- <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>2.11<a id="Jalview.2.11.0">.0</a></strong>
+ <br />
+ <em>04/07/2019</em>
+ </td>
+ <td class="new_features" align="left" valign="top">
+<ul>
+<li>Jalview Native Application and Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open source project) rather than InstallAnywhere <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 --></li>
+<li>Jalview Launcher System to auto-configure memory settings, receive over the air updates and launch specific versions via (<a href="https://github.com/threerings/getdown">Three Rings' GetDown</a>) <!-- JAL-1929 --></li>
+<li>File type associations for formats supported by Jalview (including .jvp project files) <!-- JAL-1839,JAL-3254,JAL-3260 --></li>
+<li>Jalview launch files (.jvl) to pass command line arguments and switch between different getdown channels <!-- JAL-3260 --></li>
+<li>Backup files created when saving Jalview project or alignment files <!-- JAL-3141 --></li>
+<li>Annotate nucleotide alignments from VCF data files <!-- JAL-1793 --></li>
+<li>Version of HTSJDK shipped with Jalview updated to version 2.12.0 <!-- JAL-2753 --></li>
+<li>Alternative genetic code tables for 'Translate as cDNA' <!-- JAL-2620 --></li>
+<li>Update of Ensembl Rest Client to API v10.0 <!-- JAL-3018 --></li>
+<li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
+<ul>
+<li>IntervalStoreJ (NCList implementation that allows updates) used for Sequence Feature collections <!-- JAL-3140 JAL-2446 --></li>
+<li>Sequence features can be filtered and shaded according to any associated attributes (e.g. variant attributes from VCF file, or key-value pairs imported from column 9 of GFF file) <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 --></li>
+<li>Feature Attributes and shading schemes stored and restored from Jalview Projects <!-- JAL-2879 --></li>
+<li>Use full Sequence Ontology (via BioJava) to recognise variant features <!-- JAL-3334 --></li>
+<li>Show synonymous codon variants on peptide sequences (also coloured red by default) <!-- JAL-2897,JAL-3330 --></li>
+<li>Popup window to show full report for a selected sequence feature's details <!-- JAL-2792 --></li>
+<li>More efficient sequence feature render algorithm (Z-sort/transparency and filter aware) <!-- JAL-3139,JAL-2816,JAL-1117 --></li>
+<li>Improved tooltips in Feature Settings dialog <!-- JAL-3049,JAL-3054 --></li>
+</ul>
+</li>
+<li>Symmetric score matrices for faster tree and PCA calculations <!-- JAL-3205 --></li>
+<li><strong>Principal Components Analysis Viewer</strong>
+<ul>
+<li>Principal Components Analysis results and Viewer state saved in Jalview Project <!-- JAL-1767,JAL-2647 --></li>
+<li>'Change parameters' option removed from viewer's drop-down menus <!-- JAL-2962 --></li>
+<li>Can use shift + arrow keys to rotate PCA image incrementally <!-- JAL-2975 --></li>
+<li>PCA plot is depth cued <!-- JAL-2965, JAL-1285 --></li>
+</ul>
+</li>
+<li>New 'Colour by Sequence ID' option <!-- JAL-3127 --></li>
+<li><strong>Speed and Efficiency</strong>
+<ul>
+<li>More efficient creation of selections and multiple groups when working with large alignments <!-- JAL-2185,JAL-3198 --></li>
+<li>Speedier import of annotation rows when parsing Stockholm files <!-- JAL-3200 --></li>
+</ul>
+</li>
+<li><strong>User Interface</strong>
+<ul>
+<li>Finder panel remembers last position in each view <!-- JAL-2933 --></li>
+<li>Alignment Overview now WYSIWIS (What you see is what is shown)<br/> <!-- JAL-2527 JAL-3203 -->
+Only visible regions of alignment are shown by default (can be changed in user preferences)</li>
+<li>File Chooser stays open after responding Cancel to the Overwrite Dialog <!-- JAL-3169 --></li>
+<li>Better popup menu behaviour when all sequences are hidden <!-- JAL-2420,JAL-3166 --></li>
+<li>Status bar shows bounds when dragging a selection region, and gap count when inserting or deleting gaps <!-- JAL-1244 --></li>
+<li>Status bar updates over sequence and annotation labels <!-- JAL-3132 --></li>
+<li>Annotation tooltips and popup menus are shown when in wrapped mode <!-- JAL-3093 --></li>
+<li>Can select columns by dragging left/right in a graph or histogram annotation <!-- JAL-3073 --></li>
+<li>Help button on Uniprot and PDB search panels <!-- JAL-2814,JAL-437 --></li>
+<li>Cursor changes over draggable box in Overview panel <!-- JAL-2621 --></li>
+<li>Consistent ordering of links in sequence id popup menu <!-- JAL-3181 --></li>
+<li>Red line indicating tree-cut position not shown if no subgroups are created <!-- JAL-3080 --></li>
+<li>Removed ability to configure length of search history by right-clicking search box <!-- JAL-3042 --></li>
+</ul>
+</li>
+<li>Jalview Groovy Scripting Console updated to Groovy v2.5 <!-- JAL-3232 --></li>
+<li><strong>Java 11 Support (not yet on general release)</strong>
+<ul>
+<li>OSX GUI integrations for App menu's 'About' entry and trapping CMD-Q <!-- --></li>
+</ul>
+</li>
+</ul>
+<p><em>Deprecations</em></p>
+<ul>
+<li>DAS sequence retrieval and annotation capabilities removed from the Jalview Desktop <!-- JAL-3035 --></li>
+<li>Castor library for XML marshalling and unmarshalling has been replaced by JAXB for Jalview projects and XML based data retrieval clients <!-- JAL-3063,JAL-3116 --></li>
+<li>Disable VAMSAS menu in preparation for removal <!-- JAL-3311 --></li>
+<li>Jalview Desktop no longer distributed via Java Web Start <!-- --></li>
+</ul>
+<p><em>Documentation</em></p>
+<ul>
+<li>Added remarks about transparent rendering effects not supported in EPS figure export <!-- JAL-3003 --></li>
+<li>Typos in documentation for Preferences dialog <!-- JAL-2903 --></li>
+</ul>
+<p><em>Development and Release Processes</em></p>
+<ul>
+<li>Build system migrated from Ant to Gradle <!-- JAL-3196,JAL-3179.JAL-2671 --></li>
+<li>Enhanced checks for missing and duplicated keys in Message bundles <!-- JAL-1424 --></li>
+<li>Eclipse project configuration managed with gradle-eclipse <!-- JAL-3225 --></li>
+<li>Atlassian Bamboo continuous integration for unattended Test Suite execution <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 --></li>
+<li>Memory test suite to detect leaks in common operations <!-- JAL-2864 --></li>
+<li>More unit test coverage, and minor issues resolved <!-- JAL-2360,JAL-2416 --></li>
+<li>Developer documentation migrated to markdown (with HTML rendering) <!-- JAL-3248 --></li>
+<li>HelpLinksChecker runs on Windows <!-- JAL-3287 --></li>
+<li>New URLs for publishing development versions of Jalview <!-- JAL-3289 --></li>
+</ul>
+
+ </td>
+ <td class="issues_resolved" align="left" valign="top">
+<ul>
+<li>Timeouts when retrieving data from Ensembl <!-- JAL-3143 --></li>
+<li>'View [Structure] Mappings' and structure superposition in Jmol fail on Windows <!-- JAL-3244 --></li>
+<li>Blank error dialog is displayed when discovering structures for sequences with lots of PDB structures <!-- JAL-3286 --></li>
+<li>Text misaligned in EPS or SVG image export with monospaced font <!-- JAL-3239 --></li>
+<li>Warning of 'Duplicate entry' when saving Jalview project involving multiple views <!-- JAL-3171 --></li>
+<li>Overview for complementary view in a linked CDS/Protein alignment is not updated when Hide Columns by Annotation dialog hides columns <!-- JAL-3164 --></li>
+<li>Selection highlighting in the complement of a CDS/Protein alignment stops working after making a selection in one view, then making another selection in the other view <!-- JAL-3158 --></li>
+<li>Annotations tooltip changes beyond visible columns <!-- JAL-3161 --></li>
+<li>Table Columns could be re-ordered in Feature Settings and Jalview Preferences panels <!-- JAL-3154 --></li>
+<li>Jalview hangs when closing windows, or redrawing the overview with large alignments <!-- JAL-2865 --></li>
+<li>Tree and PCA calculation fails for selected region if columns were selected by dragging right-to-left and the mouse moved to the left of the first column <!-- JAL-2750 --></li>
+<li>Couldn't hide selected columns adjacent to a hidden column marker via scale popup menu <!-- JAL-3218 --></li>
+<li>Error message for trying to load in invalid URLs doesn't tell users the invalid URL <!-- JAL-2846 --></li>
+<li>Tooltips displayed for features filtered by score from view <!-- JAL-2816 --></li>
+<li>Sequence Variants retrieved from Ensembl during show cross references or Fetch Database References are shown in red in original view <!-- JAL-3330 --></li>
+<li>stop_gained variants not shown correctly on peptide sequence (computed variant shown as p.Res.null) <!-- JAL-2898,JAL-2207 --></li>
+<li>'Graduated colour' option not offered for manually created features (where feature score is Float.NaN) <!-- JAL-2060 --></li>
+<li>Blank extra columns drawn or printed when columns are hidden <!-- JAL-3097,JAL-3099 --></li>
+<li>Regular expression error for '(' in Select Columns by Annotation description <!-- JAL-3082 --></li>
+<li>Scroll doesn't stop on mouse up after dragging out of Scale or Annotation Panel <!-- JAL-3072 --></li>
+<li>Column selection incorrect after scrolling out of scale panel <!-- JAL-3075 --></li>
+<li>Left/right drag in annotation can scroll alignment down <!-- JAL-3074 --></li>
+<li>Error if mouse moved before clicking Reveal in scale panel <!-- JAL-3108 --></li>
+<li>Column display is out by one after Page Down, Page Up in wrapped mode <!-- JAL-3002 --></li>
+<li>Finder doesn't skip hidden regions <!-- JAL-2839,JAL-781 --></li>
+<li>Finder searches in minimised alignments <!-- JAL-2932 --></li>
+<li>'Apply Colour to All Groups' not always selected on opening an alignment <!-- JAL-2250 --></li>
+<li>'Colour by Annotation' not marked selected in Colour menu <!-- JAL-3180 --></li>
+<li>Per-group Clustal colour scheme changes when different groups in the alignment are selected <!-- JAL-3201 --></li>
+<li>Internationalised colour scheme names not shown correctly in menu <!-- JAL-2717 --></li>
+<li>Colour by Annotation can go black at min/max threshold limit <!-- JAL-3206 --></li>
+<li>Value input for graduated feature colour threshold gets 'unrounded' <!-- JAL-3125 --></li>
+<li>PCA image export doesn't respect background colour <!-- JAL-2982 --></li>
+<li>PCA points don't dim when rotated about y axis <!-- JAL-2963 --></li>
+<li>PCA Print dialog continues after Cancel <!-- JAL-2959 --></li>
+<li>Cancel in Tree Font dialog resets alignment, not Tree font <!-- JAL-3078 --></li>
+<li>Associate Tree with All Views not restored from project file <!-- JAL-2964 --></li>
+<li>Scrolling of split frame is sluggish if Overview shown in complementary view <!-- JAL-2915 --></li>
+<li>Codon consensus incorrectly scaled when shown without normalisation <!-- JAL-3313 --></li>
+<li>Sequence Details report should open positioned at top of report <!-- JAL-3021 --></li>
+<li>Help page can be opened twice <!-- JAL-914 --></li>
+<li>Fuzzy text in web service status menu on OSX Mojave <!-- JAL-3333 --></li>
+</ul>
+<p><em>Editing</em></p>
+<ul>
+<li>Start and End should be updated when sequence data at beginning or end of alignment added/removed via 'Edit' sequence <!-- JAL-2822 --></li>
+<li>Delete/Cut selection doesn't relocate sequence features correctly when start of sequence is removed (Known defect since 2.10) <!-- JAL-2541,JAL-2684 (tests) --></li>
+<li>Inserting gap sequence via the Edit Sequence dialog corrupts dataset sequence <!-- JAL-2830 --></li>
+<li>Structure colours not updated when associated tree repartitions the alignment view (Regression in 2.10.5) <!-- JAL-868 --></li>
+</ul>
+<p><em>Datamodel</em></p>
+<ul>
+<li>Sequence.findIndex returns wrong value when sequence's End is greater than its length <!-- JAL-2986 --></li>
+</ul>
+<p><em>Bugs fixed for Java 11 Support (not yet on general release)</em></p>
+<ul>
+<li>Menus work properly in split-screen <!-- JAL-3288 --></li>
+</ul>
+<p><em>New Known Defects</em></p>
+<ul>
+<li>Select columns containing feature by double clicking ignores bounds of an existing selected region <!-- JAL-3340 --></li>
+<li>Codon consensus logo incorrectly scaled in gapped regions of protein alignment. <!-- JAL-3313 --></li>
+<li>Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project <!-- JAL-2647 --></li>
+<li>Alignment panel height can be too small after 'New View' <!-- JAL-3213 --></li>
+<li>Display is incorrect after removing gapped columns within hidden columns <!-- JAL-3240 --></li>
+<li>Rightmost selection is lost when mouse re-enters window after dragging left to select columns to left of visible region <!-- JAL-3314 --></li>
+<li>Features coloured according to their description string and thresholded by score in earlier versions of Jalview are not shown as thresholded features in 2.11. To workaround please create a Score filter instead. <!-- JAL-2876 --></li>
+<li>Cancel on Feature Settings dialog doesn't reset group visibility <!-- JAL-3184 --></li>
+<li>F2 doesn't enable/disable keyboard mode in linked CDS/Protein view <!-- JAL-3338 --></li>
+<li>Closing tree windows with CMD/CTRL-W for alignments with multiple views can close views unexpectedly <!-- JAL-797 --></li>
+</ul>
+<p><em>Java 11 Specific defects</em></p>
+<ul>
+<li>Jalview Properties file is not sorted alphabetically when saved <!-- JAL-3235 --></li>
+</ul>
+