X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=a6293e672bd97b726cff7dbe0eb3645680b0512e;hb=e69f7ec847b9dbbf88350521ccd3fd773c6aeaa8;hp=4c72658d6b7ac8bdc490a2fda8c4998e24b39ab5;hpb=ad31864f13259c7063cd598d4693b64b4c5fce92;p=jalview.git
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 4c72658..a6293e6 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -1,3 +1,4 @@
+
New .jalview_properties token controlling
- launch of the news browser (like -nonews argument)
-
-
- New .jalview_properties token controlling
- download of linkout URLs from
- www.jalview.org/services/identifiers
-
-
- New .jalview_properties token controlling
- download of BIOJSHTML templates
-
+
+ 2.11.2.0
+ 3/03/2022 |
+
+
+ -
+ Support for viewing 3D
+ structures with ChimeraX and Pymol in addition to Jmol and
+ Chimera.
+
+ -
+ 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
+
+ -
+ Import Genbank and EMBL format flatfiles
+
+ -
+ ENA record's mol_type honoured so RNA
+ molecules imported from ENA records are shown as RNA
+
-
+ Support for Canonical Uniprot IDs
+
+ -
+ Updated Jalview bindings for Uniprot XML
+ schema
+
+ JalviewJS
+
+ -
+ PDB structures mapped to Uniprot Sequences with
+ SIFTS
+
+ -
+
+
+ -
+
+
+ -
+
+
+ -
+ Missing message bundle keys are only
+ reported once per key (avoids excessive log output in js
+ console)
+
+ -
+ Feature type is included in the title of
+ the Feature Settings' Colour Chooser dialog
+
+
+ Development
+
+ - First integrated JalviewJS and Jalview release
+ - Updated building instructions
+ -
+ Improved JalviewJS/Jalview build process
+ 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
+
+
+
+
+ |
+
+
+ -
+ Slow structure commands can block Jalview
+ execution
+
-
- New 'Discover Web Services' option to trigger
- a one off JABAWS discovery if autodiscovery was disabled
-
- |
-
-
- |
+ Structure window's viewer-specific menu
+ disappears when only one structure is shown (and many
+ sequences:one chain mappings are present)
+
+
+ Annotation file: PROPERTIES apply only to
+ the first SEQUENCE_GROUP defined
+
+
+
+
+ Selections not
+ propagated between Linked CDS - Protein alignments and their
+ trees (known defect from 2.11.1.3)
+
+
+ Not all codon positions highlighted for
+ overlapping exon splice sites (e.g due to RNA slippage)
+
+
+ X was not being recognised as the unknown base
+ in DNA sequences
+
+
+ Removed RNAview checkbox and logic from
+ Structure Preferences
+
+
+ Tooltip behaviour improved (slightly)
+
+
+ Can edit a feature so that start > end
+
+
+ Cancel from Amend Features doesn't reset a
+ modified graduated colour
+
+
+ New View with automatic 'Show Overview'
+ preference enabled results in Null Pointer Exceptions when
+ clustal colouring is enabled
+
+ Can open multiple Preferences panels
+
+ Standard out logging broken: messages only
+ routing to stderr and appear as a raw template
+
+ JalviewJS
+
+ -
+
+
+ -
+
+
+ -
+
+
+ -
+
+
+ -
+
+
+ -
+ JalviewJS doesn't honour arguments passed
+ via Info.args when there are arguments on the URL
+
+ -
+ gradle closure-compiler not using UTF-8
+
+ -
+ Annotation file fails to load from URL in
+ JalviewJS
+
+
Development
+
+ - Gradle
+
+ - Fixed non-fatal gradle errors during build
+ -
+ Updated build.gradle for use with
+ Gradle v.6.6+
+
+
+
+
+
+
+
+
+ 2.11.1.7
+ 18/01/2022 |
+ |
+
+
+ -
+ Files open in Jalview cannot be
+ updated by Jalview or other applications (Windows, other non
+ Unix/BSD OSs)
+
+ Security
+
+ -
+ Enable AIA download of HTTPS intermediate
+ certificates.
+
+
+ |
+
+ 2.11.1.6
+ 6/01/2022 |
+
+ Security
+
+ -
+ Version bump library dependency: Log4j 2.16.0 to 2.17.0.
+
+ |
+
+ |
+
+
+ 2.11.1.5
+ 20/12/2021 |
+
+ Security
+
+ -
+ Update library dependency: Log4j 2.16.0
+ (was log4j 1.2.x).
+
Development
+
+ - Updated building instructions
+ |
+
+
+ -
+ Occupancy calculation is incorrect for
+ alignment columns with over -1+2^32 gaps (breaking filtering
+ and display)
+
+ -
+ Caps on Hi-DPI scaling to prevent crazy
+ scale factors being set with buggy window-managers (linux
+ only)
+
+ Development
+
+ - Fixed non-fatal gradle errors during build
+
+ |
+
+
+ 2.11.1.4
+ 09/03/2021 |
+ Improved control of
+ Jalview's use of network services via jalview_properties
+
+ -
+ New .jalview_properties token controlling
+ launch of the news browser (like -nonews argument)
+
+ -
+ New .jalview_properties token controlling
+ download of linkout URLs from
+ www.jalview.org/services/identifiers
+
+ -
+ New .jalview_properties token controlling
+ download of BIOJSHTML templates
+
+ -
+ New 'Discover Web Services' option to
+ trigger a one off JABAWS discovery if autodiscovery was
+ disabled
+
+ |
+
+
+ -
+ Intermittent deadlock opening structure in
+ Jmol
+
+ New Known defects
+
+ -
+ Protein Cross-Refs for Gene Sequence not
+ always restored from project (since 2.10.3)
+
+ -
+ Selections from tree built from CDS aren't
+ propagated to Protein alignment (since 2.11.1.3)
+
+
+ |
|