X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=9eaf83e4352208e8889381ece559ac222f88481d;hb=80c223c45fde0899c9794e887801dd82fffd3452;hp=965edea3f8725be155776a0a09a739e9704d5d27;hpb=92ae1457a784553ccdb842b122d481ce6c5ff24f;p=jalview.git
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-What's new ?
+
+
+What's new ?
+
-What's new ?
-If you are reading this then you will already have seen some of the recent changes
- made to Jalview.
- Jalview takes advantage of some of the more recent user interface developments
- in the Java programming language. For instance Jalview is now a multi windowed
- application, this keeps all your Jalview windows neatly together in one main
- application window.
-If you were familiar with the original Jalview, here is a list of important
- features you should know about the current development:
-
- - Editing sequences is no longer the default when mouse clicking the alignment.
- Instead, mouse clicking on the alignment creates a "selection region"
- which may be full sequences or groups of residues.
- - To insert or edit the gaps in one sequence in alignment, the
- "Shift" key must be held down when dragging the mouse.
- - To insert or edit gaps for a group of sequences, the
- "Alt" key (or in X windows the "Control"
- key) must be held down.
- - Selecting colour schemes in the colour menu either sets just the
- "background" colourscheme for the alignment, or - when
- the tickbox "Apply colour to all groups" is ticked,
- applies the scheme to the background and all groups defined on the alignment.
- - Use the right mouse button (apple and click on the Mac) whilst
- the pointer is within the selection area to access the "define" region menu to
- define a new region, give it a name, and change its colourscheme and display
- properties.
- - Conservation is automatically updated whenever the alignment is edited
- - There is no "quick draw" option
- - Edits can be undone, and redone!
-
+
+ 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
+