+ 2.11.2.0
- 3/03/2022 |
+ 10/03/2022
-
@@ -77,15 +131,6 @@ li:before {
structure mapped to positions involved in the alignment
-
- New Preferences tab for adjusting Jalview's
- memory settings at launch
-
- -
- Reverted to Jalview 'classic' drop-down
- menu for selecting which database to fetch from in sequence
- fetcher dialog.
-
- -
Structure annotation rows for all mapped
chains in 3D structures are included in the 'Reference
Annotation' for a sequence
@@ -100,6 +145,20 @@ li:before {
Support for Canonical Uniprot IDs
-
+ New Preferences tab for adjusting Jalview's
+ memory settings at launch
+
+ -
+ Sequence IDs split on '_' as well as other
+ non-alphanumerics when discovering database references with
+ 'Fetch DB Refs'
+
+ -
+ Suppressed harmless exceptions output to
+ Console whilst discovering database references for a
+ sequence
+
+ -
Updated Jalview bindings for Uniprot XML
schema
@@ -108,25 +167,98 @@ li:before {
disabled by default
-
- -nowebservicediscovery command line argument to
- prevent automatic discovery of analysis webservices on
- launch
+ Reverted to Jalview 'classic' drop-down
+ menu for selecting which database to fetch from in sequence
+ fetcher dialog.
+
+ -
+ Updated Ensembl REST Client compatibility
+ to 15.2 and revised model organism names (rat, xenopus,
+ dmelanogaster now rattus_norvegicus, xenopus_tropicalis,
+ drosophila_melanogaster)
-
- JalviewJS
+
+ -nowebservicediscovery command line
+ argument to prevent automatic discovery of analysis
+ webservices on launch
+
+
+ Allow 'App' directories to be opened when
+ locating Chimera, ChimeraX or Pymol binaries via filechooser
+ opened by double clicking the Structure Preferences' path
+ textbox
+
+
+ support for HTTP/S access via
+ proxies that require authentication
+
+
+ New mechanism for opening URLs with system
+ default browser (works on OSX and Linux as well as Windows)
+
+
+ Upgraded bundled version of Jmol
+ to 14.31.53
+
+
+ GPL license info on splash screen and About
+ text
+
+ Jalview Native App
-
- PDB structures mapped to Uniprot Sequences with
- SIFTS
+ 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.
This
+ is the recommended workaround for known issue about
+ working directory preservation when running native
+ application from command line.
+
+
+ - Notarized MacOS installer for compliance with latest
+ OSX releases (Monterey)
+ -
+ Uninstaller application for old
+ (InstallAnywhere based) Jalview installations removed from
+ the OSX disk image
+
+ -
+ Options to allow user to choose the (Swing)
+ Look and Feel (LaF) used by Jalview
+
+ -
+ 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
+ JAL-3137)
-
- setprop commandline argument reinstated for JalviewJS only
+ Getdown launcher inherits HTTP/S proxy
+ configuration from jalview_properties
-
-
+ New Jalview Develop app - making it even easier
+ to get at Jalview's development builds
-
-
+ New splashscreens for Jalview, Jalview Test
+ and Jalview Develop applications.
+
+ -
+ Jalview logos shown for Jalview Java
+ Console and other window widgets in taskbar and dock rather
+ than anonymous 'Java' icons
+
+ JalviewJS
+
+ -
+ PDB structures mapped to Uniprot Sequences
+ with SIFTS
+
+ -
+ setprop commandline argument reinstated for
+ JalviewJS only
-
Missing message bundle keys are only
@@ -137,36 +269,40 @@ li:before {
Feature type is included in the title of
the Feature Settings' Colour Chooser dialog
-
+ -
+ Build details reported in About window
+
+ -
+ Numerous minor
+ GUI additions and improvements in sync with Java
+ application.
+
Development
-
First integrated JalviewJS and Jalview release
- - Updated building instructions
+ -
+ Updated README and doc/building.md
+
-
Improved JalviewJS/Jalview build
process, added support for system package provided eclipse
installs on linux
- Install4j 9.0.x used for installer packaging
- - Notarized MacOS installer for compatibility with Big
- Sur and Monterey
- -
- Uninstaller application for old
- (InstallAnywhere based) Jalview installations removed from
- the DMG
-
-
Improved use of installers for unattended
installation with a customizedId of "JALVIEW" in install4j's
Jalview Launcher
-
+ -
+ Improved compatibility of Jalview build
+ with Java 17 (next LTS target)
+
-
|
-
+ |
-
Slow structure commands can block Jalview
@@ -180,7 +316,6 @@ li:before {
-
Annotation file: PROPERTIES apply only to
the first SEQUENCE_GROUP defined
-
-
@@ -219,26 +354,29 @@ li:before {
Can open multiple Preferences panels
-
- Standard out logging broken: messages only
- routing to stderr and appear as a raw template
-
- JalviewJS
-
- -
- Consensus profile may include zero (rounded
- down) percentage values causing a divide by zero
+ Properly configure HTTPS proxy settings
+ from Preferences
-
-
+ Standard out logging broken: messages only
+ routing to stderr and appear as a raw template
-
-
+ Entering web service parameter values in
+ numerical field doesn't update the value of the parameter
+ until return is pressed.
-
-
+ 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
+ JalviewJS
+
-
-
+ Consensus profile may include zero (rounded
+ down) percentage values causing a divide by zero
-
JalviewJS doesn't honour arguments passed
@@ -263,6 +401,14 @@ li:before {
+ Known Issues
+
+ -
+ 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)
+
|
@@ -506,6 +652,12 @@ li:before {
Improved support for Hi-DPI (4K) screens
when running on Linux (Requires Java 11+)
+