2.11.1.0
- 25/2/2020 |
+ id="Jalview.2.11.1">2.11.1.1
+ 13/07/2020
- - Feature attributes from VCF files can be exported and re-imported as GFF3 files
+
+
-
+ 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 fetched via URL
+
+
+
+ |
+
+
+ -
+ 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
-
- Record "fixed column" values POS,
- ID, QUAL, FILTER from VCF as Feature Attributes
+ 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
+
+
+ |
+
+
+ 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 (e.g. AF* attributes)
+ validation while parsing
+
+ -
+ Feature Settings dialog keeps same screen
+ position if reopened
+
+ -
+ Feature Settings dialog title includes name
+ of associated view
-
Font anti-aliasing in alignment views
enabled by default
-
-
+ Very long feature descriptions truncated in
+ tooltips and menus
+
+ -
+ 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
-
+
-
Versions for install4j and getdown and installer template version reported
in console (may be null when Jalview launched as executable jar or via conda)
-
Layout improvements for OSX .dmg Finder and higher quality background images
-
+
-
- New installer/application launcher generated with install4j 8.0.4
+ New installer/application launcher generated with install4j 8.0.4
- - Jalview File Associations shown for Unix Platforms
- - Improved defaults for maximum memory setting when running on large memory machines
+ -
+ Jalview File Associations shown for Unix Platforms
+ -
+ Improved defaults for maximum memory setting when running on large memory machines
Release processes
-
New point release version scheme - 2.11.1.0
+ -
+ 'Jalview Test' installers/apps for easier access to test-release channel builds
+
Build System
-
@@ -106,18 +192,48 @@ li:before {
Test code included in Clover coverage
report
- Deprecations
+
+ 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
-
- ID margin for CDS and Protein views not equal when split frame is first opened
+ Feature Editor dialog can be opened when
+ 'Show Sequence Features' option is not ticked
-
- Sequence position numbers in status bar not correct after editing a sequence's start position via GUI
+ Undo 'Null' operation shown after sort by
+ buttons in Feature Settings dialog are clicked when no
+ features are visible
+
+ -
+ ID margins for CDS and Protein views not
+ equal when split frame is first opened
+
+ -
+ Sequence position numbers in status bar not
+ correct after editing a sequence's start position
-
Alignment is misaligned in wrapped mode
@@ -141,29 +257,49 @@ li:before {
feature settings dialog also selects columns
-
- SpinnerNumberModel causing
+ SpinnerNumberModel causes
IllegalArgumentException in some circumstances
-
+ Multiple feature settings dialogs can be
+ opened for a view
+
+ -
+ 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 results in PDB/Uniprot FTS
+ OSX - Can't view some search results in
+ PDB/Uniprot search panel
- Installer
+ Installer
- - Jalview does not automatically 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 redundant .gitignore files from
+ removed obsolete .cvsignore files from
repository
-
- New Known Issues
+
+ Clover report generation running out of
+ memory
+
+ New Known Issues
-
OSX - Current working directory not
@@ -176,7 +312,12 @@ 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.
|