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JAL-4602
Hide the 'All' secondary structure consensus annotation when just one type is available
PAE tree always shown above the alignment view
Improve dialog when attempting to open non-existing file
allow pairwise alignment gap parameters to be adjusted
"Select format by extension" option in Jalview's "Save As" dialog's file type dropdown menuJAL-4399
Consensus annotations and Tree visualisations for sequence annotation
Improve the Find window to indicate to/allow selection by users as to what is being searched
Option to align after retrieval of sequences before display
Redesign sequence ID tooltip to improve user experienceJAL-4300
New alignment windows from aligment webservices inherit feature settings and layout from input
Copy format and layout settings from another alignment view
Hidden Column arrows are pixel-out aligned with the vertical blue line, and almost hidden at left-hand side of alignment
Fit to width alignment layout option
Automatically discover and import alphaFold or best PDBe model when retrieving proteins from Uniprot
Visible adjuster marks to grab and adjust annotation panel height and id width
make it easier to pick preferred experimental modalities for structure data
"add reference annotation" should ignore when a selection is active and not only add positions for currently highlighted columns/selection range
Automatically add JNet result as reference sequence on the original alignment
More precise control of sequence & alignment associated annotation row visibility
add reference annotation should not by default only add annotation for selected columns
Visualise hidden columns by introducing a gap in the alignment gridJAL-4179
Common nucleotide symbols turns sequence into 'protein', cannot set colour to 'nucleotide'
Allow PAE file to be loaded for an already imported structure
user preferences and structure chooser controls for automatically showing PAE annotation row along side pLDDT when loading structure from alphafold, and control secondary structure and temp factor display
Suggestion for File Save dialog
Shift-Click-Drag to adjust height of all annotation tracks of same type
easier select-by-annotation and shade-by-annotation options
Extend select/hide by annotation to offer highlight by as well
Visual indication of relationship with associated sequence to distinguish different sequence associated annotation rows
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 Window
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
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