+ <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>
+ <li>Newly created RNA secondary structure line doesn't
+ have 'display all symbols' flag set</li>
+ <li>T-COFFEE alignment score shading scheme and other
+ annotation shading not saved in Jalview project</li>
+ <li>Local file cannot be loaded in freshly downloaded
+ Jalview</li>
+ <li>Jalview icon not shown on dock in Mountain
+ Lion/Webstart</li>
+ <li>Load file from desktop file browser fails</li>
+ <li>Occasional NPE thrown when calculating large trees</li>
+ <li>Cannot reorder or slide sequences after dragging an
+ alignment onto desktop</li>
+ <li>Colour by annotation dialog throws NPE after using
+ 'extract scores' function</li>
+ <li>Loading/cut'n'pasting an empty file leads to a grey
+ alignment window</li>
+ <li>Disorder thresholds rendered incorrectly after
+ performing IUPred disorder prediction</li>
+ <li>Multiple group annotated consensus rows shown when
+ changing 'normalise logo' display setting</li>
+ <li>Find shows blank dialog after 'finished searching' if
+ nothing matches query</li>
+ <li>Null Pointer Exceptions raised when sorting by
+ feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
+ </li>
+ <li>Errors in Jmol console when structures in alignment
+ don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
+ </li>
+ <li>Not all working JABAWS services are shown in
+ Jalview's menu</li>
+ <li>JAVAWS version of Jalview fails to launch with
+ 'invalid literal/length code'</li>
+ <li>Annotation/RNA Helix colourschemes cannot be applied
+ to alignment with groups (actually fixed in 2.8.0b1)</li>
+ <li>RNA Helices and T-Coffee Scores available as default
+ colourscheme</li>
+
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Remove group option is shown even when selection is
+ not a group</li>
+ <li>Apply to all groups ticked but colourscheme changes
+ don't affect groups</li>
+ <li>Documented RNA Helices and T-Coffee Scores as valid
+ colourscheme name</li>
+ <li>Annotation labels drawn on sequence IDs when
+ Annotation panel is not displayed</li>
+ <li>Increased font size for dropdown menus on OSX and
+ embedded windows</li>
+ </ul> <em>Other</em>
+ <ul>
+ <li>Consensus sequence for alignments/groups with a
+ single sequence were not calculated</li>
+ <li>annotation files that contain only groups imported as
+ annotation and junk sequences</li>
+ <li>Fasta files with sequences containing '*' incorrectly
+ recognised as PFAM or BLC</li>
+ <li>conservation/PID slider apply all groups option
+ doesn't affect background (2.8.0b1)
+ <li></li>
+ <li>redundancy highlighting is erratic at 0% and 100%</li>
+ <li>Remove gapped columns fails for sequences with ragged
+ trailing gaps</li>
+ <li>AMSA annotation row with leading spaces is not
+ registered correctly on import</li>
+ <li>Jalview crashes when selecting PCA analysis for
+ certain alignments</li>
+ <li>Opening the colour by annotation dialog for an
+ existing annotation based 'use original colours'
+ colourscheme loses original colours setting</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
+ <em>30/1/2014</em></strong>
+ </div></td>
+ <td>
+ <ul>
+ <li>Trusted certificates for JalviewLite applet and
+ Jalview Desktop application<br />Certificate was donated by
+ <a href="https://www.certum.eu">Certum</a> to the Jalview
+ open source project).
+ </li>
+ <li>Jalview SRS links replaced by Uniprot and EBI-search
+ </li>
+ <li>Output in Stockholm format</li>
+ <li>Allow import of data from gzipped files</li>
+ <li>Export/import group and sequence associated line
+ graph thresholds</li>
+ <li>Nucleotide substitution matrix that supports RNA and
+ ambiguity codes</li>
+ <li>Allow disorder predictions to be made on the current
+ selection (or visible selection) in the same way that JPred
+ works</li>
+ <li>Groovy scripting for headless Jalview operation</li>
+ </ul> <em>Other improvements</em>
+ <ul>
+ <li>Upgrade desktop installer to InstallAnywhere 2013</li>
+ <li>COMBINE statement uses current SEQUENCE_REF and
+ GROUP_REF scope to group annotation rows</li>
+ <li>Support '' style escaping of quotes in Newick
+ files</li>
+ <li>Group options for JABAWS service by command line name</li>
+ <li>Empty tooltip shown for JABA service options with a
+ link but no description</li>
+ <li>Select primary source when selecting authority in
+ database fetcher GUI</li>
+ <li>Add .mfa to FASTA file extensions recognised by
+ Jalview</li>
+ <li>Annotation label tooltip text wrap</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Slow scrolling when lots of annotation rows are
+ displayed</li>
+ <li>Lots of NPE (and slowness) after creating RNA
+ secondary structure annotation line</li>
+ <li>Sequence database accessions not imported when
+ fetching alignments from Rfam</li>
+ <li>Incorrect SHMR submission for sequences with
+ identical IDs</li>
+ <li>View all structures does not always superpose
+ structures</li>
+ <li>Option widgets in service parameters not updated to
+ reflect user or preset settings</li>
+ <li>Null pointer exceptions for some services without
+ presets or adjustable parameters</li>
+ <li>Discover PDB IDs entry in structure menu doesn't
+ discover PDB xRefs</li>
+ <li>Exception encountered while trying to retrieve
+ features with DAS</li>
+ <li>Lowest value in annotation row isn't coloured
+ when colour by annotation (per sequence) is coloured</li>
+ <li>Keyboard mode P jumps to start of gapped region when
+ residue follows a gap</li>
+ <li>Jalview appears to hang importing an alignment with
+ Wrap as default or after enabling Wrap</li>
+ <li>'Right click to add annotations' message
+ shown in wrap mode when no annotations present</li>
+ <li>Disorder predictions fail with NPE if no automatic
+ annotation already exists on alignment</li>
+ <li>oninit javascript function should be called after
+ initialisation completes</li>
+ <li>Remove redundancy after disorder prediction corrupts
+ alignment window display</li>
+ <li>Example annotation file in documentation is invalid</li>
+ <li>Grouped line graph annotation rows are not exported
+ to annotation file</li>
+ <li>Multi-harmony analysis cannot be run when only two
+ groups created</li>
+ <li>Cannot create multiple groups of line graphs with
+ several 'combine' statements in annotation file</li>
+ <li>Pressing return several times causes Number Format
+ exceptions in keyboard mode</li>
+ <li>Multi-harmony (SHMMR) method doesn't submit
+ correct partitions for input data</li>
+ <li>Translation from DNA to Amino Acids fails</li>
+ <li>Jalview fail to load newick tree with quoted label</li>
+ <li>--headless flag isn't understood</li>
+ <li>ClassCastException when generating EPS in headless
+ mode</li>
+ <li>Adjusting sequence-associated shading threshold only
+ changes one row's threshold</li>
+ <li>Preferences and Feature settings panel panel
+ doesn't open</li>
+ <li>hide consensus histogram also hides conservation and
+ quality histograms</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
+ </div></td>
+ <td><em>Application</em>
+ <ul>
+ <li>Support for JABAWS 2.0 Services (AACon alignment
+ conservation, protein disorder and Clustal Omega)</li>
+ <li>JABAWS server status indicator in Web Services
+ preferences</li>
+ <li>VARNA (http://varna.lri.fr) viewer for RNA structures
+ in Jalview alignment window</li>
+ <li>Updated Jalview build and deploy framework for OSX
+ mountain lion, windows 7, and 8</li>
+ <li>Nucleotide substitution matrix for PCA that supports
+ RNA and ambiguity codes</li>
+
+ <li>Improved sequence database retrieval GUI</li>
+ <li>Support fetching and database reference look up
+ against multiple DAS sources (Fetch all from in 'fetch db
+ refs')</li>
+ <li>Jalview project improvements
+ <ul>
+ <li>Store and retrieve the 'belowAlignment'
+ flag for annotation</li>
+ <li>calcId attribute to group annotation rows on the
+ alignment</li>
+ <li>Store AACon calculation settings for a view in
+ Jalview project</li>
+
+ </ul>
+ </li>
+ <li>horizontal scrolling gesture support</li>
+ <li>Visual progress indicator when PCA calculation is
+ running</li>
+ <li>Simpler JABA web services menus</li>
+ <li>visual indication that web service results are still
+ being retrieved from server</li>
+ <li>Serialise the dialogs that are shown when Jalview
+ starts up for first time</li>
+ <li>Jalview user agent string for interacting with HTTP
+ services</li>
+ <li>DAS 1.6 and DAS 2.0 source support using new JDAS
+ client library</li>
+ <li>Examples directory and Groovy library included in
+ InstallAnywhere distribution</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>RNA alignment and secondary structure annotation
+ visualization applet example</li>
+ </ul> <em>General</em>
+ <ul>
+ <li>Normalise option for consensus sequence logo</li>
+ <li>Reset button in PCA window to return dimensions to
+ defaults</li>
+ <li>Allow seqspace or Jalview variant of alignment PCA
+ calculation</li>
+ <li>PCA with either nucleic acid and protein substitution
+ matrices
+ <li>Allow windows containing HTML reports to be exported
+ in HTML</li>
+ <li>Interactive display and editing of RNA secondary
+ structure contacts</li>
+ <li>RNA Helix Alignment Colouring</li>
+ <li>RNA base pair logo consensus</li>
+ <li>Parse sequence associated secondary structure
+ information in Stockholm files</li>
+ <li>HTML Export database accessions and annotation
+ information presented in tooltip for sequences</li>
+ <li>Import secondary structure from LOCARNA clustalw
+ style RNA alignment files</li>
+ <li>import and visualise T-COFFEE quality scores for an
+ alignment</li>
+ <li>'colour by annotation' per sequence option to
+ shade each sequence according to its associated alignment
+ annotation</li>
+ <li>New Jalview Logo</li>
+ </ul> <em>Documentation and Development</em>
+ <ul>
+ <li>documentation for score matrices used in Jalview</li>
+ <li>New Website!</li>
+ </ul></td>
+ <td><em>Application</em>
+ <ul>
+ <li>PDB, Unprot and EMBL (ENA) databases retrieved via
+ wsdbfetch REST service</li>
+ <li>Stop windows being moved outside desktop on OSX</li>
+ <li>Filetype associations not installed for webstart
+ launch</li>
+ <li>Jalview does not always retrieve progress of a JABAWS
+ job execution in full once it is complete</li>
+ <li>revise SHMR RSBS definition to ensure alignment is
+ uploaded via ali_file parameter</li>
+ <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
+ <li>View all structures superposed fails with exception</li>
+ <li>Jnet job queues forever if a very short sequence is
+ submitted for prediction</li>
+ <li>Cut and paste menu not opened when mouse clicked on
+ desktop window</li>
+ <li>Putting fractional value into integer text box in
+ alignment parameter dialog causes Jalview to hang</li>
+ <li>Structure view highlighting doesn't work on
+ windows 7</li>
+ <li>View all structures fails with exception shown in
+ structure view</li>
+ <li>Characters in filename associated with PDBEntry not
+ escaped in a platform independent way</li>
+ <li>Jalview desktop fails to launch with exception when
+ using proxy</li>
+ <li>Tree calculation reports 'you must have 2 or more
+ sequences selected' when selection is empty</li>
+ <li>Jalview desktop fails to launch with jar signature
+ failure when java web start temporary file caching is
+ disabled</li>
+ <li>DAS Sequence retrieval with range qualification
+ results in sequence xref which includes range qualification</li>
+ <li>Errors during processing of command line arguments
+ cause progress bar (JAL-898) to be removed</li>
+ <li>Replace comma for semi-colon option not disabled for
+ DAS sources in sequence fetcher</li>
+ <li>Cannot close news reader when JABAWS server warning
+ dialog is shown</li>
+ <li>Option widgets not updated to reflect user settings</li>
+ <li>Edited sequence not submitted to web service</li>
+ <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
+ <li>InstallAnywhere installer doesn't unpack and run
+ on OSX Mountain Lion</li>
+ <li>Annotation panel not given a scroll bar when
+ sequences with alignment annotation are pasted into the
+ alignment</li>
+ <li>Sequence associated annotation rows not associated
+ when loaded from Jalview project</li>
+ <li>Browser launch fails with NPE on java 1.7</li>
+ <li>JABAWS alignment marked as finished when job was
+ cancelled or job failed due to invalid input</li>
+ <li>NPE with v2.7 example when clicking on Tree
+ associated with all views</li>
+ <li>Exceptions when copy/paste sequences with grouped
+ annotation rows to new window</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Sequence features are momentarily displayed before
+ they are hidden using hidefeaturegroups applet parameter</li>
+ <li>loading features via javascript API automatically
+ enables feature display</li>
+ <li>scrollToColumnIn javascript API method doesn't
+ work</li>
+ </ul> <em>General</em>
+ <ul>
+ <li>Redundancy removal fails for rna alignment</li>
+ <li>PCA calculation fails when sequence has been selected
+ and then deselected</li>
+ <li>PCA window shows grey box when first opened on OSX</li>
+ <li>Letters coloured pink in sequence logo when alignment
+ coloured with clustalx</li>
+ <li>Choosing fonts without letter symbols defined causes
+ exceptions and redraw errors</li>
+ <li>Initial PCA plot view is not same as manually
+ reconfigured view</li>
+ <li>Grouped annotation graph label has incorrect line
+ colour</li>
+ <li>Grouped annotation graph label display is corrupted
+ for lots of labels</li>
+ </ul>
+ </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>
+ <ul>
+ <li>Alignment height set incorrectly when lots of
+ annotation rows are displayed</li>
+ <li>Relative URLs in feature HTML text not resolved to
+ codebase</li>
+ <li>View follows highlighting does not work for positions
+ in sequences</li>
+ <li><= shown as = in tooltip</li>
+ <li>Export features raises exception when no features
+ exist</li>
+ <li>Separator string used for serialising lists of IDs
+ for javascript api is modified when separator string
+ provided as parameter</li>
+ <li>Null pointer exception when selecting tree leaves for
+ alignment with no existing selection</li>
+ <li>Relative URLs for datasources assumed to be relative
+ to applet's codebase</li>
+ <li>Status bar not updated after finished searching and
+ search wraps around to first result</li>
+ <li>StructureSelectionManager instance shared between
+ several Jalview applets causes race conditions and memory
+ leaks</li>
+ <li>Hover tooltip and mouseover of position on structure
+ not sent from Jmol in applet</li>
+ <li>Certain sequences of javascript method calls to
+ applet API fatally hang browser</li>
+ </ul> <em>General</em>
+ <ul>
+ <li>View follows structure mouseover scrolls beyond
+ position with wrapped view and hidden regions</li>
+ <li>Find sequence position moves to wrong residue
+ with/without hidden columns</li>
+ <li>Sequence length given in alignment properties window
+ is off by 1</li>
+ <li>InvalidNumberFormat exceptions thrown when trying to
+ import PDB like structure files</li>
+ <li>Positional search results are only highlighted
+ between user-supplied sequence start/end bounds</li>
+ <li>End attribute of sequence is not validated</li>
+ <li>Find dialog only finds first sequence containing a
+ given sequence position</li>
+ <li>Sequence numbering not preserved in MSF alignment
+ output</li>
+ <li>Jalview PDB file reader does not extract sequence
+ from nucleotide chains correctly</li>
+ <li>Structure colours not updated when tree partition
+ changed in alignment</li>
+ <li>Sequence associated secondary structure not correctly
+ parsed in interleaved stockholm</li>
+ <li>Colour by annotation dialog does not restore current
+ state</li>
+ <li>Hiding (nearly) all sequences doesn't work
+ properly</li>
+ <li>Sequences containing lowercase letters are not
+ properly associated with their pdb files</li>
+ </ul> <em>Documentation and Development</em>
+ <ul>
+ <li>schemas/JalviewWsParamSet.xsd corrupted by
+ ApplyCopyright tool</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
+ </div>
+ </td>
+ <td><em>Application</em>
+ <ul>
+ <li>New warning dialog when the Jalview Desktop cannot
+ contact web services</li>
+ <li>JABA service parameters for a preset are shown in
+ service job window</li>
+ <li>JABA Service menu entries reworded</li>
+ </ul></td>
+ <td>
+ <ul>
+ <li>Modeller PIR IO broken - cannot correctly import a
+ pir file emitted by Jalview</li>
+ <li>Existing feature settings transferred to new
+ alignment view created from cut'n'paste</li>
+ <li>Improved test for mixed amino/nucleotide chains when
+ parsing PDB files</li>
+ <li>Consensus and conservation annotation rows
+ occasionally become blank for all new windows</li>
+ <li>Exception raised when right clicking above sequences
+ in wrapped view mode</li>
+ </ul> <em>Application</em>
+ <ul>
+ <li>multiple multiply aligned structure views cause cpu
+ usage to hit 100% and computer to hang</li>
+ <li>Web Service parameter layout breaks for long user
+ parameter names</li>
+ <li>Jaba service discovery hangs desktop if Jaba server
+ is down</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
+ </div>
+ </td>
+ <td><em>Application</em>
+ <ul>
+ <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
+ <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
+ (JABAWS)
+ </li>
+ <li>Web Services preference tab</li>
+ <li>Analysis parameters dialog box and user defined
+ preferences</li>
+ <li>Improved speed and layout of Envision2 service menu</li>
+ <li>Superpose structures using associated sequence
+ alignment</li>
+ <li>Export coordinates and projection as CSV from PCA
+ viewer</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>enable javascript: execution by the applet via the
+ link out mechanism</li>
+ </ul> <em>Other</em>
+ <ul>
+ <li>Updated the Jmol Jalview interface to work with Jmol
+ series 12</li>
+ <li>The Jalview Desktop and JalviewLite applet now
+ require Java 1.5</li>
+ <li>Allow Jalview feature colour specification for GFF
+ sequence annotation files</li>
+ <li>New 'colour by label' keword in Jalview feature file
+ type colour specification</li>
+ <li>New Jalview Desktop Groovy API method that allows a
+ script to check if it being run in an interactive session or
+ in a batch operation from the Jalview command line</li>
+ </ul></td>
+ <td>
+ <ul>
+ <li>clustalx colourscheme colours Ds preferentially when
+ both D+E are present in over 50% of the column</li>
+ </ul> <em>Application</em>
+ <ul>
+ <li>typo in AlignmentFrame->View->Hide->all but
+ selected Regions menu item</li>
+ <li>sequence fetcher replaces ',' for ';' when the ',' is
+ part of a valid accession ID</li>
+ <li>fatal OOM if object retrieved by sequence fetcher
+ runs out of memory</li>
+ <li>unhandled Out of Memory Error when viewing pca
+ analysis results</li>
+ <li>InstallAnywhere builds fail to launch on OS X java
+ 10.5 update 4 (due to apple Java 1.6 update)</li>
+ <li>Installanywhere Jalview silently fails to launch</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Jalview.getFeatureGroups() raises an
+ ArrayIndexOutOfBoundsException if no feature groups are
+ defined.</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
+ </div>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li>Alignment prettyprinter doesn't cope with long
+ sequence IDs</li>
+ <li>clustalx colourscheme colours Ds preferentially when
+ both D+E are present in over 50% of the column</li>
+ <li>nucleic acid structures retrieved from PDB do not
+ import correctly</li>
+ <li>More columns get selected than were clicked on when a
+ number of columns are hidden</li>
+ <li>annotation label popup menu not providing correct
+ add/hide/show options when rows are hidden or none are
+ present</li>
+ <li>Stockholm format shown in list of readable formats,
+ and parser copes better with alignments from RFAM.</li>
+ <li>CSV output of consensus only includes the percentage
+ of all symbols if sequence logo display is enabled</li>
+
+ </ul> <em>Applet</em>
+ <ul>
+ <li>annotation panel disappears when annotation is
+ hidden/removed</li>
+ </ul> <em>Application</em>
+ <ul>
+ <li>Alignment view not redrawn properly when new
+ alignment opened where annotation panel is visible but no
+ annotations are present on alignment</li>
+ <li>pasted region containing hidden columns is
+ incorrectly displayed in new alignment window</li>
+ <li>Jalview slow to complete operations when stdout is
+ flooded (fix is to close the Jalview console)</li>
+ <li>typo in AlignmentFrame->View->Hide->all but
+ selected Rregions menu item.</li>
+ <li>inconsistent group submenu and Format submenu entry
+ 'Un' or 'Non'conserved</li>
+ <li>Sequence feature settings are being shared by
+ multiple distinct alignments</li>
+ <li>group annotation not recreated when tree partition is
+ changed</li>
+ <li>double click on group annotation to select sequences
+ does not propagate to associated trees</li>
+ <li>Mac OSX specific issues:
+ <ul>
+ <li>exception raised when mouse clicked on desktop
+ window background</li>
+ <li>Desktop menu placed on menu bar and application
+ name set correctly</li>
+ <li>sequence feature settings not wide enough for the
+ save feature colourscheme button</li>
+ </ul>
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+
+ <td>
+ <div align="center">
+ <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
+ </div>
+ </td>
+ <td><em>New Capabilities</em>
+ <ul>
+ <li>URL links generated from description line for
+ regular-expression based URL links (applet and application)
+
+ <li>Non-positional feature URL links are shown in link
+ menu</li>
+ <li>Linked viewing of nucleic acid sequences and
+ structures</li>
+ <li>Automatic Scrolling option in View menu to display
+ the currently highlighted region of an alignment.</li>
+ <li>Order an alignment by sequence length, or using the
+ average score or total feature count for each sequence.</li>
+ <li>Shading features by score or associated description</li>
+ <li>Subdivide alignment and groups based on identity of
+ selected subsequence (Make Groups from Selection).</li>
+ <li>New hide/show options including Shift+Control+H to
+ hide everything but the currently selected region.</li>
+ <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
+ </ul> <em>Application</em>
+ <ul>
+ <li>Fetch DB References capabilities and UI expanded to
+ support retrieval from DAS sequence sources</li>
+ <li>Local DAS Sequence sources can be added via the
+ command line or via the Add local source dialog box.</li>
+ <li>DAS Dbref and DbxRef feature types are parsed as
+ database references and protein_name is parsed as
+ description line (BioSapiens terms).</li>
+ <li>Enable or disable non-positional feature and database
+ references in sequence ID tooltip from View menu in
+ application.</li>
+ <!-- <li>New hidden columns and rows and representatives capabilities
+ in annotations file (in progress - not yet fully implemented)</li> -->
+ <li>Group-associated consensus, sequence logos and
+ conservation plots</li>
+ <li>Symbol distributions for each column can be exported
+ and visualized as sequence logos</li>
+ <li>Optionally scale multi-character column labels to fit
+ within each column of annotation row<!-- todo for applet -->
+ </li>
+ <li>Optional automatic sort of associated alignment view
+ when a new tree is opened.</li>
+ <li>Jalview Java Console</li>
+ <li>Better placement of desktop window when moving
+ between different screens.</li>
+ <li>New preference items for sequence ID tooltip and
+ consensus annotation</li>
+ <li>Client to submit sequences and IDs to <a
+ href="webServices/index.html#envision2">Envision2</a>
+ Workflows
+ </li>
+ <li><em>Vamsas Capabilities</em>
+ <ul>
+ <li>Improved VAMSAS synchronization (Jalview archive
+ used to preserve views, structures, and tree display
+ settings)</li>
+ <li>Import of vamsas documents from disk or URL via
+ command line</li>
+ <li>Sharing of selected regions between views and
+ with other VAMSAS applications (Experimental feature!)</li>
+ <li>Updated API to VAMSAS version 0.2</li>
+ </ul></li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Middle button resizes annotation row height</li>
+ <li>New Parameters
+ <ul>
+ <li>sortByTree (true/false) - automatically sort the
+ associated alignment view by the tree when a new tree is
+ opened.</li>
+ <li>showTreeBootstraps (true/false) - show or hide
+ branch bootstraps (default is to show them if available)</li>
+ <li>showTreeDistances (true/false) - show or hide
+ branch lengths (default is to show them if available)</li>
+ <li>showUnlinkedTreeNodes (true/false) - indicate if
+ unassociated nodes should be highlighted in the tree
+ view</li>
+ <li>heightScale and widthScale (1.0 or more) -
+ increase the height or width of a cell in the alignment
+ grid relative to the current font size.</li>
+ </ul>
+ </li>
+ <li>Non-positional features displayed in sequence ID
+ tooltip</li>
+ </ul> <em>Other</em>
+ <ul>
+ <li>Features format: graduated colour definitions and
+ specification of feature scores</li>
+ <li>Alignment Annotations format: new keywords for group
+ associated annotation (GROUP_REF) and annotation row display
+ properties (ROW_PROPERTIES)</li>
+ <li>XML formats extended to support graduated feature
+ colourschemes, group associated annotation, and profile
+ visualization settings.</li></td>
+ <td>
+ <ul>
+ <li>Source field in GFF files parsed as feature source
+ rather than description</li>
+ <li>Non-positional features are now included in sequence
+ feature and gff files (controlled via non-positional feature
+ visibility in tooltip).</li>
+ <li>URL links generated for all feature links (bugfix)</li>
+ <li>Added URL embedding instructions to features file
+ documentation.</li>
+ <li>Codons containing ambiguous nucleotides translated as
+ 'X' in peptide product</li>
+ <li>Match case switch in find dialog box works for both
+ sequence ID and sequence string and query strings do not
+ have to be in upper case to match case-insensitively.</li>
+ <li>AMSA files only contain first column of
+ multi-character column annotation labels</li>
+ <li>Jalview Annotation File generation/parsing consistent
+ with documentation (e.g. Stockholm annotation can be
+ exported and re-imported)</li>
+ <li>PDB files without embedded PDB IDs given a friendly
+ name</li>
+ <li>Find incrementally searches ID string matches as well
+ as subsequence matches, and correctly reports total number
+ of both.</li>
+ <li>Application:
+ <ul>
+ <li>Better handling of exceptions during sequence
+ retrieval</li>
+ <li>Dasobert generated non-positional feature URL
+ link text excludes the start_end suffix</li>
+ <li>DAS feature and source retrieval buttons disabled
+ when fetch or registry operations in progress.</li>
+ <li>PDB files retrieved from URLs are cached properly</li>
+ <li>Sequence description lines properly shared via
+ VAMSAS</li>
+ <li>Sequence fetcher fetches multiple records for all
+ data sources</li>
+ <li>Ensured that command line das feature retrieval
+ completes before alignment figures are generated.</li>
+ <li>Reduced time taken when opening file browser for
+ first time.</li>
+ <li>isAligned check prior to calculating tree, PCA or
+ submitting an MSA to JNet now excludes hidden sequences.</li>
+ <li>User defined group colours properly recovered
+ from Jalview projects.</li>
+ </ul>
+ </li>
+ </ul>
+ </td>
+
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.4.0.b2</strong><br> 28/10/2009
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Experimental support for google analytics usage
+ tracking.</li>
+ <li>Jalview privacy settings (user preferences and docs).</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Race condition in applet preventing startup in
+ jre1.6.0u12+.</li>
+ <li>Exception when feature created from selection beyond
+ length of sequence.</li>
+ <li>Allow synthetic PDB files to be imported gracefully</li>
+ <li>Sequence associated annotation rows associate with
+ all sequences with a given id</li>
+ <li>Find function matches case-insensitively for sequence
+ ID string searches</li>
+ <li>Non-standard characters do not cause pairwise
+ alignment to fail with exception</li>
+ </ul> <em>Application Issues</em>
+ <ul>
+ <li>Sequences are now validated against EMBL database</li>
+ <li>Sequence fetcher fetches multiple records for all
+ data sources</li>
+ </ul> <em>InstallAnywhere Issues</em>
+ <ul>
+ <li>Dock icon works for Mac OS X java (Mac 1.6 update
+ issue with installAnywhere mechanism)</li>
+ <li>Command line launching of JARs from InstallAnywhere
+ version (java class versioning error fixed)</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>