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-
-
-
- - i18n Internationalisation of user interface and translation for Spanish locale
-
- Application
- - Define/Undefine group on current selection with Ctrl-G
- - Select columns containing particular features from Feature Settings dialog
-- View all 'representative' PDB structures for selected sequences
-- Interactive consensus RNA secondary structure prediction VIENNA RNAAliFold JABA 2.1 service
-
- - Jalview v2.8.1 project preserves sequence dataset and dataset annotation (e.g. hidden secondary structure annotation rows)
-
- Applet Other improvements
-
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-
- Application
+
+ |
+
+ Release
+
+ |
+
+
+ New Features
+
+ |
+
+
+ Issues Resolved
+
+ |
+
+
+ |
+ General
+
+ - Updated Java code signing certificate donated by Certum.PL.
+ - Features and annotation preserved when performing pairwise
+ alignment
+ - RNA pseudoknot annotation can be
+ imported/exported/displayed
+ - 'colour by annotation' can colour by RNA and
+ protein secondary structure
+ Application
+
+ - Extract and display secondary structure for sequences with
+ 3D structures
+ - Support for parsing RNAML
+ - Annotations menu for layout
+
+ - sort sequence annotation rows by alignment
+ - place sequence annotation above/below alignment
+ annotation
+
+ - Output in Stockholm format
+ - Internationalisation: improved Spanish (es) translation
+ - Structure viewer preferences tab
+ - Disorder and Secondary Structure annotation tracks shared
+ between alignments
+ - UCSF launch and linked highlighting from Jalview
+ - Show/hide all sequence associated annotation rows for all
+ or current selection
+ - disorder and secondary structure predictions available as
+ dataset annotation
+ - Per-sequence rna helices colouring
+
+
+ - Sequence database accessions imported when fetching
+ alignments from Rfam
+ - update VARNA version to 3.91
+
+ - New groovy scripts for exporting aligned positions,
+ conservation values, and calculating sum of pairs scores.
+ - Command line argument to set default JABAWS server
+ - include installation type in build properties and console
+ log output
+ - Updated Jalview project format to preserve dataset annotation
+ |
+
+ Application
+
+ - Distinguish alignment and sequence associated RNA
+ structure in structure->view->VARNA
+ - Raise dialog box if user deletes all sequences in an
+ alignment
+ - Pressing F1 results in documentation opening twice
+ - Sequence feature tooltip is wrapped
+ - Double click on sequence associated annotation selects
+ only first column
+ - Redundancy removal doesn't result in unlinked leaves
+ shown in tree
+ - Undos after several redundancy removals don't undo
+ properly
+ - Hide sequence doesn't hide associated annotation
+ - User defined colours dialog box too big to fit on screen
+ and buttons not visible
+ - author list isn't updated if already written to jalview
+ properties
+ - Popup menu won't open after retrieving sequence from
+ database
+ - File open window for associate PDB doesn't open
+ - Left-then-right click on a sequence id opens a browser
+ search window
+ - Cannot open sequence feature shading/sort popup menu in
+ feature settings dialog
+ - better tooltip placement for some areas of Jalview desktop
+ - Unable to add JABAWS Server which doesn't pass
+ validation
+ - Web services parameters dialog box is too large to fit on
+ screen
+ - Muscle nucleotide alignment preset obscured by tooltip
+ - JABAWS preset submenus don't contain newly defined
+ user preset
+ - MSA web services warns user if they were launched with
+ invalid input
+ - Jalview cannot contact DAS Registy when running on Java 8
+ -
+
+ 'Superpose with' submenu not shown when new view created
+
+
+ Deployment and Documentation
+
+ - 2G and 1G options in launchApp have no effect on memory
+ allocation
+ - launchApp service doesn't automatically open
+ www.jalview.org/examples/exampleFile.jar if no file is given
+ -
+
+ InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is
+ available
+
+ Application Known issues
+
+ -
+
+ corrupted or unreadable alignment display when scrolling alignment
+ to right
+
+ -
+
+ retrieval fails but progress bar continues for DAS retrieval with
+ large number of ID
+
+ -
+
+ flatfile output of visible region has incorrect sequence start/end
+
+ -
+
+ rna structure consensus doesn't update when secondary
+ structure tracks are rearranged
+
+ -
+
+ invalid rna structure positional highlighting does not highlight
+ position of invalid base pairs
+
+ -
+
+ out of memory errors are not raised when saving jalview project
+ from alignment window file menu
+
+ -
+
+ Switching to RNA Helices colouring doesn't propagate to
+ structures
+
+ -
+
+ colour by RNA Helices not enabled when user created annotation
+ added to alignment
+
+ -
+
+ Jalview icon not shown on dock in Mountain Lion/Webstart
+
+ Applet Known Issues
+
+ -
+
+ JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
+
+ -
+
+ Jalview and Jmol example not compatible with IE9
+
+
+ - Sort by annotation score doesn't reverse order when
+ selected
+
+ |
+
+
+ |
+
+
+ General
+
+ - Internationalisation of user interface (usually called
+ i18n support) and translation for Spanish locale
+ - Define/Undefine group on current selection with
+ Ctrl-G/Shift Ctrl-G
+ - Improved group creation/removal options in
+ alignment/sequence Popup menu
+ - Sensible precision for symbol distribution percentages
+ shown in logo tooltip.
+ - Annotation panel height set according to amount of
+ annotation when alignment first opened
+ Application
+
+ - Interactive consensus RNA secondary structure prediction
+ VIENNA RNAAliFold JABA 2.1 service
+ - Select columns containing particular features from Feature
+ Settings dialog
+ - View all 'representative' PDB structures for selected
+ sequences
+ - Update Jalview project format:
+
+ - New file extension for Jalview projects '.jvp'
+ - Preserve sequence and annotation dataset (to store
+ secondary structure annotation,etc)
+ - Per group and alignment annotation and RNA helix
+ colouring
+
+
+ - New similarity measures for PCA and Tree calculation
+ (PAM250)
+ - Experimental support for retrieval and viewing of flanking
+ regions for an alignment
+
+ |
+
+ Application
+
+ - logo keeps spinning and status remains at queued or
+ running after job is cancelled
+ - cannot export features from alignments imported from
+ Jalview/VAMSAS projects
+ - Buggy slider for web service parameters that take float
+ values
- Newly created RNA secondary structure line doesn't have
'display all symbols' flag set
- - T-COFFEE alignment score shading scheme not saved in
- jalview project
+ - T-COFFEE alignment score shading scheme and other
+ annotation shading not saved in jalview project
- Local file cannot be loaded in freshly downloaded Jalview
- - ??? unresolved ??? Jalview icon not shown on dock in
- Mountain Lion/Webstart
+ - Jalview icon not shown on dock in Mountain Lion/Webstart
- Load file from desktop file browser fails
- Occasional NPE thrown when calculating large trees
-
- Applet
-
+ - Cannot reorder or slide sequences after dragging an
+ alignment onto desktop
+ - Colour by annotation dialog throws NPE after using
+ 'extract scores' function
+ - Loading/cut'n'pasting an empty file leads to a grey
+ alignment window
+ - Disorder thresholds rendered incorrectly after performing
+ IUPred disorder prediction
+ - Multiple group annotated consensus rows shown when
+ changing 'normalise logo' display setting
+ - Find shows blank dialog after 'finished searching' if
+ nothing matches query
+ - Null Pointer Exceptions raised when sorting by feature
+ with lots of groups
+
+ - Errors in Jmol console when structures in alignment don't
+ overlap
+
+ - Not all working JABAWS services are shown in Jalview's
+ menu
+ - JAVAWS version of jalview fails to launch with 'invalid
+ literal/length code'
+ - Annotation/RNA Helix colourschemes cannot be applied to
+ alignment with groups (actually fixed in 2.8.0b1)
+ - RNA Helices and T-Coffee Scores available as default colourscheme
+
+ Applet
+
+ - Remove group option is shown even when selection is not a
+ group
- Apply to all groups ticked but colourscheme changes don't
affect groups
-
- Other
- |
-
-
+ - Documented RNA Helices and T-Coffee Scores as valid colourscheme name
+ - Annotation labels drawn on sequence IDs when Annotation panel is not displayed
+ - Increased font size for dropdown menus on OSX and embedded windows
+ Other
+
+ - Consensus sequence for alignments/groups with a single
+ sequence were not calculated
+ - annotation files that contain only groups imported as
+ annotation and junk sequences
+ - Fasta files with sequences containing '*' incorrectly
+ recognised as PFAM or BLC
+ - conservation/PID slider apply all groups option doesn't
+ affect background (2.8.0b1)
+
+ - redundancy highlighting is erratic at 0% and 100%
+ - Remove gapped columns fails for sequences with ragged
+ trailing gaps
+ - AMSA annotation row with leading spaces is not registered
+ correctly on import
+ - Jalview crashes when selecting PCA analysis for certain
+ alignments
+ - Opening the colour by annotation dialog for an existing
+ annotation based 'use original colours' colourscheme loses
+ original colours setting
+
+
+
+
@@ -172,10 +418,12 @@
- ClassCastException when generating EPS in headless
mode
- Adjusting sequence-associated shading threshold only
- changes one row's threshold
+ changes one row's threshold
- Preferences and Feature settings panel panel
doesn't open
-
+ - hide consensus histogram also hides conservation and
+ quality histograms
+
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