</td>
</tr>
<tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>4/09/2018</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <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>
+ </div></td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-247 -->Hidden sequence markers and representative
+ sequence bolding included when exporting alignment as EPS,
+ SVG, PNG or HTML. <em>Display of these can be
+ configured via the Format menu or in batch mode with a
+ jalview properties file.</em>
+ </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
+ </li>
+ <li>
+ <!-- JAL-3061 -->'.' written into RNA secondary structure
+ annotation when writing out Stockholm format
+ </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>
+ </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-1847 JAL-2944 -->Structure Chooser controls to
- control superposition of multiple structures and open
- structures in existing views
+ <!-- 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.2.10.4">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
</li>
<li>
<!-- JAL-2593 -->Improved performance when rendering lots
- of features
+ of features (particularly when transparency is disabled)
</li>
</ul>
</div>
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>
columns in annotation row
</li>
<li>
- <!-- JAL-2913 -->Preferences panel's ID Width control is
- honored in interactive and batch mode
+ <!-- JAL-2913 -->Preferences panel's ID Width control is not
+ honored in batch mode
</li>
<li>
<!-- JAL-2945 -->Linked sequence highlighting doesn't work
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>
with 'StringIndexOutOfBounds'
</li>
<li>
- <!-- JAL-2976 -->VAqua(4) (<a
- href="http://violetlib.org/vaqua/overview.html">download
- here</a>) provided as fallback Look and Feel for OSX
+ <!-- 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>
<!-- 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>
git://source.jalview.org / jalview.git / blobdiff