X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=9eaf83e4352208e8889381ece559ac222f88481d;hb=80c223c45fde0899c9794e887801dd82fffd3452;hp=651292e0b5fa6c4ba15bda5a770cab93160a03b1;hpb=bb105fcca41253815982584f4c8f6fae1f8e10a3;p=jalview.git
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+
What's new ?
-What's new ?
-
-Jalview Version 2.2
-Multiple views with different styles, colours, hidden regions for
-one alignment
-Easily add, amend and delete sequence features
-"Reload" alignment from File or URL to revert to
-original
-"Save" to current filename or "Save As" to
-new filename
-New "New Window" button on the
-"Output To Textbox" opens output window for quick 'sequence
-editing'.
-Set different text colour for dark or light background
-Right align sequence ids
-Set colour of lower case residues in a user defined colour scheme
-
-Menu Rearrangements: New Format for alignment
-layout and Select for region selection.
-
-Menu item accelerator keys added
-Control-V pastes sequences to active window, Control-Shift-V
-pastes to a new window.
-Raise/Minimise alignment and all associated windows from desktop
-window's window menu
-Select and colour whole branches of a tree
-'New Window' button on the 'Output to Text box' alignment output
-option to open a new alignment window after editing.
-Issues Resolved
-
-Optimisations for large alignments: faster multithreaded
-calculations and Undo/Redo system.
-Remove empty columns - if empty columns exist at the end of the
-alignment bug fixed.
-DAS feature fetching slowed down, doesn't overload DAS servers
-DAS feature fetching can be cancelled
-Correct display of > and < symbols for feature descriptions
-without explicit <html> tags.
-Zoom working in PCA viewer
-Sequence Descriptions retained after running a web service
-
-See the Release History page for
-details of all new features and resolved issues.
+
+ 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
+