+ <em>Development and deployment</em>
+ <li>Java 1.7 minimum requirement for Jalview 2.9</li>
+ <li>Include installation type and git revision in build
+ properties and console log output</li>
+ <li>Github project and web URL for storing BioJsMSA
+ Templates</li>
+ <li>Jalview's unit tests now managed with TestNG</li></td>
+ <td><em>General</em>
+ <ul>
+ </ul> <!-- issues resolved --> <em>Application</em>
+ <ul>
+ <li>Escape should close any open find dialogs</li>
+ <li>typo in select-by-features status report</li>
+ <li>Consensus RNA secondary secondary structure
+ predictions are not highlighted in amber</li>
+ <li>missing gap character means v2.7 example file appears
+ unaligned REVIEW</li>
+ <li>First switch to RNA Helices colouring doesn't colour
+ associated structure views</li>
+ <li>ID width preference option is greyed out when auto
+ width checkbox not enabled</li>
+ <li>Stopped a warning dialog from being shown when
+ creating user defined colours</li>
+ <li>'View Mapping' in structure viewer shows sequence
+ mappings for just that viewer's sequences</li>
+ <li>Workaround for superposing PDB files containing
+ multiple models in Chimera</li>
+ <li>Report sequence position in status bar when hovering
+ over Jmol structure</li>
+ <li>Cannot output gaps as '.' symbols with Selection ->
+ output to text box</li>
+ <li>Flat file exports of alignments with hidden columns
+ have incorrect sequence start/end</li>
+ <li>'Aligning' a second chain to a Chimera structure from
+ Jalview fails</li>
+ <li>Colour schemes applied to structure viewers don't
+ work for nucleotide</li>
+ <li>Loading/cut'n'pasting an empty or invalid file leads
+ to a grey/invisible alignment window</li>
+ <li>Exported Jpred annotation from a sequence region
+ imports to different position</li>
+ <li>Space at beginning of sequence feature mouseover
+ tooltip on some platforms</li>
+ <li>Chimera viewer 'View | Show Chain' menu is not
+ populated</li>
+ <li>'New View' fails with a Null Pointer Exception if
+ Chimera has been opened</li>
+ <li>Mouseover to Chimera not working</li>
+ <li>Miscellaneous ENA XML feature qualifiers not
+ retrieved</li>
+ <li>NPE in annotation renderer after 'Extract Scores'</li>
+ <li>If two structures in one Chimera window, mouseover of
+ either sequence shows on first structure</li>
+ <li>'Show annotations' options should not make
+ non-positional annotations visible</li>
+ <li>subsequence secondary structure annotation not shown
+ in right place after 'view flanking regions'</li>
+ <li>File Save As type unset when current file format is
+ unknown</li>
+ <li>Native 'Quaqua' dialogs for saving and loading files
+ on OSX</li>
+ <li>Save as '.jar' option removed for saving Jalview
+ projects</li>
+ <li>Colour by Sequence colouring in Chimera more
+ responsive</li>
+ <li>Can disable consensus calculation independently of
+ quality and conservation</li>
+ <li>Cannot 'add reference annotation' for a sequence in
+ several views on same alignment</li>
+ <li>Cannot show linked products for EMBL / ENA records</li>
+ <li>Jalview's tooltip wraps long texts containing no
+ spaces</li>
+ </ul> <em>Applet</em>
+ <li>Jmol to JalviewLite mouseover/link not working</li>
+ <li>JalviewLite can't import sequences with ID descriptions
+ containing angle brackets</li>
+ <ul>
+ </ul> <em>General</em>
+ <ul>
+ <li>Cannot export and reimport RNA secondary structure
+ via jalview annotation file</li>
+ <li>Random helix colour palette for colour by annotation
+ with RNA secondary structure</li>
+ <li>Mouseover to cDNA from STOP residue in protein
+ translation doesn't work.</li>
+ <li>hints when using the select by annotation dialog box</li>
+ <li>Jmol alignment incorrect if PDB file has alternate CA
+ positions</li>
+ <li>FontChooser message dialog appears to hang after
+ choosing 1pt font</li>
+ <li>Peptide secondary structure incorrectly imported from
+ annotation file when annotation display text includes 'e' or
+ 'h'</li>
+ <li>Cannot set colour of new feature type whilst creating
+ new feature</li>
+ <li>cDNA translation alignment should not be sequence
+ order dependent</li>
+ <li>'Show unconserved' doesn't work for lower case
+ sequences</li>
+ <li>Nucleotide ambiguity codes involving R not recognised</li>
+ </ul> <em>Deployment and Documentation</em>
+ <ul>
+
+ </ul> <em>Application Known issues</em>
+ <ul>
+ <li>Incomplete sequence extracted from PDB entry 3a6s</li>
+ <li>Misleading message appears after trying to delete
+ solid column.</li>
+ <li>Jalview icon not shown in dock after InstallAnywhere
+ version launches</li>
+ <li>Fetching EMBL reference for an RNA sequence results
+ fails with a sequence mismatch</li>
+ <li>Corrupted or unreadable alignment display when
+ scrolling alignment to right</li>
+ <li>ArrayIndexOutOfBoundsException thrown when remove
+ empty columns called on alignment with ragged gapped ends</li>
+ <li>auto calculated alignment annotation rows do not get
+ placed above or below non-autocalculated rows</li>
+ <li>Jalview dekstop becomes sluggish at full screen in
+ ultra-high resolution</li>
+ </ul> <em>Applet Known Issues</em>
+ <ul>
+ <li>Core PDB parsing code requires Jmol</li>
+ <li>Sequence canvas panel goes white when alignment
+ window is being resized
+ <li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.8.2b1">2.8.2b1</a><br /> <em>15/12/2014</em></strong>
+ </div>
+ </td>
+ <td>
+ <div align="center">
+ </div>
+ </td>
+ <td>
+ <div align="center">
+ <ul><li>Reinstated the display of default example file on startup</li>
+ <li>All pairs shown in Jalview window when viewing result of pairwise alignment</li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
+ </div></td>
+ <td><em>General</em>
+ <ul>
+ <li>Updated Java code signing certificate donated by Certum.PL.</li>
+ <li>Features and annotation preserved when performing pairwise
+ alignment</li>
+ <li>RNA pseudoknot annotation can be
+ imported/exported/displayed</li>
+ <li>'colour by annotation' can colour by RNA and
+ protein secondary structure</li>
+ <li>Warn user if 'Find' regular expression is invalid (<em>mentioned post-hoc with 2.9 release</em>)</li>
+
+ </ul> <em>Application</em>
+ <ul>
+ <li>Extract and display secondary structure for sequences with
+ 3D structures</li>
+ <li>Support for parsing RNAML</li>
+ <li>Annotations menu for layout
+ <ul>
+ <li>sort sequence annotation rows by alignment</li>
+ <li>place sequence annotation above/below alignment
+ annotation</li>
+ </ul>
+ <li>Output in Stockholm format</li>
+ <li>Internationalisation: improved Spanish (es) translation</li>
+ <li>Structure viewer preferences tab</li>
+ <li>Disorder and Secondary Structure annotation tracks shared
+ between alignments</li>
+ <li>UCSF Chimera launch and linked highlighting from Jalview</li>
+ <li>Show/hide all sequence associated annotation rows for all
+ or current selection</li>
+ <li>disorder and secondary structure predictions available as
+ dataset annotation</li>
+ <li>Per-sequence rna helices colouring</li>
+
+
+ <li>Sequence database accessions imported when fetching
+ alignments from Rfam</li>
+ <li>update VARNA version to 3.91</li>
+
+ <li>New groovy scripts for exporting aligned positions,
+ conservation values, and calculating sum of pairs scores.</li>
+ <li>Command line argument to set default JABAWS server</li>
+ <li>include installation type in build properties and console
+ log output</li>
+ <li>Updated Jalview project format to preserve dataset annotation</li>
+ </ul></td>
+ <td>
+ <!-- issues resolved --> <em>Application</em>
+ <ul>
+ <li>Distinguish alignment and sequence associated RNA
+ structure in structure->view->VARNA</li>
+ <li>Raise dialog box if user deletes all sequences in an
+ alignment</li>
+ <li>Pressing F1 results in documentation opening twice</li>
+ <li>Sequence feature tooltip is wrapped</li>
+ <li>Double click on sequence associated annotation selects
+ only first column</li>
+ <li>Redundancy removal doesn't result in unlinked leaves
+ shown in tree</li>
+ <li>Undos after several redundancy removals don't undo
+ properly</li>
+ <li>Hide sequence doesn't hide associated annotation</li>
+ <li>User defined colours dialog box too big to fit on screen
+ and buttons not visible</li>
+ <li>author list isn't updated if already written to Jalview
+ properties</li>
+ <li>Popup menu won't open after retrieving sequence from
+ database</li>
+ <li>File open window for associate PDB doesn't open</li>
+ <li>Left-then-right click on a sequence id opens a browser
+ search window</li>
+ <li>Cannot open sequence feature shading/sort popup menu in
+ feature settings dialog</li>
+ <li>better tooltip placement for some areas of Jalview desktop</li>
+ <li>Allow addition of JABAWS Server which doesn't pass
+ validation</li>
+ <li>Web services parameters dialog box is too large to fit on
+ screen</li>
+ <li>Muscle nucleotide alignment preset obscured by tooltip</li>
+ <li>JABAWS preset submenus don't contain newly defined
+ user preset</li>
+ <li>MSA web services warns user if they were launched with
+ invalid input</li>
+ <li>Jalview cannot contact DAS Registy when running on Java 8</li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
+ 'Superpose with' submenu not shown when new view created
+ </li>
+
+ </ul> <!-- <em>Applet</em>
+ <ul>
+ </ul> <em>General</em>
+ <ul>
+ </ul>--> <em>Deployment and Documentation</em>
+ <ul>
+ <li>2G and 1G options in launchApp have no effect on memory
+ allocation</li>
+ <li>launchApp service doesn't automatically open
+ www.jalview.org/examples/exampleFile.jar if no file is given</li>
+ <li>
+ <!-- [<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
+ </li>
+ </ul> <em>Application Known issues</em>
+ <ul>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
+ corrupted or unreadable alignment display when scrolling alignment
+ to right
+ </li>
+ <li>
+ <!-- [<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
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
+ flatfile output of visible region has incorrect sequence start/end
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
+ rna structure consensus doesn't update when secondary
+ structure tracks are rearranged
+ </li>
+ <li>
+ <!-- [<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
+ </li>
+ <li>
+ <!-- <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
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
+ Switching to RNA Helices colouring doesn't propagate to
+ structures
+ </li>
+ <li>
+ <!-- [<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
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
+ Jalview icon not shown on dock in Mountain Lion/Webstart
+ </li>
+ </ul> <em>Applet Known Issues</em>
+ <ul>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
+ JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
+ Jalview and Jmol example not compatible with IE9
+ </li>
+
+ <li>Sort by annotation score doesn't reverse order when
+ selected</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
+ </div></td>
+ <td>
+ <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
+ <em>General</em>
+ <ul>
+ <li>Internationalisation of user interface (usually called
+ i18n support) and translation for Spanish locale</li>
+ <li>Define/Undefine group on current selection with
+ Ctrl-G/Shift Ctrl-G</li>
+ <li>Improved group creation/removal options in
+ alignment/sequence Popup menu</li>
+ <li>Sensible precision for symbol distribution percentages
+ shown in logo tooltip.</li>
+ <li>Annotation panel height set according to amount of
+ annotation when alignment first opened</li>
+ </ul> <em>Application</em>
+ <ul>
+ <li>Interactive consensus RNA secondary structure prediction
+ VIENNA RNAAliFold JABA 2.1 service</li>
+ <li>Select columns containing particular features from Feature
+ Settings dialog</li>
+ <li>View all 'representative' PDB structures for selected
+ sequences</li>
+ <li>Update Jalview project format:
+ <ul>
+ <li>New file extension for Jalview projects '.jvp'</li>
+ <li>Preserve sequence and annotation dataset (to store
+ secondary structure annotation,etc)</li>
+ <li>Per group and alignment annotation and RNA helix
+ colouring</li>
+ </ul>
+ </li>
+ <li>New similarity measures for PCA and Tree calculation
+ (PAM250)</li>
+ <li>Experimental support for retrieval and viewing of flanking
+ regions for an alignment</li>
+ </ul>
+ </td>
+ <td>
+ <!-- issues resolved --> <em>Application</em>
+ <ul>
+ <li>logo keeps spinning and status remains at queued or
+ running after job is cancelled</li>
+ <li>cannot export features from alignments imported from
+ Jalview/VAMSAS projects</li>
+ <li>Buggy slider for web service parameters that take float
+ values</li>