-
+
+
+ -
+ Principal Components Analysis and
+ Viewer state is saved in Jalview Project
The 'Change
+ parameters' option has also been removed from the PCA
+ viewer.
+
+ -
+ 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 v9.0
+
+ -
+ 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)
+
+ -
+ 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)
+
+ -
+
+
+ Deprecations
+
+ -
+ DAS sequence retrieval and annotation
+ capabilities removed from the Jalview Desktop
+
+
+ Release Processes
+
+ - 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+ unmarshalling has been replaced by JAXB for Jalview projects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
+
+ -
+
+
+
+ |
+
+
+
+ -
+ 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.
+
+ -
+ Error message for trying to load in invalid
+ URLs doesn't tell users the invalid URL
+
+
+ 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)
+
+ -
+
+
+
+ New Known Defects
+
+ -
+ Nonpositional features lose feature group
+ on export as jalview features file
+
+ - Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project
+
+ |
+
+
+ |
+
+ |
+
+
+
+ -
+ Default memory for Jalview webstart and
+ InstallAnywhere increased to 1G.
+
+ -
+ Hidden sequence markers and representative
+ sequence bolding included when exporting alignment as EPS,
+ SVG, PNG or HTML. Display is configured via the
+ Format menu, or for command-line use via a jalview
+ properties file.
+
+ -
+ Ensembl client updated to Version 7 REST
+ API and sequence data now imported as JSON.
+
+ -
+ Change in recommended way of starting
+ Jalview via a Java command line: add jars in lib directory
+ to CLASSPATH, rather than via the deprecated java.ext.dirs
+ property.
+
+
+ Development
- |
-
-
+
+ Support added to execute test suite
+ instrumented with Open
+ Clover
+
+
+ |
+
+
+
+ -
+ Poorly scaled bar in quality annotation
+ row shown in Feredoxin Structure alignment view of example
+ alignment.
+
+ -
+ Annotation obscures sequences if lots of
+ annotation displayed.
+
+ -
+ Group conservation/consensus not shown
+ for newly created group when 'Apply to all groups'
+ selected
+
+ -
+ Corrupted display when switching to
+ wrapped mode when sequence panel's vertical scrollbar is
+ visible.
+
+ -
+ Alignment is black in exported EPS file
+ when sequences are selected in exported view.
+
+ -
+ Groups with different coloured borders
+ aren't rendered with correct colour.
+
+ -
+ Jalview could hang when importing certain
+ types of knotted RNA secondary structure.
+
+ -
+ Sequence highlight and selection in
+ trimmed VARNA 2D structure is incorrect for sequences that
+ do not start at 1.
+
+ -
+ '.' inserted into RNA secondary structure
+ annotation when columns are inserted into an alignment,
+ and when exporting as Stockholm flatfile.
+
+ -
+ Jalview annotation rows containing upper
+ and lower-case 'E' and 'H' do not automatically get
+ treated as RNA secondary structure.
+
+ -
+ .jvp should be used as default extension
+ (not .jar) when saving a jalview project file.
+
+ -
+ Mac Users: closing a window correctly
+ transfers focus to previous window on OSX
+
+
+ Java 10 Issues Resolved
- |
+
+ OSX - Can't save new files via the File
+ or export menus by typing in a name into the Save dialog
+ box.
+
+
+ Jalview now uses patched version
+ of the VAqua5
+ 'look and feel' which has improved compatibility with the
+ latest version of OSX.
+
+
+
+
|
@@ -130,7 +362,8 @@ li:before {
annotation added to view (Windows)
- Jalview Desktop is slow to start up when network connectivity is poor
+ Jalview Desktop is slow to start up when
+ network connectivity is poor
Drag URL from chrome, firefox, IE to
|