r27409 - /trunk/data_store/seq_align.py -- January 31, 2015 - 10:17

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.