X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Freleases.html;h=af417a768933d9701bb2f02602c3baff4e8fdb01;hb=10d099e29efcb19b1e32043c74fd2dd12d5d65af;hp=2096f6f590fece361df1fa6c6b119de16c9e0012;hpb=fd20059368432141b6cfe42fd3aa993a260c011b;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 2096f6f..af417a7 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -67,19 +67,217 @@ li:before {
+
+
+
+ |
+
+
+
+ -
+ Jalview doesn't hang when closing windows or the overview updates with large alignments.
+
+
+ |
+
+
+
+ -
+ DAS sequence retrieval and annotation capabilities removed from the Jalview Desktop
+
+
+ |
+
+
+
+
+ |
+
+
+
+ -
+ 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.
+
+
+ |
+
|
-
- Structure Chooser controls to
- control superposition of multiple structures and open
- structures in existing views
+ New Structure Chooser control
+ for disabling automatic superposition of multiple
+ structures and open structures in existing views
-
Mouse cursor changes to indicate Sequence
@@ -96,7 +294,7 @@ li:before {
-
Improved performance when rendering lots
- of features
+ of features (particularly when transparency is disabled)
@@ -112,6 +310,25 @@ li:before {
overlapping alignment panel
+ Overview doesn't show end of unpadded
+ sequence as gaps
+
+
+ Cross-reference handling
+ improved: CDS not handled correctly if transcript has no
+ UTR
+
+
+ Secondary structure and temperature
+ factor annotation not added to sequence when local PDB
+ file associated with it by drag'n'drop or structure
+ chooser
+
+
+ Answering 'No' to PDB Autoassociate
+ dialog doesn't import PDB files dropped on an alignment
+
+
Linked scrolling via protein horizontal
scroll bar doesn't work for some CDS/Protein views
@@ -124,8 +341,8 @@ li:before {
columns in annotation row
- Preferences panel's ID Width control is
- honored in interactive and batch mode
+ Preferences panel's ID Width control is not
+ honored in batch mode
Linked sequence highlighting doesn't work
@@ -146,6 +363,14 @@ 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
+
+
Selecting columns from highlighted regions
very slow for alignments with large numbers of sequences
@@ -154,9 +379,7 @@ li:before {
with 'StringIndexOutOfBounds'
- VAqua(4) (download
- here) provided as fallback Look and Feel for OSX
+ VAqua(4) provided as fallback Look and Feel for OSX
platforms running Java 10
@@ -170,7 +393,12 @@ li:before {
Copy consensus sequence option in applet
should copy the group consensus when popup is opened on it
-
+
+ Batch Mode
+
+ -
+ Fixed ID width preference is not respected
+
New Known Defects
|