X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=0fba08a635bc7d6afe0e37a928781aa25f40be9b;hb=1cb2d001bec9aac0da55fe770b40f034c4b071ff;hp=993fcd50737ddd23a69d7594308531d254efeda0;hpb=576d2415673f37bb083d88e3c5702fb7d71d9b7b;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 993fcd5..0fba08a 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -67,6 +67,243 @@ li:before {
+
+ |
+
+ |
+
+ 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
+
+ |
+
+
+
+ -
+ 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
+
+
+ |
+
+
+ |
+
+ |
+
+
+
+ -
+ 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.
+
+
+ |
+
+
+ |
+
+ |
+
+
+
+ -
+ Use HGVS nomenclature for variant
+ annotation retrieved from Uniprot
+
+ -
+ Windows File Shortcuts can be dragged
+ onto the Jalview Desktop
+
+
+ |
+
+
+
+ -
+ Cannot import features with multiple
+ variant elements (blocks import of some Uniprot records)
+
+ -
+ Clustal files with sequence positions in
+ right-hand column parsed correctly
+
+ -
+ Wrap view - export to SVG - IDs shown but
+ not alignment area in exported graphic
+
+ -
+ F2/Keyboard mode edits work when Overview
+ window has input focus
+
+ -
+ Annotation panel set too high when
+ annotation added to view (Windows)
+
+ -
+ Jalview Desktop is slow to start up when
+ network connectivity is poor
+
+ -
+ Drag URL from chrome, firefox, IE to
+ Jalview desktop on Windows doesn't open file
Dragging
+ the currently open URL and links from a page viewed in
+ Firefox or Chrome on Windows is now fully supported. If
+ you are using Edge, only links in the page can be
+ dragged, and with Internet Explorer, only the currently
+ open URL in the browser can be dropped onto Jalview.
+
+
+ |
+
|
@@ -165,6 +402,10 @@ li:before {
as generated by CONSURF)
+ Uniprot 'sequence variant' features
+ tooltip doesn't include a text description of mutation
+
+
Invert displayed features very slow when
structure and/or overview windows are also shown
|