Jalview 2.8.2

Version Date: 3 December 2014

Archive downloads:

New Features

Updated Java code signing certificate donated by Certum.PL.
Features and annotation preserved when performing pairwise alignment
RNA pseudoknot annotation can be imported/exported/displayed
‘colour by annotation’ can colour by RNA and protein secondary structure
Warn user if ‘Find’ regular expression is invalid (mentioned post-hoc with 2.9 release)

Extract and display secondary structure for sequences with 3D structures
Support for parsing RNAML
Annotations menu for layout
- sort sequence annotation rows by alignment
- place sequence annotation above/below alignment annotation
Output in Stockholm format
Internationalisation: improved Spanish (es) translation
Structure viewer preferences tab
Disorder and Secondary Structure annotation tracks shared between alignments
UCSF Chimera launch and linked highlighting from Jalview
Show/hide all sequence associated annotation rows for all or current selection
disorder and secondary structure predictions available as dataset annotation
Per-sequence rna helices colouring
Sequence database accessions imported when fetching alignments from Rfam
update VARNA version to 3.91
New groovy scripts for exporting aligned positions, conservation values, and calculating sum of pairs scores.
Command line argument to set default JABAWS server
include installation type in build properties and console log output
Updated Jalview project format to preserve dataset annotation

Distinguish alignment and sequence associated RNA structure in structure->view->VARNA
Raise dialog box if user deletes all sequences in an alignment
Pressing F1 results in documentation opening twice
Sequence feature tooltip is wrapped
Double click on sequence associated annotation selects only first column
Redundancy removal doesn’t result in unlinked leaves shown in tree
Undos after several redundancy removals don’t undo properly
Hide sequence doesn’t hide associated annotation
User defined colours dialog box too big to fit on screen and buttons not visible
author list isn’t updated if already written to Jalview properties
Popup menu won’t open after retrieving sequence from database
File open window for associate PDB doesn’t open
Left-then-right click on a sequence id opens a browser search window
Cannot open sequence feature shading/sort popup menu in feature settings dialog
better tooltip placement for some areas of Jalview desktop
Allow addition of JABAWS Server which doesn’t pass validation
Web services parameters dialog box is too large to fit on screen
Muscle nucleotide alignment preset obscured by tooltip
JABAWS preset submenus don’t contain newly defined user preset
MSA web services warns user if they were launched with invalid input
Jalview cannot contact DAS Registy when running on Java 8
'Superpose with' submenu not shown when new view created

2G and 1G options in launchApp have no effect on memory allocation
launchApp service doesn’t automatically open www.jalview.org/examples/exampleFile.jar if no file is given
InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is available

corrupted or unreadable alignment display when scrolling alignment to right
retrieval fails but progress bar continues for DAS retrieval with large number of ID
flatfile output of visible region has incorrect sequence start/end
rna structure consensus doesn't update when secondary structure tracks are rearranged
invalid rna structure positional highlighting does not highlight position of invalid base pairs
out of memory errors are not raised when saving Jalview project from alignment window file menu
Switching to RNA Helices colouring doesn't propagate to structures
colour by RNA Helices not enabled when user created annotation added to alignment
Jalview icon not shown on dock in Mountain Lion/Webstart