X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=79cf7c98197d9c18e8884964fbeb4c5d7f93cc17;hb=936d30a2eea9e94c2bb221025e58d7e9ed747262;hp=d9b63608533b67a993ef7586aa719e8820b03946;hpb=32254db18cc678b675db8d0cd72a525a6034bf01;p=jalview.git
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What's new ?
-
- 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
-
-
+
+ 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
+