X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=efe65205ecd9e309a2bca6d14cb59467abc43347;hb=fa87a9e2098c49021abe2456819979b8e68c9566;hp=e1402e92bf4afdeae1a5f99986c282546393b655;hpb=2a56e8d0cf14008775a197e77ed1d5be19a5f9a3;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index e1402e9..efe6520 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -67,17 +67,253 @@ li:before {
+
+ |
+
+ |
+ |
+
+
+
+ -
+ DAS sequence retrieval and annotation capabilities removed from the Jalview Desktop
+
+
+ |
+
- |
+ |
|
+
+ -
+ Windows File Shortcuts can be dragged
+ onto the Jalview Desktop
+
+
+ |
+
+
+
+ -
+ Clustal files with sequence positions in
+ right-hand column parsed correctly
+
+ -
+ F2/Keyboard mode edits work when Overview
+ window has input focus
+
+ -
+ Wrap view - export to SVG - IDs shown but
+ not alignment area in exported graphic
+
+ -
+ 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.
+
+ -
+
+
+
+ |
+
+
+ |
+
+ |
+
+
+
+ -
+ New Structure Chooser control
+ for disabling automatic superposition of multiple
+ structures and open structures in existing views
+
+ -
+ Mouse cursor changes to indicate Sequence
+ ID and annotation area margins can be click-dragged to
+ adjust them.
+
+ -
+ Jalview uses HTTPS for Uniprot, Xfam and
+ Ensembl services
+
+ -
+ Improved performance for large alignments
+ and lots of hidden columns
+
+ -
+ Improved performance when rendering lots
+ of features (particularly when transparency is disabled)
+
+
+ |
- - Alignment doesn't appear to scroll vertically via trackpad and scrollwheel
+
+ -
+ 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
+
+ -
+ Trackpad scrolling is broken on OSX on
+ Java 1.8u153 onwards and Java 1.9u4+.
+
+ -
+ Tooltip shouldn't be displayed for empty
+ columns in annotation row
+
+ -
+ Preferences panel's ID Width control is not
+ honored in batch mode
+
+ -
+ Linked sequence highlighting doesn't work
+ for structures added to existing Jmol view
+
+ -
+ 'View Mappings' includes duplicate
+ entries after importing project with multiple views
+
+ -
+ Viewing or annotating Uniprot
+ protein sequences via SIFTS from associated PDB entries
+ with negative residue numbers or missing residues fails
+
+ -
+ Exception when shading sequence with negative
+ Temperature Factor values from annotated PDB files (e.g.
+ 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'
+
+ -
+ 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
+
+ -
+ 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
+
+ -
+ Exceptions occasionally raised when
+ editing a large alignment and overview is displayed
+
+ -
+ 'Overview updating' progress bar is shown
+ 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)
+
+
+
|
+
+
+ |
+
+ |
+
+ - Updated Certum Codesigning Certificate
+ (Valid till 30th November 2018)
|
+
+ Desktop
+
+ - Only one structure is loaded when several sequences and structures are selected for viewing/superposing
+ - Alignment doesn't appear to scroll vertically via trackpad and scrollwheel
+ - Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment
+ - Helix annotation has 'notches' when scrolled into view if columns are hidden
+ - Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns
+ - User preference for disabling inclusion of sequence limits when exporting as flat file has no effect
+ - Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes
+
+ |