</tr>
<tr>
<td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.2">.2</a><br />
+ <em>19/04/2022</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3992 -->Minor documentation fixes
+ </li>
+ </ul>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3365 -->Secondary structure annotation from Pfam
+ not displayed correctly
+ </li>
+ <li>
+ <!-- JAL-3997 -->Null pointer exceptions when displaying
+ annotation tooltips whilst in wrapped mode
+ </li>
+ </ul> <!-- <em>New Known Issues</em>-->
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.1">.1</a><br />
+ <em>05/04/2022</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3973 -->Distribution Tarball includes git commit
+ and branch details
+ </li>
+ </ul>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3975 -->Keyboard mode (F2) stops working after
+ using the "Create sequence feature" dialog
+ </li>
+ <li>
+ <!-- JAL-3976 -->3D Structure chooser fails to select
+ structures from 3D-beacons and pops up a 'null' dialog
+ </li>
+ <li>
+ <!-- JAL-3985 -->PDB FTS query results in error dialog
+ containing '414' [URL too long]
+ </li>
+ <li>
+ <!-- JAL-3980 JAL-3981 -->Sequence ID tooltip not shown during
+ long running retrieval/crossref operations (affects at least
+ 2.11.1 onwards)
+ </li>
+ <li>
+ <!-- JAL-3973 -->Cannot build Jalview 2.11.2.0 via gradle
+ from its source tarball
+ </li>
+ </ul> <em>New Known Issues</em>
+ <ul>
+ <li>
+ <!-- JAL-3984 -->Keyboard mode (F2) stops working after
+ using the "Text Colour" dialog
+ </li>
+ <li>
+ <!-- JAL-3873 -->Colour by->all views doesn't allow
+ colouring same structure from different views (since
+ 2.11.2.0)
+ </li>
+ <li>
+ <!-- JAL-3886 -->Pfam and Rfam alignment retrieval as
+ gzipped stockholm doesn't work on JalviewJS build of 2.11.2
+ </li>
+ <li>
+ <!-- JAL-3972 -->Java 11 Only: Jalview 2.11.2.0 OSX install
+ not working due to VAqua requiring
+ sun.awt.image.MultiResolutionImage
+ </li>
+ <li>
+ <!-- JAL-3981 -->Sequence Details can take a long time to be
+ displayed for heavily annotated sequences (all versions)
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
- <em>8/03/2022</em></strong></td>
+ <em>10/03/2022</em></strong></td>
<td align="left" valign="top">
<ul>
<li>
structure mapped to positions involved in the alignment
</li>
<li>
- <!-- JAL-3503 -->New Preferences tab for adjusting Jalview's
- memory settings at launch
- </li>
- <li>
- <!-- JAL-3144 -->Reverted to Jalview 'classic' drop-down
- menu for selecting which database to fetch from in sequence
- fetcher dialog.
- </li>
- <li>
<!-- JAL-2226 -->Structure annotation rows for all mapped
chains in 3D structures are included in the 'Reference
Annotation' for a sequence
<!-- JAL-3863 -->Support for Canonical Uniprot IDs
</li>
<li>
+ <!-- JAL-3503 -->New Preferences tab for adjusting Jalview's
+ memory settings at launch
+ </li>
+ <li>
<!-- JAL-3881 -->Sequence IDs split on '_' as well as other
non-alphanumerics when discovering database references with
'Fetch DB Refs'
disabled by default
</li>
<li>
+ <!-- JAL-3144 -->Reverted to Jalview 'classic' drop-down
+ menu for selecting which database to fetch from in sequence
+ fetcher dialog.
+ </li>
+ <li>
+ <!-- JAL-3018 -->Updated Ensembl REST Client compatibility
+ to 15.2 and revised model organism names (rat, xenopus,
+ dmelanogaster now rattus_norvegicus, xenopus_tropicalis,
+ drosophila_melanogaster)
+ </li>
+ <li>
<!-- JAL-3530 -->-nowebservicediscovery command line
argument to prevent automatic discovery of analysis
webservices on launch
default browser (works on OSX and Linux as well as Windows)
</li>
<li>
+ <!-- JAL-3871 JAL-3874 -->Upgraded bundled version of Jmol
+ to 14.31.53
+ </li>
+ <li>
<!-- JAL-3837 -->GPL license info on splash screen and About
text
</li>
- </ul>
- <em>Jalview Native App</em>
+ </ul> <em>Jalview Native App</em>
<ul>
<li>
- <!-- JAL- -->New Jalview Develop app - making it even easier
- to get at Jalview's development builds
+ <!-- JAL-3830 -->New command line launcher scripts (.sh,
+ .ps1, .bat) usable on macOS, Linux/Unix, Windows and
+ documentation in Help. Installer wizard has option to add
+ this to PATH, or link to it in your PATH.<br /> <em>This
+ is the recommended workaround for known issue about
+ working directory preservation when running native
+ application from command line. <!-- JAL-3523 -->
+ </em>
</li>
+ <li>Notarized MacOS installer for compliance with latest
+ OSX releases (Monterey)</li>
<li>
- <!-- JAL-3594 -->New splashscreens for Jalview, Jalview Test
- and Jalview Develop applications.
+ <!-- JAL-3805 -->Uninstaller application for old
+ (InstallAnywhere based) Jalview installations removed from
+ the OSX disk image
</li>
<li>
- <!-- JAL-3728 -->Jalview logos shown for Jalview Java
- Console and other window widgets in taskbar and dock rather
- than anonymous 'Java' icons
+ <!-- JAL-3608 -->Options to allow user to choose the (Swing)
+ Look and Feel (LaF) used by Jalview
</li>
<li>
- <!-- JAL-3608 -->Options to allow user to choose the (Swing) Look and Feel (LaF) used by Jalview
+ <!-- JAL-3552, JAL-3609 -->Metal LaF used to improved
+ operation on Linux Ubuntu with HiDPI display in Java 11
+ (still known issues with HiDPI screens in java 8 and 11. see
+ <a href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)
</li>
<li>
- <!-- JAL-3552, JAL-3609 -->Metal LaF used to improved operation on Linux Ubuntu with
- HiDPI display in Java 11 (still known issues with HiDPI screens in java
- 8 and 11. see <a
- href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)
+ <!-- JAL-3633 -->Getdown launcher inherits HTTP/S proxy
+ configuration from jalview_properties
</li>
<li>
- <!-- JAL-3830 -->New command line launcher scripts (.sh, .ps1, .bat) usable on
- macOS, Linux/Unix, Windows and documentation in Help. Installer wizard has option
- to add this to PATH, or link to it in your PATH.
+ <!-- JAL- -->New Jalview Develop app - making it even easier
+ to get at Jalview's development builds
</li>
<li>
- <!-- JAL-3633 -->Getdown launcher inherits HTTP/S proxy
- configuration from jalview_properties
+ <!-- JAL-3594 -->New splashscreens for Jalview, Jalview Test
+ and Jalview Develop applications.
+ </li>
+ <li>
+ <!-- JAL-3728 -->Jalview logos shown for Jalview Java
+ Console and other window widgets in taskbar and dock rather
+ than anonymous 'Java' icons
</li>
</ul> <em>JalviewJS</em>
<ul>
<li>
- <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences with
- SIFTS
+ <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences
+ with SIFTS
</li>
<li>
- <!-- JAL-3208 -->setprop commandline argument reinstated for JalviewJS only
+ <!-- JAL-3208 -->setprop commandline argument reinstated for
+ JalviewJS only
</li>
<li>
<!-- JAL-3163 -->Missing message bundle keys are only
<!-- JAL-3168 -->Feature type is included in the title of
the Feature Settings' Colour Chooser dialog
</li>
- <li></li>
+ <li>
+ <!-- JAL-3279 -->Build details reported in About window
+ </li>
+ <li>
+ <!-- JAL-3038 JAL-3071 JAL-3263 JAL-3084 -->Numerous minor
+ GUI additions and improvements in sync with Java
+ application.
+ </li>
</ul> <em>Development</em>
<ul>
<li>
<!-- -->First integrated JalviewJS and Jalview release
</li>
- <li>Updated building instructions</li>
+ <li>
+ <!-- JAL-3841,JAL-3248 -->Updated README and doc/building.md
+ </li>
<li>
<!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
process, added support for system package provided eclipse
installs on linux
</li>
<li>Install4j 9.0.x used for installer packaging</li>
- <li>Notarized MacOS installer for compatibility with Big
- Sur and Monterey</li>
- <li>
- <!-- JAL-3805 -->Uninstaller application for old
- (InstallAnywhere based) Jalview installations removed from
- the DMG
- </li>
<li>
<!-- JAL-3930 -->Improved use of installers for unattended
installation with a customizedId of "JALVIEW" in install4j's
<!-- JAL-3907 -->Improved compatibility of Jalview build
with Java 17 (next LTS target)
</li>
-
</ul>
-
</td>
- <td>
+ <td align="left" valign="top">
<ul>
<li>
<!-- JAL-3674 -->Slow structure commands can block Jalview
<li>
<!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
the first SEQUENCE_GROUP defined
-
</li>
<li>
<!-- JAL-3949 -->Standard out logging broken: messages only
routing to stderr and appear as a raw template
</li>
- </ul> <em>JalviewJS</em>
- <ul>
- <li>
- <!-- JAL-3202 -->Consensus profile may include zero (rounded
- down) percentage values causing a divide by zero
- </li>
- <li>
- <!-- -->
- </li>
<li>
- <!-- -->
+ <!-- JAL-3739 -->Entering web service parameter values in
+ numerical field doesn't update the value of the parameter
+ until return is pressed.
</li>
<li>
- <!-- -->
+ <!-- JAL-3749 -->Resolved known issue (from 2.11.1.1)
+ concerning duplicate CDS sequences generated when protein
+ products for certain ENA records are repeatedly shown via
+ Calculate->Show Cross Refs
</li>
+ </ul> <em>JalviewJS</em>
+ <ul>
<li>
- <!-- -->
+ <!-- JAL-3202 -->Consensus profile may include zero (rounded
+ down) percentage values causing a divide by zero
</li>
<li>
<!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
</ul>
</li>
- </ul>
- <em>Known Issues</em>
+ </ul> <em>Known Issues</em>
<ul>
<li>
<!-- JAL-3764 -->Display of RESNUM sequence features are not
suppressed when structures associated with a sequence are
- viewed with an external viewer (Regression from 2.11.1 series)
+ viewed with an external viewer (Regression from 2.11.1
+ series)
</li>
</ul>
</td>
<td width="60" nowrap>
<div align="center">
<strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
- <em>7/06/2018</em></strong>
+ <em>07/06/2018</em></strong>
</div>
</td>
<td><div align="left">
</div></td>
<td><div align="left">
<em>Desktop</em>
- <ul>
<ul>
<li>
<!-- JAL-2859-->Only one structure is loaded when
<li>Export scrollable SVG in HTML page</li>
<li>Optional embedding of BioJSON data when exporting
alignment figures to HTML</li>
+ </ul>
</li>
<li>3D structure retrieval and display
<ul>
<li>Core PDB parsing code requires Jmol</li>
<li>Sequence canvas panel goes white when alignment
window is being resized</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview.2.8.2b1">2.8.2b1</a><br /> <em>15/12/2014</em></strong>
+ </div></td>
+ <td>
+ </td>
+ <td>
+ <ul>
+ <li>Reinstated the display of default example file on startup</li>
+ <li>All pairs shown in Jalview window when viewing result of pairwise alignment</li>
</ul>
</td>
</tr>
+
<tr>
<td><div align="center">
<strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
<li>Fasta files with sequences containing '*' incorrectly
recognised as PFAM or BLC</li>
<li>conservation/PID slider apply all groups option
- doesn't affect background (2.8.0b1)
- <li></li>
+ doesn't affect background (2.8.0b1)</li>
<li>redundancy highlighting is erratic at 0% and 100%</li>
<li>Remove gapped columns fails for sequences with ragged
trailing gaps</li>
<li>Fetch sequences from DAS sources supporting the
sequence command</li>
</ul> <em>Import and Export</em>
+ <ul>
<li>export annotation rows as CSV for spreadsheet import</li>
<li>Jalview projects record alignment dataset associations,
EMBL products, and cDNA sequence mappings</li>
git://source.jalview.org / jalview.git / blobdiff