X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=0abd2a7b9501e9f1fffc3bc4456f39ec4af1d50a;hb=628abf41b8573c7eb97b17656ba49bda6919c181;hp=9eaf83e4352208e8889381ece559ac222f88481d;hpb=e2b0b250d21b61c876bdb2303c34d66922336a86;p=jalview.git
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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
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 the 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 di 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 in Jalview 2.10.4 ?
+
+
+ This is the May 2018 release of Jalview, and the last in the 2.10.x series. Jalview 2.10.4 includes:
+
+
+ - Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns
+ - Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services
+ - Critical patches for running Jalview on OSX with Java 10
+ - Easier adjustment of the Alignment ID panel and Annotation panel
+ - Improved support for mapping between 3D Structures and Uniprot Protein Sequences
+ - Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs
+ - New buttons on the Structure Chooser for adding structures
+ to an existing view, and disabling automatic superposition
+ according to linked alignments
+ - Annotation transfer between Chimera and Jalview (formerly only
+ available in 'Experimental' mode)
+
+
+ The full list of bugs fixed in this release can be found in the 2.10.4
+ Release Notes.
+