X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=1fe2602739f69f4c26454d0fcdaef9400f61bf69;hb=79501a7433d7fd26f958b8574e2147e011433224;hp=441b394aedd0acc3cc73d83e7bf73c7f9d85b5ae;hpb=12c8641d36171e8c5ce40b0090bb09a8916de28b;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 441b394..1fe2602 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -21,6 +21,29 @@
-->
Release History
+
@@ -47,8 +70,116 @@
|
+ |
+
+ General
+
+ - More robust colours and shader model for alignments and groups
+ - Custom shading schemes created via groovy scripts
+
+ Application
+
+ -
+
+ Experimental Features Checkbox in Desktop's Tools
+ menu to hide or show untested features in the application.
+
+ - Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera
+ - Faster Chimera/Jalview communication by file-based command exchange
+ - URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB
+
+
+ Experimental features
+
+ -
+ New entries in the Chimera menu
+ to transfer Chimera's structure attributes as Jalview
+ features, and vice-versa.
+
+
+ Applet
+
+ Test Suite
+ Added PrivelegedAccessor to test suite
+ Prevent or clear modal dialogs raised during tests
+
+
+ |
+ General
+
+ -
+ Fixed incorrect value in BLOSUM 62 score
+ matrix - C->R should be '3'
Old matrix restored with
+ this one-line groovy script:
jalview.schemes.ResidueProperties.BLOSUM62[4][1]=3
+
+ -
+ Fixed Jalview's treatment of gaps in PCA
+ and substitution matrix based Tree calculations.
In
+ earlier versions of Jalview, gaps matching gaps were
+ penalised, and gaps matching non-gaps penalised even more.
+ In the PCA calculation, gaps were actually treated as
+ non-gaps - so different costs were applied, which mean't
+ Jalview's PCAs were different to those produced by
+ SeqSpace.
Jalview now treats gaps in the same way as
+ SeqSpace (ie it scores them as 0). To restore pre-2.10.2
+ behaviour
+ jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
+ 2.10.1 mode
+ jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
+ restore 2.10.2 mode
+
+ - Reopening Colour by annotation dialog doesn't reselect a specific sequence's associated annotation after it was used for colouring a view
+ - Hidden regions in alignment views are not coloured in linked structure views
+ - Current selection lost if popup menu opened on a region of alignment without groups
+ - Popup menu not always shown for regions of an alignment with overlapping groups
+ - Finder double counts if both a sequence's name and description match
+ - Hiding column selection containing two hidden regions results in incorrect hidden regions
+ - PCA calculation could hang when generating output report when working with highly redundant alignments
+ - Cannot configure feature colours with lightGray or darkGray via features file
+ - Overview window visible region moves erratically when hidden rows or columns are present
+ - Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring
+ - Protein specific colours only offered in colour and group colour menu for protein alignments
+ - 'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups
+ - Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds
+ - Percentage identity and conservation menu items do not show a tick or allow shading to be disabled
+ - Conservation shading or PID threshold lost when base colourscheme changed if slider not visible
+
+ Application
+
+ - Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added)
+ - Text colour threshold's 'Cancel' button doesn't restore group-specific text colour thresholds
+ - Feature settings panel does not update as new features are added to alignment
+ - Structure viewer's View -> Colour By view selection menu changes colours of alignment views
+ - Proxy server address and port always appear enabled in Preferences->Connections
+ - Spurious exceptions in console raised from alignment calculation workers after alignment has been closed
+ - Typo in selection popup menu - Create groups now 'Create Group'
+ - CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work
+ - Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'
+ - DAS registry not found exceptions removed from console output
+ - Above PID colour threshold not recovered when alignment view imported from project
+
+
+ Applet
+
+ - Features not rendered as transparent on overview or linked structure view
+ - Colour group by conservation doesn't work (since 2.8)
+
+ New Known Issues
+
+
+ |
+
+
2.10.1
- 24/11/2016
+ 29/11/2016
|
@@ -59,13 +190,10 @@
for all consensus calculations
- Updated Jmol shipped with applet and
- desktop to 14.6.4
-
-
-
+ Jmol updated to version 14.6.4 (released 3rd Oct 2016)
-
+ Updated Jalview's Certum code signing certificate
+ for 2016-2017
Application
@@ -100,14 +228,6 @@
MSAviewer
- Applet
- -->
- Build and deployment
-
- - Updated Jalview's Certum code signing certificate
- for 2016-2017
-
|
@@ -199,21 +319,14 @@
Attempting to view structure for Hen
lysozyme results in a PDB Client error dialog box
-
-
- Build and deployment
-
-
- Failing/passing unit tests
-
+ Structure View's mapping report switched ranges for PDB and sequence for SIFTS
+ SIFTS 'Not_Observed' residues mapped to non-existant coordindate data
- New Known Issues
+
|