+
+ # Execute the base class __init__() method.
+ super(Sequence_alignments, self).__init__()
+
+ # Some generic initial names.
+ self.list_name = 'sequence_alignments'
+ self.list_desc = 'List of all multiple sequence alignments'
+
def add(self, object_ids=None, models=None, molecules=None,
sequences=None, strings=None, gaps=None, msa_algorithm=None,
pairwise_algorithm=None, matrix=None, gap_open_penalty=None,
gap_extend_penalty=None, end_gap_open_penalty=None,
end_gap_extend_penalty=None):
"""Add a new sequence alignment.
@@ -175,6 +186,9 @@
@type end_gap_extend_penalty: float
"""
+ # Execute the base class __init__() method.
+ super(Alignment, self).__init__(name='sequence_alignment',
desc='Multiple sequence alignment container.')
+
# Store the values.
self.object_ids = object_ids
self.models = models
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