- 2.11
- 20/06/2019
+ 2.11.0
+ 04/07/2019
|
-
+ 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 +96,34 @@ li:before {
Update of Ensembl Rest Client to API v10.0
- 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)
+
-
+ 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)
+
+ -
+ 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 +133,23 @@ 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 +159,7 @@ li:before {
- Speed and Efficiency
-
- More efficient creation of selections and
+ More efficient creation of selections and
multiple groups when working with large alignments
-
@@ -137,8 +174,8 @@ li:before {
view
-
- Alignment Overview now WYSIWIS (What you see is
- what is shown)
Only visible region of alignment is shown by
+ Alignment Overview now WYSIWIS (What you see is
+ what is shown)
Only visible regions of alignment are shown by
default (can be changed in user preferences)
-
@@ -166,7 +203,7 @@ li:before {
annotation
-
- Help button on Uniprot and PDB search panels
+ Help button on Uniprot and PDB search panels
-
Cursor changes over draggable box in Overview
@@ -183,13 +220,10 @@ li:before {
+ - 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
@@ -197,52 +231,55 @@ li:before {
Deprecations
- -
- DAS sequence retrieval and annotation
+
- DAS sequence retrieval and annotation
capabilities removed from the Jalview Desktop
- -
- Castor library for XML marshalling and
+
- 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
+
- Added remarks about transparent rendering effects
not supported in EPS figure export
+ - Typos in documentation for Preferences dialog
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
+
-
+ Build system migrated from Ant to Gradle
+ -
+ Enhanced checks for missing and duplicated keys in Message bundles
-
- Atlassian Bamboo continuous integration for
- unattended Test Suite execution
+ Eclipse project configuration managed with
+ gradle-eclipse
+
-
- Memory test suite to detect leaks in common
- operations
+ Atlassian
+ Bamboo continuous integration for unattended Test Suite
+ execution
+
-
- IntervalStoreJ (NCList
- implementation that alows updates) used for Sequence Feature collections
- - More unit test coverage, and minor issues resolved.
+ Memory test suite to detect leaks in common
+ operations
+
+ -
+ More unit test coverage, and minor
+ issues resolved
+
+ -
+ Developer documentation migrated to
+ markdown (with HTML rendering)
+
+ -
+ HelpLinksChecker runs on Windows
+
+ -
+ New URLs for publishing development
+ versions of Jalview
+
|
@@ -285,8 +322,8 @@ li:before {
Settings and Jalview Preferences panels
- Jalview hangs when closing windows or the
- overview updates with large alignments
+ Jalview hangs when closing windows, or redrawing the
+ overview with large alignments
Tree and PCA calculation fails for selected
@@ -302,12 +339,21 @@ li:before {
doesn't tell users the invalid URL
- Nonpositional features lose feature group on
- export as Jalview features file
+ 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
+
+ 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)
+ manually created features (where feature score is Float.NaN)
Blank extra columns drawn or printed
@@ -338,7 +384,7 @@ li:before {
Page Up in wrapped mode
- Finder doesn't skip hidden regions
+ Finder doesn't skip hidden regions
Finder searches in minimised alignments
@@ -390,16 +436,19 @@ li:before {
shown in complementary view
- stop_gained variants not shown correctly on
- peptide sequence
+ Codon consensus incorrectly scaled when shown
+ without normalisation
- Sequence Details report opens positioned to top
+ 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
-
@@ -417,12 +466,30 @@ li:before {
dialog corrupts dataset sequence
-
- Codon consensus logo incorrectly scaled when
- shown without normalisation
+ 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.
-
- New Known Defects
-
-
Input Data menu entry is greyed out when PCA View
is restored from a Jalview 2.11 project
@@ -446,14 +513,23 @@ li:before {
not shown as thresholded features in 2.11. To workaround please
create a Score filter instead.
- - Java 11 Specific defects
+
-
+ Cancel on Feature Settings dialog doesn't reset group visibility
+ -
+ F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
+
+ -
+ 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
-
-
-
-
+ Jalview Properties file is not sorted
+ alphabetically when saved
+
+
|