X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=9d3c568ffc34f1867e7dfd65e2b224fe589dcbed;hb=6a1a9ecb46fa986460dbe5a85a072f97c96f9121;hp=5d3a3837a1db5863baa276f75b8a6047b7ddcab4;hpb=ef915732552933bb67aaf40559e071826f9e3e52;p=jalview.git
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 5d3a383..9d3c568 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -1,3 +1,4 @@
+
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
- 11/08/2020 |
+ 17/09/2020
-
-
Shift+arrow keys navigate to next gap or
residue in cursor mode
@@ -92,7 +247,7 @@ li:before {
EMBL flat file
-
- Improved warning messages, debug logging
+ Improved warning messages, debug logging
and fixed Retry action when Jalview encounters errors when
saving or making backup files.
@@ -116,12 +271,18 @@ li:before {
-
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)
@@ -130,6 +291,10 @@ li:before {
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
multiple EMBL gene products shown for a single contig
@@ -155,6 +320,42 @@ li:before {
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
-
@@ -162,18 +363,40 @@ li:before {
data, causing cloverReport gradle task to fail with an
OutOfMemory error.
+ -
+ Migrated the Jalview Version Checker to
+ monitor the release channel
+
New Known defects
-
+ 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)
-
- 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.
- Workaround is to try to save the file again, and if that
- fails, delete the original file and save in place.
+ 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
|