X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=d5e5dec6cb139e84ae2e950a27d837c9a278814d;hb=2a1caf440dbf484b76b944639faabf96223d0e57;hp=678b84f86bbee4987da2b1db9dd0cf1b89d8e385;hpb=b1404f0be5c24fce3c971d1e8c81e6e9f8dfcef3;p=jalview.git
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 678b84f..d5e5dec 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -24,25 +24,25 @@
Release History
@@ -68,6 +68,15 @@ li:before {
Chimera.
+ Discover 3D structure data for sequences
+ with Uniprot references via 3D-Beacons
+
+
+ Rank and select available structures for
+ Uniprot sequences according to number of residues in
+ structure mapped to positions involved in the alignment
+
+
New Preferences tab for adjusting Jalview's
memory settings at launch
@@ -77,18 +86,12 @@ li:before {
fetcher dialog.
-
-
-
-
-
-
Structure annotation rows for all mapped
chains in 3D structures are included in the 'Reference
Annotation' for a sequence
- Import Genbank and EMBL format flatfiles
+ Import Genbank and EMBL format flatfiles
ENA record's mol_type honoured so RNA
@@ -100,20 +103,64 @@ li:before {
Updated Jalview bindings for Uniprot XML
schema
- JalviewJS
+
+ Uniprot and PDBe autosearch option is
+ disabled by default
+
+
+ -nowebservicediscovery command line
+ argument to prevent automatic discovery of analysis
+ webservices on launch
+
+
+ Allow 'App' directories to be opened when
+ locating Chimera, ChimeraX or Pymol binaries via filechooser
+ opened by double clicking the Structure Preferences' path
+ textbox
+
+
+ GPL license info on splash screen and About
+ text
+
+
+ Jalview Native App
-
- PDB structures mapped to Uniprot Sequences with
- SIFTS
+ New Jalview Develop app - making it even easier
+ to get at Jalview's development builds
+
+ -
+ New splashscreens for Jalview, Jalview Test
+ and Jalview Develop applications.
-
-
+ Jalview logos shown for Jalview Java
+ Console and other window widgets in taskbar and dock rather
+ than anonymous 'Java' icons
-
-
+ Options to allow user to choose the (Swing) Look and Feel (LaF) used by Jalview
-
-
+ Metal LaF used to improved operation on Linux Ubuntu with
+ HiDPI display in Java 11 (still known issues with HiDPI screens in java
+ 8 and 11. see JAL-3137)
+
+ -
+ New command line launcher scripts (.sh, .ps1, .bat) usable on
+ macOS, Linux/Unix, Windows and documentation in Help. Installer wizard has option
+ to add this to PATH, or link to it in your PATH.
+
+
+
JalviewJS
+
+ -
+ PDB structures mapped to Uniprot Sequences with
+ SIFTS
+
+ -
+ setprop commandline argument reinstated for JalviewJS only
-
Missing message bundle keys are only
@@ -149,17 +196,21 @@ li:before {
installation with a customizedId of "JALVIEW" in install4j's
Jalview Launcher
+ -
+ Improved compatibility of Jalview build
+ with Java 17 (next LTS target)
+
-
- |
+
-
@@ -1577,8 +1689,8 @@ li:before {
columns in annotation row
-
- Preferences panel's ID Width control is not
- honored in batch mode
+ Preferences panel's ID Width control is
+ not honored in batch mode
-
Linked sequence highlighting doesn't work
@@ -1594,9 +1706,9 @@ li:before {
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)
+ Exception when shading sequence with
+ negative Temperature Factor values from annotated PDB
+ files (e.g. as generated by CONSURF)
-
Uniprot 'sequence variant' features
@@ -1607,20 +1719,22 @@ li:before {
structure and/or overview windows are also shown
-
- Selecting columns from highlighted regions
- very slow for alignments with large numbers of sequences
+ 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
+ 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
+ view appears to do nothing because the view is hidden
+ behind the alignment view
Applet
@@ -1632,9 +1746,10 @@ li:before {
Batch Mode
- -
- Fixed ID width preference is not respected
-
+ -
+ Fixed ID width preference is not
+ respected
+
New Known Defects
@@ -1654,35 +1769,64 @@ li:before {
2.10.4 is to fail back to N&W mapping)
-
- Export Annotations from File Menu with CSV
- option gives blank output
+ Export Annotations from File Menu with
+ CSV option gives blank output
-
- |
+
|
- - 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
+ - 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
+
+
+ |
@@ -1938,14 +2082,16 @@ li:before {
New features in Jalview Desktop
-
- Uniprot Sequence Fetcher now uses web API at uniprot.org
+ Uniprot Sequence Fetcher now uses web API
+ at uniprot.org
- - HTTPS used for all connections to ebi.ac.uk
+
-
+ HTTPS used for all connections to
+ ebi.ac.uk
|
-
- |
+ |
@@ -2414,9 +2560,9 @@ li:before {
recovered correctly from Jalview project file
- Feature colours in overview when first opened
- (automatically via preferences) are different to the main
- alignment panel
+ Feature colours in overview when first
+ opened (automatically via preferences) are different to
+ the main alignment panel
Data import/export
@@ -3292,7 +3438,7 @@ li:before {
column.
- Null Pointer Exception raised when
+ Null Pointer Exception raised when
pressing Add on an orphaned cut'n'paste window.
|