- 2.11
- 20/06/2019
+ 2.11.0
+ 02/07/2019
|
-
+ 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)
+
+ -
+ File type associations for
+ formats supported by jalview (including .jvp project files)
+
+ -
+ Jalview launch files (.jvl) to pass command line
+ arguments and switch between different getdown channels
+
+ -
+ Backup files created when saving Jalview project
+ or alignment files
+
+
+ -
Annotate nucleotide alignments from VCF data files
+ - Version of HTSJDK shipped with Jalview updated to version 2.12.0
-
Alternative genetic code tables for
'Translate as cDNA'
@@ -71,22 +96,35 @@ li:before {
Update of Ensembl Rest Client to API v10.0
- Enhanced visualisation and analysis of Sequence Features
+ -
+ IntervalStoreJ (NCList
+ implementation that allows updates) used for Sequence Feature collections
+ -
-
- 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)
+ 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)
+
+ -
+ Feature Attributes and shading schemes
+ stored and restored from Jalview Projects
+
+ -
+ Use full Sequence Ontology (via BioJava) to
+ recognise variant features
-
- Show synonymous codon variants on peptide
- sequences
+ Show synonymous codon variants on peptide
+ sequences (also coloured red by default)
-
Popup window to show full report for a selected sequence feature's
details
-
- More efficient sequence feature render
+ More efficient sequence feature render
algorithm (Z-sort/transparency and filter aware)
-
@@ -96,23 +134,23 @@ li:before {
-
- Backup files created when saving Jalview project
- or alignment files
-
- - Principal Components Analysis Viewer
+ Symmetric score matrices for faster
+ tree and PCA calculations
+
+ - Principal Components Analysis Viewer
-
Principal Components Analysis results
and Viewer state saved in Jalview Project
- - 'Change parameters' option removed from viewer's
+
- '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
+ PCA plot is depth cued
@@ -122,7 +160,7 @@ li:before {
- Speed and Efficiency
-
- More efficient creation of selections and
+ More efficient creation of selections and
multiple groups when working with large alignments
-
@@ -137,7 +175,7 @@ li:before {
view
-
- Alignment Overview now WYSIWIS (What you see is
+ 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)
@@ -162,8 +200,8 @@ li:before {
when in wrapped mode
-
- Can select columns by dragging left/right in
- annotations
+ Can select columns by dragging left/right in a graph or histogram
+ annotation
-
Help button on Uniprot and PDB search panels
@@ -177,17 +215,16 @@ li:before {
popup menu
-
- Sequence Details report opens positioned to top
- of report
-
+ 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
+ Jalview Groovy Scripting Console updated to Groovy v2.5
+ Java 11 Support (not yet on general release)
-
- Java 11 Native Desktop installer, standalone JAR
- and getdown release channels
-
- -
OSX GUI integrations for App menu's 'About' entry and
trapping CMD-Q
@@ -199,157 +236,308 @@ li:before {
DAS sequence retrieval and annotation
capabilities removed from the Jalview Desktop
- Jalview Desktop no longer distributed via Java Web Start
-
- 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 server 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
-
- |
-
+ 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
+
+ - Typos in documentation for Preferences dialog
+ Development and Release Processes
+ -
+ Build system migrated from Ant to Gradle
+
+ - Enhanced checks for missing and duplicated keys in Message bundles
-
- Timeouts when retrieving data from Ensembl
- -
- 'View [Structure] Mappings' and structure superposition in Jmol fail on Windows
- -
- Text misaligned in EPS or SVG image export with monospaced font
- -
- Warning of 'Duplicate entry' when saving
- Jalview project involving multiple views
- -
- Overview for complementary view in a linked
- CDS/Protein alignment is not updated when Hide Columns by
- Annotation dialog hides columns
- -
- Selection highlighting in the complement of
- a CDS/Protein alignment stops working after making a
- selection in one view, then making another selection in the
- other view
- -
- Annotations tooltip changes beyond visible columns
- -
- Table Columns could be re-ordered in
- Feature Settings and Jalview Preferences panels
- -
- Jalview hangs when closing windows
- or the overview updates with large alignments
- -
- 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
- -
- Blank extra columns drawn or
- printed when columns are hidden
- -
- Regular expression error for '(' in Select Columns by Annotation description
- -
- Scroll doesn't stop on mouse up after
- dragging out of Scale or Annotation Panel
- -
- Column selection incorrect after scrolling out of scale panel
- -
- Left/right drag in annotation can scroll alignment down
- -
- Error if mouse moved before clicking Reveal in scale panel
- -
- Column display is out by one after Page Down, Page Up in wrapped mode
- -
- Finder doesn't skip hidden regions
- -
- Finder searches in minimised alignments
- -
- 'Apply Colour to All Groups' not always selected on
- opening an alignment
- -
- 'Colour by Annotation' not marked selected in Colour menu
- -
- Per-group Clustal colour scheme changes when
- different groups in the alignment are selected
- -
- Internationalised colour scheme names not shown correctly in menu
- -
- Colour by Annotation can go black at min/max threshold limit
- -
- Value input for graduated feature colour threshold gets 'unrounded'
- -
- PCA image export doesn't respect background colour
- -
- PCA points don't dim when rotated about y axis
+ Eclipse project configuration managed with
+ gradle-eclipse
+
-
- PCA Print dialog continues after Cancel
+ Atlassian
+ Bamboo continuous integration for unattended Test Suite
+ execution
+
-
- Cancel in Tree Font dialog resets alignment, not Tree font
+ Memory test suite to detect leaks in common
+ operations
+
-
- Associate Tree with All Views not restored from project file
+ More unit test coverage, and minor
+ issues resolved.
+
-
- Scrolling of split frame is sluggish if Overview shown in complementary view
+ Developer documentation migrated to
+ markdown (with HTML rendering)
+
-
- stop_gained variants not shown correctly on peptide sequence
+ HelpLinksChecker runs on Windows
+
-
- Help page can be opened twice
-
- Editing
-
+ New URLs for publishing development
+ versions of Jalview
+
-
- Start and End should be updated when
- sequence data at beginning or end of alignment added/removed
- via 'Edit' sequence
-
- Delete/Cut selection doesn't relocate
- sequence features correctly when start of sequence is
- removed (Known defect since 2.10)
- New Known Defects
-
- -
- Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project
+ |
+
+
+ -
+ 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 Jalview
+ project involving multiple views
+
+ -
+ Overview for complementary view in a linked
+ CDS/Protein alignment is not updated when Hide Columns by
+ Annotation dialog hides columns
+
+ -
+ Selection highlighting in the complement of a
+ CDS/Protein alignment stops working after making a selection in
+ one view, then making another selection in the other view
+
+ -
+ Annotations tooltip changes beyond visible
+ columns
+
+ -
+ Table Columns could be re-ordered in Feature
+ Settings and Jalview Preferences panels
+
+ -
+ Jalview hangs when closing windows or the
+ overview updates with large alignments
+
+ -
+ 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
+
+ -
+ Tooltips displayed for features filtered by
+ score from view
+
+ -
+ Sequence Variants retrieved from Ensembl during
+ show cross references or Fetch Database References are shown in
+ red in original view
+
-
- Alignment panel height can be too small after 'New View'
+ stop_gained variants not shown correctly on
+ peptide sequence (computed variant shown as p.Res.null)
+
+ -
+ '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
+
+ -
+ Regular expression error for '(' in Select
+ Columns by Annotation description
+
+ -
+ Scroll doesn't stop on mouse up after dragging
+ out of Scale or Annotation Panel
+
+ -
+ Column selection incorrect after scrolling out of
+ scale panel
+
+ -
+ Left/right drag in annotation can scroll
+ alignment down
+
+ -
+ Error if mouse moved before clicking Reveal in
+ scale panel
+
+ -
+ Column display is out by one after Page Down,
+ Page Up in wrapped mode
+
+ -
+ Finder doesn't skip hidden regions
+
+ -
+ Finder searches in minimised alignments
+
+ -
+ 'Apply Colour to All Groups' not always selected
+ on opening an alignment
+
+ -
+ 'Colour by Annotation' not marked selected in
+ Colour menu
+
+ -
+ Per-group Clustal colour scheme changes when
+ different groups in the alignment are selected
+
+ -
+ Internationalised colour scheme names not shown
+ correctly in menu
+
+ -
+ Colour by Annotation can go black at min/max
+ threshold limit
+
+ -
+ Value input for graduated feature colour
+ threshold gets 'unrounded'
+
+ -
+ PCA image export doesn't respect background
+ colour
+
+ -
+ PCA points don't dim when rotated about y axis
+
+ -
+ PCA Print dialog continues after Cancel
+
+ -
+ Cancel in Tree Font dialog resets alignment, not
+ Tree font
+
+ -
+ Associate Tree with All Views not restored from
+ project file
+
+ -
+ Scrolling of split frame is sluggish if Overview
+ shown in complementary view
+
+ -
+ Codon consensus incorrectly scaled when shown
+ without normalisation
+
+ -
+ Sequence Details report should open positioned at top
+ of report
+
+ -
+ Help page can be opened twice
+
+ -
+ Fuzzy text in web service status menu on OSX Mojave
+
+ Editing
+
+ -
+ Start and End should be updated when sequence
+ data at beginning or end of alignment added/removed via 'Edit'
+ sequence
+
+ -
+ Delete/Cut selection doesn't
+ relocate sequence features correctly when start of sequence is
+ removed (Known defect since 2.10)
+
+ -
+ Inserting gap sequence via the Edit Sequence
+ dialog corrupts dataset sequence
+
+ -
+ Structure colours not updated when associated tree
+ repartitions the alignment view (Regression in 2.10.5)
+
+
+ Datamodel
+
+ -
+ Sequence.findIndex returns wrong value when
+ sequence's End is greater than its length
+
+ - Bugs fixed for Java 11 Support (not
+ yet on general release)
+
+ -
+ Menus work properly in split-screen
+
+
+ New Known Defects
+
+ - Select columns containing feature by double clicking ignores bounds of an existing selected region
+
+ -
+ Codon consensus logo incorrectly scaled in gapped
+ regions of protein alignment.
+
+ -
+ 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
+
+ -
+ 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.
+
+ - Cancel on Feature Settings dialog doesn't reset group visibility
+ -
+ F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
+
-
- Display is incorrect after removing gapped columns within hidden columns
+ Closing tree windows with CMD/CTRL-W for
+ alignments with multiple views can close views unexpectedly
+
+ - Java 11 Specific defects
+
+ -
+ Jalview Properties file is not sorted
+ alphabetically when saved
+
+
+
- |
-
+
+