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JAL-4138
user preference for automatically showing PAE annotation row along side pLDDT when loading structure from alphafoldJAL-4112
Suggestion for File Save dialog
Shift-Click-Drag to adjust height of all annotation tracks of same type
Extend select/hide by annotation to offer highlight by as well
Visual indication of relationship with associated sequence to distinguish different sequence associated annotation rowsJAL-4087
Jalview GUI adapted for Touch and Gesture interactions
Highlight aligned positions on all associated structures when mousing over a column
Interactive highlights of sites on 3D structure corresponding for pAE matrix regions
Sequence extent shows start-end for visible sequence range when residues at start or end are hidden
nightingale style contact prediction trackJAL-4055
Should we retire the Jalview Desktop WindowJAL-4053
The prev and next page buttons in the Sequence Fetcher FTS panel are often hidden
Disable Autosearch for index change in FTS Sequence Fetcher when autosearch is deselected
Make the 3D-Beacons Search button more buttony and logic for Uniprot search
Select/Fetch all button for database query results
Autosearch disabled by default
quick annotation of a structure via sequence features (that can be undone)
total number of sequences in alignment not obvious when first loaded
Prompt to save unsaved Alignment windows on close or 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'
Loading a gzipped file and saving it leaves the new file uncompressed
Preferences window can be opened more than once
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 presentJAL-3311
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
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