X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=3e701f93b46d038c07e907ba2a85de5980877825;hb=11ca0240a5792724d5e890de9fbd63cb2f11093a;hp=81e75eaec85650832f1ed877dfdb422fb0bcb728;hpb=a990c2c6facfd04d61d316dcafba31d03747d162;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 81e75ea..3e701f9 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -70,8 +70,136 @@ 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
+ - Start/End limits are shown in Pairwise Alignment report
+ - Sequence fetcher's Free text 'autosearch' feature can be disabled
+ - Retrieve IDs tab added for UniProt and PDB easier retrieval of sequences for lists of IDs
+ - Short names for sequences retrieved from Uniprot
+
+ Scripting
+
+ - Groovy interpreter updated to 2.4.12
+ - 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
+ - Export of features doesn't always respect group visibility
+ - Jumping from column 1 to column 100,000 takes a long time in Cursor mode
+
+ 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
+ - Revised Ensembl REST API CDNA query
+ - 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
+ - Pairwise alignment of selected regions of each selected sequence do not have correct start/end positions
+ - Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog
+ - Show cross-references not enabled after restoring project until a new view is created
+ - Warning popup about use of SEQUENCE_ID in URL links appears when only default EMBL-EBI link is configured (since 2.10.2b2)
+ - Overview redraws whole window when box position is adjusted
+ - Structure viewer doesn't map all chains in a multi-chain structure when viewing alignment involving more than one chain (since 2.10)
+ - Double residue highlights in cursor mode if new selection moves alignment window
+ - Alignment vanishes when using arrow key in cursor mode to pass hidden column marker
+
+ > Applet
+
+ - Concurrent modification exception when closing alignment panel
+
+ BioJSON
+
+ -
+ BioJSON export does not preserve non-positional features
+
+
+ New Known Issues
+
+ - Delete/Cut selection doesn't relocate sequence features correctly (for many previous versions of Jalview)
+ - Cursor mode unexpectedly scrolls when using cursor in wrapped panel other than top
+ - Select columns containing feature ignores graduated colour threshold
+ - Edit sequence operation doesn't always preserve numbering and sequence features
+
+ Known Java 9 Issues
+
+ - Groovy Console very slow to open and is
+ not responsive when entering characters (Webstart, Java 9.01,
+ OSX 10.10)
+
+
+ |
+
+
+ |
+
+ |
+
+ New features in Jalview Desktop
+
+ -
+ Uniprot Sequence Fetcher now uses web API at uniprot.org
+
+ - HTTPS used for all connections to ebi.ac.uk
+
+
+ |
+
+ |
+
+
+ |
+
|
@@ -82,26 +210,72 @@ 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
+
+
|
-
+ Overview window redraws every hidden
+ column region row by row
+
+ -
duplicate protein sequences shown after
retrieving Ensembl crossrefs for sequences from Uniprot
- - Overview window throws NPE if show boxes
+
-
+ Overview window throws NPE if show boxes
format setting is unticked
-
Groups are coloured wrongly in overview
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
+
+ -
+ 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
+
|
-
+
|
@@ -1356,6 +1530,10 @@ 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.
+
|