2.11
- 14/05/2019 (final due date !)
+ 20/06/2019
|
-
Annotate nucleotide alignments from VCF data files
-
- Optional automatic backups when saving
- Jalview project or alignment files
- -
- Principal Components Analysis and
- Viewer state is saved in Jalview Project
The 'Change
- parameters' option has also been removed from the PCA viewer
- -
- New 'Colour by Sequence ID' (subgroup) option
- -
- Alternative genetic code tables supported for
+ Alternative genetic code tables for
'Translate as cDNA'
-
- Finder panel remembers last position in each view
- -
- More efficient creation of selections and
- multiple groups when working with large alignments
- -
- Speedier import of annotation rows when
- parsing stockholm files
- -
Update of Ensembl Rest Client to API v10.0
- -
- Sequence features can be filtered and
- shaded according to any associated attributes (e.g. variant
- attributes from VCF file, or key-value pairs imported from
- column 9 of GFF file)
- -
- Show synonymous codon variants on peptide sequences
- -
- Popup report of a selected sequence feature's details
- -
- More efficient sequence feature render
- algorithm (Z-sort/transparency and filter aware)
- -
- Alignment Overview now by default shows
- only visible region of alignment (this can be changed in
- user preferences)
- -
- File Chooser stays open after Cancel overwrite
- -
- Better popup menu behaviour when
- all sequences are hidden
- -
- Status bar shows bounds when dragging a selection
- region, and gap count when inserting or deleting gaps
- -
- Status bar updates over sequence and annotation labels
- -
- Show annotation tooltips and popup menus in wrapped mode
- -
- Can select columns by dragging left/right in annotations
- -
- Improved tooltips in Feature Settings dialog
- -
- Help button on Uniprot and PDB search panels
- -
- Cursor changes over draggable box in Overview panel
- -
- Overview panel default changed to not show hidden regions
- -
- Consistent ordering of links in sequence id popup menu
- -
- Sequence Details report opens positioned to top of report
- -
- Scale panel popup menu allows Hide selected columns adjacent
- to a hidden column marker
- -
- Can use shift + arrow keys to rotate PCA image incrementally
- -
- PCA depth cueing with graduated colours
-
+ Enhanced visualisation and analysis of Sequence Features
+
+ -
+ Sequence features can be filtered and
+ shaded according to any associated attributes (e.g. variant
+ attributes from VCF file, or key-value pairs imported from
+ column 9 of GFF file)
+
+ -
+ Show synonymous codon variants on peptide
+ sequences
+
+ -
+ Popup window to show full report for a selected sequence feature's
+ details
+
+ -
+ More efficient sequence feature render
+ algorithm (Z-sort/transparency and filter aware)
+
+ -
+ Improved tooltips in Feature Settings
+ dialog
+
+
+
+
+ Backup files created when saving Jalview project
+ or alignment files
+
+ Principal Components Analysis Viewer
+
+ -
+ Principal Components Analysis results
+ and Viewer state saved in Jalview Project
+
+ - 'Change parameters' option removed from viewer's
+ drop-down menus
+ -
+ Can use shift + arrow keys to rotate PCA image
+ incrementally
+
+ -
+ PCA plot is depth cued
+
+
+
+
+ New 'Colour by Sequence ID' option
+
+ Speed and Efficiency
+
+ -
+ More efficient creation of selections and
+ multiple groups when working with large alignments
+
+ -
+ Speedier import of annotation rows when parsing
+ Stockholm files
+
+
+ User Interface
+
+ -
+ Finder panel remembers last position in each
+ view
+
+ -
+ Alignment Overview now WYSIWIS (What you see is
+ what is shown)
Only visible region of alignment is shown by
+ default (can be changed in user preferences)
+
+ -
+ File Chooser stays open after responding Cancel
+ to the Overwrite Dialog
+
+ -
+ Better popup menu behaviour when all
+ sequences are hidden
+
+ -
+ Status bar shows bounds when dragging a
+ selection region, and gap count when inserting or deleting gaps
+
+ -
+ Status bar updates over sequence and annotation
+ labels
+
+ -
+ Annotation tooltips and popup menus are shown
+ when in wrapped mode
+
+ -
+ Can select columns by dragging left/right in a graph or histogram
+ annotation
+
+ -
+ Help button on Uniprot and PDB search panels
+
+ -
+ Cursor changes over draggable box in Overview
+ panel
+
+ -
+ Consistent ordering of links in sequence id
+ popup menu
+
+ -
+ Red line indicating tree-cut position not shown if no subgroups are created
+ -
+ Removed ability to configure length of search history by right-clicking search box
+
+
+
+ Java 11 Support
+
+ -
+ Java 11 Native Desktop installer, standalone JAR
+ and getdown release channels
+
+ -
+ OSX GUI integrations for App menu's 'About' entry and
+ trapping CMD-Q
+
+
+
Deprecations
-
DAS sequence retrieval and annotation
capabilities removed from the Jalview Desktop
-
- Release Processes
-
-
- Atlassian Bamboo continuous integration server for
+ Castor library for XML marshalling and
+ unmarshalling has been replaced by JAXB for Jalview projects
+ and XML based data retrieval clients
+ - Disable VAMSAS menu in preparation for removal
+ - Jalview Desktop no longer distributed via Java Web Start
+ Documentation
+
+ -
+ Added remarks about transparent rendering effects
+ not supported in EPS figure export
+
+ Development and Release Processes
+
+ -
+ Jalview Native Application and
+ Installers built with Install4j (licensed to the Jalview open
+ source project) rather than InstallAnywhere
+
+ -
+ Jalview Launcher System to auto-configure memory
+ settings, receive over the air updates and launch specific
+ versions via (Three
+ Rings' GetDown)
+
+ -
+ Build system migrated from Ant to Gradle
+
+ -
+ Eclipse project configuration managed with
+ gradle-eclipse
+
+ -
+ Atlassian Bamboo continuous integration for
unattended Test Suite execution
-
Memory test suite to detect leaks in common
operations
-
- IntervalStoreJ (new updatable NCList
- implementation) used for Sequence Feature collections
- -
- Castor library for XML marshalling and
- unmarshalling has been replaced by JAXB for Jalview projects
- and XML based data retrieval clients
+ IntervalStoreJ (NCList
+ implementation that alows updates) used for Sequence Feature collections
+ - More unit test coverage, and minor issues resolved.
|
@@ -166,7 +251,11 @@ li:before {
Timeouts when retrieving data from Ensembl
'View [Structure] Mappings' and structure superposition in Jmol fail on Windows
-
+
+ Blank error dialog is displayed when discovering
+ structures for sequences with lots of PDB structures
+
+
Text misaligned in EPS or SVG image export with monospaced font
Warning of 'Duplicate entry' when saving
@@ -192,13 +281,20 @@ li:before {
Tree and PCA calculation fails for selected
region if columns were selected by dragging right-to-left
and the mouse moved to the left of the first column
+
+ Couldn't hide selected columns adjacent
+ to a hidden column marker via scale popup menu
Error message for trying to load in invalid
URLs doesn't tell users the invalid URL
Nonpositional features lose feature group
on export as Jalview features file
-
+
+ 'Graduated colour' option not offered for
+ manually created features (where if feature score is Float.NaN)
+
+
Blank extra columns drawn or
printed when columns are hidden
@@ -247,6 +343,8 @@ li:before {
stop_gained variants not shown correctly on peptide sequence
+ Sequence Details report opens positioned to top of report
+
Help page can be opened twice
Editing
@@ -256,19 +354,35 @@ li:before {
sequence data at beginning or end of alignment added/removed
via 'Edit' sequence
- Delete/Cut selection doesn't relocate
+ Delete/Cut selection doesn't relocate
sequence features correctly when start of sequence is
removed (Known defect since 2.10)
-
- New Known Defects
+
+ Inserting gap sequence via the Edit Sequence
+ dialog corrupts dataset sequence
+
+ New Known Defects
-
Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project
-
- Alignment panel height can be too small after 'New View'
- -
- Display is incorrect after removing gapped columns within hidden columns
-
+ Alignment panel height can be too small after 'New View'
+
+ Display is incorrect after removing gapped
+ columns within hidden columns
+
+
+ Rightmost selection is lost when mouse re-enters
+ window after dragging left to select columns to left of visible
+ region
+
+
+ Features coloured according to their description
+ string and thresholded by score in earlier versions of Jalview are
+ not shown as thresholded features in 2.11. To workaround please
+ create a Score filter instead.
+
+
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