+ <!-- 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>
+ </ul>
+ <ul><li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li></ul>
+ </td>
+ <td><div align="left">
+ <em></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>
+ </ul>
+ </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>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