<!-- JAL-1933 -->Occupancy annotation row shows number of
ungapped positions in each column of the alignment.
</li>
+ <li>
+ <!-- JAL-2533 -->File extension pruned from Sequence ID
+ for sequences derived from structure files without
+ embedded database accession
+ </li>
+ <li>
+ <!-- JAL-1476 -->Status bar message shown when not enough
+ aligned positions were available to create a 3D structure
+ superposition.
+ </li>
+ <li>
+ <!-- JAL-2507 -->More robust per-sequence positional
+ annotation input/output via stockholm flatfile
+ </li>
+
</ul>
<em>Application</em>
<ul>
format sequence substitution matrices
</li>
<li>
- <!-- JAL-2375 -->Structure chooser automatically shows Cached Structures rather than querying the PDBe if structures are already available for sequences
+ <!-- JAL-2375 -->Structure chooser automatically shows
+ Cached Structures rather than querying the PDBe if
+ structures are already available for sequences
</li>
+ <li>
+ <!-- JAL-2520 -->Structures imported via URL are cached in
+ the Jalview project rather than downloaded again when the
+ project is reopened.
+ </li>
+
</ul>
<em>Experimental features</em>
<ul>
during tests
</li>
<li>
+ <!-- JAL-2485, -->External service integration tests for
+ Uniprot REST Free Text Search Client
+ </li>
+ <li>
<!-- --> <em>Scripting</em>
<ul>
<li>
constants)
</li>
<li>
- <!-- JAL- -->
+ <!-- JAL-2228 -->FeatureCounter script refactored for
+ efficiency when counting all displayed features (not
+ backwards compatible with 2.10.1)
</li>
+ <li></li>
</ul>
restore 2.10.2 mode
</li>
<li>
+ <!-- JAL-2424 -->Fixed off-by-one bug that affected
+ scaling of branch lengths for trees computed using
+ Sequence Feature Similarity.
+ </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
overview when features overlaid on alignment
</li>
<li>
- <!-- JAL- -->
+ <!-- JAL-2473 -->Minimum size set for Jalview windows so
+ widgets don't permanently disappear
</li>
<li>
- <!-- JAL- -->
+ <!-- JAL-2503 -->Cannot select or filter quantitative
+ annotation that are shown only as column labels (e.g.
+ T-Coffee column reliability scores)
</li>
<li>
- <!-- JAL- -->
+ <!-- JAL-2589 -->Gap colours in user-defined colourschemes
+ are not shown
</li>
<li>
- <!-- JAL- -->
+ <!-- JAL-2594 -->Exception thrown if trying to create a
+ sequence feature on gaps only
+ </li>
+ <li>
+ <!-- JAL-2544 --> Sort by features includes features to
+ right of selected region when gaps present on right-hand
+ boundary
+ </li>
+ <li>
+ <!-- JAL-2504 -->Features created with 'New feature'
+ button from a Find inherit previously defined feature type
+ rather than the Find query string
+ </li>
+ <li>
+ <!-- JAL-2423 -->incorrect title in output window when
+ exporting tree calculated in Jalview
+ </li>
+ <li>
+ <!-- JAL-2507 -->Per-sequence RNA secondary structures
+ added after a sequence was imported are not written to
+ Stockholm File
+ </li>
+ <li>
+ <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
+ when importing RNA secondary structure via Stockholm
+ </li>
+ <li>
+ <!-- JAL-2509 -->Secondary structure arrows for [] and {}
+ not shown in correct direction for simple pseudoknots
+ </li>
+ <li>
+ <!-- JAL-2437 -->Hiding sequences at bottom of alignment
+ and then revealing them reorders sequences on the
+ alignment
+ </li>
+ <li>
+ <!-- JAL-964 -->Group panel in sequence feature settings
+ doesn't update to reflect available set of groups after
+ interactively adding or modifying features
+ </li>
+ <li>
+ <!-- JAL-2225 -->Sequence Database chooser unusable on
+ Linux
+ </li>
+ <li>
+ <!-- JAL -->
+ </li>
+ <li>
+ <!-- JAL -->
+ </li>
+ <li>
+ <!-- JAL -->
</li>
</ul>
<strong>Documentation</strong>
<!-- JAL-2339 -->Release notes reformatted for readibility
with the built-in Java help viewer
</li>
+ <li>
+ <!-- JAL-1644 -->Find documentation updated with 'search
+ sequence description' option
+ </li>
</ul>
<em>Application</em>
<ul>
<li>
+ <!-- JAL-2225 -->Sequence Database chooser doesn't show
+ available databases panel on Linux
+ </li>
+ <li>
+ <!-- JAL-2519 -->EnsemblGenomes example failing after
+ release of Ensembl v.88
+ </li>
+ <li>
+ <!-- JAL-2361 -->User Defined Colours not added to Colour
+ menu
+ </li>
+ <li>
<!-- JAL-2401 -->Easier creation of colours for all 'Lower
case' residues (button in colourscheme editor debugged and
new documentation and tooltips added)
new features are added to alignment
</li>
<li>
+ <!-- JAL-2532 -->Cancel in feature settings reverts
+ changes to feature colours via the Amend features dialog
+ </li>
+ <li>
+ <!-- JAL-2506 -->Null pointer exception when attempting to
+ edit graduated feature colour via amend features dialog
+ box
+ </li>
+ <li>
<!-- JAL-2436 -->Structure viewer's View -> Colour By view
selection menu changes colours of alignment views
</li>
when alignment view imported from project
</li>
<li>
- <!-- JAL-2465 -->No mappings generated between structure
- and sequences extracted from structure files imported via
- URL
+ <!-- JAL-2520,JAL-2465 -->No mappings generated between
+ structure and sequences extracted from structure files
+ imported via URL and viewed in Jmol
</li>
<li>
<!-- JAL-2520 -->Structures loaded via URL are saved in
proteins
</li>
<li>
- <!-- JAL-2431 -->cDNA Consensus not shown
+ <!-- JAL-2482 -->Incorrect PDB-Uniprot mappings created
+ from SIFTs for April 2017 update due to 'null' strings in
+ RESNUM mapping field
</li>
jalview.ws.jabaws.RNAStructExportImport setup fails
</li>
<li>
- <!-- JAL- -->
+ <!-- JAL-2307 -->Unit test failure:
+ jalview.ws.sifts.SiftsClientTest due to compatibility
+ problems with deep array comparison equality asserts in
+ successive versions of TestNG
</li>
+ <li>
+ <!-- JAL-2479 -->Relocated StructureChooserTest and
+ ParameterUtilsTest Unit tests to Network suite
+ </li>
+
</ul>
</div>
+
<tr>
<td width="60" nowrap>
<div align="center">
git://source.jalview.org / jalview.git / blobdiff