X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=f0516e985d52673126d0463dab27489062b18131;hb=738f79179e4135a7225fc5c36e1ac4118aff0efb;hp=fa70d64fb06077f44dc1cadfc4a5671754dbab18;hpb=c7a6b7267536fdb9bb9c61eb2971c4ef4c805edb;p=jalview.git
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index fa70d64..f0516e9 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -57,14 +57,162 @@ li:before {
2.11.1.1
+ 11/08/2020 |
+
+
+
+ -
+ Shift+arrow keys navigate to next gap or
+ residue in cursor mode
+
+ -
+ Support import of VCF 4.3 by updating
+ HTSJDK from 2.12 to 2.23
+
+ -
+ IntervalStore library updated to v.1.1:
+ optimisations and improvements suggested by Bob Hanson and
+ improved compatibility with JalviewJS
+
+ -
+ Retrieve GZipped stockholm formatted
+ alignments from Pfam and Rfam
+
+ -
+ Recognise GZipped content for URLs and File
+ import (no longer based on .gz extension)
+
+ -
+ Updated Spanish Translation for 2.11.1
+
+ -
+ Migrate EMBL record retrieval to use latest
+ 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
+
+
+ |
+
+
+ -
+ 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, just sequence under cursor
+
+ -
+ Peptide-to-CDS tracking broken when
+ multiple EMBL gene products shown for a single contig
+
+ -
+ Errors encountered when processing variants
+ from VCF files yield "Error processing VCF: Format specifier
+ '%s'" on the console
+
+ -
+ Count of features not shown can be wrong
+ when there are both local and complementary features mapped
+ 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)
+
+ -
+ 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
+
+ Developing Jalview
+
+ -
+ Fixed issue with cleaning up old coverage
+ data, causing cloverReport gradle task to fail with an
+ OutOfMemory error.
+
+ New Known defects
+
+ -
+ Co-located features exported and re-imported
+ are ordered differently when shown on alignment and in
+ tooltips. (Also affects v2.11.1.0)
+
+ -
+ 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.
+
+ -
+ Drag and drop of alignment file onto
+ alignment window not working correctly when in a HiDPI
+ scaled mode in Linux
+
+ -
+ Stale build data in jalview standalone jar
+ builds (only affects 2.11.1.1 branch)
+
+
+ |
+
+
+ 2.11.1.0
- 27/03/2020 |
+ 22/04/2020
-
- Map 'virtual'
- codon features shown on protein (or vice versa) for display
- in alignments, on structure views and for export.
+ Map
+ 'virtual' codon features shown on protein (or vice versa)
+ for display in alignments, on structure views (including
+ transfer to UCSF chimera), in feature reports and for
+ export.
-
Feature attributes from VCF files can be
@@ -83,6 +231,10 @@ li:before {
position if reopened
-
+ Feature Settings dialog title includes name
+ of associated view
+
+ -
Font anti-aliasing in alignment views
enabled by default
@@ -94,6 +246,9 @@ li:before {
Warn if Sort by Score or Density attempted
with no feature types visible
+ -
+ Improved support for filtering feature attributes with large integer values
+
Jalview Installer
-
@@ -115,6 +270,9 @@ li:before {
-
New point release version scheme - 2.11.1.0
+ -
+ 'Jalview Test' installers/apps for easier access to test-release channel builds
+
Build System
-
@@ -125,20 +283,36 @@ li:before {
report
-
- Groovy Scripts
-
- -
- exportconsensus.groovy prints a FASTA
- file to stdout containing the consensus sequence for each
- alignment in a Jalview session
-
-
+ Groovy Scripts
+
+ -
+ exportconsensus.groovy prints a FASTA file
+ to stdout containing the consensus sequence for each
+ alignment in a Jalview session
+
+ -
+ ComputePeptideVariants.groovy to translate
+ genomic sequence_variant annotation from CDS as
+ missense_variant or synonymous_variant on protein products.
+
|
-
+ Hidden sequence markers still visible when
+ 'Show hidden markers' option is not ticked
+
+ -
+ Hidden sequence markers not shown in EPS and
+ PNG output when 'Automatically set ID width' is set in
+ jalview preferences or properties file
+
+ -
+ Feature Editor dialog can be opened when
+ 'Show Sequence Features' option is not ticked
+
+ -
Undo 'Null' operation shown after sort by
buttons in Feature Settings dialog are clicked when no
features are visible
@@ -188,6 +362,11 @@ li:before {
Credits missing some authors in Jalview
help documentation for 2.11.0 release
+ -
+ Export of Pfam alignment as Stockholm
+ includes Pfam ID as sequence's accession rather than its
+ Uniprot Accession
+
Java 11 Compatibility issues
-
@@ -226,6 +405,10 @@ li:before {
Jalview Installation type always reports
'Source' in console output
+ -
+ Test Suite: Certain Functional tests fail on jalview's
+ bamboo server but run fine locally.
+
|