X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=d9b63608533b67a993ef7586aa719e8820b03946;hb=32254db18cc678b675db8d0cd72a525a6034bf01;hp=b099c3b142e676a55f94a5e7b02980c082d85cd8;hpb=2eeea2f43d7bbaafd79ebd4185b42fc60646d9e3;p=jalview.git
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-
-What's new ?
-
-What's new ?
-Jalview Version 2.1
-The multiple sequence alignment program MAFFT
- is available from the default Web Service list.
-The sequence feature retrieval system using DBFetch from EBI has been replaced
- with DAS Feature fetching capabilities.
-Hide sequences and columns
-Export Annotations and Features
-GFF file reading / writing
-Associate structures with sequences from local PDB files
-Add sequences to existing alignment
-Recently opened files / URL lists
-Applet can launch the full application
-Applet has transparency for features (Java 1.2 required)
-Applet has user defined colours parameter
-
-Issues Resolved
-Redundancy Panel reinstalled in the Applet
-Monospaced font - EPS / rescaling bug fixed
-Annotation files with sequence references bug fixed
-
-See the Release History page for details of all
- new features and resolved issues.
-
-
+
+
+
+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
+
+
+
+