X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Freleases.html;h=86a1100c909cad066b4cef2378e6deb28cce5b4c;hb=51a7eedfc7d55c6f2dae8a75dcda6c4ccbe81893;hp=1fe2602739f69f4c26454d0fcdaef9400f61bf69;hpb=32cac3efee2758195a3315ff427c792ad18db050;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 1fe2602..86a1100 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -71,7 +71,7 @@ li:before {
|
@@ -79,6 +79,20 @@ li:before {
- More robust colours and shader model for alignments and groups
- Custom shading schemes created via groovy scripts
+ - 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
+ - Graduated feature colour style example included in the example feature file
Application
@@ -90,7 +104,7 @@ li:before {
- 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
@@ -105,7 +119,7 @@ li:before {
Test Suite
- Added PrivelegedAccessor to test suite
+ Added PrivilegedAccessor to test suite
Prevent or clear modal dialogs raised during tests
@@ -114,8 +128,8 @@ li:before {
-
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
+ matrix - C->R should be '-3' Old matrix restored with
+ this one-line groovy script: jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
-
Fixed Jalview's treatment of gaps in PCA
@@ -123,7 +137,7 @@ li:before {
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
+ non-gaps - so different costs were applied, which meant
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
@@ -147,7 +161,16 @@ 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
+ - Graduated feature colour threshold not restored to UI when feature colour is edited
+ - Feature colour thresholds not respected when rendered on overview and structures when opacity at 100%
+ - Structure and alignment overview update as graduate feature colour settings are modified via the dialog box
+ - Vertical scrollbar jumps one page-width at a time when scrolling vertically in wrapped mode.
+ - Overview window doesn't always update when a group defined on the alignment is resized
+ - Mouseovers on left/right scale region in wrapped view result in positional status updates
+ - Status bar shows position for ambiguous amino acid and nucleotide symbols
Application
@@ -162,16 +185,27 @@ 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
+ - Cannot load Newick trees from eggnog ortholog database
|