X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=8dbb2b7d4da693db9608855705196a63db1cb9d9;hb=e560da393ef730e8d9931d8916cab34b903c86a8;hp=dd7a3f8885df6235b5e4986a79dc3c7e97a8f4ef;hpb=a9f2db2f1688164dd54da7521509c135d7fdf042;p=jalview.git
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index dd7a3f8..8dbb2b7 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -1,3 +1,4 @@
+
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
+
+ -
+ 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
+
+ -
+ Consensus profile may include zero (rounded
+ down) percentage values causing a divide by zero
+
+ -
+
+
+ -
+
+
+ -
+
+
+ -
+
+
+ -
+ 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)
+
+
+ |
+
+
+ 2.11.1.3
+ 29/10/2020 |
+
+
+ |
+
+
+ -
+ Find doesn't always highlight all matching
+ positions in a sequence (bug introduced in 2.11.1.2)
+
+ -
+ Alignments containing one or more protein
+ sequences can be classed as nucleotide
+
+ -
+ CDS alignment doesn't match original CDS
+ sequences after alignment of protein products (known defect
+ first reported for 2.11.1.0)
+
+ -
+ No tooltip or popup menu for genomic
+ features outwith CDS shown overlaid on protein
+
+ -
+ Overlapping CDS in ENA accessions are not
+ correctly mapped by Jalview (e.g. affects viral CDS with
+ ribosomal slippage, since 2.9.0)
+
+ -
+ Spliced transcript CDS sequences don't show
+ CDS features
+
+ -
+ Selections in CDS sequence panel don't
+ always select corresponding protein sequences
+
+ -
+ Make groups from selection for a
+ column selection doesn't always ignore hidden columns
+
+ Installer
+
+ -
+ Space character in Jalview install path on
+ Windows prevents install4j launching getdown
+
+ Development
+
+ -
+ Fixed typos and specified compatible gradle
+ version numbers in doc/building.md
+
+
+ |
+
+
+ 2.11.1.2
+ 25/09/2020 |
+
+
+ |
+
+
+ -
+ Fresh install of Jalview 2.11.1.1 reports
+ "Encountered problems opening
+ https://www.jalview.org/examples/exampleFile_2_7.jvp"
+
+
+ |
+
+
+ 2.11.1.1
17/09/2020 |
@@ -185,6 +567,14 @@ li:before {
file again, and if that fails, delete the original file and
save in place.)
+
+ Cannot process alignments from HTTPS urls
+ via command line
+
+
+ References to http://www.jalview.org in
+ program and documentation
+
Launching Jalview
-
@@ -229,6 +619,11 @@ li:before {
Sequence ID colourscheme not re-applied
when alignment view restored from project (since Jalview 2.11.0)
+ -
+ Duplicate CDS sequences are generated when
+ protein products for certain ENA records are repeatedly
+ shown via Calculate->Show Cross Refs
+
|