X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Freleases.html;h=86a1100c909cad066b4cef2378e6deb28cce5b4c;hb=51a7eedfc7d55c6f2dae8a75dcda6c4ccbe81893;hp=ebe5df93947d8d3aa1c5ffbe0d434e8d5f4e8e3e;hpb=1c885fe60d7db401d40b8d14ecb1b375f51f2eef;p=jalview.git
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@@ -21,6 +21,29 @@
-->
Release History
+
@@ -47,35 +70,355 @@
+ |
+
+ 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
+
+
+
+ |
+
+
+ |
+
+ General
+
+ -
+ Improved memory usage: sparse arrays used
+ for all consensus calculations
+
+ -
+ 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 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.
+
+ -
+ Cancel button and escape listener on
+ dialog warning user about disconnecting Jalview from a
+ Chimera session
+
+ -
+ Jalview's Chimera control window closes if
+ the Chimera it is connected to is shut down
+
+ -
+ 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
+
+
+ |
+
+
+ General
+
+ -
+ Columns with more than one modal residue
+ are not coloured or thresholded according to percent
+ identity (first observed in Jalview 2.8.2)
+
+ -
+ Threonine incorrectly reported as not
+ hydrophobic
+
+ -
+ Updates to documentation pages (above PID
+ threshold, amino acid properties)
+
+ -
+ Lower case residues in sequences are not
+ reported as mapped to residues in a structure file in the
+ View Mapping report
+
+ -
+ Identical features with non-numeric scores
+ could be added multiple times to a sequence
+
+ -
+ Disulphide
+ bond features shown as two highlighted residues rather
+ 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
+
+ -
+ Custom URL links for specific database
+ names without regular expressions also offer links from
+ Sequence ID
+
+ -
+ Removing a single configured link in the
+ URL links pane in Connections preferences doesn't actually
+ update Jalview configuration
+
+ -
+ CTRL-Click on a selected region to open
+ the alignment area popup menu doesn't work on El-Capitan
+
+ -
+ Jalview doesn't offer to associate mmCIF
+ files with similarly named sequences if dropped onto the
+ alignment
+
+ -
+ Additional mappings are shown for PDB
+ entries where more chains exist in the PDB accession than
+ are reported in the SIFTS file
+
+ -
+ Certain structures do not get mapped to
+ the structure view when displayed with Chimera
+
+ -
+ No chains shown in the Chimera view
+ panel's View->Show Chains submenu
+
+ -
+ Export as HTML with embedded SVG doesn't
+ work for wrapped alignment views
+
+ -
+ Rename UI components for running JPred
+ predictions from 'JNet' to 'JPred'
+
+ -
+ Export as PNG or SVG is
+ corrupted when annotation panel vertical scroll is not at
+ first annotation row
+
+ -
+ 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
+
+
+
+ |
+
+
+
|
Application
- - 3D Structure chooser opens with 'Cached structures' view if structures already loaded
- - Progress bar reports models as they are loaded to structure views
+ - 3D Structure chooser opens with 'Cached structures'
+ view if structures already loaded
+ - Progress bar reports models as they are loaded to
+ structure views
|
General
- - Colour by conservation always enabled and no tick shown in menu when PID shading applied
+ - Colour by conservation always enabled and no tick
+ shown in menu when BLOSUM or PID shading applied
+ - FER1_ARATH and FER2_ARATH labels were switched in
+ example sequences/projects/trees
Application
- - Multiple structure views can be opened and superposed without timeout for structures with multiple models or multiple sequences in alignment
- - Cannot import or associated local PDB files without a PDB ID HEADER line
- - RMSD is not output in Jmol console when superposition is performed
- - Drag and drop of URL from Browser fails for Linux and OSX versions earlier than El Capitan
+ - Jalview projects with views of local PDB structure
+ files saved on Windows cannot be opened on OSX
+ - Multiple structure views can be opened and
+ superposed without timeout for structures with multiple
+ models or multiple sequences in alignment
+ - Cannot import or associated local PDB files without
+ a PDB ID HEADER line
+ - RMSD is not output in Jmol console when
+ superposition is performed
+ - Drag and drop of URL from Browser fails for Linux
+ and OSX versions earlier than El Capitan
- ENA client ignores invalid content from ENA server
- - Exceptions are not raised in console when ENA client attempts to fetch non-existent IDs via Fetch DB Refs UI option
- - Exceptions are not raised in console when a new view is created on the alignment
+ - Exceptions are not raised in console when ENA
+ client attempts to fetch non-existent IDs via Fetch DB
+ Refs UI option
+ - Exceptions are not raised in console when a new
+ view is created on the alignment
+ - OSX right-click fixed for group selections:
+ CMD-click to insert/remove gaps in groups and CTRL-click
+ to open group pop-up menu
- New Known Issues
- - Drag and drop from URL links in browsers do not work on Windows
Build and deployment
- - URL link checker now copes with multi-line anchor tags
+
+ - URL link checker now copes with multi-line anchor
+ tags
+
+ New Known Issues
+
+ - Drag and drop from URL links in browsers do not
+ work on Windows
+
|
@@ -378,6 +721,10 @@
Quality and Conservation are now shown on
load even when Consensus calculation is disabled
+
+ Remove right on penultimate column of
+ alignment does nothing
+
Application
@@ -524,6 +871,14 @@
Incorrect start and end reported for PDB
to sequence mapping in 'View Mappings' report
+ -
+ Unable to read old Jalview projects that
+ contain non-XML data added after Jalvew wrote project.
+
+ - Newly created annotation row reorders
+ after clicking on it to create new annotation for a
+ column.
+
@@ -592,6 +947,9 @@
Applet
- Split frame example added to applet examples page
+
Build and Deployment
+
+ - New ant target for running Jalview's test suite
|