--- /dev/null
+---
+channel: release
+version: 2.8.2
+date: 2014-12-03
+---
+
+## New Features
+
+
+
+### General
+- Updated Java code signing certificate donated by Certum.PL.
+- Features and annotation preserved when performing pairwise alignment
+- RNA pseudoknot annotation can be imported/exported/displayed
+- 'colour by annotation' can colour by RNA and protein secondary structure
+- Warn user if 'Find' regular expression is invalid (*mentioned post-hoc with 2.9 release*)
+
+
+### Application
+- Extract and display secondary structure for sequences with 3D structures
+- Support for parsing RNAML
+- Annotations menu for layout
+ - sort sequence annotation rows by alignment
+ - place sequence annotation above/below alignment annotation
+- Output in Stockholm format
+- Internationalisation: improved Spanish (es) translation
+- Structure viewer preferences tab
+- Disorder and Secondary Structure annotation tracks shared between alignments
+- UCSF Chimera launch and linked highlighting from Jalview
+- Show/hide all sequence associated annotation rows for all or current selection
+- disorder and secondary structure predictions available as dataset annotation
+- Per-sequence rna helices colouring
+- Sequence database accessions imported when fetching alignments from Rfam
+- update VARNA version to 3.91
+- New groovy scripts for exporting aligned positions, conservation values, and calculating sum of pairs scores.
+- Command line argument to set default JABAWS server
+- include installation type in build properties and console log output
+- Updated Jalview project format to preserve dataset annotation
+
+
+## Issues Resolved
+
+
+
+### Application
+- Distinguish alignment and sequence associated RNA structure in structure->view->VARNA
+- Raise dialog box if user deletes all sequences in an alignment
+- Pressing F1 results in documentation opening twice
+- Sequence feature tooltip is wrapped
+- Double click on sequence associated annotation selects only first column
+- Redundancy removal doesn't result in unlinked leaves shown in tree
+- Undos after several redundancy removals don't undo properly
+- Hide sequence doesn't hide associated annotation
+- User defined colours dialog box too big to fit on screen and buttons not visible
+- author list isn't updated if already written to Jalview properties
+- Popup menu won't open after retrieving sequence from database
+- File open window for associate PDB doesn't open
+- Left-then-right click on a sequence id opens a browser search window
+- Cannot open sequence feature shading/sort popup menu in feature settings dialog
+- better tooltip placement for some areas of Jalview desktop
+- Allow addition of JABAWS Server which doesn't pass validation
+- Web services parameters dialog box is too large to fit on screen
+- Muscle nucleotide alignment preset obscured by tooltip
+- JABAWS preset submenus don't contain newly defined user preset
+- MSA web services warns user if they were launched with invalid input
+- Jalview cannot contact DAS Registy when running on Java 8
+- <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] --> 'Superpose with' submenu not shown when new view created
+
+
+### Deployment and Documentation
+- 2G and 1G options in launchApp have no effect on memory allocation
+- launchApp service doesn't automatically open www.jalview.org/examples/exampleFile.jar if no file is given
+- <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] --> InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is available
+
+
+### Application Known issues
+- <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] --> corrupted or unreadable alignment display when scrolling alignment to right
+- <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] --> retrieval fails but progress bar continues for DAS retrieval with large number of ID
+- <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] --> flatfile output of visible region has incorrect sequence start/end
+- <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] --> rna structure consensus doesn't update when secondary structure tracks are rearranged
+- <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] --> invalid rna structure positional highlighting does not highlight position of invalid base pairs
+- <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] --> out of memory errors are not raised when saving Jalview project from alignment window file menu
+- <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] --> Switching to RNA Helices colouring doesn't propagate to structures
+- <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] --> colour by RNA Helices not enabled when user created annotation added to alignment
+- <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] --> Jalview icon not shown on dock in Mountain Lion/Webstart
+
+
+### Applet Known Issues
+- <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] --> JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
+- <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] --> Jalview and Jmol example not compatible with IE9
+- Sort by annotation score doesn't reverse order when selected
git://source.jalview.org / jalview.git / blobdiff