+ <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>
+ <li>
+ <!-- JAL-1933 -->Occupancy annotation row shows number of
+ ungapped positions in each column of the alignment.
+ </li>
+ <li>
+ <!-- JAL-1476 -->Status bar message shown when not enough
+ aligned positions were available to create a 3D structure
+ superposition.
+ </li>
+ </ul>
+ <em>Application</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-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>
+ <li>
+ <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
+ 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
+ </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>
+ <ul>
+ <li>
+ <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
+ </li>
+ <li>
+ <!-- JAL-2326 -->Prevent or clear modal dialogs raised
+ during tests
+ </li>
+ <li>
+ <!-- --> <em>Scripting</em>
+ <ul>
+ <li>
+ <!-- JAL-2344 -->FileFormatI interface for describing
+ and identifying file formats (instead of String
+ constants)
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+
+
+ </ul>
+ </ul>
+ </div></td>
+ <td><div align="left">
+ <em>General</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>
+ <!-- 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-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>
+ <li>
+ <!-- JAL-2602 -->Copy consensus sequence failed if
+ alignment included gapped columns
+ </li>
+ <li>
+ <!-- JAL-2589 -->User defined gap colour not shown in
+ overview when features overlaid on alignment
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ </ul>
+ <strong>Documentation</strong>
+ <ul>
+ <li>
+ <!-- JAL-2339 -->Release notes reformatted for readibility
+ with the built-in Java help viewer
+ </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>
+ <li>
+ <!-- JAL-2582 -->Cannot retrieve protein products from
+ Ensembl by Peptide ID
+ </li>
+ <li>
+ <!-- JAL-2431 -->cDNA Consensus annotation not shown in
+ CDS/Protein view after CDS sequences added for aligned
+ proteins
+ </li>
+ <li>
+ <!-- JAL-2431 -->cDNA Consensus not shown
+ </li>
+
+
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <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>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 Newick trees from eggnog
+ ortholog database
+ </li>
+ </ul>
+ <em>Test Suite</em>
+ <ul>
+ <li>
+ <!-- JAL-2314 -->Unit test failure:
+ jalview.ws.jabaws.RNAStructExportImport setup fails
+ </li>
+ <li>
+ <!-- JAL- -->
+ </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>
+ </tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
+ <em>25/10/2016</em></strong>
+ </div>
+ </td>
+ <td><em>Application</em>
+ <ul>
+ <li>3D Structure chooser opens with 'Cached structures'
+ view if structures already loaded</li>
+ <li>Progress bar reports models as they are loaded to
+ structure views</li>
+ </ul></td>
+ <td>
+ <div align="left">
+ <em>General</em>