- <tr>
- <td width="60" nowrap>
- <div align="center">
- <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
- </div>
- </td>
- <td><div align="left">
- <em>Calculations</em>
- <ul>
-
- <li>
- <!-- JAL-1933 -->Occupancy annotation row shows number of
- ungapped positions in each column of the alignment.
- </li>
- <li>
- <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
- a calculation dialog box
- </li>
- <li>
- <!-- JAL-2379 -->Revised implementation of PCA for speed
- and memory efficiency (~30x faster)
- </li>
- <li>
- <!-- JAL-2403 -->Revised implementation of sequence
- similarity scores as used by Tree, PCA, Shading Consensus
- and other calculations
- </li>
- <li>
- <!-- JAL-2416 -->Score matrices are stored as resource
- files within the Jalview codebase
- </li>
- <li>
- <!-- JAL-2500 -->Trees computed on Sequence Feature
- Similarity may have different topology due to increased
- precision
- </li>
- </ul>
- <em>Rendering</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>
- </ul>
- <em>Overview</em>
- <ul>
- <li>
- <!-- JAL-2526 -->Efficiency improvements for interacting
- with alignment and overview windows
- </li>
- <li>
- <!-- JAL-2514 -->Scrolling of wrapped alignment views via
- overview
- </li>
- <li>
- <!-- JAL-2388 -->Hidden columns and sequences can be
- omitted in Overview
- </li>
- <li>
- <!-- JAL-2611 -->Click-drag in visible area allows fine
- adjustment of visible position
- </li>
- </ul>
-
- <em>Data import/export</em>
- <ul>
- <li>
- <!-- JAL-2535 -->Posterior probability annotation from
- Stockholm files imported as sequence associated annotation
- </li>
- <li>
- <!-- JAL-2507 -->More robust per-sequence positional
- annotation input/output via stockholm flatfile
- </li>
- <li>
- <!-- JAL-2533 -->Sequence names don't include file
- extension when importing structure files without embedded
- names or PDB accessions
- </li>
- <li>
- <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
- format sequence substitution matrices
- </li>
- </ul>
- <em>User Interface</em>
- <ul>
- <li>
- <!-- JAL-2447 --> Experimental Features Checkbox in
- Desktop's Tools menu to hide or show untested features in
- the application.
- </li>
- <li>
- <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
- via Overview or sequence motif search operations
- </li>
- <li>
- <!-- JAL-2547 -->Amend sequence features dialog box can be
- opened by double clicking gaps within sequence feature
- extent
- </li>
- <li>
- <!-- JAL-1476 -->Status bar message shown when not enough
- aligned positions were available to create a 3D structure
- superposition.
- </li>
- </ul>
- <em>3D Structure</em>
- <ul>
- <li>
- <!-- JAL-2430 -->Hidden regions in alignment views are not
- coloured in linked structure views
- </li>
- <li>
- <!-- JAL-1596 -->Faster Chimera/Jalview communication by
- file-based command exchange
- </li>
- <li>
- <!-- 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>
- <li>
- <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
- to transfer Chimera's structure attributes as Jalview
- features, and vice-versa (<strong>Experimental
- Feature</strong>)
- </li>
- </ul>
- <em>Web Services</em>
- <ul>
- <li>
- <!-- JAL-2549 -->Updated JABAWS client to v2.2
- </li>
- <li>
- <!-- JAL-2335 -->Filter non-standard amino acids and
- nucleotides when submitting to AACon and other MSA
- Analysis services
- </li>
- <li>
- <!-- JAL-2316, -->URLs for viewing database
- cross-references provided by identifiers.org and the
- EMBL-EBI's MIRIAM DB
- </li>
- </ul>
-
- <em>Scripting</em>
- <ul>
- <li>
- <!-- JAL-2344 -->FileFormatI interface for describing and
- identifying file formats (instead of String constants)
- </li>
- <li>
- <!-- JAL-2228 -->FeatureCounter script refactored for
- efficiency when counting all displayed features (not
- backwards compatible with 2.10.1)
- </li>
- </ul>
- <em>Example files</em>
- <ul>
- <li>
- <!-- JAL-2631 -->Graduated feature colour style example
- included in the example feature file
- </li>
- </ul>
- <em>Documentation</em>
- <ul>
- <li>
- <!-- JAL-2339 -->Release notes reformatted for readability
- with the built-in Java help viewer
- </li>
- <li>
- <!-- JAL-1644 -->Find documentation updated with 'search
- sequence description' option
- </li>
- </ul>
- <em>Test Suite</em>
- <ul>
- <li>
- <!-- JAL-2485, -->External service integration tests for
- Uniprot REST Free Text Search Client
- </li>
- <li>
- <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
- </li>
- <li>
- <!-- JAL-2326 -->Prevent or clear modal dialogs raised
- during tests
- </li>
- </ul>
- </div></td>
- <td><div align="left">
- <em>Calculations</em>
- <ul>
- <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><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
- Jalview's treatment of gaps in PCA and substitution matrix
- based Tree calculations.<br /> <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). <br /> <br />Enter the following in the
- Groovy console to restore pre-2.10.2 behaviour:<br />
- jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
- // for 2.10.1 mode <br />
- jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
- // to restore 2.10.2 mode <br /> <br /> <em>Note:
- these settings will affect all subsequent tree and PCA
- calculations (not recommended)</em></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-2377 -->PCA calculation could hang when
- generating output report when working with highly
- redundant alignments
- </li>
- <li>
- <!-- JAL-2544 --> Sort by features includes features to
- right of selected region when gaps present on right-hand
- boundary
- </li>
- </ul>
- <em>User Interface</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-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-2386 -->'Apply to all groups' setting when
- changing colour does not apply Conservation slider value
- to all groups
- </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-2623 -->Graduated feature colour threshold not
- restored to UI when feature colour is edited
- </li>
- <li>
- <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
- a time when scrolling vertically in wrapped mode.
- </li>
- <li>
- <!-- JAL-2630 -->Structure and alignment overview update
- as graduate feature colour settings are modified via the
- dialog box
- </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 doesn't show position for
- ambiguous amino acid and nucleotide symbols
- </li>
- <li>
- <!-- JAL-2602 -->Copy consensus sequence failed if
- alignment included gapped columns
- </li>
- <li>
- <!-- JAL-2473 -->Minimum size set for Jalview windows so
- widgets don't permanently disappear
- </li>
- <li>
- <!-- 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-2594 -->Exception thrown if trying to create a
- sequence feature on gaps only
- </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-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-2291 -->Hide insertions in PopUp->Selection menu
- only excluded gaps in current sequence and ignored
- selection.
- </li>
- </ul>
- <em>Rendering</em>
- <ul>
- <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-2385 -->Colour threshold slider doesn't update to
- reflect currently selected view or group's shading
- thresholds
- </li>
- <li>
- <!-- JAL-2624 -->Feature colour thresholds not respected
- when rendered on overview and structures when opacity at
- 100%
- </li>
- <li>
- <!-- JAL-2589 -->User defined gap colour not shown in
- overview when features overlaid on alignment
- </li>
- <li>
- <!-- JAL-2567 -->Feature settings for different views not
- recovered correctly from Jalview project file
- </li>
- <li>
- <!-- JAL-2256 -->Feature colours in overview when first opened
- (automatically via preferences) are different to the main
- alignment panel
- </li>
- </ul>
- <em>Data import/export</em>
- <ul>
- <li>
- <!-- JAL-2576 -->Very large alignments take a long time to
- load
- </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-2365,JAL-2642 -->Cannot configure feature colours
- with lightGray or darkGray via features file (but can
- specify lightgray)
- </li>
- <li>
- <!-- JAL-2383 -->Above PID colour threshold not recovered
- when alignment view imported from project
- </li>
- <li>
- <!-- 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
- Jalview Projects rather than fetched via URL again when
- the project is loaded and the structure viewed
- </li>
- </ul>
- <em>Web Services</em>
- <ul>
- <li>
- <!-- JAL-2519 -->EnsemblGenomes example failing after
- release of Ensembl v.88
- </li>
- <li>
- <!-- JAL-2366 -->Proxy server address and port always
- appear enabled in Preferences->Connections
- </li>
- <li>
- <!-- JAL-2461 -->DAS registry not found exceptions
- removed from console output
- </li>
- <li>
- <!-- JAL-2582 -->Cannot retrieve protein products from
- Ensembl by Peptide ID
- </li>
- <li>
- <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
- created from SIFTs, and spurious 'Couldn't open structure
- in Chimera' errors raised after April 2017 update (problem
- due to 'null' string rather than empty string used for
- residues with no corresponding PDB mapping).
- </li>
- </ul>
- <em>Application UI</em>
- <ul>
- <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)
- </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-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>
- <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-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-2431 -->cDNA Consensus annotation not shown in
- CDS/Protein view after CDS sequences added for aligned
- proteins
- </li>
- <li>
- <!-- JAL-2592 -->User defined colourschemes called 'User
- Defined' don't appear in Colours menu
- </li>
- </ul>
- <em>Applet</em>
- <ul>
- <li>
- <!-- JAL-2468 -->Switching between Nucleotide and Protein
- score models doesn't always result in an updated PCA plot
- </li>
- <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>Test Suite</em>
- <ul>
- <li>
- <!-- JAL-2314 -->Unit test failure:
- jalview.ws.jabaws.RNAStructExportImport setup fails
- </li>
- <li>
- <!-- 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>
- <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>
- <li>
- <!-- JAL-2590 -->Cannot load and display Newick trees
- reliably from eggnog Ortholog database
- </li>
- <li>
- <!-- JAL-2468 -->Status bar shows 'Marked x columns
- containing features of type Highlight' when 'B' is pressed
- to mark columns containing highlighted regions.
- </li>
- <li>
- <!-- JAL-2321 -->Dropping a PDB file onto a sequence
- doesn't always add secondary structure annotation.
- </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">
- <em>General</em>
- <ul>
- <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-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>
- </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>Application</em>
- <ul>
- <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>
- <ul>
- <li></li>
- </ul> -->
- </div>
+
+ <td class="release" align="center" valign="top" nowrap>
+ <strong>2.10<a id="Jalview.2.10.3">.3</a></strong>
+ <br />
+ <em>17/11/2017</em>
+ </td>
+ <td class="new_features" align="left" valign="top">
+<ul>
+<li>Faster and more efficient management and rendering of sequence features <!-- JAL-2446 --></li>
+<li>More reliable Ensembl fetching with HTTP 429 rate limit request hander <!-- JAL 2523--></li>
+<li>Structure views don't get updated unless their colours have changed <!-- JAL-2773 --></li>
+<li>All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera) <!-- JAL-2495 --></li>
+<li>'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs <!-- JAL-2790 --></li>
+<li>Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references <!-- JAL-2617 --></li>
+<li>Start/End limits are shown in Pairwise Alignment report <!-- JAL-2685 --></li>
+<li>Sequence fetcher's Free text 'autosearch' feature can be disabled <!-- JAL-2810 --></li>
+<li>Retrieve IDs tab added for UniProt and PDB easier retrieval of sequences for lists of IDs <!-- JAL-2810 --></li>
+<li>Short names for sequences retrieved from Uniprot <!-- JAL-2758 --></li>
+</ul>
+<p><em>Scripting</em></p>
+<ul>
+<li>Groovy interpreter updated to 2.4.12</li>
+<li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li>
+</ul>
+<p><em>Testing and Deployment</em></p>
+<ul>
+<li>Test to catch memory leaks in Jalview UI <!-- JAL-2727 --></li>
+</ul>
+
+ </td>
+ <td class="issues_resolved" align="left" valign="top">
+<p><em>General</em></p>
+<ul>
+<li>Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view <!-- JAL-2643 --></li>
+<li>Race condition when parsing sequence ID strings in parallel <!-- JAL-2682 --></li>
+<li>Overview windows are also closed when alignment window is closed <!-- JAL-2608 --></li>
+<li>Export of features doesn't always respect group visibility <!-- JAL-2548 --></li>
+<li>Jumping from column 1 to column 100,000 takes a long time in Cursor mode <!-- JAL-2831 --></li>
+</ul>
+<p><em>Desktop</em></p>
+<ul>
+<li>Structures with whitespace chainCode cannot be viewed in Chimera <!-- JAL-2777 --></li>
+<li>Protein annotation panel too high in CDS/Protein view <!-- JAL-2728 --></li>
+<li>Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs <!-- JAL-2757 --></li>
+<li>Slow EnsemblGenome ID lookup <!-- JAL-2253 --></li>
+<li>Revised Ensembl REST API CDNA query <!-- JAL-2529 --></li>
+<li>Hidden column marker in last column not rendered when switching back from Wrapped to normal view <!-- JAL-2739 --></li>
+<li>Annotation display corrupted when scrolling right in unwapped alignment view <!-- JAL-2768 --></li>
+<li>Existing features on subsequence incorrectly relocated when full sequence retrieved from database <!-- JAL-2542 --></li>
+<li>Last reported memory still shown when Desktop->Show Memory is unticked (OSX only) <!-- JAL-2733 --></li>
+<li>Amend Features dialog doesn't allow features of same type and group to be selected for amending <!-- JAL-2658 --></li>
+<li>Jalview becomes sluggish in wide alignments when hidden columns are present <!-- JAL-2524 --></li>
+<li>Jalview freezes when loading and displaying several structures <!-- JAL-2392 --></li>
+<li>Black outlines left after resizing or moving a window <!-- JAL-2732 --></li>
+<li>Unable to minimise windows within the Jalview desktop on OSX <!-- JAL-1900,JAL-1625 --></li>
+<li>Mouse wheel doesn't scroll vertically when in wrapped alignment mode <!-- JAL-2667 --></li>
+<li>Scale mark not shown when close to right hand end of alignment <!-- JAL-2636 --></li>
+<li>Pairwise alignment of selected regions of each selected sequence do not have correct start/end positions <!-- JAL-2684 --></li>
+<li>Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog <!-- JAL-2793 --></li>
+<li>Show cross-references not enabled after restoring project until a new view is created <!-- JAL-2036 --></li>
+<li>Warning popup about use of SEQUENCE_ID in URL links appears when only default EMBL-EBI link is configured (since 2.10.2b2) <!-- JAL-2756 --></li>
+<li>Overview redraws whole window when box position is adjusted <!-- JAL-2775 --></li>
+<li>Structure viewer doesn't map all chains in a multi-chain structure when viewing alignment involving more than one chain (since 2.10) <!-- JAL-2225 --></li>
+<li>Double residue highlights in cursor mode if new selection moves alignment window <!-- JAL-2811 --></li>
+<li>Alignment vanishes when using arrow key in cursor mode to pass hidden column marker <!-- JAL-2837,JAL-2840 --></li>
+<li>Ensembl Genomes example ID changed to one that produces correctly annotated transcripts and products <!-- JAL-2679 --></li>
+<li>Toggling a feature group after first time doesn't update associated structure view <!-- JAL-2776 --></li>
+</ul>
+<p><em>Applet</em></p>
+<ul>
+<li>Concurrent modification exception when closing alignment panel <!-- JAL-2687 --></li>
+</ul>
+<p><em>BioJSON</em></p>
+<ul>
+<li>BioJSON export does not preserve non-positional features <!-- JAL-2546 --></li>
+</ul>
+<p><em>New Known Issues</em></p>
+<ul>
+<li>Delete/Cut selection doesn't relocate sequence features correctly (for many previous versions of Jalview) <!-- JAL-2541 --></li>
+<li>Cursor mode unexpectedly scrolls when using cursor in wrapped panel other than top <!-- JAL-2841 --></li>
+<li>Select columns containing feature ignores graduated colour threshold <!-- JAL-2791 --></li>
+<li>Edit sequence operation doesn't always preserve numbering and sequence features <!-- JAL-2822,JAL-2823 --></li>
+</ul>
+<p><em>Known Java 9 Issues</em></p>
+<ul>
+<li>Groovy Console very slow to open and is not responsive when entering characters (Webstart, Java 9.01, OSX 10.10) <!-- JAL-2902 --></li>
+</ul>
+