X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;fp=help%2Fhtml%2FwhatsNew.html;h=79cf7c98197d9c18e8884964fbeb4c5d7f93cc17;hb=8a3915baf2a22618346a5a2ecd38f7fbca5d4a44;hp=b81031da3a77ef5ba1792f561e8463c9a157d1f3;hpb=211d3c57e8cd7dd1529a6ecd3ba15372d35baff8;p=jalview.git
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
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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 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 ?
Jalview 2.8.0b1 is a bugfix
+ release for Jalview version 2.8.
As usual you can find the
+ highlights below, and the comprehensive list is given in the Jalview 2.8.0b1 Release Notes.
+
+
+ This bug fix release includes numerous minor enhancements made over
+ the last 12 months. Importantly, it is also the first release that
+ provides Jalview as a trusted application, signed with a certificate
+ donated to us by Certum.
+
+ Enhancements and new features
+
+ - Allow disorder predictions to be made on the current
+ selection (or visible selection) in the same way that JPred works
+ - allow import of data from gzipped files
+ - Improved per-sequence 'colour-by-annotation' performance
+ - Support '' style escaping of quotes in Newick files
+ - group options for JABAWS service by command line name
+ - Select primary source when selecting authority in database
+ fetcher GUI
+ - COMBINE statement uses current SEQUENCE_REF and GROUP_REF
+ scope to group annotation rows
+ - add .mfa to FASTA file extensions recognised by Jalview
+ - groovy scripting for headless jalview operation
+ - Output in Stockholm format
+
+ Bug fixes
+
+ - Uniprot and PDB database cross-reference fetching works
+ properly
+ - 'View all structures' in the desktop is more reliable
+ - Web services parameter dialog box shows the options enabled
+ for different presets
+ - Interactive creation of RNA secondary structure works more
+ smoothly
+ - Keyboard mode 'P' command jumps to the right place
+ - Improved support for parsing database cross-references via
+ Stockholm and Rfam database
+ - Improved semantics in annotation files for grouping
+ annotation rows associated with particular sequences and groups
+ - More robust DNA->Amino acid translation
+ - Improved Headless-mode operation for DAS annotation
+ retrieval, groovy script execution and alignment figure generation
+ - annotation label tooltip text needs to be wrapped
+