</tr>
<tr>
<td width="60" align="center" nowrap>
- <strong><a name="Jalview.2.11">2.11</a><br />
- <em>27/06/2019</em></strong>
+ <strong><a name="Jalview.2.11.1">2.11.1</a><br />
+ <em>19/11/2019</em></strong>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ <li><!-- -->
+ </li>
+ </ul>
+ <em>Deprecations</em>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ </ul>
+ <em>Java 11 Compatibility issues</em>
+ <ul>
+ <li>
+ <!-- JAL-2987 -->OSX - Can't view results in PDB/Uniprot FTS
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap>
+ <strong><a name="Jalview.2.11.0">2.11.0</a><br />
+ <em>04/07/2019</em></strong>
</td>
<td align="left" valign="top">
<ul>
</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
<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
- shaded according to any associated attributes (e.g. variant
- attributes from VCF file, or key-value pairs imported from
- column 9 of GFF file)
+ <!-- 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
+ file, or key-value pairs imported from column 9 of GFF
+ file)
+ </li>
+ <li>
+ <!-- JAL-2879 -->Feature Attributes and shading schemes
+ stored and restored from Jalview Projects
+ </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
+ <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
+ sequences (also coloured red by default)
</li>
<li>
<!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
<!-- 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
</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>
annotation
</li>
<li>
- <!-- JAL-2814 -->Help button on Uniprot and PDB search panels
+ <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
</li>
<li>
<!-- JAL-2621 -->Cursor changes over draggable box in Overview
</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-3225 -->Eclipse project configuration managed with
- gradle-eclipse
- </li>
- <li><!-- JAL-3174,JAL-2886,JAL-2729 -->
- Atlassian Bamboo continuous integration for
- unattended Test Suite execution</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
+ </li>
+ <li>
+ <!-- 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
+ operations
+ </li>
<li>
- <!-- 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.</li>
- <li><!-- JAL-3248 -->Developer documentation migrated to markdown (with HTML rendering)</li>
+ <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
+ issues resolved
+ </li>
+ <li>
+ <!-- JAL-3248 -->Developer documentation migrated to
+ markdown (with HTML rendering)
+ </li>
+ <li>
+ <!-- JAL-3287 -->HelpLinksChecker runs on Windows
+ </li>
+ <li>
+ <!-- JAL-3289 -->New URLs for publishing development
+ versions of Jalview
+ </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
doesn't tell users the invalid URL
</li>
<li>
- <!-- JAL-3178 -->Nonpositional features lose feature group on
- export as Jalview features file
- </li>
- <li>
<!-- 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,JAL-2207 -->stop_gained variants not shown correctly on
+ peptide sequence (computed variant shown as p.Res.null)
+ </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
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>
<li>
- <!-- JAL-3021 -->Sequence Details report opens positioned to top
+ <!-- JAL-3021 -->Sequence Details report should open positioned at top
of report
</li>
<li>
<!-- JAL-914 -->Help page can be opened twice
</li>
+ <li>
+ <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
+ </li>
</ul> <em>Editing</em>
<ul>
<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>
- <ul>
+ </ul> <em>Datamodel</em>
+ <ul>
+ <li>
+ <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
+ sequence's End is greater than its length
+ </li>
+ </ul> <em>Bugs fixed for Java 11 Support (not yet on
+ general release)</em>
+ <ul>
+ <li>
+ <!-- JAL-3288 -->Menus work properly in split-screen
+ </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.
not shown as thresholded features in 2.11. To workaround please
create a Score filter instead.
</li>
- <li><strong>Java 11 Specific defects</strong>
+ <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>
+ <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
+ alignments with multiple views can close views unexpectedly
+ </li>
+ </ul>
+ <em>Java 11 Specific defects</em>
<ul>
<li>
- <!-- JAL-3235 -->Jalview Properties file is not sorted alphabetically when saved</li>
-
- </ul></li>
-
- </ul>
+ <!-- JAL-3235 -->Jalview Properties file is not sorted
+ alphabetically when saved
+ </li>
+ </ul>
</td>
</tr>
<tr>
<!-- 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