X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=86a1100c909cad066b4cef2378e6deb28cce5b4c;hb=51a7eedfc7d55c6f2dae8a75dcda6c4ccbe81893;hp=abfefa267c83a5b29f18b13a37c3f4bc8be28842;hpb=c168623cf7396b5aa41d78d19ab801a9f757b103;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index abfefa2..86a1100 100755
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+++ b/help/html/releases.html
@@ -21,6 +21,29 @@
-->
Release History
+
@@ -47,8 +70,150 @@
+ |
+
+ General
+
+ - 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
+
+ -
+
+ 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.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[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 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
+ 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
+ - 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
+
+ - 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
+ - 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
+
+
+
+ |
+
+
2.10.1
- 24/11/2016
+ 29/11/2016
|
@@ -59,25 +224,22 @@
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
-
- Sequence ID tool tips have been tamed
- (databases sorted alphabetically, abridged ID sets)
+ Sequence ID tool tip presents abridged
+ set of database cross-references, sorted alphabetically
-
New replacement token for creating URLs just
from database cross references. Users with custom links
- will receive a warning dialog asking them to update their
- preferences.
+ will receive a warning
+ dialog asking them to update their preferences.
-
Cancel button and escape listener on
@@ -85,35 +247,20 @@
Chimera session
-
- Jalview's chimera control window closes if
+ Jalview's Chimera control window closes if
the Chimera it is connected to is shut down
-
- Custom URL links for database
- cross-references are matched to database name regardless
- of case
-
- -
- Select highlighted columns menu item and
- keystroke (B) to mark columns containing highlighted
- regions from structure selections or results of a Find
- operation
+ New keystroke (B) and Select highlighted
+ columns menu item to mark columns containing
+ highlighted regions (e.g. from structure selections or results
+ of a Find operation)
-
Command line option for batch-generation
of HTML pages rendering alignment data with the BioJS
MSAviewer
-
-
-
- Applet
-
- Build and deployment
-
- - Updated Jalview's Certum code signing certificate
- for 2016-2017
|
@@ -148,6 +295,11 @@
than a range in linked structure views, and treated
correctly when selecting and computing trees from features
+
+ Custom URL links for database
+ cross-references are matched to database name regardless
+ of case
+
Application
@@ -201,20 +353,14 @@
Attempting to view structure for Hen
lysozyme results in a PDB Client error dialog box
-
- Applet
-
- 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
+
|