<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>3/03/2022</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'
+ </li>
+ <li>
+ <!-- JAL-3884 -->Suppressed harmless exceptions output to
+ Console whilst discovering database references for a
+ sequence
+ </li>
+ <li>
<!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
schema
</li>
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
opened by double clicking the Structure Preferences' path
textbox
</li>
- </ul>
- <em>Jalview Native App</em>
+ <li>
+ <!-- JAL-3632 JAL-3633 -->support for HTTP/S access via
+ proxies that require authentication
+ </li>
+ <li>
+ <!-- JAL-3103 -->New mechanism for opening URLs with system
+ 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>
<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.<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-3805 -->Uninstaller application for old
+ (InstallAnywhere based) Jalview installations removed from
+ the OSX disk image
+ </li>
+ <li>
+ <!-- JAL-3608 -->Options to allow user to choose the (Swing)
+ Look and Feel (LaF) used by Jalview
+ </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>)
+ </li>
+ <li>
+ <!-- JAL-3633 -->Getdown launcher inherits HTTP/S proxy
+ configuration from jalview_properties
+ </li>
+ <li>
<!-- JAL- -->New Jalview Develop app - making it even easier
to get at Jalview's development builds
</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
- </li>
- <li>
- <!-- JAL- -->
- </li>
- <li>
- <!-- JAL- -->
+ <!-- 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>
<ul>
<li>
<!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
the first SEQUENCE_GROUP defined
-
</li>
<li>
<!-- JAL-3275 -->Can open multiple Preferences panels
</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
+ <!-- JAL-3633 -->Properly configure HTTPS proxy settings
+ from Preferences
</li>
<li>
- <!-- -->
+ <!-- JAL-3949 -->Standard out logging broken: messages only
+ routing to stderr and appear as a raw template
</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>
+ <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)
+ </li>
</ul>
</td>
</tr>
<!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
when running on Linux (Requires Java 11+)
</li>
+ <li>
+ <!-- JAL-1842 JAL-3509 -->RESNUM sequence features (the
+ green ones) are not automatically displayed when associated
+ structures are displayed or for sequences retrieved from the
+ PDB.
+ </li>
</ul> <em>Launching Jalview</em>
<ul>
<li>
save in place.)
</li>
<li>
+ <!-- JAL-3509 -->Dragging a PDB file onto an alignment with
+ sequence features displayed causes displayed features to be
+ hidden.
+ </li>
+ <li>
<!-- JAL-3750 -->Cannot process alignments from HTTPS urls
via command line
</li>
git://source.jalview.org / jalview.git / blobdiff