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padding-left: 10px;
padding-bottom: 4px;
}
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/* separate the items from eachother */
- margin-left: -3px;
- padding-bottom: 3px;
- padding-left: 6px;
+ margin-left: -3px;
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</head>
<body>
<tr>
<td width="60" nowrap>
<div align="center">
- <strong><a name="Jalview.2.10.2">2.10.2</a><br />
- <em>30/5/2017</em></strong>
+ <strong><a name="Jalview.2.10.3">2.10.3</a><br />
+ <em>14/11/2017</em></strong>
</div>
</td>
<td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-2446 -->Faster and more efficient management and
+ rendering of sequence features
+ </li>
+ <li>
+ <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
+ 429 rate limit request hander
+ </li>
+ <li>
+ <!-- JAL-2773 -->Structure views don't get updated unless
+ their colours have changed
+ </li>
+ <li><!-- JAL-2495 -->All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)</li>
+ <li><!-- JAL-2790 -->'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
+ </li>
+
+ <li><!-- JAL-2617 -->Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references</li>
+ <li><!-- JAL-2685 -->Start/End limits are shown in Pairwise Alignment report</li>
+ <li><!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch' feature can be disabled</li>
+ <li><!-- JAL-2810 -->Retrieve IDs tab added for UniProt and PDB easier retrieval of sequences for lists of IDs</li>
+
+ </ul>
+ <em>Scripting</em>
+ <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>
+ <em>Testing and Deployment</em>
+ <ul><li><!-- JAL-2727 -->Test to catch memory leaks in Jalview UI</li></ul>
+ </div>
+ </td>
+ <td><div align="left">
<em>General</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>
- <li><!-- JAL-2491 -->linked scrolling of CDS/Protein views via Overview or sequence motif search operations</li>
- <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-2643 -->Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view</li>
+ <li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
+ <li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
+ <li><!-- JAL-2548 -->Export of features doesn't always respect group visibility</li>
+ </ul>
+ <em>Desktop</em>
+ <ul>
+ <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
+ <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
+ </li>
+ <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
+ </li>
+ <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
+ <li><!-- JAL-2529 -->Revised Ensembl REST API CDNA query</li>
+ <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
+ <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
+ <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
+ <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
+ <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
+ <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
+ <li><!-- JAL-2392 -->Jalview freezes when loading and displaying several structures</li>
+ <li><!-- JAL-2732 -->Black outlines left after resizing or moving a window</li>
+ <li><!-- JAL-1900,JAL-1625 -->Unable to minimise windows within the Jalview desktop on OSX</li>
+ <li><!-- JAL-2667 -->Mouse wheel doesn't scroll vertically when in wrapped alignment mode</li>
+ <li><!-- JAL-2636 -->Scale mark not shown when close to right hand end of alignment</li>
+ <li><!-- JAL-2684 -->Pairwise alignment only aligns selected regions of each selected sequence</li>
+ <li><!-- JAL-2973 -->Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog</li>
+ <li><!-- JAL-2036 -->Show cross-references not enabled after restoring project until a new view is created</li>
+ <li><!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in URL links appears when only default EMBL-EBI link is configured (since 2.10.2b2)</li>
+ <li><!-- JAL-2775 -->Overview redraws whole window when box position is adjusted</li>
+ <li><!-- JAL-2225 -->Structure viewer doesn't map all chains in a multi-chain structure when viewing alignment involving more than one chain (since 2.10)</li>
+ </ul>
+ <strong><em>Applet</em></strong><br/>
+ <ul>
+ <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
+ </ul>
+ <strong><em>BioJSON</em></strong><br/>
+ <ul>
+ <li>
+ <!-- JAL-2546 -->BioJSON export does not preserve non-positional features
+ </li>
+ </ul>
+ <strong>Known Java 9 Issues</strong>
+ <ul>
+ <li><!-- JAL-2902 -->Groovy Console very slow to open and is
+ not responsive when entering characters (Webstart, Java 9.01,
+ OSX 10.10)
+ </li>
+ </ul>
+ <strong>New Known Issues</strong>
+ <ul>
+ <li><!-- JAL- --></li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
+ <em>2/10/2017</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <em>New features in Jalview Desktop</em>
+ <ul>
+ <li>
+ <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
+ </li>
+ <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
+ </li>
+ </ul>
+ </div></td>
+ <td><div align="left">
+ </div></td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
+ <em>7/9/2017</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-2588 -->Show gaps in overview window by colouring
+ in grey (sequences used to be coloured grey, and gaps were
+ white)
+ </li>
+ <li>
+ <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
+ Preferences
+ </li>
+ <li>
+ <!-- JAL-2587 -->Overview updates immediately on increase
+ in size and progress bar shown as higher resolution
+ overview is recalculated
+ </li>
+
+ </ul>
+ </div></td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-2664 -->Overview window redraws every hidden
+ column region row by row
+ </li>
+ <li>
+ <!-- JAL-2681 -->duplicate protein sequences shown after
+ retrieving Ensembl crossrefs for sequences from Uniprot
+ </li>
+ <li>
+ <!-- JAL-2603 -->Overview window throws NPE if show boxes
+ format setting is unticked
+ </li>
+ <li>
+ <!-- JAL-2610 -->Groups are coloured wrongly in overview
+ if group has show boxes format setting unticked
+ </li>
+ <li>
+ <!-- JAL-2672,JAL-2665 -->Redraw problems when
+ autoscrolling whilst dragging current selection group to
+ include sequences and columns not currently displayed
+ </li>
+ <li>
+ <!-- JAL-2691 -->Not all chains are mapped when multimeric
+ assemblies are imported via CIF file
+ </li>
+ <li>
+ <!-- JAL-2704 -->Gap colour in custom colourscheme is not
+ displayed when threshold or conservation colouring is also
+ enabled.
+ </li>
+ <li>
+ <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
+ server version
+ </li>
+ <li>
+ <!-- JAL-2673 -->Jalview continues to scroll after
+ dragging a selected region off the visible region of the
+ alignment
+ </li>
+ <li>
+ <!-- JAL-2724 -->Cannot apply annotation based
+ colourscheme to all groups in a view
+ </li>
+ <li>
+ <!-- JAL-2511 -->IDs don't line up with sequences
+ initially after font size change using the Font chooser or
+ middle-mouse zoom
+ </li>
+ </ul>
+ </div></td>
+ </tr>
+ <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>Application</em>
+ <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.
+ <!-- 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>
- <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>
</ul>
- <em>Experimental features</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.
+ features, and vice-versa (<strong>Experimental
+ Feature</strong>)
</li>
</ul>
- <em>Applet</em>
+ <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><!-- --></li>
+ <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>
- <li><!-- JAL-2474 -->Added PrivelegedAccessor to test suite</li>
- <li><!-- JAL-2326 -->Prevent or clear modal dialogs raised during tests</li>
- <li><!-- -->
+ <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>General</em>
+ </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.schemes.ResidueProperties.BLOSUM62[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 mean't
- 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>
+ 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>Application</em>
+ <em>User Interface</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-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>
+ </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-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>
+ <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-2563 -->Status bar doesn't show positions for ambiguous amino acids</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-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>
+ </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>
+ <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
</div>
</td>
<td><div align="left">
for all consensus calculations
</li>
<li>
- <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released 3rd Oct 2016)
+ <!-- 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>
</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)
+ 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
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>
+ <!-- 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>
+ <!-- <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>
+ <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>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>
+ <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>
<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>
+ <li>
+ <!-- JAL-1980 -->Null Pointer Exception raised when
+ pressing Add on an orphaned cut'n'paste window.
+ </li>
<!-- may exclude, this is an external service stability issue JAL-1941
-- > RNA 3D structure not added via DSSR service</li> -->
</ul>
</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