Details
-
Type:
Bug
-
Status: Open
-
Priority:
Critical
-
Resolution: Unresolved
-
Affects Version/s: 2.10.4b1, 2.10.5, 2.11.0
-
Fix Version/s: None
-
Component/s: annotation
-
Labels:None
-
Environment:Jalview Version: 2.10.4b1
Jalview Installation: installAnywhere git-commit:1253fe4 [releases/Release_2_10_4_Branch]
Build Date: 07 June 2018
Java version: 1.8.0_92
x86_64 Mac OS X 10.13.6
Description
Discovered from going through Exercise 14 in the manual. Fails at step 14.f.
Load http://www.jalview.org/tutorial/alignment.fa
Create a new annotation row and add a helix or sheet. Export this either through "Export Annotation" in the context menu for this annotation row label or Alignment Window: File=>Export Annotations...
Now re-load this file with Alignment Window: File=>Load Features/Annotations...
and it appears to be a misinterpreted RNA secondary structure. See screenshot of before and after.
The exported file looks okay, but a textbox export of the AFTER (re-imported) row shows information has been lost when read back in:
JALVIEW_ANNOTATION
# Created: Mon Sep 24 12:15:52 BST 2018
NO_GRAPH annotation row AFTER ||||||||A||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NO_GRAPH annotation row BEFORE ||||||||H,A||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Possibly linked withJAL-2313. Similar looking loss/swap of information between display character and secondary structure characters.
Load http://www.jalview.org/tutorial/alignment.fa
Create a new annotation row and add a helix or sheet. Export this either through "Export Annotation" in the context menu for this annotation row label or Alignment Window: File=>Export Annotations...
Now re-load this file with Alignment Window: File=>Load Features/Annotations...
and it appears to be a misinterpreted RNA secondary structure. See screenshot of before and after.
The exported file looks okay, but a textbox export of the AFTER (re-imported) row shows information has been lost when read back in:
JALVIEW_ANNOTATION
# Created: Mon Sep 24 12:15:52 BST 2018
NO_GRAPH annotation row AFTER ||||||||A||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NO_GRAPH annotation row BEFORE ||||||||H,A||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Possibly linked with
