--- /dev/null
+---
+channel: release
+version: 2.8
+date: 2012-11-12
+---
+
+## New Features
+
+
+
+### Application
+- Support for JABAWS 2.0 Services (AACon alignment conservation, protein disorder and Clustal Omega)
+- JABAWS server status indicator in Web Services preferences
+- VARNA (http://varna.lri.fr) viewer for RNA structures in Jalview alignment window
+- Updated Jalview build and deploy framework for OSX mountain lion, windows 7, and 8
+- Nucleotide substitution matrix for PCA that supports RNA and ambiguity codes
+- Improved sequence database retrieval GUI
+- Support fetching and database reference look up against multiple DAS sources (Fetch all from in 'fetch db refs')
+- Jalview project improvements
+ - Store and retrieve the 'belowAlignment' flag for annotation
+ - calcId attribute to group annotation rows on the alignment
+ - Store AACon calculation settings for a view in Jalview project
+- horizontal scrolling gesture support
+- Visual progress indicator when PCA calculation is running
+- Simpler JABA web services menus
+- visual indication that web service results are still being retrieved from server
+- Serialise the dialogs that are shown when Jalview starts up for first time
+- Jalview user agent string for interacting with HTTP services
+- DAS 1.6 and DAS 2.0 source support using new JDAS client library
+- Examples directory and Groovy library included in InstallAnywhere distribution
+
+
+### Applet
+- RNA alignment and secondary structure annotation visualization applet example
+
+
+### General
+- Normalise option for consensus sequence logo
+- Reset button in PCA window to return dimensions to defaults
+- Allow seqspace or Jalview variant of alignment PCA calculation
+- PCA with either nucleic acid and protein substitution matrices
+- Allow windows containing HTML reports to be exported in HTML
+- Interactive display and editing of RNA secondary structure contacts
+- RNA Helix Alignment Colouring
+- RNA base pair logo consensus
+- Parse sequence associated secondary structure information in Stockholm files
+- HTML Export database accessions and annotation information presented in tooltip for sequences
+- Import secondary structure from LOCARNA clustalw style RNA alignment files
+- import and visualise T-COFFEE quality scores for an alignment
+- 'colour by annotation' per sequence option to shade each sequence according to its associated alignment annotation
+- New Jalview Logo
+
+
+### Documentation and Development
+- documentation for score matrices used in Jalview
+- New Website!
+
+
+## Issues Resolved
+
+
+
+### Application
+- 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
+- revise SHMR RSBS definition to ensure alignment is uploaded via ali_file parameter
+- Jalview 2.7 is incompatible with Jmol-12.2.2
+- View all structures superposed fails with exception
+- Jnet job queues forever if a very short sequence is submitted for prediction
+- Cut and paste menu not opened when mouse clicked on desktop window
+- Putting fractional value into integer text box in alignment parameter dialog causes Jalview to hang
+- Structure view highlighting doesn't work on windows 7
+- View all structures fails with exception shown in structure view
+- Characters in filename associated with PDBEntry not escaped in a platform independent way
+- 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
+- Jalview desktop fails to launch with jar signature failure when java web start temporary file caching is disabled
+- DAS Sequence retrieval with range qualification results in sequence xref which includes range qualification
+- Errors during processing of command line arguments cause progress bar (JAL-898) to be removed
+- Replace comma for semi-colon option not disabled for DAS sources in sequence fetcher
+- Cannot close news reader when JABAWS server warning dialog is shown
+- Option widgets not updated to reflect user settings
+- Edited sequence not submitted to web service
+- Jalview 2.7 Webstart does not launch on mountain lion
+- InstallAnywhere installer doesn't unpack and run on OSX Mountain Lion
+- 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
+- Browser launch fails with NPE on java 1.7
+- JABAWS alignment marked as finished when job was cancelled or job failed due to invalid input
+- NPE with v2.7 example when clicking on Tree associated with all views
+- Exceptions when copy/paste sequences with grouped annotation rows to new window
+
+
+### 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
+
+
+### General
+- Redundancy removal fails for rna alignment
+- PCA calculation fails when sequence has been selected and then deselected
+- 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
+- Grouped annotation graph label has incorrect line colour
+- Grouped annotation graph label display is corrupted for lots of labels
git://source.jalview.org / jalview.git / blobdiff