X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=17ac27510659f2b4c483dd02eaf7b4a83cbd79c5;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=39ef82f1fc460d65c7c71428206cf72002eb3c3a;hpb=f6a7e5514230be7ea8c2d4cccb504b4ed95f80ef;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 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 JABAWS client and new JABAWS 2.0 Services
-
-
- - Support for 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 Tomassi 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 new JDAS Distributed Annotation client library)
- - 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
-
+
+ What's new ?
+
+
+ Jalview 2.9.0b1 is a bug fix release for Jalview 2.9, which has been in development since December 2014. In addition
+ to a multitude of bug fixes and minor improvements (both small, and
+ rather big!), it also brings major new capabilities for codon-level
+ analysis of protein alignments and the retrieval and manipulation of
+ structural data.
For the patches since version 2.9 was release, see the
+ Jalview 2.9.0b1 Release Notes.
+
+
+ Highlights in Jalview 2.9
+
+ - Visualisation, editing and analysis of
+ cDNA and Protein alignments
A new Split View window allows linked
+ protein and nucleotide sequence alignments to be viewed, edited,
+ and analysed as one.
cDNA alignments can also be
+ reconstructed from protein alignments calculated by Jalview's web
+ services, and update in response to edits in the amino acid view.
To
+ start experimenting with cDNA/Protein analysis, jut drop a file
+ containing cDNA sequences which code for proteins in an existing
+ alignment, and Jalview will do the rest.
+ - Enhanced Integration of UCSF Chimera
Jalview
+ 2.9 provides full support for the use of Chimera to view 3D
+ structures linked to alignment views in the Jalview Desktop. We've
+ also included support for saving Chimera sessions in Jalview
+ project files.
Jalview and Chimera communicate using local
+ web server connections, which may cause firewall alerts on some
+ systems, but has the advantage of allowing bidirectional
+ communication. Communication between Jalview and Chimera is now
+ much more responsive, and selected regions in Chimera are now
+ shown as highlighted regions in the Jalview desktop.
+ - Interactive querying of the PDBe
Jalview
+ users can now browse and retrieve 3D structure data from the PDB
+ via the PDBe
+ Search API (Gutmanas
+ et al 2014). Developed in collaboration with the PDBe group at
+ EMBL-EBI, the interface allows both structured and free-text
+ queries to be performed, and allows automatic selection of the
+ most relevant structures for an alignment acording to a variety of
+ criteria.
+ - Improved support for RNA visualisation
Jalview
+ 2.9 integrates the latest version of the VARNA RNA Viewer, and VARNA views
+ can also now be stored in Jalview projects. We've also dealt with
+ a number of lingering bugs in the VARNA/Jalview interface,
+ including the loss of pseudoknots when RNA secondary structure is
+ shown VARNA.
+ - Protein Secondary Structure predictions
+ with JPred4
Jalview includes a number of new features for
+ working with secondary structure predictions from the JPred4
+ server. These include new popup menu actions to automatically hide insertions and highlight
+ mutations in an alignment with respect to a Reference
+ Sequence. Jalview 2.9's new scrollable
+ SVG HTML export was also developed specifically for the JPred4
+ server.
+
-
-
- 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
-
- -
- Choosing
- fonts without letter symbols defined causes exceptions and redraw
- errors
-
- -
- Initial
- PCA plot view is not same as manually reconfigured view
-
-