react-msaview 6.0.0 → 6.1.0

package/dist/columnCounts.d.ts

@@ -15,6 +15,13 @@ export declare class ColumnCounts {
      * are skipped, so this is ~the number of distinct residues, not 32.
      */
     forEachResidue(col: number, cb: (slot: number, count: number) => void): void;
+    /**
+     * Shannon entropy of a column in bits, taken over its non-gap residues only:
+     * a column of two residues and eight gaps is a two-way choice, not a ten-way
+     * one, and gap occupancy is accounted for separately by every caller. 0 for
+     * an all-gap column.
+     */
+    entropy(col: number): number;
     /** non-gap [letter, count] pairs for one column, for display */
     residueEntries(col: number): [string, number][];
     /** the distinct non-gap letters appearing anywhere in the alignment */

package/dist/columnCounts.js

@@ -92,6 +92,24 @@ export class ColumnCounts {
             }
         }
     }
+    /**
+     * Shannon entropy of a column in bits, taken over its non-gap residues only:
+     * a column of two residues and eight gaps is a two-way choice, not a ten-way
+     * one, and gap occupancy is accounted for separately by every caller. 0 for
+     * an all-gap column.
+     */
+    entropy(col) {
+        const nonGapTotal = this.total(col) - this.gapCount(col);
+        if (nonGapTotal === 0) {
+            return 0;
+        }
+        let entropy = 0;
+        this.forEachResidue(col, (_slot, count) => {
+            const freq = count / nonGapTotal;
+            entropy -= freq * Math.log2(freq);
+        });
+        return entropy;
+    }
     /** non-gap [letter, count] pairs for one column, for display */
     residueEntries(col) {
         const entries = [];

package/dist/columnCounts.js.map

@@ -1 +1 @@
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package/dist/components/DragHandle.d.ts

@@ -0,0 +1,25 @@
+import React from 'react';
+export declare const scrollbarThumbFill = "rgba(66,119,127,0.3)";
+declare const variants: Record<'thumb' | 'resizer', {
+    fill: string;
+    fillHovered: string;
+    cursor: (axis: 'x' | 'y') => string;
+    position: React.CSSProperties['position'];
+    zIndex?: number;
+}>;
+/**
+ * A handle dragged along a single axis. `getStart` is read at mousedown and
+ * handed back to `onDrag` alongside the pixel delta since, so a caller only
+ * supplies the dimension it drives and where the handle sits.
+ *
+ * Memoize `onDrag` (useCallback) so the document listeners are not re-attached
+ * on every render.
+ */
+export default function DragHandle({ axis, variant, getStart, onDrag, style, }: {
+    axis: 'x' | 'y';
+    variant: keyof typeof variants;
+    getStart: () => number;
+    onDrag: (delta: number, startValue: number) => void;
+    style: React.CSSProperties;
+}): React.JSX.Element;
+export {};

package/dist/components/DragHandle.js

@@ -0,0 +1,49 @@
+import React, { useState } from 'react';
+import { useDragScroll } from '../useDragScroll.js';
+export const scrollbarThumbFill = 'rgba(66,119,127,0.3)';
+// The scroll thumbs (minimap, vertical scrollbar) and the resize dividers are
+// one widget -- press, drag along an axis, report the pixel delta -- differing
+// only in the affordance they present, so the variant carries the whole
+// difference rather than a second copy of the drag wiring.
+const variants = {
+    thumb: {
+        fill: scrollbarThumbFill,
+        fillHovered: 'rgba(66,119,127,0.6)',
+        cursor: () => 'pointer',
+        position: 'absolute',
+        zIndex: 100,
+    },
+    resizer: {
+        fill: 'rgba(200,200,200)',
+        fillHovered: 'rgba(150,150,150)',
+        cursor: axis => (axis === 'x' ? 'ew-resize' : 'ns-resize'),
+        position: 'relative',
+    },
+};
+/**
+ * A handle dragged along a single axis. `getStart` is read at mousedown and
+ * handed back to `onDrag` alongside the pixel delta since, so a caller only
+ * supplies the dimension it drives and where the handle sits.
+ *
+ * Memoize `onDrag` (useCallback) so the document listeners are not re-attached
+ * on every render.
+ */
+export default function DragHandle({ axis, variant, getStart, onDrag, style, }) {
+    const [hovered, setHovered] = useState(false);
+    const { startDrag } = useDragScroll(axis, onDrag);
+    const { fill, fillHovered, cursor, position, zIndex } = variants[variant];
+    return (React.createElement("div", { onMouseEnter: () => {
+            setHovered(true);
+        }, onMouseLeave: () => {
+            setHovered(false);
+        }, onMouseDown: event => {
+            startDrag(event, getStart());
+        }, style: {
+            position,
+            zIndex,
+            cursor: cursor(axis),
+            background: hovered ? fillHovered : fill,
+            ...style,
+        } }));
+}
+//# sourceMappingURL=DragHandle.js.map

package/dist/components/DragHandle.js.map

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

@@ -1,11 +1,13 @@
 import React from 'react';
 import type { MsaViewModel } from '../model.ts';
+import type { TrackKind } from '../types.ts';
 export declare const VerticalResizeHandle: ({ model, }: {
     model: MsaViewModel;
 }) => React.JSX.Element;
 export declare const HorizontalResizeHandle: ({ model, }: {
     model: MsaViewModel;
 }) => React.JSX.Element;
-export declare const ConservationTrackResizeHandle: ({ model, }: {
+export declare const TrackResizeHandle: ({ model, kind, }: {
     model: MsaViewModel;
-}) => React.JSX.Element;
+    kind: TrackKind;
+}) => React.JSX.Element | null;

package/dist/components/ResizeHandles.js

@@ -1,52 +1,49 @@
-import React, { useCallback, useState } from 'react';
+import React, { useCallback } from 'react';
 import { observer } from 'mobx-react';
-import { useDragScroll } from '../useDragScroll.js';
-const handleBg = 'rgba(200,200,200)';
-const handleBgHover = 'rgba(150,150,150)';
-/**
- * A draggable divider. `getStart` is read at mousedown and handed back to
- * `onDrag` alongside the pixel delta since, so each handle below only has to say
- * which model dimension it resizes and where it sits.
- */
-function ResizeHandle({ axis, getStart, onDrag, style, }) {
-    const [hovered, setHovered] = useState(false);
-    const { startDrag } = useDragScroll(axis, onDrag);
-    return (React.createElement("div", { onMouseDown: event => {
-            startDrag(event, getStart());
-        }, onMouseEnter: () => {
-            setHovered(true);
-        }, onMouseLeave: () => {
-            setHovered(false);
-        }, style: {
-            position: 'relative',
-            cursor: axis === 'x' ? 'ew-resize' : 'ns-resize',
-            background: hovered ? handleBgHover : handleBg,
-            ...style,
-        } }));
-}
+import DragHandle from './DragHandle.js';
 export const VerticalResizeHandle = observer(function ({ model, }) {
     const onDrag = useCallback((delta, startWidth) => {
         model.setTreeAreaWidth(startWidth + delta);
     }, [model]);
-    return (React.createElement(ResizeHandle, { axis: "x", getStart: () => model.treeAreaWidth, onDrag: onDrag, style: { width: model.resizeHandleWidth } }));
+    return (React.createElement(DragHandle, { axis: "x", variant: "resizer", getStart: () => model.treeAreaWidth, onDrag: onDrag, style: { width: model.resizeHandleWidth } }));
 });
 export const HorizontalResizeHandle = observer(function ({ model, }) {
     const onDrag = useCallback((delta, startHeight) => {
         model.setHeight(startHeight + delta);
     }, [model]);
-    return (React.createElement(ResizeHandle, { axis: "y", getStart: () => model.height, onDrag: onDrag, style: { width: '100%', height: model.resizeHandleWidth } }));
+    return (React.createElement(DragHandle, { axis: "y", variant: "resizer", getStart: () => model.height, onDrag: onDrag, style: { width: '100%', height: model.resizeHandleWidth } }));
 });
-export const ConservationTrackResizeHandle = observer(function ({ model, }) {
+// The height behind each resizable track kind. Both bar tracks read one height
+// so conservation and property conservation stay directly comparable; the logo
+// keeps its own, being taller by default. Text tracks are absent: they are one
+// alignment row tall and follow rowHeight, so the zoom controls already size
+// them.
+const trackHeights = {
+    bar: {
+        get: model => model.conservationTrackHeight,
+        set: (model, height) => {
+            model.setConservationTrackHeight(height);
+        },
+    },
+    logo: {
+        get: model => model.sequenceLogoTrackHeight,
+        set: (model, height) => {
+            model.setSequenceLogoTrackHeight(height);
+        },
+    },
+};
+export const TrackResizeHandle = observer(function ({ model, kind, }) {
+    const height = trackHeights[kind];
     const onDrag = useCallback((delta, startHeight) => {
-        model.setConservationTrackHeight(Math.max(10, startHeight + delta));
-    }, [model]);
-    return (React.createElement(ResizeHandle, { axis: "y", getStart: () => model.conservationTrackHeight, onDrag: onDrag, style: {
+        height?.set(model, Math.max(10, startHeight + delta));
+    }, [model, height]);
+    return height ? (React.createElement(DragHandle, { axis: "y", variant: "resizer", getStart: () => height.get(model), onDrag: onDrag, style: {
             position: 'absolute',
             bottom: 0,
             left: 0,
             width: '100%',
             height: model.resizeHandleWidth,
             zIndex: 1,
-        } }));
+        } })) : null;
 });
 //# sourceMappingURL=ResizeHandles.js.map

package/dist/components/ResizeHandles.js.map

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package/dist/components/VerticalScrollbar.js

@@ -1,6 +1,6 @@
 import React, { useCallback } from 'react';
 import { observer } from 'mobx-react';
-import ScrollbarThumb from './ScrollbarThumb.js';
+import DragHandle from './DragHandle.js';
 const width = 20;
 const VerticalScrollbar = observer(({ model }) => {
     const { msaAreaHeight, scrollY, totalHeight } = model;
@@ -18,7 +18,7 @@ const VerticalScrollbar = observer(({ model }) => {
             borderTop: '1px solid #555',
             boxSizing: 'border-box',
         } },
-        React.createElement(ScrollbarThumb, { axis: "y", getStart: () => model.scrollY, onDrag: onDrag, style: {
+        React.createElement(DragHandle, { axis: "y", variant: "thumb", getStart: () => model.scrollY, onDrag: onDrag, style: {
                 top: Math.max(0, t),
                 left: 0,
                 boxSizing: 'border-box',

package/dist/components/VerticalScrollbar.js.map

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package/dist/components/dialogs/InterProScanDialog.js

@@ -5,133 +5,56 @@ import { Button, DialogActions, DialogContent, Typography } from '@mui/material'
 import { observer } from 'mobx-react';
 import { getUngappedSequence } from 'msa-parsers';
 import { launchInterProScan } from '../../launchInterProScan.js';
+const FAMILIES = 'Families, domains, sites & repeats';
+const FEATURES = 'Other sequence features';
+const STRUCTURAL = 'Structural domains';
+const OTHER = 'Other category';
+// The analyses the EBI iprscan5 endpoint accepts, all on by default. Static, so
+// it lives out here rather than being rebuilt on every render of the dialog.
+const interProScanPrograms = [
+    {
+        name: 'NCBIfam',
+        category: FAMILIES,
+        description: 'NCBI RefSeq FAMs including TIGRFAMs',
+    },
+    {
+        name: 'SFLD',
+        category: FAMILIES,
+        description: 'Structure function linkage database',
+    },
+    {
+        name: 'Phobius',
+        category: FEATURES,
+        description: 'A combined transmembrane topology and signal peptide predictor',
+    },
+    { name: 'SignalP', category: FEATURES },
+    { name: 'SignalP_EUK', category: OTHER },
+    { name: 'SignalP_GRAM_POSITIVE', category: OTHER },
+    { name: 'SignalP_GRAM_NEGATIVE', category: OTHER },
+    { name: 'SuperFamily', category: STRUCTURAL },
+    { name: 'Panther', category: FAMILIES },
+    { name: 'Gene3d', category: STRUCTURAL },
+    { name: 'HAMAP', category: FAMILIES },
+    { name: 'PrositeProfiles', category: FAMILIES },
+    { name: 'PrositePatterns', category: FAMILIES },
+    { name: 'Coils', category: FEATURES },
+    { name: 'SMART', category: FAMILIES },
+    {
+        name: 'CDD',
+        category: FAMILIES,
+        description: 'Conserved Domains Database',
+    },
+    { name: 'PRINTS', category: FAMILIES },
+    { name: 'PfamA', category: FAMILIES },
+    { name: 'MobiDBLite', category: FEATURES },
+    { name: 'PIRSF', category: OTHER },
+    { name: 'TMHMM', category: FEATURES },
+    { name: 'AntiFam', category: OTHER },
+    { name: 'FunFam', category: OTHER },
+    { name: 'PIRSR', category: FAMILIES },
+].map(program => ({ ...program, checked: true }));
 const InterProScanDialog = observer(function ({ handleClose, model, }) {
-    const [vals, setVals] = useState([
-        {
-            name: 'NCBIfam',
-            description: 'NCBI RefSeq FAMs including TIGRFAMs',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'SFLD',
-            description: 'Structure function linkage database',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'Phobius',
-            checked: true,
-            description: 'A combined transmembrane topology and signal peptide predictor',
-            category: 'Other sequence features',
-        },
-        {
-            name: 'SignalP',
-            checked: true,
-            category: 'Other sequence features',
-        },
-        {
-            name: 'SignalP_EUK',
-            category: 'Other category',
-            checked: true,
-        },
-        {
-            name: 'SignalP_GRAM_POSITIVE',
-            category: 'Other category',
-            checked: true,
-        },
-        {
-            name: 'SignalP_GRAM_NEGATIVE',
-            checked: true,
-            category: 'Other category',
-        },
-        {
-            name: 'SuperFamily',
-            category: 'Structural domains',
-            checked: true,
-        },
-        {
-            name: 'Panther',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'Gene3d',
-            category: 'Structural domains',
-            checked: true,
-        },
-        {
-            name: 'HAMAP',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'PrositeProfiles',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'PrositePatterns',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'Coils',
-            category: 'Other sequence features',
-            checked: true,
-        },
-        {
-            name: 'SMART',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'CDD',
-            description: 'Conserved Domains Database',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'PRINTS',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'PfamA',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'MobiDBLite',
-            checked: true,
-            category: 'Other sequence features',
-        },
-        {
-            name: 'PIRSF',
-            checked: true,
-            category: 'Other category',
-        },
-        {
-            name: 'TMHMM',
-            checked: true,
-            category: 'Other sequence features',
-        },
-        {
-            name: 'AntiFam',
-            checked: true,
-            category: 'Other category',
-        },
-        {
-            name: 'FunFam',
-            checked: true,
-            category: 'Other category',
-        },
-        {
-            name: 'PIRSR',
-            checked: true,
-            category: 'Families, domains, sites & repeats',
-        },
-    ]);
+    const [vals, setVals] = useState(interProScanPrograms);
     const programs = vals.filter(e => e.checked).map(e => e.name);
     const [show, setShow] = useState(false);
     return (React.createElement(Dialog, { maxWidth: "xl", title: "Query InterProScan API for domains", onClose: () => {
@@ -156,14 +79,14 @@ const InterProScanDialog = observer(function ({ handleClose, model, }) {
                 React.createElement("table", null,
                     React.createElement("tbody", null, vals
                         .toSorted((a, b) => a.category.localeCompare(b.category))
-                        .map(({ name, checked, category }) => (React.createElement("tr", { key: name },
+                        .map(({ name, checked, category, description }) => (React.createElement("tr", { key: name },
                         React.createElement("td", null,
-                            React.createElement("input", { type: "checkbox", key: name, checked: checked, onChange: () => {
+                            React.createElement("input", { type: "checkbox", checked: checked, onChange: () => {
                                     setVals(vals.map(e => e.name === name
                                         ? { ...e, checked: !e.checked }
                                         : e));
                                 } })),
-                        React.createElement("td", null, name),
+                        React.createElement("td", { title: description }, name),
                         React.createElement("td", null, category)))))))) : null),
         React.createElement(DialogActions, null,
             React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {

package/dist/components/dialogs/InterProScanDialog.js.map

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package/dist/components/header/settingsMenuItems.js

@@ -8,9 +8,24 @@ function toggle(label, checked, set) {
         },
     };
 }
+// Every track the alignment can show, with its current state. Without this the
+// "Close" item on a track's own dropdown is a one-way door -- there is nowhere
+// else in the UI to turn a track back on.
+function tracksSubMenu(model) {
+    const shown = new Set(model.turnedOnTracks.map(t => t.model.id));
+    return model.tracks.map(({ model: { id, name } }) => toggle(name, shown.has(id), () => {
+        model.toggleTrack(id);
+    }));
+}
 export function msaSettingsMenuItems(model) {
     const { drawMsaLetters, hideGaps, bgColor, showColumnStats } = model;
     return [
+        {
+            label: 'Tracks',
+            type: 'subMenu',
+            subMenu: tracksSubMenu(model),
+        },
+        { type: 'divider' },
         toggle('Show column statistics on hover', showColumnStats, arg => {
             model.setShowColumnStats(arg);
         }),

package/dist/components/header/settingsMenuItems.js.map

@@ -1 +1 @@
-{"version":3,"file":"settingsMenuItems.js","sourceRoot":"","sources":["../../../src/components/header/settingsMenuItems.ts"],"names":[],"mappings":"AAGA,SAAS,MAAM,CAAC,KAAa,EAAE,OAAgB,EAAE,GAA2B;IAC1E,OAAO;QACL,KAAK;QACL,IAAI,EAAE,UAAmB;QACzB,OAAO;QACP,OAAO,EAAE,GAAG,EAAE;YACZ,GAAG,CAAC,CAAC,OAAO,CAAC,CAAA;QACf,CAAC;KACF,CAAA;AACH,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,KAAmB;IACtD,MAAM,EAAE,cAAc,EAAE,QAAQ,EAAE,OAAO,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IACpE,OAAO;QACL,MAAM,CAAC,iCAAiC,EAAE,eAAe,EAAE,GAAG,CAAC,EAAE;YAC/D,KAAK,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAA;QAC/B,CAAC,CAAC;QACF,MAAM,CAAC,cAAc,EAAE,cAAc,EAAE,GAAG,CAAC,EAAE;YAC3C,KAAK,CAAC,iBAAiB,CAAC,GAAG,CAAC,CAAA;QAC9B,CAAC,CAAC;QACF,2EAA2E;QAC3E,wEAAwE;QACxE,MAAM,CAAC,8CAA8C,EAAE,CAAC,OAAO,EAAE,GAAG,CAAC,EAAE;YACrE,KAAK,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;QACF,MAAM,CAAC,8BAA8B,EAAE,QAAQ,EAAE,GAAG,CAAC,EAAE;YACrD,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;KACH,CAAA;AACH,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,KAAmB;IACvD,MAAM,EACJ,QAAQ,EACR,aAAa,EACb,gBAAgB,EAChB,eAAe,EACf,UAAU,GACX,GAAG,KAAK,CAAA;IACT,OAAO;QACL,MAAM,CAAC,oBAAoB,EAAE,aAAa,EAAE,GAAG,CAAC,EAAE;YAChD,KAAK,CAAC,gBAAgB,CAAC,GAAG,CAAC,CAAA;QAC7B,CAAC,CAAC;QACF,MAAM,CAAC,WAAW,EAAE,QAAQ,EAAE,GAAG,CAAC,EAAE;YAClC,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;QACF,MAAM,CAAC,yCAAyC,EAAE,eAAe,EAAE,GAAG,CAAC,EAAE;YACvE,KAAK,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAA;QAC/B,CAAC,CAAC;QACF,MAAM,CAAC,yBAAyB,EAAE,gBAAgB,EAAE,GAAG,CAAC,EAAE;YACxD,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAA;QAChC,CAAC,CAAC;QACF,MAAM,CAAC,aAAa,EAAE,UAAU,EAAE,GAAG,CAAC,EAAE;YACtC,KAAK,CAAC,aAAa,CAAC,GAAG,CAAC,CAAA;QAC1B,CAAC,CAAC;KACH,CAAA;AACH,CAAC"}
+{"version":3,"file":"settingsMenuItems.js","sourceRoot":"","sources":["../../../src/components/header/settingsMenuItems.ts"],"names":[],"mappings":"AAGA,SAAS,MAAM,CAAC,KAAa,EAAE,OAAgB,EAAE,GAA2B;IAC1E,OAAO;QACL,KAAK;QACL,IAAI,EAAE,UAAmB;QACzB,OAAO;QACP,OAAO,EAAE,GAAG,EAAE;YACZ,GAAG,CAAC,CAAC,OAAO,CAAC,CAAA;QACf,CAAC;KACF,CAAA;AACH,CAAC;AAED,+EAA+E;AAC/E,+EAA+E;AAC/E,0CAA0C;AAC1C,SAAS,aAAa,CAAC,KAAmB;IACxC,MAAM,KAAK,GAAG,IAAI,GAAG,CAAC,KAAK,CAAC,cAAc,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAA;IAChE,OAAO,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,EAAE,EAAE,CAClD,MAAM,CAAC,IAAI,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,GAAG,EAAE;QAC/B,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;IACvB,CAAC,CAAC,CACH,CAAA;AACH,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,KAAmB;IACtD,MAAM,EAAE,cAAc,EAAE,QAAQ,EAAE,OAAO,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IACpE,OAAO;QACL;YACE,KAAK,EAAE,QAAQ;YACf,IAAI,EAAE,SAAkB;YACxB,OAAO,EAAE,aAAa,CAAC,KAAK,CAAC;SAC9B;QACD,EAAE,IAAI,EAAE,SAAkB,EAAE;QAC5B,MAAM,CAAC,iCAAiC,EAAE,eAAe,EAAE,GAAG,CAAC,EAAE;YAC/D,KAAK,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAA;QAC/B,CAAC,CAAC;QACF,MAAM,CAAC,cAAc,EAAE,cAAc,EAAE,GAAG,CAAC,EAAE;YAC3C,KAAK,CAAC,iBAAiB,CAAC,GAAG,CAAC,CAAA;QAC9B,CAAC,CAAC;QACF,2EAA2E;QAC3E,wEAAwE;QACxE,MAAM,CAAC,8CAA8C,EAAE,CAAC,OAAO,EAAE,GAAG,CAAC,EAAE;YACrE,KAAK,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;QACF,MAAM,CAAC,8BAA8B,EAAE,QAAQ,EAAE,GAAG,CAAC,EAAE;YACrD,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;KACH,CAAA;AACH,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,KAAmB;IACvD,MAAM,EACJ,QAAQ,EACR,aAAa,EACb,gBAAgB,EAChB,eAAe,EACf,UAAU,GACX,GAAG,KAAK,CAAA;IACT,OAAO;QACL,MAAM,CAAC,oBAAoB,EAAE,aAAa,EAAE,GAAG,CAAC,EAAE;YAChD,KAAK,CAAC,gBAAgB,CAAC,GAAG,CAAC,CAAA;QAC7B,CAAC,CAAC;QACF,MAAM,CAAC,WAAW,EAAE,QAAQ,EAAE,GAAG,CAAC,EAAE;YAClC,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;QACF,MAAM,CAAC,yCAAyC,EAAE,eAAe,EAAE,GAAG,CAAC,EAAE;YACvE,KAAK,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAA;QAC/B,CAAC,CAAC;QACF,MAAM,CAAC,yBAAyB,EAAE,gBAAgB,EAAE,GAAG,CAAC,EAAE;YACxD,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAA;QAChC,CAAC,CAAC;QACF,MAAM,CAAC,aAAa,EAAE,UAAU,EAAE,GAAG,CAAC,EAAE;YACtC,KAAK,CAAC,aAAa,CAAC,GAAG,CAAC,CAAA;QAC1B,CAAC,CAAC;KACH,CAAA;AACH,CAAC"}

package/dist/components/minimap/Minimap.js

@@ -1,10 +1,36 @@
 import React, { useCallback } from 'react';
+import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
-import ScrollbarThumb, { scrollbarThumbFill } from '../ScrollbarThumb.js';
+import { useCanvasAutorun } from '../../useCanvasAutorun.js';
+import DragHandle, { scrollbarThumbFill } from '../DragHandle.js';
+import { msaThumbnail } from '../msa/msaRaster.js';
 import { MINIMAP_BAR_HEIGHT, getMinimapLayout } from './minimapLayout.js';
 const Minimap = observer(function ({ model }) {
-    const { minimapHeight, msaCanvasWidth } = model;
+    const { minimapHeight, msaCanvasWidth, highResScaleFactor } = model;
+    const theme = useTheme();
     const { unit, s, w, polygonHeight, polygonPoints } = getMinimapLayout(model, msaCanvasWidth);
+    // the whole alignment, sampled down to the bar: it says where the conserved
+    // blocks and the gappy stretches are, which is what a scroll aims at
+    const barWidth = Math.round(msaCanvasWidth * highResScaleFactor);
+    const barHeight = Math.round(MINIMAP_BAR_HEIGHT * highResScaleFactor);
+    const ref = useCanvasAutorun({
+        draw: ctx => {
+            ctx.resetTransform();
+            ctx.clearRect(0, 0, barWidth, barHeight);
+            const thumbnail = msaThumbnail({
+                model,
+                theme,
+                height: MINIMAP_BAR_HEIGHT,
+            });
+            if (thumbnail) {
+                ctx.imageSmoothingEnabled = true;
+                ctx.drawImage(thumbnail, 0, 0, thumbnail.width, thumbnail.height, 0, 0, barWidth, barHeight);
+            }
+        },
+        width: barWidth,
+        height: barHeight,
+        deps: [model, theme],
+    });
     const onDrag = useCallback((delta, startScroll) => {
         model.setScrollX(startScroll - delta / unit);
     }, [model, unit]);
@@ -14,12 +40,14 @@ const Minimap = observer(function ({ model }) {
             width: msaCanvasWidth,
             flexShrink: 0,
         } },
-        React.createElement("div", { style: {
+        React.createElement("canvas", { ref: ref, width: barWidth, height: barHeight, style: {
+                display: 'block',
+                width: msaCanvasWidth,
                 height: MINIMAP_BAR_HEIGHT,
                 boxSizing: 'border-box',
                 border: '1px solid #555',
             } }),
-        React.createElement(ScrollbarThumb, { axis: "x", getStart: () => model.scrollX, onDrag: onDrag, style: {
+        React.createElement(DragHandle, { axis: "x", variant: "thumb", getStart: () => model.scrollX, onDrag: onDrag, style: {
                 top: 0,
                 left: Math.max(0, s),
                 height: MINIMAP_BAR_HEIGHT,

package/dist/components/minimap/Minimap.js.map

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