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JAL-3943
Select/Fetch all button for database query resultsJAL-3926
Autosearch disabled by defaultJAL-3925
quick annotation of a structure via sequence features (that can be undone)
total number of sequences in alignment not obvious when first loadedJAL-3772
Unsaved Alignment windows close without prompting to save, individually or at application quit.
Rendering multiple windows at once
Java Console (and other independent JFrames) appear with default Java icon
Find should report greedy matches only for conditional Regex
Find dialog's 'Ignore hidden regions' setting isn't 'wysiwyg'JAL-3699
Loading a gzipped file and saving it leaves the new file uncompressed
Preferences window can be opened more than onceJAL-3664
UX for working with HMMs in Jalview
Next/Previous region navigation buttons
Combined row-wise and positional per-sequence annotation shading
Multiple Structure Viewer Support in Jalview 2.11.2
Find dialog and prompts indicate when a selection was searched rather than whole alignment
Id width doesn't adjust for font size change
Visual indicator to show where mouse can change width of sequence label column or height of annotation area
Bundle a well-designed font to use by default
Import GFF of loci and browse to open views of aligned transcripts and reference
Better management of many sequence features popup windows
Automatically hide alignment calculation rows when only one sequence is present
Sunset VAMSAS and rescue functionality
Make it easier to modify colour for a group or all groups via the Colours menu
Remove 'Variable Colour' from Sequence Features popup menu
Different terminology between Preferences and Format menu for show unconserved
Make 'Input path' text fields easier to complete for novices
Allow structures to be opened in a specific structure view
Jump to nearest visible column rather than hide cursor when jumping to hidden region in keyboard mode
Optionally disable 'autosearch' on FTS
Offer 'Open Groovy Console' as well as Run Groovy Script from Calculations
Visual analytics for non-positional sequence annotation and metadata
Sort alignment for non-positional features
Keystrokes for Increase/Decrease font size in alignment view
Position UCSF Chimera window adjacent to Jalview desktop
Quick navigation buttons to jump to reference seuqence
Dynamically determine UI components minimum size based on platform
Highlight matching region from a find in complementary CDS/Protein view
Enlarging a group does not update Blosum62 colours until mouse up
Right-click on blue triangle to reveal hidden sequences
Expanded sort by PID functionality
Add ability to limit cache size and clear cache items
Import of files other than alignment files by Desktop->Import-> or drag'n'drop
report number of highlighted positions in status bar and mention 'B' for selecting them
option to enable/disable 'experimental' options in Jalview's UI
filter/threshold annotation rows by percentile or absolute numbers
'Reveal all' offered in alignment area popup menu when sequences are hidden
Provide options for controlling side-effects of setting a reference sequence
merging group and view specific shader settings with the colour by annotation dialog
Support feature type ontologies for control, display, and analysis of sequence features
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