X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Freleases.html;h=97d6789b4b2cb756b292915b5f0f2c59daa41974;hb=bf3206cc56a3bff812f96967a81cc9cff54a57b1;hp=aa589e9e7a2de0c06048ac0ef0b44c730146c4c5;hpb=d8bf5506216e7a0726a1fa5baa6b4d244f035741;p=jalview.git
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@@ -70,6 +70,140 @@ li:before {
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+ |
+
+ 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
+
+ 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 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
+ - 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
+
+ - 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
+
+
+ |
+ |
+
@@ -211,6 +345,9 @@ li:before {
Attempting to view structure for Hen
lysozyme results in a PDB Client error dialog box
+
+ Structure View's mapping report switched ranges for PDB and sequence for SIFTS
+ SIFTS 'Not_Observed' residues mapped to non-existant coordindate data
|