All notable changes to aform-rs will be documented in this file.
- Multi-alignment Stockholm file support with alignment selection
- Adopted ratatui ecosystem widgets for scrollbars, list, and text input
- Faster, non-blocking sequence clustering with a corrected dendrogram
- SVG export command (
:svg <path>) for saving alignment views as SVG images - Light mode support for base colors and popup overlays
- Migrated docs from mkdocs to zensical via pixi
- Switched to peaceiris/actions-gh-pages for deployment
- Clippy unnecessary_unwrap and formatting issues
- Auto-configure display for protein alignments: base coloring, consensus, and conservation bar are enabled automatically on file load
- Index out of bounds when deleting sequences with active clustering and collapsed identical sequences
- Visual Line mode (
V) for selecting whole sequences with annotations - Split panes with separate alignments for sequence extraction workflow
- Yank sequences in Visual Line mode captures complete sub-alignment (#=GS, #=GR, #=GC, #=GF)
:newcommand to create empty alignment in split pane:clipboardcommand to inspect clipboard contents- Paste (
p) in secondary pane appends sequences from clipboard
- Ctrl-w + arrow keys now correctly switches between split panes
- Clustering commands (
:cluster,:collapse,:tree) are not supported in secondary pane
- Light mode theme support: auto-detects terminal background and uses appropriate colors
- Auto-enable structure coloring for RNA files with SS_cons annotation
- Updated
tomldependency to 0.9
- Improved dendrogram tree display with collapsed sequences
- Minimal dots style for dendrogram tree display
- Use musl for static Linux binaries
- Trackpad scroll support for navigation
- Configurable UI theme via
aform.toml - Base-pair ruler display showing paired column positions
- Support for simpler color formats in config (hex
#RRGGBBand CSVr,g,b)
- Multi-sequence deletion in visual mode with row ID highlighting
- PP (posterior probability) coloring
- Gap column hiding (
:hidegaps/:showgaps) - Info overlay (
?key)
- Correct sequence indexing in clustered view
- Recompute clustering after sequence deletion
- CLI flags for display options (
--consensus,--conservation,--ruler,--rownum,--shortid) - CLI flags for clustering (
--cluster,--collapse,--tree) - Tab completion for file paths in
:ecommand
- Upgraded to ratatui 0.30
- Search history with Up/Down arrow navigation
- Improved code organization and reduced duplication
- Gzip file support (
.stk.gz,.sto.gz) - Protein sequence support with automatic detection
- Collapse identical sequences (
:collapse) - Consensus sequence display (
:consensus) - Conservation bar display (
:conservation)
- Collapse counts with clustering
- Height-varying bars for conservation display
- Stay in command mode when backspacing to empty
- Sequence clustering by similarity (
:cluster,:uncluster) - Dendrogram tree visualization (
:tree) - Scrollbar widgets for position feedback
- Clippy warnings
- Initial release
- Stockholm format parsing and writing
- Vim-style modal editing (Normal, Insert, Command, Search, Visual modes)
- RNA secondary structure visualization with helix coloring
- Multiple color schemes: none, structure, base, conservation, compensatory
- Split screen view (
:split,:vsplit) - Visual block selection and trim commands
- Sequence search with
/andn/Nnavigation (U/T tolerance) - File browser with
:ecommand - Column ruler and row numbers
- Base-pair highlighting
- Help overlay (
?) - Command history
- Splash screen with rainbow RNA helix logo