What's new ?
Jalview 2.8 includes a brand new logo, which you'll see in file
browsers, splash screens, and also on the new look Jalview site.
In addition to our new look, Jalview 2.8 includes a number of new
features.. some of which have been in development since July 2010. The
highlights are below, and - as usual, for a comprehensive list, take a
look at the Jalview 2.8 Release
Notes.
Highlights in Jalview Version 2.8
- Improved JABA client and new JABAWS 2.0 Services
- AACon alignment conservation
- Protein disorder - DisEMBL, RONN, GlobPlot and IUPred
- Clustal Omega - huge protein alignments
- Support for RNA
- Import sequence and alignment associated WUSS or VIENNA
secondary structure notation from stockholm and clustalW files or
as jalview annotation.
- Interactive editing of RNA secondary structure annotation
- Colour scheme for purine/pyrimidine and to highlight RNA
helices
- RNA canonical base pair consensus score and sequence logo
- Embedded VARNA RNA
secondary structure viewer in the Desktop
See Nucleic Acid Support for full
details.
- Parse and display T-COFFEE alignment quality scores
- Shade individual sequence positions according to alignment
annotation scores
- Enhanced PCA viewer: more export options, and switch between
different PCA modes and residue score models
- New Jalview Desktop database fetcher GUI
- Support for DAS 1.6 and DAS 2.0 sources
- Export sequence database annotation as HTML report
- Normalised Sequence Logo Display
Issues Resolved (a select list - see the release history for full details)
Issues in the Jalview Desktop
- PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch
REST service
-
Stop
windows being moved outside desktop on OSX
-
Filetype
associations not installed for webstart launch
-
Jalview
does not always retrieve progress of a JABAWS job execution in full
once it is complete
-
View
all structures superposed fails with exception
-
Jnet
job queues forever if a very short sequence is submitted for
prediction
-
Structure
view highlighting doesn't work on windows 7
-
Jalview
desktop fails to launch with exception when using proxy
-
Tree
calculation reports 'you must have 2 or more sequences
selected' when selection is empty
-
DAS
Sequence retrieval with range qualification results in sequence xref
which includes range qualification
-
Cannot
close news reader when JABAWS server warning dialog is shown
-
Edited
sequence not submitted to web service
-
Jalview
2.7 Webstart and InstallAnywhere installer doesn't unpack and run
on OSX Mountain Lion
- The workaround for webstart is to go into the Security
panel (gatekeeper symbol) under System settings, and select the
'allow any code to run' setting.
-
Annotation
panel not given a scroll bar when sequences with alignment annotation
are pasted into the alignment
-
Sequence
associated annotation rows not associated when loaded from jalview
project
-
Exceptions
when copy/paste sequences with grouped annotation rows to new window
-
Browser
launch fails with NPE on java 1.7
Issues specific to the JalviewLite Applet
-
Sequence
features are momentarily displayed before they are hidden using
hidefeaturegroups applet parameter
-
loading
features via javascript API automatically enables feature display
-
scrollToColumnIn
javascript API method doesn't work
Issues affecting both applet and application
General
-
Redundancy
removal fails for rna alignment
-
PCA
window shows grey box when first opened on OSX
-
Letters
coloured pink in sequence logo when alignment coloured with clustalx
-
Choosing
fonts without letter symbols defined causes exceptions and redraw
errors
-
Initial
PCA plot view is not same as manually reconfigured view