X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FwhatsNew.html;h=9eaf83e4352208e8889381ece559ac222f88481d;hb=d83db1c05bf39e076ce0cd53635bedf7e89afed1;hp=bd57b81b2859697831859af7babf8ebab04729d5;hpb=b5edbd2a03d16372bc3e8019ddbf3840dcfe38ed;p=jalview.git
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-
-What's new ?
-
-What's new ?
-Jalview Version 2.07
-Sequence Fetcher has been added to quickly
- retrieve sequences with known ids from several databases.
-Sequence Features enhanced to allow
- the user to display all features of a Uniprot file on the alignment and subsequently
- colour, hide or show overlapping features.
-Choose to omit /start-end from sequences when
- saving files. This is important for saving files to be used by some programs
- which cannot read the original Jalview sequence output with the appended /start-end.
-PDB structure viewer enhanced. Mapping
- between sequence and structure has been enhanced, colours on the alignment are
- reflected in the structure viewer.
-Jalview Applet can read
- in feature files, PDB files be used as input to HTML form See the website
- to find out the new parameters available for the Applet Version of Jalview.
-
-Issues Resolved
-Group Editing is possible with Control and mouse click. Alt key and mouse press
- does not work as this translates as the middle mouse button, which since 2.04
- is now used to scroll the alignment and change the font size.
-HTML export now writes groups and features which were previously missing.
-
-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 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
+
+
+