X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=97d6789b4b2cb756b292915b5f0f2c59daa41974;hb=bf3206cc56a3bff812f96967a81cc9cff54a57b1;hp=2f983fa0ac2e6485ed6e438e817c257d0ae3056e;hpb=a299290c8f04a6bb68b18f8335b8f9f28486b54f;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 2f983fa..97d6789 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -71,7 +71,7 @@ li:before {
2.10.2
- 30/5/2017
+ 20/6/2017
|
@@ -79,26 +79,56 @@ li:before {
- More robust colours and shader model for alignments and groups
- Custom shading schemes created via groovy scripts
- - Test suite expanded and debugged (over 940 functional unit tests, only 3 failing due to ongoing work!)
+
- linked scrolling of CDS/Protein views via Overview or sequence motif search operations
+ - Efficiency improvements for interacting with alignment and overview windows
+ - Hidden columns and sequences can be omitted in Overview
+ -
+ Posterior probability annotation from
+ Stockholm files imported as sequence associated annotation
+
+ -
+ Sequence names don't include file
+ extension when importing structure files without embedded
+ names or PDB accessions
+
+ - Amend sequence features dialog box can be opened by double clicking gaps within sequence feature extent
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
-
+ - Updated JABAWS client to v2.2
+
+ Experimental features
+
+ -
+ New entries in the Chimera menu
+ to transfer Chimera's structure attributes as Jalview
+ features, and vice-versa.
+
Applet
+ Test Suite
+ Added PrivilegedAccessor 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
+ this one-line groovy script: jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
-
Fixed Jalview's treatment of gaps in PCA
@@ -130,7 +160,10 @@ li:before {
- '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
+ - Conservation shading or PID threshold lost when base colourscheme changed if slider not visible
+ - Sequence features shown in tooltip for gaps before start of features
+ - Very large alignments take a long time to load
+ - Cannot load Newick trees from eggnog ortholog database
Application
@@ -145,16 +178,26 @@ li:before {
- 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
-
+ - No mappings generated between structure and sequences extracted from structure files imported via URL
+ -
+ Structures loaded via URL are saved in
+ Jalview Projects rather than fetched via URL again when
+ the project is loaded and the structure viewed
+
+ - Trackpad horizontal scroll gesture adjusts start position in wrap mode
+ - Status bar doesn't show positions for ambiguous amino acids
+ - Hide insertions in PopUp menu excludes gaps in selection, current sequence and only within selected columns
Applet
- Features not rendered as transparent on overview or linked structure view
- Colour group by conservation doesn't work (since 2.8)
+ - Hitting Cancel after applying user-defined colourscheme doesn't restore original colourscheme
New Known Issues
-
+ - Protein/CDS view scrolling not always in phase after a sequence motif find operation
+ - Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS rna secondary structure symbols
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