</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>
<li>
+ <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
+ Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
+ source project) rather than InstallAnywhere
+ </li>
+ <li>
+ <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
+ settings, receive over the air updates and launch specific
+ versions via (<a href="https://github.com/threerings/getdown">Three
+ Rings' GetDown</a>)
+ </li>
+ <li>
+ <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
+ formats supported by jalview (including .jvp project files)
+ </li>
+ <li>
+ <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
+ arguments and switch between different getdown channels
+ </li>
+ <li>
+ <!-- JAL-3141 -->Backup files created when saving Jalview project
+ or alignment files
+ </li>
+
+ <li>
<!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
+ <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
<li>
<!-- JAL-2620 -->Alternative genetic code tables for
'Translate as cDNA'</li>
<!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
<li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
<ul>
+ <li>
+ <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
+ implementation that allows updates) used for Sequence Feature collections</li>
+ <li>
<li>
- <!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
+ <!-- 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-2897 -->Show synonymous codon variants on peptide
- sequences
+ <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
+ recognise variant features
+ </li>
+ <li>
+ <!-- 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
details
</li>
<li>
- <!-- JAL-3139,JAL-2816 -->More efficient sequence feature render
+ <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
algorithm (Z-sort/transparency and filter aware)
</li>
<li>
</ul>
</li>
<li>
- <!-- JAL-3141 -->Backup files created when saving Jalview project
- or alignment files
- </li>
- <li><strong>Principal Components Analysis Viewer</strong>
+ <!-- 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
incrementally
</li>
<li>
- <!-- JAL-2965 -->PCA plot is depth cued
+ <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
</li>
</ul>
</li>
<li><strong>Speed and Efficiency</strong>
<ul>
<li>
- <!-- JAL-3198 -->More efficient creation of selections and
+ <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
multiple groups when working with large alignments
</li>
<li>
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>
</ul></li>
- <li><strong>Java 11 Support</strong>
+ <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
+ <li><strong>Java 11 Support (not yet on general release)</strong>
<ul>
<li>
- <!-- JAL- -->Java 11 Native Desktop installer, standalone JAR
- and getdown release channels
- </li>
- <li>
<!-- -->OSX GUI integrations for App menu's 'About' entry and
trapping CMD-Q
</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-3007 -->Jalview Native Application and
- Installers built with Install4j (licensed to the Jalview open
- source project) rather than InstallAnywhere
- </li>
- <li>
- <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
- settings, receive over the air updates and launch specific
- versions via (<a href="https://github.com/threerings/getdown">Three
- Rings' GetDown</a>)
- </li>
- <li>
- <!-- JAL-3196,JAL-3179 -->Build system migrated from Ant to Gradle
+ <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
</li>
- <li>
+ <li><!-- JAL-3174,JAL-2886,JAL-2729 -->
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 JAL-2446 -->IntervalStoreJ (NCList
- implementation that alows updates) used for Sequence Feature collections</li>
- <li><!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor issues resolved.</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>
</ul>
</td>
<td align="left" valign="top">
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,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)
Page Up in wrapped mode
</li>
<li>
- <!-- JAL-2839 -->Finder doesn't skip hidden regions
+ <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
</li>
<li>
<!-- JAL-2932 -->Finder searches in minimised alignments
shown in complementary view
</li>
<li>
- <!-- JAL-2898 -->stop_gained variants not shown correctly on
- peptide sequence
+ <!-- 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-2830 -->Inserting gap sequence via the Edit Sequence
dialog corrupts dataset sequence
</li>
+ <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>
+ <li>
<!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
is restored from a Jalview 2.11 project
</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>
+ <!-- JAL-3235 -->Jalview Properties file is not sorted alphabetically when saved</li>
+
+ </ul></li>
+
</ul>
</td>
</tr>
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>
git://source.jalview.org / jalview.git / blobdiff