</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.2.10.4">2.10.4</a><br /> <em>1/05/2018</em></strong>
+ <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-984 -->Mouse cursor changes to indicate Sequence ID and annotation area margins can be click-dragged to adjust them.</li>
+ <!-- JAL-2920 -->Use HGVS nomenclature for variant
+ annotation retrieved from Uniprot
+ </li>
<li>
- <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and Ensembl services
+ <!-- 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-2759 -->Improved performance for large alignments and lots of hidden columns
+ <!-- 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>
+ </div></td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <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-2778 -->Slow redraw when Overview panel shown overlapping alignment panel
+ <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
+ for disabling automatic superposition of multiple
+ structures and open structures in existing views
</li>
<li>
- <!-- JAL-2666 -->Linked scrolling via protein horizontal scroll bar doesn't work for some CDS/Protein views
+ <!-- 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>
- <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 honored in interactive and batch mode</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>
- </div>
+ </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>
git://source.jalview.org / jalview.git / blobdiff