X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=09595b08b570208fa9b15a0187499f8a263249cf;hb=2e78324ac6e6dba9f3db8939df4e777a0b097300;hp=a0efc10fb505fdb154e9700816ff1a91c74ff648;hpb=d8488297d82c4a5e2d87a589ce26e2b4c4258235;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index a0efc10..09595b0 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -70,8 +70,95 @@ li:before {
|
+ |
+
+
+
+ -
+ Faster and more efficient management and
+ rendering of sequence features
+
+ -
+ More reliable Ensembl fetching with HTTP
+ 429 rate limit request hander
+
+ -
+ Structure views don't get updated unless
+ their colours have changed
+
+ - All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)
+ - 'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
+
+
+ - Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references
+
+ - Example groovy script for generating a matrix of percent identity scores for current alignment.
+ Testing and Deployment
+ - Test to catch memory leaks in Jalview UI
+ |
+
+ General
+
+ - Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view
+ - Race condition when parsing sequence ID strings in parallel
+ - Overview windows are also closed when alignment window is closed
+
+ Desktop
+
+ - Structures with whitespace chainCode cannot be viewed in Chimera
+ - Protein annotation panel too high in CDS/Protein view
+
+ - Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
+
+ - Slow EnsemblGenome ID lookup
+ - Hidden column marker in last column not rendered when switching back from Wrapped to normal view
+ - Annotation display corrupted when scrolling right in unwapped alignment view
+ - Existing features on subsequence incorrectly relocated when full sequence retrieved from database
+ - Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)
+ - Amend Features dialog doesn't allow features of same type and group to be selected for amending
+ - Jalview becomes sluggish in wide alignments when hidden columns are present
+ - Jalview freezes when loading and displaying several structures
+ - Black outlines left after resizing or moving a window
+ - Unable to minimise windows within the Jalview desktop on OSX
+ - Mouse wheel doesn't scroll vertically when in wrapped alignment mode
+ - Scale mark not shown when close to right hand end of alignment
+
+ Applet
+
+ - Concurrent modification exception when closing alignment panel
+
+ |
+
+
+ |
+
+ |
+
+ New features in Jalview Desktop
+
+ -
+ Uniprot Sequence Fetcher now uses web API at uniprot.org
+
+ - HTTPS used for all connections to ebi.ac.uk
+
+
+ |
+
+ |
+
+
+ |
+
|
@@ -82,7 +169,16 @@ li:before {
in grey (sequences used to be coloured grey, and gaps were
white)
- Overview tab in Jalview Desktop Preferences
+
+ Overview tab in Jalview Desktop
+ Preferences
+
+
+ Overview updates immediately on increase
+ in size and progress bar shown as higher resolution
+ overview is recalculated
+
+
|
@@ -105,13 +201,40 @@ li:before {
if group has show boxes format setting unticked
- Redraw problems when autoscrolling whilst
- dragging current selection group to include sequences and
- columns not currently displayed
+ Redraw problems when
+ autoscrolling whilst dragging current selection group to
+ include sequences and columns not currently displayed
+
+
+ Not all chains are mapped when multimeric
+ assemblies are imported via CIF file
+
+
+ Gap colour in custom colourscheme is not
+ displayed when threshold or conservation colouring is also
+ enabled.
+
+
+ JABAWS 2.2 services report wrong JABAWS
+ server version
+
+
+ Jalview continues to scroll after
+ dragging a selected region off the visible region of the
+ alignment
+
+
+ Cannot apply annotation based
+ colourscheme to all groups in a view
+
+
+ IDs don't line up with sequences
+ initially after font size change using the Font chooser or
+ middle-mouse zoom
|
-
+
|
@@ -1366,6 +1489,10 @@ li:before {
after clicking on it to create new annotation for a
column.
+
+ Null Pointer Exception raised when
+ pressing Add on an orphaned cut'n'paste window.
+
|