X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=e16949e9709ef0a36e22945c21cb632fbfd748da;hb=3d5d8043f5eaa6e5ca903289a7d136125d3ed1c1;hp=5d00e193e35918a376d012edd2cd0629fa9d422f;hpb=0bce27989320cd0b44a13151269749614d5cd312;p=jalview.git
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What's new ?
-
- What's new ?
- Jalview 2.8 includes a number of enhancements and new features that
- have been in development since July 2010. It is also the first Jalview
- release to incorporate RNA visualization features developed by Lauren
- Lui and Jan Engelhart during their Google Summer of Code projects
- (http://code.google.com/soc/). As usual, you can find some highlights
- below, but to see the comprehensive list, take a look at the look at
- the Jalview 2.8 Release Notes.
-
- Highlights in Jalview Version 2.8
-
- - Improved JABAWS
- client and new JABAWS 2.0 Services
-
-
- - RNA
-
- - Import sequence and alignment associated WUSS or VIENNA
- dot-bracket notation from files and the RFAM
- database
-
- - 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
-
-
- - Parse and display T-COFFEE
- alignment quality scores (thanks to Paolo Tomasso of the Notredame
- Group)
-
- - Per
- sequence alignment annotation shading
- - 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 (thanks to the new
- JDAS Distributed Annotation client library (see
- http://code.google.com/p/jdas))
- - Export sequence database annotation as an HTML report
- - Normalised Sequence
- Logo Display
-
-
- Issues resolved in the Jalview Desktop
-
-
- - PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch
- REST service
- - Stop windows being moved outside desktop on OSX
- - 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
- - 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 InstallAnywhere installer doesn't unpack and run
- on OSX Mountain Lion
-
- - If you use webstart then you may need to go into the
- Security panel (a.k.a the gatekeeper) in your System
- Settings, and select the 'allow any code to run' option.
-
-
-
-
-
- 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
-
-
- - 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
-
+
+ What's new ?
Jalview 2.8.1 includes a range of new features developed in the last 12 months.
As usual you can find the
+ highlights below, and the comprehensive list is given in the Jalview 2.8.1 Release Notes.
+
+ Internationalisation
+
+ In August 2013, David Róldan-Martinez took on the task of
+ internationalising Jalview's user interface. He also recruited Sara
+ Hernández DÃaz and Laura Ferrandis Martinez who created Jalview's
+ first spanish user interface translation.
If you notice any
+ problems, or would like to help translate Jalview's user interface
+ into other languages, please sign up at issues.jalview.org and put in
+ a feature request for your translation to the i18n component, and
+ David or Jim will get in contact with you.
+
+ Enhancements and new features
+
+ -
+
- Extended the feature settings dialog to allow columns to be selected containing particular sequence features.
+
+ Bug fixes
+