-->
<head>
<title>Release History</title>
+<style>
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+ /* remove bullets, narrower indent */
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+
+li {
+ /* separate the items from eachother */
+ margin-left: -3px;
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+ padding-left: 6px;
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+ /* doesnt get processed in javahelp */
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</head>
<body>
<p>
<tr>
<td width="60" nowrap>
<div align="center">
- <strong><a name="Jalview.2.10.1">2.10.1</a><br />
- <em>22/11/2016</em></strong>
+ <strong><a name="Jalview.2.10.2">2.10.2</a><br />
+ <em>8/8/2017</em></strong>
</div>
</td>
<td><div align="left">
- <em>General</em>
- <ul>
- <li><!-- JAL-98 -->Improved memory usage: sparse arrays used for all consensus calculations</li>
- <li><!-- JAL- --></li>
+ <em>General</em>
+ <ul>
+ <li><!-- JAL-2360,JAL-2371, -->More robust colours and shader model for alignments and groups</li>
+ <li><!-- JAL-384 -->Custom shading schemes created via groovy scripts</li>
+ <li><!-- JAL-2491 -->linked scrolling of CDS/Protein views via Overview or sequence motif search operations</li>
+ <li><!-- JAL-2526 -->Efficiency improvements for interacting with alignment and overview windows</li>
+ <li><!-- JAL-2388 -->Hidden columns and sequences can be omitted in Overview</li>
+ <li>
+ <!-- JAL-2535 -->Posterior probability annotation from
+ Stockholm files imported as sequence associated annotation
+ </li>
+ <li>
+ <!-- JAL-2533 -->Sequence names don't include file
+ extension when importing structure files without embedded
+ names or PDB accessions
+ </li>
+ <li><!-- JAL-2547 -->Amend sequence features dialog box can be opened by double clicking gaps within sequence feature extent</li>
+ <li><!-- JAL-2631 -->Graduated feature colour style example included in the example feature file</li>
</ul>
<em>Application</em>
<ul>
- <li><!-- JAL-1723 -->Sequence ID tool tips have been tamed (databases sorted alphabetically, abridged ID sets) </li>
- <li><!-- JAL-2282-->New replacement token for creating URLs <em>just</em> from database cross references. Users with custom links will receive a warning dialog asking them to update their preferences.</li>
- <li><!-- JAL-2287-->Cancel button and escape listener on dialog warning user about disconnecting Jalview from a Chimera session</li>
- <li><!-- JAL-2281-->Custom URL links for database cross-references are matched to database name regardless of case</li>
- <li></li>
-
-
+ <li>
+ <!-- JAL-2447 -->
+ Experimental Features Checkbox in Desktop's Tools
+ menu to hide or show untested features in the application.
+ </li>
+ <li><!-- JAL-1476 -->Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera</li>
+ <li><!-- JAL-1596 -->Faster Chimera/Jalview communication by file-based command exchange</li>
+ <li><!-- JAL-2316, -->URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB</li>
+ <li><!-- JAL-2549 -->Updated JABAWS client to v2.2</li>
+ </ul>
+ <em>Experimental features</em>
+ <ul>
+ <li>
+ <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
+ to transfer Chimera's structure attributes as Jalview
+ features, and vice-versa.
+ </li>
</ul>
<em>Applet</em>
<ul>
+ <li><!-- --></li>
</ul>
- <em>Build and deployment</em>
+ <em>Test Suite</em>
+ <li><!-- JAL-2474 -->Added PrivilegedAccessor to test suite</li>
+ <li><!-- JAL-2326 -->Prevent or clear modal dialogs raised during tests</li>
+ <li><!-- -->
+ </ul>
+ </div></td><td><div align="left">
+ <em>General</em>
<ul>
- <li></li>
+ <li>
+ <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
+ matrix - C->R should be '-3'<br />Old matrix restored with
+ this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
+ </li>
+ <li>
+ <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
+ and substitution matrix based Tree calculations.<br />In
+ earlier versions of Jalview, gaps matching gaps were
+ penalised, and gaps matching non-gaps penalised even more.
+ In the PCA calculation, gaps were actually treated as
+ non-gaps - so different costs were applied, which meant
+ Jalview's PCAs were different to those produced by
+ SeqSpace.<br />Jalview now treats gaps in the same way as
+ SeqSpace (ie it scores them as 0). To restore pre-2.10.2
+ behaviour<br />
+ jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
+ 2.10.1 mode<br />
+ jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
+ restore 2.10.2 mode
+ </li>
+ <li><!-- JAL-2346 -->Reopening Colour by annotation dialog doesn't reselect a specific sequence's associated annotation after it was used for colouring a view</li>
+ <li><!-- JAL-2430 -->Hidden regions in alignment views are not coloured in linked structure views</li>
+ <li><!-- JAL-2419 -->Current selection lost if popup menu opened on a region of alignment without groups</li>
+ <li><!-- JAL-2374 -->Popup menu not always shown for regions of an alignment with overlapping groups</li>
+ <li><!-- JAL-2310 -->Finder double counts if both a sequence's name and description match</li>
+ <li><!-- JAL-2370 -->Hiding column selection containing two hidden regions results in incorrect hidden regions</li>
+ <li><!-- JAL-2377 -->PCA calculation could hang when generating output report when working with highly redundant alignments</li>
+ <li><!-- JAL-2365 -->Cannot configure feature colours with lightGray or darkGray via features file</li>
+ <li><!-- JAL-2421 -->Overview window visible region moves erratically when hidden rows or columns are present</li>
+ <li><!-- JAL-2362 -->Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring</li>
+ <li><!-- JAL-2405 -->Protein specific colours only offered in colour and group colour menu for protein alignments</li>
+ <li><!-- JAL-2386 -->'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups</li>
+ <li><!-- JAL-2385 -->Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds</li>
+ <li><!-- JAL-2373 -->Percentage identity and conservation menu items do not show a tick or allow shading to be disabled</li>
+ <li><!-- JAL-2385 -->Conservation shading or PID threshold lost when base colourscheme changed if slider not visible</li>
+ <li><!-- JAL-2547 -->Sequence features shown in tooltip for gaps before start of features</li>
+ <li><!-- JAL-2576 -->Very large alignments take a long time to load</li>
+ <li><!-- JAL-2590 -->Cannot load Newick trees from eggnog ortholog database</li>
+ <li><!-- JAL-2623 -->Graduated feature colour threshold not restored to UI when feature colour is edited</li>
+ <li><!-- JAL-2624 -->Feature colour thresholds not respected when rendered on overview and structures when opacity at 100%</li>
+ <li><!-- JAL-2630 -->Structure and alignment overview update as graduate feature colour settings are modified via the dialog box</li>
+ <li><!-- JAL-147 -->Vertical scrollbar jumps one page-width at a time when scrolling vertically in wrapped mode.</li>
+ <li><!-- JAL-2034 -->Overview window doesn't always update when a group defined on the alignment is resized</li>
+ <li><!-- JAL-2605 -->Mouseovers on left/right scale region in wrapped view result in positional status updates</li>
+ </ul>
+ <em>Application</em>
+ <ul>
+ <li><!-- JAL-2401 -->Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added)</li>
+ <li><!-- JAL-2399-->Text colour threshold's 'Cancel' button doesn't restore group-specific text colour thresholds</li>
+ <li><!-- JAL-2243 -->Feature settings panel does not update as new features are added to alignment</li>
+ <li><!-- JAL-2436 -->Structure viewer's View -> Colour By view selection menu changes colours of alignment views</li>
+ <li><!-- JAL-2366 -->Proxy server address and port always appear enabled in Preferences->Connections</li>
+ <li><!-- JAL-2426 -->Spurious exceptions in console raised from alignment calculation workers after alignment has been closed</li>
+ <li><!-- JAL-1608 -->Typo in selection popup menu - Create groups now 'Create Group'</li>
+ <li><!-- JAL-1608 -->CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work</li>
+ <li><!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'</li>
+ <li><!-- JAL-2461 -->DAS registry not found exceptions removed from console output</li>
+ <li><!-- JAL-2383 -->Above PID colour threshold not recovered when alignment view imported from project</li>
+ <li><!-- JAL-2465 -->No mappings generated between structure and sequences extracted from structure files imported via URL</li>
+ <li>
+ <!-- JAL-2520 -->Structures loaded via URL are saved in
+ Jalview Projects rather than fetched via URL again when
+ the project is loaded and the structure viewed
+ </li>
+ <li><!-- JAL-1256 -->Trackpad horizontal scroll gesture adjusts start position in wrap mode</li>
+ <li><!-- JAL-2563 -->Status bar doesn't show positions for ambiguous amino acids</li>
+ <li><!-- JAL-2291 -->Hide insertions in PopUp menu excludes gaps in selection, current sequence and only within selected columns</li>
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <li><!-- JAL-2442 -->Features not rendered as transparent on overview or linked structure view</li>
+ <li><!-- JAL-2372 -->Colour group by conservation doesn't work (since 2.8)</li>
+ <li><!-- JAL-2517 -->Hitting Cancel after applying user-defined colourscheme doesn't restore original colourscheme</li>
</ul>
- </div>
+ <em>New Known Issues</em>
+ <ul>
+ <li><!-- JAL-2566 -->Protein/CDS view scrolling not always in phase after a sequence motif find operation</li>
+ <li><!-- JAL-2550 -->Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS rna secondary structure symbols</li>
+ </ul>
+
+ </div>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.1">2.10.1</a><br />
+ <em>29/11/2016</em></strong>
+ </div>
</td>
- <td>
- <div align="left">
+ <td><div align="left">
<em>General</em>
<ul>
- <li><!-- JAL-2286 -->Columns with more than one modal residue are not coloured or thresholded according to percent identity (first observed in Jalview 2.8.2)</li>
- <li><!-- JAL-2301 -->Threonine incorrectly reported as not hydrophobic</li>
- <li><!-- JAL-2318 -->Updates to documentation pages (above PID threshold, amino acid properties)</li>
- <li><!-- JAL-2292 -->Lower case residues in sequences are not reported as mapped to residues in a structure file in the View Mapping report</li>
+ <li>
+ <!-- JAL-98 -->Improved memory usage: sparse arrays used
+ for all consensus calculations
+ </li>
+ <li>
+ <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released 3rd Oct 2016)
+ </li>
+ <li>Updated Jalview's Certum code signing certificate
+ for 2016-2017</li>
</ul>
<em>Application</em>
<ul>
- <li><!-- JAL-2282-->Custom URL links for specific database names without regular expressions also offer invalid links from Sequence ID</li>
- <li><!-- JAL-2315-->Removing a single configured link in the URL links pane in Connections preferences doesn't actually update Jalview configuration</li>
- <li><!-- JAL-2272-->CTRL-Click on a selected region to open the alignment area popup menu doesn't work on El-Capitan</li>
- <li><!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF files with similarly named sequences if dropped onto the alignment</li>
- <li><!-- JAL-2312 -->Additional mappings are shown for PDB entries where more chains exist in the PDB accession than are reported in the SIFTS file</li>
- <li><!-- JAL-2317-->Certain structures do not get mapped to the structure view when displayed with Chimera</li>
- <li><!-- JAL-2317-->No chains shown in the Chimera view panel's View->Show Chains submenu</li>
-
- <li><!-- --></li>
- <li><!-- --></li>
+ <li>
+ <!-- JAL-1723 -->Sequence ID tool tip presents abridged
+ set of database cross-references, sorted alphabetically
+ </li>
+ <li>
+ <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
+ from database cross references. Users with custom links
+ will receive a <a href="webServices/urllinks.html#warning">warning
+ dialog</a> asking them to update their preferences.
+ </li>
+ <li>
+ <!-- JAL-2287-->Cancel button and escape listener on
+ dialog warning user about disconnecting Jalview from a
+ Chimera session
+ </li>
+ <li>
+ <!-- JAL-2320-->Jalview's Chimera control window closes if
+ the Chimera it is connected to is shut down
+ </li>
+ <li>
+ <!-- JAL-1738-->New keystroke (B) and Select highlighted
+ columns menu item to mark columns containing
+ highlighted regions (e.g. from structure selections or results
+ of a Find operation)
+ </li>
+ <li>
+ <!-- JAL-2284-->Command line option for batch-generation
+ of HTML pages rendering alignment data with the BioJS
+ MSAviewer
+ </li>
</ul>
- <em>Applet</em>
+ </div></td>
+ <td>
+ <div align="left">
+ <em>General</em>
<ul>
+ <li>
+ <!-- JAL-2286 -->Columns with more than one modal residue
+ are not coloured or thresholded according to percent
+ identity (first observed in Jalview 2.8.2)
+ </li>
+ <li>
+ <!-- JAL-2301 -->Threonine incorrectly reported as not
+ hydrophobic
+ </li>
+ <li>
+ <!-- JAL-2318 -->Updates to documentation pages (above PID
+ threshold, amino acid properties)
+ </li>
+ <li>
+ <!-- JAL-2292 -->Lower case residues in sequences are not
+ reported as mapped to residues in a structure file in the
+ View Mapping report
+ </li>
+ <li>
+ <!--JAL-2324 -->Identical features with non-numeric scores
+ could be added multiple times to a sequence
+ </li>
+ <li>
+ <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
+ bond features shown as two highlighted residues rather
+ than a range in linked structure views, and treated
+ correctly when selecting and computing trees from features
+ </li>
+ <li>
+ <!-- JAL-2281-->Custom URL links for database
+ cross-references are matched to database name regardless
+ of case
+ </li>
+
</ul>
- <em>Build and deployment</em>
+ <em>Application</em>
<ul>
- <li><!-- JAL-2308, -->Failing/passing unit tests</li>
+ <li>
+ <!-- JAL-2282-->Custom URL links for specific database
+ names without regular expressions also offer links from
+ Sequence ID
+ </li>
+ <li>
+ <!-- JAL-2315-->Removing a single configured link in the
+ URL links pane in Connections preferences doesn't actually
+ update Jalview configuration
+ </li>
+ <li>
+ <!-- JAL-2272-->CTRL-Click on a selected region to open
+ the alignment area popup menu doesn't work on El-Capitan
+ </li>
+ <li>
+ <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
+ files with similarly named sequences if dropped onto the
+ alignment
+ </li>
+ <li>
+ <!-- JAL-2312 -->Additional mappings are shown for PDB
+ entries where more chains exist in the PDB accession than
+ are reported in the SIFTS file
+ </li>
+ <li>
+ <!-- JAL-2317-->Certain structures do not get mapped to
+ the structure view when displayed with Chimera
+ </li>
+ <li>
+ <!-- JAL-2317-->No chains shown in the Chimera view
+ panel's View->Show Chains submenu
+ </li>
+ <li>
+ <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
+ work for wrapped alignment views
+ </li>
+ <li>
+ <!--JAL-2197 -->Rename UI components for running JPred
+ predictions from 'JNet' to 'JPred'
+ </li>
+ <li>
+ <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
+ corrupted when annotation panel vertical scroll is not at
+ first annotation row
+ </li>
+ <li>
+ <!--JAL-2332 -->Attempting to view structure for Hen
+ lysozyme results in a PDB Client error dialog box
+ </li>
+ <li>
+ <!-- JAL-2319 -->Structure View's mapping report switched ranges for PDB and sequence for SIFTS</li>
+ <!-- JAL-2319 -->SIFTS 'Not_Observed' residues mapped to non-existant coordindate data</li>
</ul>
- <em>New Known Issues</em>
+<!-- <em>New Known Issues</em>
<ul>
<li></li>
- </ul>
+ </ul> -->
</div>
</td>
</tr>
<!-- JAL-2284 -->Unable to read old Jalview projects that
contain non-XML data added after Jalvew wrote project.
</li>
+ <li><!-- JAL-2118 -->Newly created annotation row reorders
+ after clicking on it to create new annotation for a
+ column.
+ </li>
<!-- may exclude, this is an external service stability issue JAL-1941
-- > RNA 3D structure not added via DSSR service</li> -->
</ul>