-<p><strong>Release History</strong></p>
-<table border="1">
- <tr>
- <td width="60" nowrap>
- <div align="center"><em><strong>Release</strong></em></div>
- </td>
- <td>
- <div align="center"><em><strong>New Features</strong></em></div>
- </td>
- <td>
- <div align="center"><em><strong>Issues Resolved</strong></em></div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">
- <strong><a name="Jalview2.7">2.7</a>
- </strong><br> <em>27/09/2011</em>
- </div></td>
- <td><em>Application</em>
- <ul>
- <li>Jalview Desktop News Reader</li>
- <li>Tweaked default layout of web services menu</li>
- <li>View/alignment association menu to enable user to easily
- specify which alignment a multi-structure view takes its
- colours/correspondences from</li>
- <li>Allow properties file location to be specified as URL </li>
- <li>Extend jalview project to preserve associations between
- many alignment views and a single Jmol display</li>
- <li>Store annotation row height in jalview project file</li>
- <li>Annotation row column label formatting attributes stored
- in project file</li>
- <li>Annotation row order for auto-calculated annotation rows
- preserved in jalview project file</li>
- <li>Visual progress indication when Jalview state is saved
- using Desktop window menu</li>
- <li>Visual indication that command line arguments are still
- being processed</li>
- <li>Groovy script execution from URL</li>
- <li>Colour by annotation default min and max colours in
- preferences</li>
- <li>Automatically associate PDB files dragged onto an
- alignment with sequences that have high similarity and matching
- IDs</li>
- <li>Update JGoogleAnalytics to latest release (0.3)</li>
- <li>'view structures' option to open many structures
- in same window</li>
- <li>Sort associated views menu option for tree panel</li>
- <li>Group all JABA and non-JABA services for a particular
- analysis function in its own submenu</li>
- </ul> <em>Applet</em>
- <ul>
- <li>Userdefined and autogenerated annotation rows for groups</li>
- <li>Adjustment of alignment annotation pane height</li>
- <li>Annotation scrollbar for annotation panel</li>
- <li>Drag to reorder annotation rows in annotation panel</li>
- <li>'automaticScrolling' parameter</li>
- <li>Allow sequences with partial ID string matches to be
- annotated from GFF/jalview features files</li>
- <li>Sequence logo annotation row in applet</li>
- <li>Absolute paths relative to host server in applet
- parameters are treated as such</li>
- <li>New in the JalviewLite javascript API:
- <ul>
- <li>JalviewLite.js javascript library</li>
- <li>Javascript callbacks for
- <ul>
- <li>Applet initialisation</li>
- <li>Sequence/alignment mouse-overs and selections</li>
- </ul>
- </li>
- <li>scrollTo row and column alignment scrolling functions</li>
- <li>Select sequence/alignment regions from javascript</li>
- <li>javascript structure viewer harness to pass messages
- between Jmol and Jalview when running as distinct applets</li>
- <li>sortBy method</li>
- <li>Set of applet and application examples shipped with
- documentation</li>
- <li>New example to demonstrate jalviewLite and Jmol
- javascript message exchange</li>
- </ul>
- </ul> <em>General</em>
- <ul>
- <li>Enable Jmol displays to be associated with multiple
- multiple alignments</li>
- <li>Option to automatically sort alignment with new tree</li>
- <li>User configurable link to enable redirects to a
- www.jalview.org mirror</li>
- <li>Jmol colours option for Jmol displays</li>
- <li>Configurable newline string when writing alignment and
- other flat files</li>
- <li>Allow alignment annotation description lines to contain
- html tags</li>
- </ul> <em>Documentation and Development</em>
- <ul>
- <li>Add groovy test harness for bulk load testing to examples
- </li>
- <li>Groovy script to load and align a set of sequences using a
- web service before displaying the result in the Jalview desktop</li>
- <li>Restructured javascript and applet api documentation</li>
- <li>Ant target to publish example html files with applet archive</li>
- <li>Netbeans project for building jalview from source</li>
- <li>ant task to create online javadoc for jalview source</li>
- </ul></td>
- <td><em>Application</em>
- <ul>
- <li>User defined colourscheme throws exception when current
- built in colourscheme is saved as new scheme</li>
- <li>AlignFrame->Save in application pops up save dialog for
- valid filename/format</li>
- <li>Cannot view associated structure for Uniprot sequence</li>
- <li>PDB file association breaks for Uniprot sequence P37173</li>
- <li>Associate PDB from file dialog does not tell you which
- sequence is to be associated with the file</li>
- <li>Find All raises null pointer exception when query only
- matches sequence IDs</li>
- <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
- <li>Jalview project with Jmol views created with Jalview 2.4
- cannot be loaded</li>
- <li>Filetype associations not installed for webstart launch</li>
- <li>Two or more chains in a single PDB file associated with
- sequences in different alignments do not get coloured by their
- associated sequence</li>
- <li>Visibility status of autocalculated annotation row not
- preserved when project is loaded</li>
- <li>Annotation row height and visibility attributes not stored
- in jalview project</li>
- <li>Tree bootstraps are not preserved when saved as a jalview
- project</li>
- <li>Envision2 workflow tooltips are corrupted</li>
- <li>Enabling show group conservation also enables colour by
- conservation</li>
- <li>Duplicate group associated conservation or consensus
- created on new view</li>
- <li>Annotation scrollbar not displayed after 'show all
- hidden annotation rows' option selected</li>
- <li>Alignment quality not updated after alignment annotation
- row is hidden then shown</li>
- <li>Preserve colouring of structures coloured by sequences in pre
- jalview 2.7 projects</li>
- <li>Web service job parameter dialog is not laid out properly
- </li>
- <li>Web services menu not refreshed after 'reset
- services' button is pressed in preferences</li>
- <li>Annotation off by one in jalview v2_3 example project</li>
- <li>Structures imported from file and saved in project get
- name like jalview_pdb1234.txt when reloaded</li>
- <li>Jalview does not always retrieve progress of a JABAWS job
- execution in full once it is complete</li>
- </ul> <em>Applet</em>
+ <p>
+ <strong>Release History</strong>
+ </p>
+ <table border="1">
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <em><strong>Release</strong></em>
+ </div>
+ </td>
+ <td>
+ <div align="center">
+ <em><strong>New Features</strong></em>
+ </div>
+ </td>
+ <td>
+ <div align="center">
+ <em><strong>Issues Resolved</strong></em>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>20/9/2016</em></strong>
+ </div>
+ </td>
+ <td><em>General</em>
+ <ul>
+ <li><!-- JAL-2164,JAL-1919,-->Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.</li>
+ <li><!-- JAL-192 --->Alignment ruler shows positions relative to reference sequence</li>
+ <li><!-- JAL-2202 -->Position/residue shown in status bar when mousing over sequence associated annotation</li>
+ <li><!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket' for manual entry</li>
+ <li><!-- JAL-2214 -->RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column</li>
+ </ul> <em>Application</em>
+ <ul>
+ <li><!-- JAL---></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL-2079 -->Updated download sites used for Rfam and Pfam sources to xfam.org</li>
+ <li><!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher</li>
+ <li><!-- JAL-2123 -->Show residue labels in Chimera when mousing over sequences in Jalview</li>
+ <li><!-- JAL-2027-->Support for reverse-complement coding regions in ENA and EMBL</li>
+ <li><!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for ENA record retrieval</li>
+ <li><!-- JAL-2027 -->Support for ENA CDS records with reverse complement operator</li>
+ <li><!-- JAL-1812 -->New 'execute Groovy script' option in an alignment window's Calculate menu</li>
+ <li><!-- JAL-1812 -->Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode</li>
+ <li><!-- JAL-2068 -->Support for creating new alignment calculation workers from groovy scripts</li>
+ <li><!-- JAL-1369 --->Store/restore reference sequence in Jalview projects</li>
+ <li><!-- JAL-1803-->Chain codes for a sequence's PDB associations are now saved/restored from project</li>
+ <li><!-- JAL-2183-->Double click on an entry in Jalview's database chooser opens a sequence fetcher</li>
+ <li><!-- JAL-1563-->Free-text search client for UniProt using the UniProt REST API</li>
+
+
+ </ul> <em>Applet</em>
+ <ul>
+ <li><!-- JAL---></li>
+ </ul></td>
+ <td>
+ <div align="left">
+ <em>General</em>
+ <ul>
+ <li><!-- JAL-2077 -->reinstate CTRL-click for opening pop-up menu on OSX</li>
+ <li><!-- JAL-2018-->Export features in Jalview format (again) includes graduated colourschemes</li>
+ <li><!-- JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
+ <li><!-- JAL-2053-->Hidden column markers not always rendered at right of alignment window</li>
+ <li><!-- JAL-2067, JAL- -->Tidied up links in help file table of contents</li>
+ <li><!-- JAL-2072 -->Feature based tree calculation not shown for DNA alignments</li>
+ <li><!-- JAL-2075 -->Hidden columns ignored during feature based tree calculation</li>
+ <li><!-- JAL-2065 -->Alignment view stops updating when show unconserved enabled for group on alignment</li>
+ <li><!-- JAL-2086 -->Cannot insert gaps into sequence when set as reference</li>
+ <li><!-- JAL-2146 -->Alignment column in status incorrectly shown as "Sequence position" when mousing over annotation</li>
+ <li><!-- JAL-2099 -->Incorrect column numbers in ruler when hidden columns present</li>
+ <li><!-- JAL-1577 -->Colour by RNA Helices not enabled when user created annotation added to alignment</li>
+ <li><!-- JAL-1841 -->RNA Structure consensus only computed for '()' base pair annotation</li>
+ <li><!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus</li>
+
+
+ </ul>
+ <em>Application</em>
+ <ul>
+ <li><!-- JAL-1944 not yet fixed Error thrown when exporting a view with hidden sequences as flat-file alignment--></li>
+ <li><!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms</li>
+ <li><!-- JAL-1552-->URLs and links can imported by drag'n'drop on OSX webstart</li>
+ <li><!-- JAL-2030-->InstallAnywhere distribution fails when launching Chimera</li>
+ <li><!-- JAL-2080-->Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)</li>
+ <li><!-- JAL-2085 -->Cannot save project when view has a reference sequence defined</li>
+ <li><!-- JAL-1011 -->Columns are suddenly selected in other alignments and views when revealing hidden columns</li>
+ <li><!-- JAL-1989 -->Hide columns not mirrored in complement view in a cDNA/Protein splitframe</li>
+ <li><!-- JAL-1369 -->Cannot save/restore representative sequence from project when only one sequence is represented</li>
+ <li><!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option in Structure Chooser</li>
+ <li><!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel</li>
+ <!-- may exclude, this is an external service stability issue JAL-1941 /> RNA 3D structure not added via DSSR service</li> -->
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <li><!-- --></li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
+ <em>16/10/2015</em></strong>
+ </div>
+ </td>
+ <td><em>General</em>
+ <ul>
+ <li>Time stamps for signed Jalview application and applet
+ jars</li>
+ </ul></td>
+ <td>
+ <div align="left">
+ <em>Application</em>
+ <ul>
+ <li>Duplicate group consensus and conservation rows
+ shown when tree is partitioned</li>
+ <li>Erratic behaviour when tree partitions made with
+ multiple cDNA/Protein split views</li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
+ <em>8/10/2015</em></strong>
+ </div>
+ </td>
+ <td><em>General</em>
+ <ul>
+ <li>Updated Spanish translations of localized text for
+ 2.9</li>
+ </ul> <em>Application</em>
+ <ul>
+ <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
+ <li>Signed OSX InstallAnywhere installer<br></li>
+ <li>Support for per-sequence based annotations in BioJSON</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Split frame example added to applet examples page</li>
+ </ul></td>
+ <td>
+ <div align="left">
+ <em>General</em>
+ <ul>
+ <li>Mapping of cDNA to protein in split frames
+ incorrect when sequence start > 1</li>
+ <li>Broken images in filter column by annotation dialog
+ documentation</li>
+ <li>Feature colours not parsed from features file</li>
+ <li>Exceptions and incomplete link URLs recovered when
+ loading a features file containing HTML tags in feature
+ description</li>
+
+ </ul>
+ <em>Application</em>
+ <ul>
+ <li>Annotations corrupted after BioJS export and
+ reimport</li>
+ <li>Incorrect sequence limits after Fetch DB References
+ with 'trim retrieved sequences'</li>
+ <li>Incorrect warning about deleting all data when
+ deleting selected columns</li>
+ <li>Patch to build system for shipping properly signed
+ JNLP templates for webstart launch</li>
+ <li>EMBL-PDBe fetcher/viewer dialogs do not offer
+ unreleased structures for download or viewing</li>
+ <li>Tab/space/return keystroke operation of EMBL-PDBe
+ fetcher/viewer dialogs works correctly</li>
+ <li>Disabled 'minimise' button on Jalview windows
+ running on OSX to workaround redraw hang bug</li>
+ <li>Split cDNA/Protein view position and geometry not
+ recovered from jalview project</li>
+ <li>Initial enabled/disabled state of annotation menu
+ sorter 'show autocalculated first/last' corresponds to
+ alignment view</li>
+ <li>Restoring of Clustal, RNA Helices and T-Coffee
+ color schemes from BioJSON</li>
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <li>Reorder sequences mirrored in cDNA/Protein split
+ frame</li>
+ <li>Applet with Jmol examples not loading correctly</li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
+ </div></td>
+ <td><em>General</em>
+ <ul>
+ <li>Linked visualisation and analysis of DNA and Protein
+ alignments:
+ <ul>
+ <li>Translated cDNA alignments shown as split protein
+ and DNA alignment views</li>
+ <li>Codon consensus annotation for linked protein and
+ cDNA alignment views</li>
+ <li>Link cDNA or Protein product sequences by loading
+ them onto Protein or cDNA alignments</li>
+ <li>Reconstruct linked cDNA alignment from aligned
+ protein sequences</li>
+ </ul>
+ </li>
+ <li>Jmol integration updated to Jmol v14.2.14</li>
+ <li>Import and export of Jalview alignment views as <a
+ href="features/bioJsonFormat.html">BioJSON</a></li>
+ <li>New alignment annotation file statements for
+ reference sequences and marking hidden columns</li>
+ <li>Reference sequence based alignment shading to
+ highlight variation</li>
+ <li>Select or hide columns according to alignment
+ annotation</li>
+ <li>Find option for locating sequences by description</li>
+ <li>Conserved physicochemical properties shown in amino
+ acid conservation row</li>
+ <li>Alignments can be sorted by number of RNA helices</li>
+ </ul> <em>Application</em>
+ <ul>
+ <li>New cDNA/Protein analysis capabilities
+ <ul>
+ <li>Get Cross-References should open a Split Frame
+ view with cDNA/Protein</li>
+ <li>Detect when nucleotide sequences and protein
+ sequences are placed in the same alignment</li>
+ <li>Split cDNA/Protein views are saved in Jalview
+ projects</li>
+ </ul>
+ </li>
+
+ <li>Use REST API to talk to Chimera</li>
+ <li>Selected regions in Chimera are highlighted in linked
+ Jalview windows</li>
+
+ <li>VARNA RNA viewer updated to v3.93</li>
+ <li>VARNA views are saved in Jalview Projects</li>
+ <li>Pseudoknots displayed as Jalview RNA annotation can
+ be shown in VARNA</li>
+
+ <li>Make groups for selection uses marked columns as well
+ as the active selected region</li>
+
+ <li>Calculate UPGMA and NJ trees using sequence feature
+ similarity</li>
+ <li>New Export options
+ <ul>
+ <li>New Export Settings dialog to control hidden
+ region export in flat file generation</li>
+
+ <li>Export alignment views for display with the <a
+ href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
+
+ <li>Export scrollable SVG in HTML page</li>
+ <li>Optional embedding of BioJSON data when exporting
+ alignment figures to HTML</li>
+ </li>
+ <li>3D structure retrieval and display
+ <ul>
+ <li>Free text and structured queries with the PDBe
+ Search API</li>
+ <li>PDBe Search API based discovery and selection of
+ PDB structures for a sequence set</li>
+ </ul>
+ </li>
+
+ <li>JPred4 employed for protein secondary structure
+ predictions</li>
+ <li>Hide Insertions menu option to hide unaligned columns
+ for one or a group of sequences</li>
+ <li>Automatically hide insertions in alignments imported
+ from the JPred4 web server</li>
+ <li>(Nearly) Native 'Quaqua' dialogs for browsing file
+ system on OSX<br />LGPL libraries courtesy of <a
+ href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
+ </li>
+ <li>changed 'View nucleotide structure' submenu to 'View
+ VARNA 2D Structure'</li>
+ <li>change "View protein structure" menu option to "3D
+ Structure ..."</li>
+
+ </ul> <em>Applet</em>
+ <ul>
+ <li>New layout for applet example pages</li>
+ <li>New parameters to enable SplitFrame view
+ (file2,enableSplitFrame, scaleProteinAsCdna)</li>
+ <li>New example demonstrating linked viewing of cDNA and
+ Protein alignments</li>
+ </ul> <em>Development and deployment</em>
+ <ul>
+ <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>Jalview Github organisation, and new github site for
+ storing BioJsMSA Templates</li>
+ <li>Jalview's unit tests now managed with TestNG</li>
+ </ul></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 in v2.7 example file means
+ alignment appears unaligned when pad-gaps is not enabled</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 tooltips shown
+ on some platforms</li>
+ <li>Chimera viewer 'View | Show Chain' menu is not
+ populated</li>
+ <li>'New View' fails with a Null Pointer Exception in
+ console 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>Save as '.jar' option removed for saving Jalview
+ projects</li>
+ <li>Colour by Sequence colouring in Chimera more
+ responsive</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>
+ <ul>
+ <li>Jmol to JalviewLite mouseover/link not working</li>
+ <li>JalviewLite can't import sequences with ID
+ descriptions containing angle brackets</li>
+ </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>
+ <li>Applet example pages appear different to the rest of
+ www.jalview.org</li>
+ </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>
+ <li>Cannot disable consensus calculation independently of
+ quality and conservation</li>
+ <li>Mouseover highlighting between cDNA and protein can
+ become sluggish with more than one splitframe shown</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><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>