</tr>
<tr>
<td width="60" align="center" nowrap>
- <strong><a name="Jalview.2.11">2.11</a><br />
- <em>20/06/2019</em></strong>
+ <strong><a name="Jalview.2.11.0">2.11.0</a><br />
+ <em>02/07/2019</em></strong>
</td>
<td align="left" valign="top">
<ul>
<ul>
<li>
<!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
- implementation that alows updates) used for Sequence Feature collections</li>
+ implementation that allows updates) used for Sequence Feature collections</li>
<li>
<li>
<!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
column 9 of GFF file)
</li>
<li>
+ <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
+ recognise variant features
+ </li>
+ <li>
<!-- JAL-2897 -->Show synonymous codon variants on peptide
sequences
</li>
</li>
</ul>
</li>
- <li><strong>Principal Components Analysis Viewer</strong>
+ <li>
+ <!-- JAL-3205 -->Symmetric score matrices for faster
+ tree and PCA calculations
+ </li>
+ <li><strong>Principal Components Analysis Viewer</strong>
<ul>
<li>
<!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
and Viewer state saved in Jalview Project
</li>
- <li>'Change parameters' option removed from viewer's
+ <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
drop-down menus</li>
<li>
<!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
view
</li>
<li>
- <!-- JAL-2527 -->Alignment Overview now WYSIWIS (What you see is
+ <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
what is shown)<br />Only visible region of alignment is shown by
default (can be changed in user preferences)
</li>
<!-- JAL-3003 -->Added remarks about transparent rendering effects
not supported in EPS figure export
</li>
+ <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
</ul> <em>Development and Release Processes</em>
<ul>
<li>
<!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
</li>
+ <li><!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
<li>
<!-- JAL-3225 -->Eclipse project configuration managed with
gradle-eclipse
doesn't tell users the invalid URL
</li>
<li>
- <!-- JAL-3178 -->Nonpositional features lose feature group on
- export as Jalview features file
+ <!-- JAL-2816 -->Tooltips displayed for features filtered by
+ score from view
+ </li>
+ <li>
+ <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
+ show cross references or Fetch Database References are shown in
+ red in original view
</li>
+ <li>
+ <!-- JAL-2898 -->stop_gained variants not shown correctly on
+ peptide sequence
+ </li>
<li>
<!-- JAL-2060 -->'Graduated colour' option not offered for
manually created features (where if feature score is Float.NaN)
shown in complementary view
</li>
<li>
- <!-- JAL-2898 -->stop_gained variants not shown correctly on
- peptide sequence
- </li>
- <li>
<!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
without normalisation
</li>
<!-- JAL-868 -->Structure colours not updated when associated tree
repartitions the alignment view (Regression in 2.10.5)
</li>
-
</ul>
- <em>New Known Defects</em>
+ <em>Datamodel</em>
<ul>
<li>
+ <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
+ sequence's End is greater than its length
+ </li>
+ </ul> <em>New Known Defects</em>
+ <ul>
+ <li><!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
+ </li>
+ <li>
<!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
regions of protein alignment.
</li>
not shown as thresholded features in 2.11. To workaround please
create a Score filter instead.
</li>
+ <li><!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
+ <li>
+ <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
+ </li>
<li><strong>Java 11 Specific defects</strong>
<ul>
<li>
open URL in the browser can be dropped onto Jalview.</em>
</li>
</ul>
+ <em>New Known Defects</em>
+ <ul>
+ <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
+ </ul>
</div></td>
</tr>
<tr>
Sequences' enabled) or Ensembl isoforms (Workaround in
2.10.4 is to fail back to N&W mapping)
</li>
- </ul>
+ <li>
+ <!-- JAL-2990 -->Export Annotations from File Menu with CSV
+ option gives blank output
+ </li>
+ </ul>
</div>
</td>
</tr>