react-msaview 9.1.0 → 9.2.0

package/dist/constants.js

@@ -42,6 +42,9 @@ export const defaultScrollZoomAxis = 'both';
 // frame. A sprite atlas measured slower.
 export const minLetterRowHeight = 8;
 export const minLetterColWidth = 5;
+// A wheel-zoom frame draws a block's letters only when the block holds at most
+// this many cells; the settle redraw after the gesture draws the rest
+export const zoomFrameMaxLetters = 2000;
 // A feature span draws its label at two pixels under its height, capped at 11,
 // so a span shorter than this holds no readable text: an underline bar, a
 // sub-row band or a features panel over small rows
@@ -57,8 +60,10 @@ export const labelFitFontSize = fontSizeFor(defaultRowHeight);
 // zoom-in buttons (which otherwise grow unbounded). minColWidth/minRowHeight are
 // the smooth-zoom floors.
 export const minColWidth = 0.2;
-export const minRowHeight = 1;
+export const minRowHeight = 0.2;
 export const maxCellSize = 80;
+// the settings panel's width, which it takes out of the view's
+export const settingsPanelWidth = 280;
 // MSA model defaults
 export const defaultBgColor = true;
 export const defaultColorSchemeName = 'maeditor';
@@ -86,6 +91,7 @@ export const defaultDrawTree = true;
 export const defaultDrawNodeBubbles = true;
 export const defaultDrawNodeLabels = false;
 export const defaultShowTreeOverview = false;
+export const defaultShowTreeScaleBar = false;
 export const defaultOverviewHeight = 120;
 // Neighbor joining does not run above this many rows. The distance matrix is
 // O(n^2*L) and the join loop O(n^3), both on the main thread with no progress

package/dist/constants.js.map

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package/dist/darkReader.d.ts

@@ -0,0 +1,7 @@
+import type { Theme } from '@mui/material';
+/**
+ * The theme a canvas draws in: the surrounding MUI theme, or a dark one while
+ * Dark Reader darkens a light page. The DOM keeps the surrounding theme, which
+ * Dark Reader restyles itself, and the SVG export keeps it too.
+ */
+export declare function useCanvasTheme(): Theme;

package/dist/darkReader.js

@@ -0,0 +1,42 @@
+import { useSyncExternalStore } from 'react';
+import { createJBrowseTheme } from '@jbrowse/core/ui/theme';
+import { useTheme } from '@mui/material';
+// Dark Reader's Dynamic mode rewrites the page's CSS and leaves canvas pixels
+// alone, so a light theme's black letters land on the dark page it paints.
+// Inlined from @jbrowse/core/util/systemColorScheme, which an older host core
+// lacks (see CLAUDE.md on externals).
+const DARK_READER_ATTRIBUTE = 'data-darkreader-scheme';
+function darkReaderIsDark() {
+    return (typeof document !== 'undefined' &&
+        document.documentElement.getAttribute(DARK_READER_ATTRIBUTE) === 'dark');
+}
+function onDarkReaderChange(listener) {
+    if (typeof MutationObserver !== 'function' ||
+        typeof document === 'undefined') {
+        return () => { };
+    }
+    const observer = new MutationObserver(listener);
+    observer.observe(document.documentElement, {
+        attributes: true,
+        attributeFilter: [DARK_READER_ATTRIBUTE],
+    });
+    return () => {
+        observer.disconnect();
+    };
+}
+let darkTheme;
+/**
+ * The theme a canvas draws in: the surrounding MUI theme, or a dark one while
+ * Dark Reader darkens a light page. The DOM keeps the surrounding theme, which
+ * Dark Reader restyles itself, and the SVG export keeps it too.
+ */
+export function useCanvasTheme() {
+    const theme = useTheme();
+    const darkReader = useSyncExternalStore(onDarkReaderChange, darkReaderIsDark, () => false);
+    if (darkReader && theme.palette.mode !== 'dark') {
+        darkTheme ??= createJBrowseTheme({ palette: { mode: 'dark' } });
+        return darkTheme;
+    }
+    return theme;
+}
+//# sourceMappingURL=darkReader.js.map

package/dist/darkReader.js.map

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

@@ -1,5 +1,15 @@
 import { when } from 'mobx';
 import { mount } from './mount.js';
+const dataProperties = [
+    'msa',
+    'tree',
+    'gff',
+    'features',
+    'colorScheme',
+    'highlights',
+    'columnTracks',
+    'residueMappings',
+];
 const ownAttributes = [
     'msa-url',
     'tree-url',
@@ -72,53 +82,18 @@ export function defineMsaElement(tagName = 'jbrowse-msa') {
         #rangePending = false;
         #reported;
         #data = {};
-        get msa() {
-            return this.#data.msa;
-        }
-        set msa(value) {
-            this.#setData({ msa: value });
-        }
-        get tree() {
-            return this.#data.tree;
-        }
-        set tree(value) {
-            this.#setData({ tree: value });
-        }
-        get gff() {
-            return this.#data.gff;
-        }
-        set gff(value) {
-            this.#setData({ gff: value });
-        }
-        get features() {
-            return this.#data.features;
-        }
-        set features(value) {
-            this.#setData({ features: value });
-        }
-        get colorScheme() {
-            return this.#data.colorScheme;
-        }
-        set colorScheme(value) {
-            this.#setData({ colorScheme: value });
-        }
-        get highlights() {
-            return this.#data.highlights;
-        }
-        set highlights(value) {
-            this.#setData({ highlights: value });
-        }
-        get columnTracks() {
-            return this.#data.columnTracks;
-        }
-        set columnTracks(value) {
-            this.#setData({ columnTracks: value });
-        }
-        get residueMappings() {
-            return this.#data.residueMappings;
-        }
-        set residueMappings(value) {
-            this.#setData({ residueMappings: value });
+        static {
+            for (const key of dataProperties) {
+                Object.defineProperty(MsaElement.prototype, key, {
+                    configurable: true,
+                    get() {
+                        return this.#data[key];
+                    },
+                    set(value) {
+                        this.#setData({ [key]: value });
+                    },
+                });
+            }
         }
         // the viewer's selection, which the reader's drags change
         get selection() {

package/dist/element.js.map

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

@@ -0,0 +1,37 @@
+import type { ScaleSpec } from './scales.ts';
+import type { Annotation, DomainBand, RowFeaturesSpec, RowPanelSpan, RowPanelSpec } from './types.ts';
+export declare function rowPanelWidth(panel: RowPanelSpec, view: {
+    rowHeight: number;
+}): number;
+export declare function stringFields(row: unknown): Record<string, string> | undefined;
+export declare function colorByRow(rowData: Record<string, Record<string, string> | undefined>, field: string, colorOf: (value: string) => string | undefined): Map<string, string>;
+export declare function featureColorMap(annotations: Annotation[], encoding: {
+    field: string;
+    colorOf: (value: string) => string | undefined;
+} | undefined, fillPalette: Record<string, string>): Map<Annotation, {
+    fill: string;
+    stroke: string;
+}>;
+export declare function featureLabelMap(annotations: Annotation[], field: string): Map<Annotation, string>;
+/**
+ * The spans a `features` panel draws, keyed by row name and measured in the
+ * panel's own pixels. `column` takes the bands the overlay draws, at the
+ * alignment's column width. `position` packs each row's features in its own
+ * residue positions, shifted by an `align` transform, and maps the extent they
+ * cover across every row onto the panel width, so a row with no alignment
+ * still has an x.
+ */
+export declare function featurePanelSpans({ panel, width, colWidth, domainBands, annotationsByRow, shifts, }: {
+    panel: RowFeaturesSpec;
+    width: number;
+    colWidth: number;
+    domainBands: Map<string, DomainBand[]>;
+    annotationsByRow: Record<string, Annotation[]>;
+    shifts: Map<string, number> | undefined;
+}): Map<string, RowPanelSpan[]>;
+export declare function resolveFeatureScale(field: string, scale: ScaleSpec | undefined, annotations: Annotation[], drawn: Annotation[]): {
+    kind: 'categorical';
+    colorOf: (value: string) => string | undefined;
+    field: string;
+    legend: import("./types.ts").LegendEntry[];
+};

package/dist/featurePanels.js

@@ -0,0 +1,187 @@
+import { notEmpty } from '@jbrowse/core/util';
+import { packDomainLanes } from './components/msa/packDomainLanes.js';
+import { defaultFeaturePanelWidth } from './constants.js';
+import { featureField } from './featureFields.js';
+import { resolveScale } from './scales.js';
+import { outlineColor } from './util.js';
+// the fill of a span under a scale that gives its value no color, such as a
+// gene a `map` over gene names leaves out
+const UNSCALED_FEATURE = '#d9d9d9';
+// the fraction of a span a following one may cover before it takes a lane of
+// its own in a `features` panel
+const laneOverlap = 0.1;
+// a row panel's own width, or a default: the row height, which makes a strip
+// cell square, and a gene neighborhood's width for a features panel. The row
+// height is read only when used, so a panel with a width of its own does not
+// recompute on a vertical zoom
+export function rowPanelWidth(panel, view) {
+    return (panel.width ??
+        (panel.kind === 'features' ? defaultFeaturePanelWidth : view.rowHeight));
+}
+// one row of the row table as the channels read it. A number or a boolean
+// reads as its string, the way a GFF value does, and null or an object drops
+export function stringFields(row) {
+    if (typeof row !== 'object' || row === null) {
+        return undefined;
+    }
+    const fields = {};
+    for (const [field, value] of Object.entries(row)) {
+        if (typeof value === 'string') {
+            fields[field] = value;
+        }
+        else if (typeof value === 'number' || typeof value === 'boolean') {
+            fields[field] = String(value);
+        }
+    }
+    return fields;
+}
+// the color each row takes from a field of the row table under a scale
+export function colorByRow(rowData, field, colorOf) {
+    const colors = new Map();
+    for (const [name, row] of Object.entries(rowData)) {
+        const value = row?.[field];
+        const color = value === undefined ? undefined : colorOf(value);
+        if (color) {
+            colors.set(name, color);
+        }
+    }
+    return colors;
+}
+// the fill and outline of every feature in a list: its own GFF `color=` first,
+// then the scale an encoding resolves over one of its fields, then the
+// accession palette
+export function featureColorMap(annotations, encoding, fillPalette) {
+    const strokes = new Map();
+    const strokeOf = (fill) => {
+        const hit = strokes.get(fill);
+        if (hit !== undefined) {
+            return hit;
+        }
+        const stroke = outlineColor(fill);
+        strokes.set(fill, stroke);
+        return stroke;
+    };
+    return new Map(annotations.map(annotation => {
+        const value = encoding
+            ? featureField(annotation, encoding.field)
+            : undefined;
+        const fill = annotation.color ??
+            (value === undefined ? undefined : encoding.colorOf(value)) ??
+            (encoding ? UNSCALED_FEATURE : fillPalette[annotation.accession]);
+        return [annotation, { fill, stroke: strokeOf(fill) }];
+    }));
+}
+// the text a label channel draws inside each span, for the features carrying
+// the field it names
+export function featureLabelMap(annotations, field) {
+    const labels = new Map();
+    for (const annotation of annotations) {
+        const value = featureField(annotation, field);
+        if (value !== undefined) {
+            labels.set(annotation, value);
+        }
+    }
+    return labels;
+}
+/**
+ * Lanes for `position: "strandpile"`, gggenomes' `position_strandpile`: the
+ * forward features stack above the line and the reverse below it, each strand
+ * packing on its own. The deepest row on each side sets the grid every row lays
+ * out on, so the line between the strands sits at one height down the panel and
+ * a reader can scan it. A feature with no strand piles with the forward ones.
+ */
+function strandpileLanes(rows) {
+    const piled = rows.map(([name, bands]) => {
+        const reverse = packDomainLanes(bands.filter(b => b.annotation.strand === -1));
+        const forward = packDomainLanes(bands.filter(b => b.annotation.strand !== -1));
+        return { name, forward, reverse };
+    });
+    const up = Math.max(0, ...piled.map(p => p.forward[0]?.laneCount ?? 0));
+    const down = Math.max(0, ...piled.map(p => p.reverse[0]?.laneCount ?? 0));
+    const laneCount = up + down;
+    return new Map(piled.map(({ name, forward, reverse }) => [
+        name,
+        [
+            // forward level 0 is the lane just above the line, stacking upward
+            ...forward.map(b => ({ ...b, lane: up - 1 - b.lane, laneCount })),
+            ...reverse.map(b => ({ ...b, lane: up + b.lane, laneCount })),
+        ],
+    ]));
+}
+/** one row's spans laid out by the panel's `position` */
+function panelLanes(panel, rows) {
+    return panel.position === 'strandpile'
+        ? strandpileLanes(rows)
+        : new Map(rows.map(([name, bands]) => [name, packDomainLanes(bands)]));
+}
+/**
+ * The spans a `features` panel draws, keyed by row name and measured in the
+ * panel's own pixels. `column` takes the bands the overlay draws, at the
+ * alignment's column width. `position` packs each row's features in its own
+ * residue positions, shifted by an `align` transform, and maps the extent they
+ * cover across every row onto the panel width, so a row with no alignment
+ * still has an x.
+ */
+export function featurePanelSpans({ panel, width, colWidth, domainBands, annotationsByRow, shifts, }) {
+    if (panel.x === 'column') {
+        return panelLanes(panel, [...domainBands].map(([name, bands]) => [
+            name,
+            bands.map(band => ({
+                ...band,
+                xStart: band.startCol * colWidth,
+                xEnd: band.endCol * colWidth,
+            })),
+        ]));
+    }
+    const shifted = Object.entries(annotationsByRow).map(([name, annotations]) => {
+        const shift = shifts?.get(name) ?? 0;
+        return [
+            name,
+            annotations.map(annotation => ({
+                annotation,
+                start: annotation.start - 1 + shift,
+                end: annotation.end + shift,
+            })),
+        ];
+    });
+    let min = Infinity;
+    let max = -Infinity;
+    for (const [, features] of shifted) {
+        for (const { start, end } of features) {
+            min = Math.min(min, start);
+            max = Math.max(max, end);
+        }
+    }
+    // a gene arrow ends where its feature does, so the extent maps onto the whole
+    // panel less the pixel the rightmost stroke needs
+    const drawable = Math.max(1, width - 1);
+    const scale = max > min ? drawable / (max - min) : 0;
+    // a lane opens where a span covers more than a tenth of the one before it,
+    // which keeps the genes of an operon on one lane: adjacent genes commonly
+    // share a few bases, and a stop codon overlapping the next start reads as a
+    // second lane over the whole row
+    return panelLanes(panel, shifted.map(([name, features]) => [
+        name,
+        features.map(({ annotation, start, end }) => ({
+            annotation,
+            xStart: (start - min) * scale,
+            xEnd: (end - min) * scale,
+            startCol: start,
+            endCol: end - (end - start) * laneOverlap,
+        })),
+    ]));
+}
+// a scale over the values a field takes across every feature loaded, so hiding
+// a type in the filter dialog leaves the rest in their colors, and a legend of
+// the values the features drawn carry
+export function resolveFeatureScale(field, scale, annotations, drawn) {
+    const valuesOf = (list) => list.map(a => featureField(a, field)).filter(notEmpty);
+    const resolved = resolveScale(scale, valuesOf(annotations));
+    const shown = new Set(valuesOf(drawn));
+    return {
+        field,
+        ...resolved,
+        legend: resolved.legend.filter(entry => shown.has(entry.id)),
+    };
+}
+//# sourceMappingURL=featurePanels.js.map

package/dist/featurePanels.js.map

@@ -0,0 +1 @@
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package/dist/filehandleLoader.d.ts

@@ -0,0 +1,41 @@
+import type { FetchStatus } from './fetchUtils.ts';
+import type { FileLocation } from '@jbrowse/core/util/types';
+import type { IStateTreeNode } from '@jbrowse/mobx-state-tree';
+interface LoaderHost extends IStateTreeNode {
+    setStatus: (status?: FetchStatus) => void;
+    setError: (error?: unknown) => void;
+    addWarning: (warning: string) => void;
+}
+interface FilehandleLoader {
+    /** the layer's name in a failure message */
+    what: string;
+    getFilehandle: () => FileLocation | undefined;
+    onLoad: (text: string) => void;
+    setLoading?: (loading: boolean) => void;
+    /** runs after a local file loads, since a blob has no URL to refetch, and on cancel */
+    clearFilehandle?: () => void;
+    /** a failure adds a warning instead of an error */
+    optional?: boolean;
+}
+/**
+ * Latest-wins abort rotation, after `createAbortRotation` in
+ * jbrowse-components. Each `begin()` aborts the previous fetch and returns a
+ * signal with an `isCurrent()` guard; gate every write after an await on it so a
+ * superseded or torn-down fetch cannot overwrite fresher data. `end()` in the
+ * `finally` closes the guard of a fetch that completed.
+ */
+export declare function createAbortRotation(self: IStateTreeNode): {
+    /** aborts the running fetch, and returns whether one was running */
+    cancel(): boolean;
+    begin(): {
+        controller: AbortController;
+        isCurrent: () => boolean;
+        end(): void;
+    };
+};
+/**
+ * Fetches the filehandle whenever it changes and hands the text to `onLoad`. A
+ * superseded or cleared request is aborted and clears its status line.
+ */
+export declare function installFilehandleLoader(self: LoaderHost, { what, getFilehandle, onLoad, setLoading, clearFilehandle, optional, }: FilehandleLoader): void;
+export {};

package/dist/filehandleLoader.js

@@ -0,0 +1,99 @@
+import { openLocation } from '@jbrowse/core/util/io';
+import { addDisposer, isAlive } from '@jbrowse/mobx-state-tree';
+import { autorun, transaction } from 'mobx';
+import { fetchTextWithProgress, isAbortError } from './fetchUtils.js';
+/**
+ * Latest-wins abort rotation, after `createAbortRotation` in
+ * jbrowse-components. Each `begin()` aborts the previous fetch and returns a
+ * signal with an `isCurrent()` guard; gate every write after an await on it so a
+ * superseded or torn-down fetch cannot overwrite fresher data. `end()` in the
+ * `finally` closes the guard of a fetch that completed.
+ */
+export function createAbortRotation(self) {
+    let current;
+    return {
+        /** aborts the running fetch, and returns whether one was running */
+        cancel() {
+            const running = current !== undefined && !current.ended;
+            current?.controller.abort();
+            current = undefined;
+            return running;
+        },
+        begin() {
+            current?.controller.abort();
+            const mine = { controller: new AbortController(), ended: false };
+            current = mine;
+            return {
+                controller: mine.controller,
+                isCurrent: () => !mine.ended && mine === current && isAlive(self),
+                end() {
+                    mine.ended = true;
+                },
+            };
+        },
+    };
+}
+/**
+ * Fetches the filehandle whenever it changes and hands the text to `onLoad`. A
+ * superseded or cleared request is aborted and clears its status line.
+ */
+export function installFilehandleLoader(self, { what, getFilehandle, onLoad, setLoading, clearFilehandle, optional = false, }) {
+    const rotation = createAbortRotation(self);
+    const cancel = () => {
+        if (rotation.cancel() && isAlive(self)) {
+            self.setStatus(undefined);
+        }
+    };
+    addDisposer(self, cancel);
+    addDisposer(self, autorun(async () => {
+        const filehandle = getFilehandle();
+        cancel();
+        if (!filehandle) {
+            setLoading?.(false);
+            return;
+        }
+        const { controller, isCurrent, end } = rotation.begin();
+        try {
+            setLoading?.(true);
+            if (!optional) {
+                self.setError(undefined);
+            }
+            const text = await fetchTextWithProgress(openLocation(filehandle), status => {
+                if (isCurrent()) {
+                    self.setStatus(status);
+                }
+            }, { controller });
+            if (isCurrent()) {
+                transaction(() => {
+                    onLoad(text);
+                    if (filehandle.locationType === 'BlobLocation') {
+                        clearFilehandle?.();
+                    }
+                });
+            }
+        }
+        catch (e) {
+            if (isCurrent()) {
+                if (isAbortError(e)) {
+                    clearFilehandle?.();
+                }
+                else {
+                    console.error(e);
+                    if (optional) {
+                        self.addWarning(`The ${what} did not load: ${e}`);
+                    }
+                    else {
+                        self.setError(e);
+                    }
+                }
+            }
+        }
+        finally {
+            if (isCurrent()) {
+                setLoading?.(false);
+            }
+            end();
+        }
+    }));
+}
+//# sourceMappingURL=filehandleLoader.js.map

package/dist/filehandleLoader.js.map

@@ -0,0 +1 @@
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package/dist/index.d.ts

@@ -6,9 +6,11 @@ export { maxNeighborJoiningRows } from './constants.ts';
 export { expandSpec, residueLabel } from './expandSpec.ts';
 export type { ColumnTrackShorthand, HighlightShorthand, MsaSpec, RegionShorthand, } from './expandSpec.ts';
 export { default as MSAView } from './components/Loading.tsx';
+export type { ToolbarSlots } from './components/header/Header.tsx';
 export { default as MSAViewer } from './components/MSAViewer.tsx';
 export type { MSAViewerProps } from './components/MSAViewer.tsx';
 export { resolveTheme, viewerSnapshot } from './viewerSnapshot.ts';
+export { schemeResidueColor } from './schemeResidueColor.ts';
 export { mount } from './mount.tsx';
 export { defineMsaElement } from './element.ts';
 export { useMsaSvgFigure } from './useMsaSvgFigure.ts';
@@ -20,5 +22,6 @@ export type { HierarchyNode, LaidOutNode, TreeScale } from './hierarchy.ts';
 export type { InterProScanResults } from 'msa-parsers';
 export type { ColumnCounts } from './columnCounts.ts';
 export type { ColumnStats } from './columnStats.ts';
+export type { ZoomSnapshot } from './zoomSnapshot.ts';
 export type { ResolvedScale, ScaleSpec } from './scales.ts';
 export type { Accession, Annotation, Arc, ArcSpec, ArcTrackModel, BasicTrack, BasicTrackModel, Cell, Clade, CladeMark, ColorScheme, ColumnTrackSpec, DomainBand, Encoding, EncodingChannel, Feature, Highlight, Legend, LegendEntry, MsaSelection, Node, MappedStructure, NodeWithIds, NodeWithIdsAndLength, Region, ResidueEncoding, ResidueMapping, ResidueMappingProblem, ResidueSegment, ResolvedClade, ResolvedEncoding, ResolvedHighlight, ResolvedRowPanel, ResolvedSelection, RowDataInput, RowPanelSpec, RowResidue, StructureResidue, TextTrackModel, TidyDomainAnnotation, TrackKind, TreeOrder, TreeRoot, UnshareableData, Viewport, } from './types.ts';