2.11.1.0
- 27/03/2020 |
+ id="Jalview.2.11.1">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.
+
-
- Option to show 'virtual' codon features on
- protein (or vice versa)
+ Enhanced Jalview Java Console:
- -
- Option to export virtual features if
- shown
-
- -
- Option to transfer virtual features to
- Chimera
-
+ - Jalview's logging level can be configured
+ - Copy to Clipboard Buttion
-
- Feature attributes from VCF files can be exported and re-imported as GFF3 files
+ 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, 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)
+
+ -
+ Sequence ID colourscheme not re-applied
+ when alignment view restored from project (since Jalview 2.11.0)
+
+
+ |
+
+
+ 2.11.1.0
+ 22/04/2020 |
+
+
+ -
+ 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
+ exported and re-imported as GFF3 files
+
+ -
+ Capture VCF "fixed column" values
+ POS, ID, QUAL, FILTER as Feature Attributes
+
+ -
+ More robust VCF numeric data field
+ validation while parsing
-
- Capture VCF "fixed column" values POS,
- ID, QUAL, FILTER as Feature Attributes
+ Feature Settings dialog keeps same screen
+ position if reopened
-
- More robust VCF numeric data field validation while parsing
+ Feature Settings dialog title includes name
+ of associated view
-
- Feature Settings dialog keeps same screen position if reopened
-
+ Font anti-aliasing in alignment views
+ enabled by default
+
-
- Font anti-aliasing in alignment views enabled by default
-
+ Very long feature descriptions truncated in
+ tooltips and menus
+
-
- Very long feature descriptions truncated in tooltips and menus
-
+ Warn if Sort by Score or Density attempted
+ with no feature types visible
+
-
- 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
@@ -118,6 +280,9 @@ 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
-
@@ -128,20 +293,36 @@ 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
@@ -180,34 +361,45 @@ li:before {
IllegalArgumentException in some circumstances
-
- Multiple feature settings dialogs can be opened for a view
+ Multiple feature settings dialogs can be
+ opened for a view
-
- Feature Settings dialog is orphaned if alignment window is closed
+ Feature Settings dialog is orphaned if
+ alignment window is closed
-
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
-
- OSX - Can't view some search results in PDB/Uniprot search panel
+ OSX - Can't view some search results in
+ PDB/Uniprot search panel
- Installer
+ Installer
- - Jalview should not create file associations for 3D structure files (.pdb, .mmcif. .cif)
+
-
+ Jalview should not create file associations
+ for 3D structure files (.pdb, .mmcif. .cif)
Repository and Source Release
-
- removed obsolete .cvsignore files from repository
+ removed obsolete .cvsignore files from
+ repository
-
- Clover report generation running out of memory
+ Clover report generation running out of
+ memory
-
- New Known Issues
+ New Known Issues
-
OSX - Current working directory not
@@ -220,7 +412,12 @@ li:before {
enabled
-
- Jalview Installation type always reports 'Source' in console output
+ Jalview Installation type always reports
+ 'Source' in console output
+
+ -
+ Test Suite: Certain Functional tests fail on jalview's
+ bamboo server but run fine locally.
|