</li>
<li>
<!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
- formats supported by jalview (including .jvp project files)
+ formats supported by Jalview (including .jvp project files)
</li>
<li>
<!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
<!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
implementation that allows updates) used for Sequence Feature collections</li>
<li>
- <li>
<!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
features can be filtered and shaded according to any
associated attributes (e.g. variant attributes from VCF
</li>
<li>
<!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
- what is shown)<br />Only visible region of alignment is shown by
+ what is shown)<br />Only visible regions of alignment are shown by
default (can be changed in user preferences)
</li>
<li>
</ul>
<em>Deprecations</em>
<ul>
- <li>
- <!-- JAL-3035 -->DAS sequence retrieval and annotation
+ <li><!-- 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
+ <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unmarshalling has been replaced by JAXB for Jalview projects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>Documentation</em>
<ul>
- <li>
- <!-- JAL-3003 -->Added remarks about transparent rendering effects
+ <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
+ <!-- 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-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
<li>
- <!-- JAL-3225 -->Eclipse project configuration managed with
+ <!-- JAL-3225 -->Eclipse project configuration managed with
gradle-eclipse
</li>
<li>
- <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 --> Atlassian
+ <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
Bamboo continuous integration for unattended Test Suite
execution
</li>
<li>
- <!-- JAL-2864 -->Memory test suite to detect leaks in common
+ <!-- JAL-2864 -->Memory test suite to detect leaks in common
operations
</li>
<li>
- <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
- issues resolved.
+ <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
+ issues resolved
</li>
<li>
- <!-- JAL-3248 -->Developer documentation migrated to
+ <!-- JAL-3248 -->Developer documentation migrated to
markdown (with HTML rendering)
</li>
<li>
- <!-- JAL-3287 -->HelpLinksChecker runs on Windows
+ <!-- JAL-3287 -->HelpLinksChecker runs on Windows
</li>
<li>
- <!-- JAL-3289 -->New URLs for publishing development
+ <!-- JAL-3289 -->New URLs for publishing development
versions of Jalview
</li>
- <li>
- <li>
</ul>
</td>
<td align="left" valign="top">
Settings and Jalview Preferences panels
</li>
<li>
- <!-- JAL-2865 -->Jalview hangs when closing windows or the
- overview updates with large alignments
+ <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
+ overview with large alignments
</li>
<li>
<!-- JAL-2750 -->Tree and PCA calculation fails for selected
</li>
<li>
<!-- JAL-2060 -->'Graduated colour' option not offered for
- manually created features (where if feature score is Float.NaN)
+ manually created features (where feature score is Float.NaN)
</li>
<li>
<!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
</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>
+ <!-- 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
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-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>
<!-- 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
+ Format menu, or for command-line use via a Jalview
properties file.</em>
</li>
<li>
</li>
<li>
<!-- JAL-3106 -->.jvp should be used as default extension
- (not .jar) when saving a jalview project file.
+ (not .jar) when saving a Jalview project file.
</li>
<li>
<!-- JAL-3105 -->Mac Users: closing a window correctly
git://source.jalview.org / jalview.git / blobdiff