Add vim mode

docs/index.md

@@ -62,6 +62,7 @@ For more detail, see:
 install
 supported-files
 navigation
+vim-mode
 contig-actions
 theme-editor
 comparison-view

docs/vim-mode.md

@@ -0,0 +1,219 @@
+# 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`.
+
+## Search result navigation
+
+After using the search panel or Vim `/` search, use:
+
+- `n` for the next hit
+- `N` for the previous hit
+
+Counts are supported, such as `5n` or `2N`.
+
+The command bar shows the selected search result as `search hit x/y`. Clicking a
+search result in the search panel also updates this Vim message.
+
+## 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:
+
+```text
+: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:
+
+```text
+:open
+:open /path/to/foo.fasta
+:open "/path/to/foo bar.fasta"
+```
+
+Download example:
+
+```text
+: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:
+
+```text
+/a gene1
+/an contig1 gene1
+/annot contig2 foo bar
+```
+
+DNA search examples:
+
+```text
+/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:
+
+```text
+/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.

project.godot

@@ -73,6 +73,97 @@ seqhiker_close_right_panel={
 "events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":4194305,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
 ]
 }
+seqhiker_vim_scroll_left={
+"deadzone": 0.5,
+"events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":72,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
+]
+}
+seqhiker_vim_scroll_right={
+"deadzone": 0.5,
+"events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":76,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
+]
+}
+seqhiker_vim_zoom_out={
+"deadzone": 0.5,
+"events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":74,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
+]
+}
+seqhiker_vim_zoom_in={
+"deadzone": 0.5,
+"events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":75,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
+]
+}
+seqhiker_vim_command={
+"deadzone": 0.5,
+"events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":58,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
+, Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":true,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":59,"physical_keycode":0,"key_label":0,"unicode":58,"location":0,"echo":false,"script":null)
+]
+}
+seqhiker_vim_search={
+"deadzone": 0.5,
+"events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":47,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
+]
+}
+seqhiker_vim_search_next={
+"deadzone": 0.5,
+"events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":78,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
+]
+}
+seqhiker_vim_search_previous={
+"deadzone": 0.5,
+"events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":true,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":78,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
+]
+}
+seqhiker_vim_feature_next={
+"deadzone": 0.5,
+"events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":87,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
+]
+}
+seqhiker_vim_feature_previous={
+"deadzone": 0.5,
+"events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":66,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
+]
+}
+seqhiker_vim_go_prefix={
+"deadzone": 0.5,
+"events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":71,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
+]
+}
+seqhiker_vim_go_end={
+"deadzone": 0.5,
+"events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":true,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":71,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
+]
+}
+seqhiker_vim_contig_next={
+"deadzone": 0.5,
+"events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":67,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
+]
+}
+seqhiker_vim_contig_previous={
+"deadzone": 0.5,
+"events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":true,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":67,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
+]
+}
+seqhiker_vim_contig_next_prefix={
+"deadzone": 0.5,
+"events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":93,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
+]
+}
+seqhiker_vim_contig_previous_prefix={
+"deadzone": 0.5,
+"events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":91,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
+]
+}
+seqhiker_vim_mark_save={
+"deadzone": 0.5,
+"events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":77,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
+]
+}
+seqhiker_vim_mark_load={
+"deadzone": 0.5,
+"events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":39,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
+]
+}
 seqhiker_toggle_search={
 "deadzone": 0.5,
 "events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":true,"meta_pressed":false,"pressed":false,"keycode":70,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
@@ -85,6 +176,11 @@ seqhiker_go={
 , Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":false,"meta_pressed":true,"pressed":false,"keycode":71,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
 ]
 }
+seqhiker_toggle_view_mode={
+"deadzone": 0.5,
+"events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":true,"meta_pressed":false,"pressed":false,"keycode":4194306,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)
+]
+}
 seqhiker_view_slot_load_1={
 "deadzone": 0.5,
 "events": [Object(InputEventKey,"resource_local_to_scene":false,"resource_name":"","device":0,"window_id":0,"alt_pressed":false,"shift_pressed":false,"ctrl_pressed":false,"meta_pressed":false,"pressed":false,"keycode":49,"physical_keycode":0,"key_label":0,"unicode":0,"location":0,"echo":false,"script":null)

scenes/Main.tscn

@@ -590,6 +590,11 @@ max_value = 3.0
 step = 0.05
 value = 1.5
 
+[node name="VimModeToggle" type="CheckButton" parent="Root/ContentMargin/ViewportLayer/SettingsPanel/SettingsMargin/SettingsLayout/SettingsScroll/SettingsPadding/SettingsContent"]
+custom_minimum_size = Vector2(0, 24)
+layout_mode = 2
+text = "Vim Mode"
+
 [node name="SoundsToggle" type="CheckButton" parent="Root/ContentMargin/ViewportLayer/SettingsPanel/SettingsMargin/SettingsLayout/SettingsScroll/SettingsPadding/SettingsContent"]
 layout_mode = 2
 tooltip_text = "Do your genoming like in the movies!
@@ -668,3 +673,31 @@ autowrap_mode = 3
 
 [node name="FeaturePanel" parent="Root/ContentMargin/ViewportLayer" instance=ExtResource("3_30wbj")]
 layout_mode = 1
+
+[node name="VimCommandBar" type="PanelContainer" parent="Root"]
+visible = false
+custom_minimum_size = Vector2(0, 34)
+layout_mode = 2
+size_flags_horizontal = 3
+
+[node name="VimCommandMargin" type="MarginContainer" parent="Root/VimCommandBar"]
+layout_mode = 2
+theme_override_constants/margin_left = 10
+theme_override_constants/margin_top = 4
+theme_override_constants/margin_right = 10
+theme_override_constants/margin_bottom = 4
+
+[node name="VimCommandRow" type="HBoxContainer" parent="Root/VimCommandBar/VimCommandMargin"]
+layout_mode = 2
+theme_override_constants/separation = 4
+
+[node name="VimCommandPrefix" type="Label" parent="Root/VimCommandBar/VimCommandMargin/VimCommandRow"]
+custom_minimum_size = Vector2(12, 0)
+layout_mode = 2
+text = ""
+
+[node name="VimCommandEdit" type="LineEdit" parent="Root/VimCommandBar/VimCommandMargin/VimCommandRow"]
+layout_mode = 2
+size_flags_horizontal = 3
+editable = false
+virtual_keyboard_enabled = false