2.11.0
- 02/07/2019
+ 04/07/2019
|
@@ -75,7 +75,7 @@ li:before {
-
File type associations for
- formats supported by jalview (including .jvp project files)
+ formats supported by Jalview (including .jvp project files)
-
Jalview launch files (.jvl) to pass command line
@@ -100,19 +100,23 @@ li:before {
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
@@ -171,7 +175,7 @@ li:before {
-
Alignment Overview now WYSIWIS (What you see is
- what is shown)
Only visible region of alignment is shown by
+ what is shown)
Only visible regions of alignment are shown by
default (can be changed in user preferences)
-
@@ -199,7 +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
@@ -227,41 +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unmarshalling has been replaced by JAXB for Jalview projects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
-
- Build system migrated from Ant to Gradle
-
- - Enhanced checks for missing and duplicated keys in Message bundles
- -
- Eclipse project configuration managed with
- gradle-eclipse
+ Build system migrated from Ant to Gradle
- -
- Atlassian Bamboo continuous integration for
- unattended Test Suite execution
+ -
+ Enhanced checks for missing and duplicated keys in Message bundles
-
- 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)
+ 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
+
+ -
+ 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
+
|
@@ -304,8 +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
@@ -330,12 +348,12 @@ li:before {
red in original view
- stop_gained variants not shown correctly on
- peptide sequence
+ 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
@@ -422,12 +440,15 @@ li:before {
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
-
@@ -448,16 +469,22 @@ li:before {
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
-
- New Known Defects
-
- - Select columns containing feature by double clicking ignores bounds of an existing selected region
+
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
@@ -486,18 +513,23 @@ li:before {
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
+ -
+ Cancel on Feature Settings dialog doesn't reset group visibility
-
F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
- - Java 11 Specific defects
+
-
+ 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
+
+
|