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- JAL-4466
allow pairwise alignment gap parameters to be adjusted - JAL-4461
"Select format by extension" option in Jalview's "Save As" dialog's file type dropdown menu - JAL-4399
Consensus annotations and Tree visualisations for sequence annotation - JAL-4365
Improve the Find window to indicate to/allow selection by users as to what is being searched - JAL-4324
Option to align after retrieval of sequences before display - JAL-4309
Redesign sequence ID tooltip to improve user experience - JAL-4300
New alignment windows from aligment webservices inherit feature settings and layout from input - JAL-4299
Copy format and layout settings from another alignment view - JAL-4294
Hidden Column arrows are pixel-out aligned with the vertical blue line, and almost hidden at left-hand side of alignment - JAL-4292
Fit to width alignment layout option - JAL-4287
Automatically discover and import alphaFold or best PDBe model when retrieving proteins from Uniprot - JAL-4273
Visible adjuster marks to grab and adjust annotation panel height and id width - JAL-4231
make it easier to pick preferred experimental modalities for structure data - JAL-4213
"add reference annotation" should ignore when a selection is active and not only add positions for currently highlighted columns/selection range - JAL-4209
Automatically add JNet result as reference sequence on the original alignment - JAL-4204
More precise control of sequence & alignment associated annotation row visibility - JAL-4198
add reference annotation should not by default only add annotation for selected columns - JAL-4183
Visualise hidden columns by introducing a gap in the alignment grid - JAL-4179
Common nucleotide symbols turns sequence into 'protein', cannot set colour to 'nucleotide' - JAL-4174
Allow PAE file to be loaded for an already imported structure - JAL-4138
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 - JAL-4112
Suggestion for File Save dialog - JAL-4094
Shift-Click-Drag to adjust height of all annotation tracks of same type - JAL-4093
easier select-by-annotation and shade-by-annotation options - JAL-4092
Extend select/hide by annotation to offer highlight by as well - JAL-4091
Visual indication of relationship with associated sequence to distinguish different sequence associated annotation rows - JAL-4087
Jalview GUI adapted for Touch and Gesture interactions - JAL-4086
Highlight aligned positions on all associated structures when mousing over a column - JAL-4084
Interactive highlights of sites on 3D structure corresponding for pAE matrix regions - JAL-4069
Sequence extent shows start-end for visible sequence range when residues at start or end are hidden - JAL-4060
nightingale style contact prediction track - JAL-4055
Should we retire the Jalview Desktop Window - JAL-4053
The prev and next page buttons in the Sequence Fetcher FTS panel are often hidden - JAL-4051
Disable Autosearch for index change in FTS Sequence Fetcher when autosearch is deselected - JAL-4034
Make the 3D-Beacons Search button more buttony and logic for Uniprot search - JAL-3943
Select/Fetch all button for database query results - JAL-3926
Autosearch disabled by default - JAL-3925
quick annotation of a structure via sequence features (that can be undone) - JAL-3924
total number of sequences in alignment not obvious when first loaded - JAL-3772
Prompt to save unsaved Alignment windows on close or quit - JAL-3755
Rendering multiple windows at once - JAL-3728
Java Console (and other independent JFrames) appear with default Java icon - JAL-3710
Find should report greedy matches only for conditional Regex - JAL-3709
Find dialog's 'Ignore hidden regions' setting isn't 'wysiwyg' - JAL-3699
Loading a gzipped file and saving it leaves the new file uncompressed - JAL-3693
Preferences window can be opened more than once - JAL-3664
UX for working with HMMs in Jalview - JAL-3637
Next/Previous region navigation buttons - JAL-3623
Combined row-wise and positional per-sequence annotation shading - JAL-3616
Multiple Structure Viewer Support in Jalview 2.11.2
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