X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=3266aaea28b37855bdae75ffd33f634ddd00386e;hp=6820883ca021833370b2acdf38b15a19d494cd3b;hb=a40669b2eeb34a6c760b63c172a31a194b456f24;hpb=03c3f8e7a5593159371fd91fdf30d9f246961da5
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 6820883..3266aae 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -55,13 +55,120 @@ li:before {
| New Features |
Issues Resolved |
+ 2.11.1.4
+ 26/02/2021 |
+ 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
+
+ |
+
+
+ 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
- 13/07/2020 |
+ 17/09/2020
-
-
Shift+arrow keys navigate to next gap or
residue in cursor mode
@@ -91,23 +198,53 @@ li:before {
ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
EMBL flat file
+ -
+ Improved warning messages, debug logging
+ and fixed Retry action when Jalview encounters errors when
+ saving or making backup files.
+
+ -
+ Enhanced Jalview Java Console:
+
+ - Jalview's logging level can be configured
+ - Copy to Clipboard Buttion
+
+
+ -
+ Improved support for Hi-DPI (4K) screens
+ when running on Linux (Requires Java 11+)
+
Launching Jalview
-
Configure Jalview Desktop's look and feel
through a system property
+ -
+ Improved built-in documentation and command
+ line help for configuring Jalview's memory
+
|
-
+ Conservation and Quality tracks are shown
+ but not calculated and no protein or DNA score models are
+ available for tree/PCA calculation when launched with
+ Turkish language locale
+
+ -
Escape does not clear highlights on the
alignment (Since Jalview 2.10.3)
-
Alt+Left or Right arrow in cursor mode
- doesn't slide selected sequences
+ doesn't slide selected sequences, just sequence under cursor
+
+ -
+ Alt+Up/Down in cursor mode doesn't move
+ sequence under the cursor
-
Peptide-to-CDS tracking broken when
@@ -124,13 +261,94 @@ li:before {
to the position under the cursor
-
+ Sequence ID for reference sequence is
+ clipped when Right align Sequence IDs enabled
+
+ -
Slider with negative range values not
rendered correctly in VAqua4 (Since 2.10.4)
-
- New Known defects
+
+ Single quotes not displayed correctly in
+ internationalised text for some messages and log output
+
+
+ Find doesn't report matches that span
+ hidden gapped columns
+
+
+ Resolved memory leaks in Tree and PCA
+ panels, Alignment viewport and annotation renderer.
+
+
+ Jalview ignores file format parameter
+ specifying output format when exporting an alignment via the
+ command line
+
+
+ Windows 10: For a minority of users, if
+ backups are not enabled, Jalview sometimes fails to
+ overwrite an existing file and raises a warning dialog. (in
+ 2.11.0, and 2.11.1.0, the workaround is to try to save the
+ 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
+
+ -
+ Jalview application fails when launched the
+ first time for a version that has different jars to the
+ previous launched version.
+
+ Developing Jalview
+
+ -
+ Fixed issue with cleaning up old coverage
+ data, causing cloverReport gradle task to fail with an
+ OutOfMemory error.
+
+ -
+ Migrated the Jalview Version Checker to
+ monitor the release channel
+
+ New Known defects
- - Stale build data in jalview standalone jar builds (only affects 2.11.1.1 branch)
+
-
+ CDS shown in result of submitting proteins
+ in a CDS/Protein alignment to a web service is wrong when
+ proteins share a common transcript sequence (e.g.
+ genome of RNA viruses)
+
+ -
+ Co-located features exported and re-imported
+ are ordered differently when shown on alignment and in
+ tooltips. (Also affects v2.11.1.0)
+
+ -
+ Drag and drop of alignment file onto
+ alignment window when in a HiDPI scaled mode in Linux only
+ works for the top left quadrant of the alignment window
+
+ -
+ Stale build data in jalview standalone jar
+ builds (only affects 2.11.1.1 branch)
+
+ -
+ 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
|