+ <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>
+ <li>
+ <!-- JAL-2831 -->Jumping from column 1 to column 100,000
+ takes a long time in Cursor mode
+ </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 of selected regions of
+ each selected sequence do not have correct start/end
+ positions
+ </li>
+ <li>
+ <!-- JAL-2793 -->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>
+ <li>
+ <!-- JAL-2811 -->Double residue highlights in cursor mode
+ if new selection moves alignment window
+ </li>
+ <li>
+ <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
+ arrow key in cursor mode to pass hidden column marker
+ </li>
+ <li>
+ <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
+ that produces correctly annotated transcripts and products
+ </li>
+ <li>
+ <!-- JAL-2776 -->Toggling a feature group after first time
+ doesn't update associated structure view
+ </li>
+ </ul>
+ <em>Applet</em><br />
+ <ul>
+ <li>
+ <!-- JAL-2687 -->Concurrent modification exception when
+ closing alignment panel
+ </li>
+ </ul>
+ <em>BioJSON</em><br />
+ <ul>
+ <li>
+ <!-- JAL-2546 -->BioJSON export does not preserve
+ non-positional features
+ </li>
+ </ul>
+ <em>New Known Issues</em>
+ <ul>
+ <li>
+ <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
+ sequence features correctly (for many previous versions of
+ Jalview)
+ </li>
+ <li>
+ <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
+ using cursor in wrapped panel other than top
+ </li>
+ <li>
+ <!-- JAL-2791 -->Select columns containing feature ignores
+ graduated colour threshold
+ </li>
+ <li>
+ <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
+ always preserve numbering and sequence features
+ </li>
+ </ul>
+ <em>Known Java 9 Issues</em>
+ <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>
+ </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>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>