nucleotide substitution matrix</a>, or by sequence percentage identity,
or sequence feature similarity.
</p>
- <img src="pcaviewer.gif">
+ <img src="pcaviewer.png">
<p>
<strong>The PCA Viewer</strong>
</p>
towards the front of the view.</p>
<p>
The 3d view can be rotated by dragging the mouse with the <strong>left
- mouse button</strong> pressed. The view can also be zoomed in and out with
+ mouse button</strong> pressed, or with the <strong>arrow
+ keys</strong> when <strong>SHIFT</strong> is pressed. The
+ view can also be zoomed in and out with
the up and down <strong>arrow keys</strong> (and the roll bar of the
mouse if present). Labels will be shown for each sequence if the
entry in the View menu is checked, and the plot background colour
<p>
Initially, the display shows the first three components of the
similarity space, but any eigenvector can be used by changing the
- selected dimension for the x, y, or z axis through each ones menu
+ selected dimension for the x, y, or z axis through each one's menu
located below the 3d display. The <strong><em>Reset</em></strong>
button will reset axis and rotation settings to their defaults.
</p>
<em>The output of points and transformed point coordinates was
added to the Jalview desktop in v2.7.</em> <em>The Reset button
and Change Parameters menu were added in Jalview 2.8.</em> <em>Support
- for PAM250 based PCA was added in Jalview 2.8.1.</em>
+ for PAM250 based PCA was added in Jalview 2.8.1.</em><em>In Jalview 2.11, support for saving and restoring PCAs in Project files was added, and the Change parameters menu removed.</em>
</p>
<p>
<strong>Reproducing PCA calculations performed with older
<!-- JAL-3181 -->Consistent ordering of links in sequence id
popup menu
</li>
- <li>
- <!-- JAL-3021 -->Sequence Details report opens positioned to top
- of report
- </li>
</ul></li>
<li><strong>Java 11 Support</strong>
<ul>
<!-- JAL-3035 -->DAS sequence retrieval and annotation
capabilities removed from the Jalview Desktop
</li>
+ <li>
+ <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
+ unmarshalling has been replaced by JAXB for Jalview projects
+ and XML based data retrieval clients</li>
+ <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
<li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
</ul>
<em>Development and Release Processes</em>
gradle-eclipse
</li>
<li>
- Atlassian Bamboo continuous integration server for
+ Atlassian Bamboo continuous integration for
unattended Test Suite execution</li>
<li>
<!-- JAL-2864 -->Memory test suite to detect leaks in common
operations</li>
<li>
- <!-- JAL-3140 -->IntervalStoreJ (new updatable NCList
- implementation) used for Sequence Feature collections</li>
- <li>
- <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
- unmarshalling has been replaced by JAXB for Jalview projects
- and XML based data retrieval clients</li>
+ <!-- JAL-3140 -->IntervalStoreJ (NCList
+ implementation that alows updates) used for Sequence Feature collections</li>
</ul>
</td>
<td align="left" valign="top">
<li>
<!-- JAL-2898 -->stop_gained variants not shown correctly on peptide sequence</li>
<li>
+ <!-- JAL-3021 -->Sequence Details report opens positioned to top of report</li>
+ <li>
<!-- JAL-914 -->Help page can be opened twice</li>
</ul>
<em>Editing</em>