</td>
</tr>
<tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>6/09/2018</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-3101 -->Default memory for Jalview webstart and
+ InstallAnywhere increased to 1G.
+ </li>
+ <li>
+ <!-- JAL-247 -->Hidden sequence markers and representative
+ sequence bolding included when exporting alignment as EPS,
+ SVG, PNG or HTML. <em>Display is configured via the
+ Format menu, or for command-line use via a jalview
+ properties file.</em>
+ </li>
+ <li>
+ <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
+ API and sequence data now imported as JSON.
+ </li>
+ <li>
+ <!-- JAL-3065 -->Change in recommended way of starting
+ Jalview via a Java command line: add jars in lib directory
+ to CLASSPATH, rather than via the deprecated java.ext.dirs
+ property.
+ </li>
+ </ul>
+ <em>Development</em>
+ <ul>
+ <li>
+ <!-- JAL-3047 -->Support added to execute test suite
+ instrumented with <a href="http://openclover.org/">Open
+ Clover</a>
+ </li>
+ </ul>
+ </div></td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-3104 -->Poorly scaled bar in quality annotation
+ row shown in Feredoxin Structure alignment view of example
+ alignment.
+ </li>
+ <li>
+ <!-- JAL-2854 -->Annotation obscures sequences if lots of
+ annotation displayed.
+ </li>
+ <li>
+ <!-- JAL-3107 -->Group conservation/consensus not shown
+ for newly created group when 'Apply to all groups'
+ selected
+ </li>
+ <li>
+ <!-- JAL-3087 -->Corrupted display when switching to
+ wrapped mode when sequence panel's vertical scrollbar is
+ visible.
+ </li>
+ <li>
+ <!-- JAL-3003 -->Alignment is black in exported EPS file
+ when sequences are selected in exported view.</em>
+ </li>
+ <li>
+ <!-- JAL-3059 -->Groups with different coloured borders
+ aren't rendered with correct colour.
+ </li>
+ <li>
+ <!-- JAL-3092 -->Jalview could hang when importing certain
+ types of knotted RNA secondary structure.
+ </li>
+ <li>
+ <!-- JAL-3095 -->Sequence highlight and selection in
+ trimmed VARNA 2D structure is incorrect for sequences that
+ do not start at 1.
+ </li>
+ <li>
+ <!-- JAL-3061 -->'.' inserted into RNA secondary structure
+ annotation when columns are inserted into an alignment,
+ and when exporting as Stockholm flatfile.
+ </li>
+ <li>
+ <!-- JAL-3053 -->Jalview annotation rows containing upper
+ and lower-case 'E' and 'H' do not automatically get
+ treated as RNA secondary structure.
+ </li>
+ <li>
+ <!-- JAL-3106 -->.jvp should be used as default extension
+ (not .jar) when saving a jalview project file.
+ </li>
+ <li>
+ <!-- JAL-3105 -->Mac Users: closing a window correctly
+ transfers focus to previous window on OSX
+ </li>
+ </ul>
+ <em>Java 10 Issues</em>
+ <ul>
+ <li>
+ <!-- JAL-2988 -->OSX - Can't save new files via the File
+ or export menus by typing in a name into the Save dialog
+ box.
+ </li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
+ <em>7/06/2018</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-2920 -->Use HGVS nomenclature for variant
+ annotation retrieved from Uniprot
+ </li>
+ <li>
+ <!-- JAL-1460 -->Windows File Shortcuts can be dragged
+ onto the Jalview Desktop
+ </li>
+ </ul>
+ </div></td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-3017 -->Cannot import features with multiple
+ variant elements (blocks import of some Uniprot records)
+ </li>
+ <li>
+ <!-- JAL-2997 -->Clustal files with sequence positions in
+ right-hand column parsed correctly
+ </li>
+ <li>
+ <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
+ not alignment area in exported graphic
+ </li>
+ <li>
+ <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
+ window has input focus
+ </li>
+ <li>
+ <!-- JAL-2992 -->Annotation panel set too high when
+ annotation added to view (Windows)
+ </li>
+ <li>
+ <!-- JAL-3009 -->Jalview Desktop is slow to start up when
+ network connectivity is poor
+ </li>
+ <li>
+ <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
+ Jalview desktop on Windows doesn't open file<br /> <em>Dragging
+ the currently open URL and links from a page viewed in
+ Firefox or Chrome on Windows is now fully supported. If
+ you are using Edge, only links in the page can be
+ dragged, and with Internet Explorer, only the currently
+ open URL in the browser can be dropped onto Jalview.</em>
+ </li>
+ </ul>
+ </div></td>
+ </tr>
+ <tr>
<td width="60" nowrap>
<div align="center">
- <strong><a name="Jalview.2.10.3">2.10.3</a><br />
- <em>17/11/2017</em></strong>
+ <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
+ for disabling automatic superposition of multiple
+ structures and open structures in existing views
+ </li>
+ <li>
+ <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
+ ID and annotation area margins can be click-dragged to
+ adjust them.
+ </li>
+ <li>
+ <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
+ Ensembl services
+ </li>
+ <li>
+ <!-- JAL-2759 -->Improved performance for large alignments
+ and lots of hidden columns
+ </li>
+ <li>
+ <!-- JAL-2593 -->Improved performance when rendering lots
+ of features (particularly when transparency is disabled)
+ </li>
+ </ul>
+ </div>
+ </td>
+ <td><div align="left">
+ <ul>
+ <li>
+ <!-- JAL-2899 -->Structure and Overview aren't updated
+ when Colour By Annotation threshold slider is adjusted
+ </li>
+ <li>
+ <!-- JAL-2778 -->Slow redraw when Overview panel shown
+ overlapping alignment panel
+ </li>
+ <li>
+ <!-- JAL-2929 -->Overview doesn't show end of unpadded
+ sequence as gaps
+ </li>
+ <li>
+ <!-- JAL-2789, JAL-2893 -->Cross-reference handling
+ improved: CDS not handled correctly if transcript has no
+ UTR
+ </li>
+ <li>
+ <!-- JAL-2321 -->Secondary structure and temperature
+ factor annotation not added to sequence when local PDB
+ file associated with it by drag'n'drop or structure
+ chooser
+ </li>
+ <li>
+ <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
+ dialog doesn't import PDB files dropped on an alignment
+ </li>
+ <li>
+ <!-- JAL-2666 -->Linked scrolling via protein horizontal
+ scroll bar doesn't work for some CDS/Protein views
+ </li>
+ <li>
+ <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
+ Java 1.8u153 onwards and Java 1.9u4+.
+ </li>
+ <li>
+ <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
+ columns in annotation row
+ </li>
+ <li>
+ <!-- JAL-2913 -->Preferences panel's ID Width control is not
+ honored in batch mode
+ </li>
+ <li>
+ <!-- JAL-2945 -->Linked sequence highlighting doesn't work
+ for structures added to existing Jmol view
+ </li>
+ <li>
+ <!-- JAL-2223 -->'View Mappings' includes duplicate
+ entries after importing project with multiple views
+ </li>
+ <li>
+ <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
+ protein sequences via SIFTS from associated PDB entries
+ with negative residue numbers or missing residues fails
+ </li>
+ <li>
+ <!-- JAL-2952 -->Exception when shading sequence with negative
+ Temperature Factor values from annotated PDB files (e.g.
+ as generated by CONSURF)
+ </li>
+ <li>
+ <!-- JAL-2920 -->Uniprot 'sequence variant' features
+ tooltip doesn't include a text description of mutation
+ </li>
+ <li>
+ <!-- JAL-2922 -->Invert displayed features very slow when
+ structure and/or overview windows are also shown
+ </li>
+ <li>
+ <!-- JAL-2954 -->Selecting columns from highlighted regions
+ very slow for alignments with large numbers of sequences
+ </li>
+ <li>
+ <!-- JAL-2925 -->Copy Consensus fails for group consensus
+ with 'StringIndexOutOfBounds'
+ </li>
+ <li>
+ <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
+ platforms running Java 10
+ </li>
+ <li>
+ <!-- JAL-2960 -->Adding a structure to existing structure
+ view appears to do nothing because the view is hidden behind the alignment view
+ </li>
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <li>
+ <!-- JAL-2926 -->Copy consensus sequence option in applet
+ should copy the group consensus when popup is opened on it
+ </li>
+ </ul>
+ <em>Batch Mode</em>
+ <ul>
+ <li>
+ <!-- JAL-2913 -->Fixed ID width preference is not respected
+ </li>
+ </ul>
+ <em>New Known Defects</em>
+ <ul>
+ <li>
+ <!-- JAL-2973 --> Exceptions occasionally raised when
+ editing a large alignment and overview is displayed
+ </li>
+ <li>
+ <!-- JAL-2974 -->'Overview updating' progress bar is shown
+ repeatedly after a series of edits even when the overview
+ is no longer reflecting updates
+ </li>
+ <li>
+ <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
+ structures for protein subsequence (if 'Trim Retrieved
+ Sequences' enabled) or Ensembl isoforms (Workaround in
+ 2.10.4 is to fail back to N&W mapping)
+ </li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <ul><li>Updated Certum Codesigning Certificate
+ (Valid till 30th November 2018)</li></ul></div></td>
+ <td><div align="left">
+ <em>Desktop</em><ul>
+ <ul>
+ <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
+ <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
+ <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
+ <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
+ <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
+ <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
+ <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
</div>
</td>
<td><div align="left">
<!-- 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>
+ <!-- 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>
+ <li>
+ <!-- JAL-2758 -->Short names for sequences retrieved from
+ Uniprot
</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>
- <li><!-- JAL-2758 -->Short names for sequences retrieved from Uniprot</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>
+ <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>
+ <li>
+ <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
+ </li>
</ul>
- </div>
- </td>
+ </div></td>
<td><div align="left">
<em>General</em>
<ul>
- <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>
+ <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 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>
- <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>
- </ul>
- <strong><em>Applet</em></strong><br/>
- <ul>
- <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
+ <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>
- <strong><em>BioJSON</em></strong><br/>
+ <em>Applet</em><br />
<ul>
- <li>
- <!-- JAL-2546 -->BioJSON export does not preserve non-positional features
- </li>
+ <li>
+ <!-- JAL-2687 -->Concurrent modification exception when
+ closing alignment panel
+ </li>
</ul>
- <strong>Known Java 9 Issues</strong>
+ <em>BioJSON</em><br />
<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>
+ <!-- JAL-2546 -->BioJSON export does not preserve
+ non-positional features
</li>
</ul>
- <strong>New Known Issues</strong>
+ <em>New Known Issues</em>
<ul>
- <li><!-- JAL- --></li>
+ <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>
- </div>
- </td>
+ <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>
git://source.jalview.org / jalview.git / blobdiff