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+ General
- - Internationalisation of user interface (usually called i18n support) and
- translation for Spanish locale
+ - 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
-
+ - 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:
-
- 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
- Applet
- Other improvements
- - Sensible precision for symbol distribution percentages shown in logo tooltip.
- - Annotation panel height set according to amount of annotation when alignment first opened
+ - 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
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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
+
- 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 and other annotation shading 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
- - cannot reorder or slide sequences after dragging an
+
- 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
+ IUPred disorder prediction
- Multiple group annotated consensus rows shown when
changing 'normalise logo' display setting
- - Annotation/RNA Helix colourschemes cannot be applied to alignment
- with groups (2.8.0b1)
- - 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'
+ - 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 shown in applet when selection is not a group
+ - Remove group option is shown even when selection is not a
+ group
- Apply to all groups ticked but colourscheme changes don't
affect groups
+ - 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
+
+ - 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
@@ -121,15 +141,19 @@
affect background (2.8.0b1)
- redundancy highlighting is erratic at 0% and 100%
- - remove gapped columns fails for sequences with ragged
+
- 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
+ - 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
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-