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<strong><a name="Jalview.2.10.2">2.10.2</a><br />
- <em>30/5/2017</em></strong>
+ <em>8/8/2017</em></strong>
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<em>General</em>
<ul>
<li><!-- JAL-2360,JAL-2371, -->More robust colours and shader model for alignments and groups</li>
- <li><!-- JAL-384 -->Custom BLOSUM/Clustal type shading schemes can be created via groovy scripts</li>
-
- <li><!-- JAL-2314, -->Test suite expanded and debugged (over 940 functional unit tests, only 3 failing due to ongoing work!)
+ <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><!-- --></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>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><!-- 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-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-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-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>
+ <li><!-- JAL-2563 -->Status bar shows position for ambiguous amino acid and nucleotide symbols</li>
</ul>
<em>Application</em>
<ul>
<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-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>
<em>New Known Issues</em>
<ul>
- <li></li>
+ <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>
+ <li><!-- JAL-2590 -->Cannot load Newick trees from eggnog ortholog database</li>
</ul>
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git://source.jalview.org / jalview.git / blobdiff