-->
<head>
<title>Release History</title>
+<style>
+ul {
+ /* remove bullets, narrower indent */
+ list-style-type: none;
+ margin: 0;
+ padding-left: 10px;
+ padding-bottom: 4px;
+}
+
+li {
+ /* separate the items from eachother */
+ margin-left: -3px;
+ padding-bottom: 3px;
+ padding-left: 6px;
+}
+
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+ /* doesnt get processed in javahelp */
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+</style>
</head>
<body>
<p>
<tr>
<td width="60" nowrap>
<div align="center">
- <strong><a name="Jalview.2.10.1">2.10.1</a><br />
- <em>24/11/2016</em></strong>
+ <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
+ <em>TBA</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 -->Updated Jmol shipped with applet and desktop to 14.6.4</li>
- <li><!-- --></li>
-
+ <em></em>
+ <ul>
</ul>
- <em>Application</em>
+ </div></td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ </ul>
+ </div></td>
+
+ <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-1723 -->Sequence ID tool tips have been tamed (databases sorted alphabetically, abridged ID sets) </li>
- <li><!-- JAL-2282-->New replacement token for creating URLs <em>just</em> from database cross references. Users with custom links will receive a warning dialog 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-2281-->Custom URL links for database cross-references are matched to database name regardless of case</li>
- <li><!-- JAL-1738-->Select highlighted columns menu item and keystroke (B) to mark columns containing highlighted regions 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>
-
+ <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>Applet</em>
+ <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>Build and deployment</em>
+ <em>Overview</em>
<ul>
- <li></li>
+ <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>
- </div>
- </td>
- <td>
- <div align="left">
- <em>General</em>
+
+ <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-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-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>Application</em>
+ <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-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-2335 -->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-2197 -->Rename UI components for running JPred predictions from 'JNet' to 'JPred'</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-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- --></li>
-
- <li><!-- --></li>
- <li><!-- --></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>
+ </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>Build and deployment</em>
+ <em>Test Suite</em>
<ul>
- <li><!-- JAL-2308, -->Failing/passing unit tests</li>
+ <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></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 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>
- </td>
- </tr>
+ </div><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>
+ <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</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">
+ <td><div align="left">
<em>General</em>
<ul>
- <li>Colour by conservation always enabled and no tick
- shown in menu when BLOSUM or PID shading applied</li>
- <li>FER1_ARATH and FER2_ARATH labels were switched in
- example sequences/projects/trees</li>
+ <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>Jalview projects with views of local PDB structure
- files saved on Windows cannot be opened on OSX</li>
- <li>Multiple structure views can be opened and
- superposed without timeout for structures with multiple
- models or multiple sequences in alignment</li>
- <li>Cannot import or associated local PDB files without
- a PDB ID HEADER line</li>
- <li>RMSD is not output in Jmol console when
- superposition is performed</li>
- <li>Drag and drop of URL from Browser fails for Linux
- and OSX versions earlier than El Capitan</li>
- <li>ENA client ignores invalid content from ENA server</li>
- <li>Exceptions are not raised in console when ENA
- client attempts to fetch non-existent IDs via Fetch DB
- Refs UI option</li>
- <li>Exceptions are not raised in console when a new
- view is created on the alignment</li>
- <li>OSX right-click fixed for group selections:
- CMD-click to insert/remove gaps in groups and CTRL-click
- to open group pop-up menu</li>
+ <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>
- <em>Build and deployment</em>
+ </div></td>
+ <td>
+ <div align="left">
+ <em>General</em>
<ul>
- <li>URL link checker now copes with multi-line anchor
- tags</li>
+ <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>New Known Issues</em>
+ <em>Application</em>
<ul>
- <li>Drag and drop from URL links in browsers do not
- work on Windows</li>
+ <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>
+ <ul>
+ <li>Colour by conservation always enabled and no tick
+ shown in menu when BLOSUM or PID shading applied</li>
+ <li>FER1_ARATH and FER2_ARATH labels were switched in
+ example sequences/projects/trees</li>
+ </ul>
+ <em>Application</em>
+ <ul>
+ <li>Jalview projects with views of local PDB structure
+ files saved on Windows cannot be opened on OSX</li>
+ <li>Multiple structure views can be opened and superposed
+ without timeout for structures with multiple models or
+ multiple sequences in alignment</li>
+ <li>Cannot import or associated local PDB files without a
+ PDB ID HEADER line</li>
+ <li>RMSD is not output in Jmol console when superposition
+ is performed</li>
+ <li>Drag and drop of URL from Browser fails for Linux and
+ OSX versions earlier than El Capitan</li>
+ <li>ENA client ignores invalid content from ENA server</li>
+ <li>Exceptions are not raised in console when ENA client
+ attempts to fetch non-existent IDs via Fetch DB Refs UI
+ option</li>
+ <li>Exceptions are not raised in console when a new view
+ is created on the alignment</li>
+ <li>OSX right-click fixed for group selections: CMD-click
+ to insert/remove gaps in groups and CTRL-click to open group
+ pop-up menu</li>
+ </ul>
+ <em>Build and deployment</em>
+ <ul>
+ <li>URL link checker now copes with multi-line anchor
+ tags</li>
+ </ul>
+ <em>New Known Issues</em>
+ <ul>
+ <li>Drag and drop from URL links in browsers do not work
+ on Windows</li>
+ </ul>
+ </div>
+ </td>
+ </tr>
<tr>
<td width="60" nowrap>
<div align="center">
<td><em>General</em>
<ul>
<li>
- <!-- JAL-2124 -->Updated Spanish translations.
- </li>
+ <!-- JAL-2124 -->Updated Spanish translations.
+ </li>
<li>
<!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
for importing structure data to Jalview. Enables mmCIF and
load even when Consensus calculation is disabled
</li>
<li>
- <!-- JAL-1932 -->Remove right on penultimate column of
+ <!-- JAL-1932 -->Remove right on penultimate column of
alignment does nothing
</li>
</ul>
</li>
<li>
<!-- JAL-2036 -->Enable 'Get Cross-References' in menu
- after fetching cross-references, and restoring from project
+ after fetching cross-references, and restoring from
+ project
</li>
<li>
<!-- JAL-2032 -->Mouseover of a copy of a sequence is not
<!-- JAL-2284 -->Unable to read old Jalview projects that
contain non-XML data added after Jalvew wrote project.
</li>
- <li><!-- JAL-2118 -->Newly created annotation row reorders
+ <li>
+ <!-- JAL-2118 -->Newly created annotation row reorders
after clicking on it to create new annotation for a
column.
</li>
</ul> <em>Applet</em>
<ul>
<li>Split frame example added to applet examples page</li>
- </ul><em>Build and Deployment</em>
+ </ul> <em>Build and Deployment</em>
<ul>
- <li><!-- JAL-1888 -->New ant target for running Jalview's test suite</li>
+ <li>
+ <!-- JAL-1888 -->New ant target for running Jalview's test
+ suite
+ </li>
</ul></td>
<td>
<div align="left">
</li>
</ul> <!-- <em>Applet</em>
- <ul>
- </ul> <em>General</em>
- <ul>
- </ul>--> <em>Deployment and Documentation</em>
+ <ul>
+ </ul> <em>General</em>
+ <ul>
+ </ul>--> <em>Deployment and Documentation</em>
<ul>
<li>2G and 1G options in launchApp have no effect on
memory allocation</li>
<a href="https://www.certum.eu">Certum</a> to the Jalview
open source project).
</li>
- <li>Jalview SRS links replaced by UniProt and EBI-search
- </li>
+ <li>Jalview SRS links replaced by UniProt and EBI-search</li>
<li>Output in Stockholm format</li>
<li>Allow import of data from gzipped files</li>
<li>Export/import group and sequence associated line
<ul>
<li>URL links generated from description line for
regular-expression based URL links (applet and application)
-
-
-
-
-
<li>Non-positional feature URL links are shown in link
menu</li>
<li>Enable or disable non-positional feature and database
references in sequence ID tooltip from View menu in
application.</li>
- <!-- <li>New hidden columns and rows and representatives capabilities
- in annotations file (in progress - not yet fully implemented)</li> -->
+ <!-- <li>New hidden columns and rows and representatives capabilities
+ in annotations file (in progress - not yet fully implemented)</li> -->
<li>Group-associated consensus, sequence logos and
conservation plots</li>
<li>Symbol distributions for each column can be exported
<li>Cancel button for DAS Feature Fetching
<li>PCA and PDB Viewers zoom via mouse roller
<li>User-defined sub-tree colours and sub-tree selection
-
-
-
-
-
<li>'New Window' button on the 'Output to Text box'
</ul>
<li>Fixed Remove Empty Columns Bug (empty columns at end
of alignment)
<li>Slowed DAS Feature Fetching for increased robustness.
-
-
-
-
-
<li>Made angle brackets in ASCII feature descriptions
display correctly
<li>WsDbFetch query/result association resolved
<li>Tree leaf to sequence mapping improved
<li>Smooth fonts switch moved to FontChooser dialog box.
-
-
-
-
-
</ul>
</td>
git://source.jalview.org / jalview.git / blobdiff