+ 2.11.1.1
- 13/07/2020 |
+ 17/09/2020
+
+ 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)
-
+
+ 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, 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
+
+
+ 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
+
+
+ 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
+
+ -
+ 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)
+
+
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