X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=c566aae2e099be8a95dcf21388354df8a60a92bd;hb=b18564cbc54fd371132693fdc2a94b962c711655;hp=8e8813959c25d050e5b42792f0dabe730b88720d;hpb=7dd64f49322e3902d14a498a32e341191d2ba676;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 8e88139..c566aae 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -68,18 +68,116 @@ li:before {
+ |
+
+ |
+ |
+
+
+
+ -
+ Hidden sequence markers and representative
+ sequence bolding included when exporting alignment as EPS,
+ SVG, PNG or HTML. Display of these can be
+ configured via the Format menu or in batch mode with a
+ jalview properties file.
+
+ -
+ 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 in trimmed VARNA 2D structure is incorrect for sequences that do not start at 1
+
+
+ |
+
+
+ |
+
+ |
+
+
+
+ -
+ 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 +194,7 @@ li:before {
-
Improved performance when rendering lots
- of features
+ of features (particularly when transparency is disabled)
@@ -104,10 +202,33 @@ li:before {
|
-
+ Structure and Overview aren't updated
+ when Colour By Annotation threshold slider is adjusted
+
+ -
Slow redraw when Overview panel shown
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
@@ -120,8 +241,8 @@ 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
@@ -142,19 +263,29 @@ 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
- - Copy Consensus fails for group consensus with 'StringIndexOutOfBounds'
- - New Defects
-
- -
- 'SIFTS Mapping Error' when viewing
- structures for protein subsequence (if 'Trim Retrieved
- Sequences' enabled) or Ensembl isoforms (Workaround in
- 2.10.4 is to fail back to N&W mapping)
-
-
+ -
+ Copy Consensus fails for group consensus
+ with 'StringIndexOutOfBounds'
+
+ -
+ VAqua(4) provided as fallback Look and Feel for OSX
+ platforms running Java 10
+
+ -
+ Adding a structure to existing structure
+ view appears to do nothing because the view is hidden behind the alignment view
+
Applet
@@ -162,7 +293,12 @@ 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
@@ -175,6 +311,12 @@ li:before {
repeatedly after a series of edits even when the overview
is no longer reflecting updates
+ -
+ 'SIFTS Mapping Error' when viewing
+ structures for protein subsequence (if 'Trim Retrieved
+ Sequences' enabled) or Ensembl isoforms (Workaround in
+ 2.10.4 is to fail back to N&W mapping)
+
|