+ 2.11.2.0
- 3/03/2022 |
+ 10/03/2022
-
@@ -77,15 +163,6 @@ 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 +177,20 @@ 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
@@ -108,6 +199,17 @@ li:before {
disabled by default
-
+ 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)
+
+ -
-nowebservicediscovery command line
argument to prevent automatic discovery of analysis
webservices on launch
@@ -118,10 +220,56 @@ li:before {
opened by double clicking the Structure Preferences' path
textbox
-
- Jalview Native App
+
+ 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
-
+ 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)
+
+ -
+ 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
@@ -137,17 +285,12 @@ li:before {
JalviewJS
-
- PDB structures mapped to Uniprot Sequences with
- SIFTS
-
- -
- setprop commandline argument reinstated for JalviewJS only
-
- -
-
+ PDB structures mapped to Uniprot Sequences
+ with SIFTS
-
-
+ setprop commandline argument reinstated for
+ JalviewJS only
-
Missing message bundle keys are only
@@ -158,26 +301,28 @@ 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
@@ -187,11 +332,9 @@ li:before {
Improved compatibility of Jalview build
with Java 17 (next LTS target)
-
-
|
-
+ |
-
Slow structure commands can block Jalview
@@ -205,7 +348,6 @@ li:before {
-
Annotation file: PROPERTIES apply only to
the first SEQUENCE_GROUP defined
-
-
@@ -244,26 +386,29 @@ li:before {
Can open multiple Preferences panels
-
- Standard out logging broken: messages only
- routing to stderr and appear as a raw template
+ Properly configure HTTPS proxy settings
+ from Preferences
- JalviewJS
-
-
- Consensus profile may include zero (rounded
- down) percentage values causing a divide by zero
-
- -
-
+ 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
@@ -288,6 +433,14 @@ 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)
+
|
@@ -531,6 +684,12 @@ li:before {
Improved support for Hi-DPI (4K) screens
when running on Linux (Requires Java 11+)
+
-
@@ -611,6 +770,11 @@ li:before {
save in place.)
-
+ Dragging a PDB file onto an alignment with
+ sequence features displayed causes displayed features to be
+ hidden.
+
+ -
Cannot process alignments from HTTPS urls
via command line
@@ -1534,7 +1698,7 @@ li:before {
|
@@ -1777,7 +1941,6 @@ li:before {
|
Desktop
-
-
Only one structure is loaded when
@@ -3620,6 +3783,7 @@ li:before {
- Export scrollable SVG in HTML page
- Optional embedding of BioJSON data when exporting
alignment figures to HTML
+
- 3D structure retrieval and display
@@ -3781,10 +3945,24 @@ li:before {
- Core PDB parsing code requires Jmol
- Sequence canvas panel goes white when alignment
window is being resized
+
+ |
+
+
+ |
+
+ |
+
+
+ - Reinstated the display of default example file on startup
+ - All pairs shown in Jalview window when viewing result of pairwise alignment
|
+
2.8.2
3/12/2014
@@ -4073,8 +4251,7 @@ li:before {
- Fasta files with sequences containing '*' incorrectly
recognised as PFAM or BLC
- conservation/PID slider apply all groups option
- doesn't affect background (2.8.0b1)
-
+ doesn't affect background (2.8.0b1)
- redundancy highlighting is erratic at 0% and 100%
- Remove gapped columns fails for sequences with ragged
trailing gaps
@@ -4951,6 +5128,7 @@ li:before {
- Fetch sequences from DAS sources supporting the
sequence command
Import and Export
+
- export annotation rows as CSV for spreadsheet import
- Jalview projects record alignment dataset associations,
EMBL products, and cDNA sequence mappings
|