Vim Mode¶

Vim mode adds keyboard-driven navigation and commands. Enable it from the settings panel with the Vim Mode toggle. When Vim mode is off, these Vim keys are ignored and the normal app shortcuts keep their usual behavior.

When Vim mode is on, a single-line command bar is shown at the bottom of the window. It is used for commands, searches, counts, and short status messages.

Normal-mode keys¶

These keys work when Vim mode is enabled and the command bar is not actively editing a : command or / search.

Key	Action
`h`	Pan left by one pan step.
`l`	Pan right by one pan step.
`j`	Zoom out one step.
`k`	Zoom in one step.
`gg`	Jump to the start of the current sequence.
`<number>gg`	Jump to that 1-based position in the current sequence. For example, `500gg` jumps to position 500.
`G`	Jump to the end of the current sequence.
`gc`, `]c`	Jump to the start of the next contig.
`gC`, `[c`	Jump to the start of the previous contig.
`n`	Move to the next search hit.
`N`	Move to the previous search hit.
`w`	Move to the next annotation feature when a feature is selected.
`b`	Move to the previous annotation feature when a feature is selected.
`m<letter>`	Save the current view as a mark. For example, `ma` sets mark `a`.
`'<letter>`	Load a mark. For example, `'a` jumps to mark `a`.
`gv`	Toggle between single genome view and comparison view.
`ZZ`	Quit the app.
`:`	Open the Vim command prompt.
`/`	Open the Vim search prompt.

The pan and zoom keys apply to the active view. Browser-only navigation, such as gg, G, contig jumps, feature jumps, go, and Vim / search, requires the single genome browser view.

Counts¶

Counts can be typed before several normal-mode commands. The count is shown in the command bar while it is being entered.

Supported counted commands:

Command	Meaning
`<number>h`	Pan left by that many pan steps.
`<number>l`	Pan right by that many pan steps.
`<number>n`	Move forward by that many search hits.
`<number>N`	Move backward by that many search hits.
`<number>gg`	Jump to that position in the current sequence.
`<number>gc`, `<number>]c`	Jump forward by that many contigs.
`<number>gC`, `<number>[c`	Jump backward by that many contigs.
`<number>w`	Move forward by that many annotation features.
`<number>b`	Move backward by that many annotation features.

Contig navigation clamps at the first or last contig. Feature navigation clamps at the first or last feature. In concatenate view, feature navigation continues across contig boundaries and skips contigs that have no annotation features.

Marks¶

Marks save and restore view positions.

m<letter> saves the current view to a mark.
'<letter> loads that mark.

For example:

ma saves mark a
'a jumps to mark a

When a mark is saved, the command bar shows mark <letter> set. When a mark is loaded, it shows jumped to mark <letter>.

Marks use the same view-state saving code as the numbered temporary view slots. Browser view and comparison view keep separate saved-view banks.

Annotation feature navigation¶

Feature navigation works after selecting an annotation feature.

w selects the next annotation feature.
b selects the previous annotation feature.
Counts work, such as 5w or 3b.

In concatenate view, moving past the final feature of one contig continues to the first feature of the next contig with annotations. Moving backward from the first feature of a contig continues to the previous contig with annotations.

The command bar shows the selected feature label and its position within the current contig’s feature list, such as geneA 12/80. At the ends, it shows first feature or last feature.

Command prompt¶

Press : to type a Vim command. Press Enter to run it. Press Escape to exit the prompt without running it.

If a : command is active, Escape only exits the command prompt. It does not also close panels. If the command prompt is not active, Escape keeps the app’s normal behavior.

Implemented commands:

Command	Action
`:go <position>`	Jump to a 1-based position in the current sequence.
`:go <start>-<end>`	Jump to a range in the current sequence.
`:go <sequence>:<position>`	Jump to a position in a named sequence.
`:go <sequence>:<start>-<end>`	Jump to a range in a named sequence.
`:go <sequence> <position>`	Space-separated form for a named sequence.
`:go <sequence> <start>-<end>`	Space-separated range form for a named sequence.
`:open`	Open the native file picker, like pressing the open file button.
`:open <path>`	Open a file from a filesystem path.
`:download <accession>`	Open the download panel, fill the accession box, and start download-and-load.
`:colorscheme <theme>`	Switch to a theme. This uses standard Vim-style `colorscheme` syntax.
`:view single`	Switch to single genome view.
`:view comparison`	Switch to comparison view.
`:q`	Quit the app.
`:quit`	Quit the app.

Position and range examples:

:go 123
:go 100-250
:go contig1:123
:go contig1:100-250
:go sample:contig1:500
:go sample:contig1 500

The colon form is the preferred sequence syntax. The space-separated sequence form is also available when it is clearer for sequence names that contain colons.

Open examples:

:open
:open /path/to/foo.fasta
:open "/path/to/foo bar.fasta"

Download example:

:download GCF_000005845.2

Search prompt¶

Press / to type a search. Press Enter to run it. Press Escape to exit the prompt without running it.

Searches open the search panel with the results.

The first word chooses the search type:

annotation, or any unambiguous prefix such as a, an, or annot
dna, or any unambiguous prefix such as d or dn

Annotation search examples:

/a gene1
/an contig1 gene1
/annot contig2 foo bar

DNA search examples:

/d ACGT
/dna contig24 gtcgtacgtcag

If the search prompt contains a single word made only of A, C, G, and T characters, it is treated as a whole-genome DNA search:

/ACGT

For annotation and DNA searches, if the first word after the search type matches a sequence name, the search is restricted to that sequence. Otherwise the search runs across all sequences and the rest of the text is treated as the query.

Completion and history¶

Press Tab in the command bar to cycle through available completions.

Completion is implemented for:

: command names, such as go, open, download, colorscheme, view, q, and quit
sequence names after :go
theme names after :colorscheme
single and comparison after :view
sequence names after the search target in /annotation or /dna searches

Press Up and Down in the command bar to move through prompt history. History is session-only, keeps the last 100 commands, and is stored separately for : commands and / searches.