react-msaview 7.0.0 → 8.1.0

package/dist/types.d.ts

@@ -1,3 +1,4 @@
+import type { ResolvedScale, ScaleSpec } from './scales.ts';
 import type { Annotation } from 'msa-parsers';
 export interface Accession {
     accession: string;
@@ -5,12 +6,19 @@ export interface Accession {
     description: string;
 }
 export type TrackKind = 'text' | 'bar' | 'logo' | 'arc' | 'ruler';
+/**
+ * Which channel the color scheme paints. `fill` colors the cell a residue sits
+ * in, `color` colors the letter itself, the same distinction a grammar of
+ * graphics draws between a shape's interior and its own ink.
+ */
+export type ResidueEncoding = 'fill' | 'color';
 export interface BasicTrackModel {
     id: string;
     name: string;
     associatedRowName?: string;
     height: number;
     kind: TrackKind;
+    heightKey?: string;
     defaultOff?: boolean;
 }
 export interface TextTrackModel extends BasicTrackModel {
@@ -51,6 +59,102 @@ export interface ColumnTrackSpec {
     row?: string;
     height?: number;
 }
+/**
+ * A strip panel: one cell per row, colored from a `rowData` field through
+ * `scale`, which is ggtree's `gheatmap`. `width` is in pixels and defaults to
+ * the row height, and `header` labels the column and defaults to the field.
+ * `legend` titles the strip's legend and defaults to the field, and strips
+ * naming one title share one legend.
+ */
+export interface RowStripSpec {
+    kind: 'strip';
+    field: string;
+    scale?: ScaleSpec;
+    width?: number;
+    header?: string;
+    legend?: string;
+}
+/** the channels a `features` panel reads off the feature table */
+export interface FeatureEncodingSpec {
+    color?: {
+        field: string;
+        scale?: ScaleSpec;
+    };
+    label?: string;
+}
+/**
+ * Shifts each row so that the first feature named `on` starts at zero, which
+ * is gggenes' `make_alignment_dummies`. Only `x: "position"` reads it.
+ */
+export interface AlignTransform {
+    type: 'align';
+    on: string;
+}
+/**
+ * A features panel: the GFF's spans per row, as arrows where they carry a
+ * strand. `x: "column"` draws them in the alignment's columns, and
+ * `x: "position"` in each row's own residue positions on one linear scale, so
+ * a genome with no alignment has an x.
+ */
+export interface RowFeaturesSpec {
+    kind: 'features';
+    x: 'column' | 'position';
+    width?: number;
+    header?: string;
+    encoding?: FeatureEncodingSpec;
+    transform?: AlignTransform[];
+    /** how overlapping features share the row's height; see docs/layers.md */
+    position?: 'identity' | 'strandpile';
+}
+/**
+ * A panel left of the alignment on the row scale, the counterpart of
+ * ColumnTrackSpec on the column scale. See docs/layers.md
+ */
+export type RowPanelSpec = RowStripSpec | RowFeaturesSpec;
+interface ResolvedPanelBase {
+    id: string;
+    header: string;
+    width: number;
+    offsetX: number;
+    legend: LegendEntry[];
+    /** the legend this panel's entries go under; absent means the domain key */
+    legendTitle?: string;
+}
+/**
+ * A strip with its scale resolved: the color each row takes, keyed by row
+ * name, and the pixel column the panel draws in.
+ */
+export interface ResolvedStripPanel extends ResolvedPanelBase {
+    kind: 'strip';
+    field: string;
+    colors: Map<string, string>;
+}
+/** one feature of a features panel, at its pixel span inside the panel */
+export interface RowPanelSpan {
+    annotation: Annotation;
+    xStart: number;
+    xEnd: number;
+    lane: number;
+    laneCount: number;
+}
+/**
+ * A features panel with its x mapping and its scale resolved: the spans per
+ * row name in panel pixels, the fill and outline of each feature, and the
+ * label its `label` channel draws. `field` is the field its color scale reads,
+ * which its legend is titled by.
+ */
+export interface ResolvedFeaturePanel extends ResolvedPanelBase {
+    kind: 'features';
+    x: 'column' | 'position';
+    field?: string;
+    spans: Map<string, RowPanelSpan[]>;
+    colors: Map<Annotation, {
+        fill: string;
+        stroke: string;
+    }>;
+    labels?: Map<Annotation, string>;
+}
+export type ResolvedRowPanel = ResolvedStripPanel | ResolvedFeaturePanel;
 export interface ResidueSegment {
     rowStart: number;
     rowEnd: number;
@@ -64,21 +168,16 @@ export interface MappedStructure {
     url?: string;
 }
 /**
- * Which residue of which structure a row's residue is, as data. Computed by
- * whatever knows how -- SIFTS, an AlphaFold model, a curator -- and carried in
- * the snapshot, because the viewer cannot work it out: matching a row to a
- * structure by sequence equality fails for a construct with an expression tag,
- * a truncation, an engineered residue, or a row that is a subsequence of the
- * entry, and it fails in the direction that looks like it worked.
+ * The structure residue for each residue of a row, computed outside the viewer
+ * (SIFTS, an AlphaFold model, a curator). Sequence equality misplaces tagged
+ * constructs, truncations and subsequence rows; see docs/layers.md.
  *
  * Positions are 1-based and inclusive on both sides, as GFF and `highlights`
  * are. Structure positions are `label_seq_id`, the index into the entity's
- * SEQRES; author numbering carries insertion codes and stays out.
+ * SEQRES; author numbering carries insertion codes and is not used.
  *
  * `unobserved` is in structure positions: present in SEQRES with no
- * coordinates. Worth distinguishing from unmapped, because "the
- * crystallographer could not see it" and "this protein does not have that
- * residue" mean different things to a reader.
+ * coordinates, as distinct from a residue the structure lacks.
  */
 export interface ResidueMapping {
     row: string;
@@ -87,11 +186,9 @@ export interface ResidueMapping {
     segments: ResidueSegment[];
     unobserved?: [number, number][];
     /**
-     * ungapped length of the row this was computed against. Optional, and worth
-     * setting: a mapping outlives the alignment it was made for, and pointing at
-     * residue 58 of a sequence that has since been re-aligned, revised or swapped
-     * is the failure this whole layer exists to avoid. Declared here, the viewer
-     * can notice and refuse instead of answering from stale arithmetic.
+     * ungapped length of the row this was computed against. When set, the viewer
+     * ignores the mapping if the loaded row's length differs, as it does after a
+     * re-alignment, revision or swapped sequence.
      */
     rowLength?: number;
     generated?: {
@@ -104,9 +201,8 @@ export interface ResidueMappingProblem {
     row: string;
     structureId: string;
     /**
-     * `mapping` means the whole mapping is out: the evidence is about the row it
-     * claims, so nothing it says can be trusted. `segment` takes only that
-     * segment, since the rest of the mapping still describes residues that exist.
+     * `mapping` ignores the whole mapping, because the problem concerns its row.
+     * `segment` ignores only that segment and keeps the rest.
      */
     scope: 'mapping' | 'segment';
     reason: string;
@@ -121,9 +217,8 @@ export interface RowResidue {
     seqPos: number;
 }
 /**
- * One loaded document that the snapshot leaves behind, and how big it is.
- * `what` names it the way the import form does, since that is where the reader
- * would go to load it differently.
+ * One loaded document that the snapshot omits, and its size. `what` uses the
+ * import form's names for the documents.
  */
 export interface UnshareableData {
     what: 'alignment' | 'tree' | 'annotations' | 'row metadata' | 'data tracks';
@@ -136,6 +231,27 @@ export interface DomainBand {
     startCol: number;
     endCol: number;
     stackIndex: number;
+    lane: number;
+    laneCount: number;
+}
+/**
+ * One swatch of a categorical color key. `id` is the value the scale read, and
+ * `label` is the text drawn beside the swatch.
+ */
+export interface LegendEntry {
+    id: string;
+    label: string;
+    color: string;
+}
+/**
+ * A categorical color key, drawn by the on-screen overlay and reserved as a
+ * column in the SVG export. `title` names the legend where the viewer draws
+ * more than one.
+ */
+export interface Legend {
+    id: string;
+    title: string;
+    entries: LegendEntry[];
 }
 /**
  * A persistent, labeled highlight. Coordinates are 1-based and inclusive, as
@@ -150,6 +266,90 @@ export interface Highlight {
     label?: string;
     color?: string;
 }
+/**
+ * What the viewer draws over a clade. `highlight` fills the rows behind it,
+ * across the tree and the alignment. `bracket` draws a bar and the clade's
+ * `label` in the gutter right of the tip labels. `collapse` and `focus` seed
+ * the collapsed list and the subtree in focus at load.
+ */
+export type CladeMark = 'highlight' | 'bracket' | 'collapse' | 'focus';
+/**
+ * A clade of the tree and the mark drawn over it. `mrca` names tips whose most
+ * recent common ancestor is the clade; `range` names the first and last tip of
+ * a run in display order, in either order. `tips` is the leaf count the
+ * producer measured, and a clade that resolves to a different count is dropped.
+ * `label` names the clade beside a bracket, and a highlight carrying one draws
+ * the label without the bar. See docs/layers.md
+ */
+export interface Clade {
+    mrca?: string[];
+    range?: [string, string];
+    tips: number;
+    mark: CladeMark;
+    color?: string;
+    label?: string;
+}
+/**
+ * A Clade resolved to the rows it covers, with its fill color settled. `color`
+ * is the highlight fill; `markColor` is the producer's own color for a bracket
+ * bar and its label, unset where the theme's text color stands. `nodeId` is the
+ * node an `mrca` resolved to, which `collapse` and `focus` seed themselves
+ * with, and a `range` record has none.
+ */
+export interface ResolvedClade {
+    rows: [number, number];
+    mark: CladeMark;
+    color: string;
+    markColor?: string;
+    label?: string;
+    nodeId?: string;
+}
+/**
+ * A span in Highlight coordinates: 1-based inclusive residues of `row`, or
+ * columns of the file without it
+ */
+export interface Region {
+    row?: string;
+    start: number;
+    end: number;
+}
+/**
+ * A cell of the alignment in the host's coordinates, 1-based like Highlight:
+ * `column` counts every column of the file, hidden gappy ones included, and
+ * `residue` counts the row's own letters, absent on a gap. A pointer over a
+ * track has a column and no row.
+ */
+export interface Cell {
+    column: number;
+    row?: string;
+    residue?: number;
+    letter?: string;
+}
+/** the alignment columns on screen, 1-based and inclusive */
+export interface Viewport {
+    startColumn: number;
+    endColumn: number;
+}
+/**
+ * A channel of a mark the viewer always draws. `tipLabel` colors each tip label
+ * in the tree, `rowTint` washes the row across the tree gutter and the
+ * alignment, and `branch` colors a tree edge whose tips all share one value;
+ * all three read a field of `rowData`. `featureFill` colors each span of the
+ * annotation overlay and `featureLabel` names the field drawn inside a span,
+ * both from a field of the feature table.
+ */
+export type EncodingChannel = 'tipLabel' | 'rowTint' | 'branch' | 'featureFill' | 'featureLabel';
+/**
+ * A channel, the field feeding it, and the scale it reads that field through.
+ * See docs/layers.md
+ */
+export interface Encoding {
+    channel: EncodingChannel;
+    field: string;
+    scale?: ScaleSpec;
+}
+/** an Encoding with its scale resolved against the values in the table */
+export type ResolvedEncoding = Encoding & ResolvedScale;
 /** a Highlight resolved to visible column indices and row indices */
 export interface ResolvedHighlight {
     startCol?: number;

package/dist/umd.d.ts

@@ -1,6 +1,8 @@
 import * as React from 'react';
 export { destroy } from '@jbrowse/mobx-state-tree';
 export { default as MSAView } from './components/Loading.tsx';
+export { mount } from './mount.tsx';
+export { defineMsaElement } from './element.ts';
 export { type MsaViewModel, default as MSAModelF } from './model.ts';
 export * from 'react-dom/client';
 export { React };

package/dist/umd.js

@@ -1,8 +1,10 @@
 import * as React from 'react';
-// a host that swaps models (the R htmlwidget on re-render) has to destroy the
-// old one, or the disposers its autoruns registered never run
+// a page that builds models with MSAModelF destroys each one it replaces, so
+// the disposers its autoruns registered run
 export { destroy } from '@jbrowse/mobx-state-tree';
 export { default as MSAView } from './components/Loading.js';
+export { mount } from './mount.js';
+export { defineMsaElement } from './element.js';
 export { default as MSAModelF } from './model.js';
 export * from 'react-dom/client';
 export { React };

package/dist/umd.js.map

@@ -1 +1 @@
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package/dist/useCanvasAutorun.d.ts

@@ -1,17 +1,12 @@
 import type React from 'react';
 /**
  * Wires a canvas ref to a mobx autorun: grabs the 2d context once the canvas
- * mounts and re-runs `draw` whenever any observable it reads changes. Collapses
- * the getContext/null-guard/autorun-dispose boilerplate repeated by every canvas
- * block host.
+ * mounts and re-runs `draw` whenever any observable it reads changes.
  *
- * `width`/`height` are the canvas *backing store* size the caller renders onto
- * the element (logical size times the high-res scale factor), and they are load
- * bearing rather than informational. Assigning either resets the canvas bitmap,
- * and React assigns them on every commit where they changed -- which lands
- * *after* the mobx reaction that already redrew at the old size. Without a redraw
- * on the far side of that commit the canvas is left blank: it is what blanked the
- * tree on a tree-area resize and the consensus tracks on a vertical zoom.
+ * `width`/`height` are the canvas backing store size (logical size times the
+ * high-res scale factor). Assigning either clears the bitmap, and React assigns
+ * them after the mobx reaction has drawn at the old size, so the effect redraws
+ * when they change.
  *
  * `deps` covers everything else the effect should re-subscribe on, matching a
  * normal useEffect dep array.

package/dist/useCanvasAutorun.js

@@ -2,17 +2,12 @@ import { useEffect, useRef } from 'react';
 import { autorun } from 'mobx';
 /**
  * Wires a canvas ref to a mobx autorun: grabs the 2d context once the canvas
- * mounts and re-runs `draw` whenever any observable it reads changes. Collapses
- * the getContext/null-guard/autorun-dispose boilerplate repeated by every canvas
- * block host.
+ * mounts and re-runs `draw` whenever any observable it reads changes.
  *
- * `width`/`height` are the canvas *backing store* size the caller renders onto
- * the element (logical size times the high-res scale factor), and they are load
- * bearing rather than informational. Assigning either resets the canvas bitmap,
- * and React assigns them on every commit where they changed -- which lands
- * *after* the mobx reaction that already redrew at the old size. Without a redraw
- * on the far side of that commit the canvas is left blank: it is what blanked the
- * tree on a tree-area resize and the consensus tracks on a vertical zoom.
+ * `width`/`height` are the canvas backing store size (logical size times the
+ * high-res scale factor). Assigning either clears the bitmap, and React assigns
+ * them after the mobx reaction has drawn at the old size, so the effect redraws
+ * when they change.
  *
  * `deps` covers everything else the effect should re-subscribe on, matching a
  * normal useEffect dep array.

package/dist/useCanvasAutorun.js.map

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package/dist/useMsaSvgFigure.d.ts

@@ -0,0 +1,20 @@
+import type { MsaViewModel } from './model.ts';
+import type { Theme } from '@mui/material';
+export interface MsaSvgFigure {
+    /** the SVG document for what is on screen, once the first draw finishes */
+    svg?: string;
+    error?: unknown;
+}
+/**
+ * The viewer's SVG export of its viewport, as markup for the page to insert.
+ * It redraws after the view settles: `delay` ms after the last scroll, zoom,
+ * resize or change to the snapshot. A draw a later one overtakes is dropped.
+ *
+ * The figure's row names and letters are SVG text, so the browser's find
+ * locates them, a reader can select them, and print stylesheets apply.
+ */
+export declare function useMsaSvgFigure(model: MsaViewModel, { theme, includeTracks, delay, }?: {
+    theme?: Theme;
+    includeTracks?: boolean;
+    delay?: number;
+}): MsaSvgFigure;

package/dist/useMsaSvgFigure.js

@@ -0,0 +1,46 @@
+import { useEffect, useState } from 'react';
+import { createJBrowseTheme } from '@jbrowse/core/ui/theme';
+import { getSnapshot } from '@jbrowse/mobx-state-tree';
+import { compareStructural, reaction } from 'mobx';
+import { renderToSvg } from './renderToSvg.js';
+/**
+ * The viewer's SVG export of its viewport, as markup for the page to insert.
+ * It redraws after the view settles: `delay` ms after the last scroll, zoom,
+ * resize or change to the snapshot. A draw a later one overtakes is dropped.
+ *
+ * The figure's row names and letters are SVG text, so the browser's find
+ * locates them, a reader can select them, and print stylesheets apply.
+ */
+export function useMsaSvgFigure(model, { theme, includeTracks = false, delay = 300, } = {}) {
+    const [figure, setFigure] = useState({});
+    useEffect(() => {
+        let latest = 0;
+        const dispose = reaction(() => model.viewInitialized && model.dataInitialized
+            ? [getSnapshot(model), model.width, model.height]
+            : undefined, key => {
+            if (!key) {
+                return;
+            }
+            const draw = ++latest;
+            renderToSvg(model, {
+                theme: theme ?? createJBrowseTheme(),
+                exportType: 'viewport',
+                includeTracks,
+            }).then(svg => {
+                if (draw === latest) {
+                    setFigure({ svg });
+                }
+            }, (error) => {
+                if (draw === latest) {
+                    setFigure({ error });
+                }
+            });
+        }, { delay, fireImmediately: true, equals: compareStructural });
+        return () => {
+            latest = -1;
+            dispose();
+        };
+    }, [model, theme, includeTracks, delay]);
+    return figure;
+}
+//# sourceMappingURL=useMsaSvgFigure.js.map

package/dist/useMsaSvgFigure.js.map

@@ -0,0 +1 @@
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package/dist/useWheelScroll.js

@@ -116,10 +116,6 @@ export function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, scrollZoom,
         };
     }, [mouseDragging, onScrollX, onScrollY]);
     function onMouseDown(event) {
-        const target = event.target;
-        if (target.draggable || target.dataset.resizer) {
-            return;
-        }
         if (event.button === 0) {
             prevX.current = event.clientX;
             prevY.current = event.clientY;

package/dist/useWheelScroll.js.map

@@ -1 +1 @@
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package/dist/util.d.ts

@@ -1,17 +1,16 @@
 import type { Theme } from '@mui/material';
 export declare function adjustColorForContrast(color: string, bg: string): string;
+export declare function withAlpha(color: string, alpha: number): string;
+export declare function outlineColor(fill: string): string;
 export declare function transform<T>(obj: Record<string, T>, cb: (arg0: [string, T]) => [string, T]): {
     [k: string]: T;
 };
 /**
  * Readable letter color over a given cell color, memoized per theme.
  *
- * A dynamic scheme colors a cell from its column, so there is no letter->color
- * table to precompute a contrast table from; asking per cell color covers the
- * dynamic schemes, the static ones and a track's own `colors` alike. An
- * uncolored cell sits on the theme's background, where the theme's own text
- * color is what stays readable -- `black` turned every gap and every uncolored
- * cell invisible in the dark theme.
+ * Keyed by cell color, since a dynamic scheme has no letter->color table; this
+ * covers static schemes and a track's own `colors` too. An uncolored cell gets
+ * the theme's text color, which stays readable in the dark theme.
  */
 export declare function contrastTextFn(theme: Theme): (color: string | undefined) => string;
 export declare function dropBlanks<T>(blanks: number[], arr: T[]): T[];

package/dist/util.js

@@ -23,6 +23,16 @@ export function adjustColorForContrast(color, bg) {
     contrastAdjustCache.set(cacheKey, result);
     return result;
 }
+// a wash over the alignment or the tree: a color carrying its own alpha draws
+// at that alpha, and one with none takes `alpha` so the marks under it stay
+// readable
+export function withAlpha(color, alpha) {
+    const parsed = colord(color);
+    return parsed.alpha() === 1 ? parsed.alpha(alpha).toRgbString() : color;
+}
+export function outlineColor(fill) {
+    return colord(fill).darken(0.1).toHex();
+}
 export function transform(obj, cb) {
     return Object.fromEntries(Object.entries(obj).map(cb));
 }
@@ -30,12 +40,9 @@ const contrastTextCaches = new WeakMap();
 /**
  * Readable letter color over a given cell color, memoized per theme.
  *
- * A dynamic scheme colors a cell from its column, so there is no letter->color
- * table to precompute a contrast table from; asking per cell color covers the
- * dynamic schemes, the static ones and a track's own `colors` alike. An
- * uncolored cell sits on the theme's background, where the theme's own text
- * color is what stays readable -- `black` turned every gap and every uncolored
- * cell invisible in the dark theme.
+ * Keyed by cell color, since a dynamic scheme has no letter->color table; this
+ * covers static schemes and a track's own `colors` too. An uncolored cell gets
+ * the theme's text color, which stays readable in the dark theme.
  */
 export function contrastTextFn(theme) {
     let cache = contrastTextCaches.get(theme);

package/dist/util.js.map

@@ -1 +1 @@
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package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "7.0.0";
+export declare const version = "8.1.0";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '7.0.0';
+export const version = '8.1.0';
 //# sourceMappingURL=version.js.map