Author: bugman
Date: Sat Jan 31 10:17:58 2015
New Revision: 27409
URL: http://svn.gna.org/viewcvs/relax?rev=27409&view=rev
Log:
Sequence alignments can now be retrieved without supplying the algorithm
settings.
This is in the data_store.seq_align.Sequence_alignments.find_alignment()
method. The change allows
for the retrieval of pre-existing sequence alignments at any stage.
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=27409&r1=27408&r2=27409&view=diff
==============================================================================
--- trunk/data_store/seq_align.py (original)
+++ trunk/data_store/seq_align.py Sat Jan 31 10:17:58 2015
@@ -132,19 +132,19 @@
continue
# Check the alignment settings for mismatches.
- if self[i].msa_algorithm != msa_algorithm:
- continue
- if self[i].pairwise_algorithm != pairwise_algorithm:
- continue
- if self[i].matrix != matrix:
- continue
- if self[i].gap_open_penalty != gap_open_penalty:
- continue
- if self[i].gap_extend_penalty != gap_extend_penalty:
- continue
- if self[i].end_gap_open_penalty != end_gap_open_penalty:
- continue
- if self[i].end_gap_extend_penalty != end_gap_extend_penalty:
+ if msa_algorithm and self[i].msa_algorithm != msa_algorithm:
+ continue
+ if pairwise_algorithm and self[i].pairwise_algorithm !=
pairwise_algorithm:
+ continue
+ if matrix and self[i].matrix != matrix:
+ continue
+ if gap_open_penalty != None and self[i].gap_open_penalty !=
gap_open_penalty:
+ continue
+ if gap_extend_penalty != None and self[i].gap_extend_penalty !=
gap_extend_penalty:
+ continue
+ if end_gap_open_penalty != None and self[i].end_gap_open_penalty
!= end_gap_open_penalty:
+ continue
+ if end_gap_extend_penalty != None and
self[i].end_gap_extend_penalty != end_gap_extend_penalty:
continue
# No mismatches, so this must be the alignment.
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