react-msaview 5.10.0 → 6.1.0

package/dist/clustalX.js

@@ -16,33 +16,33 @@ const CYAN = 'rgb(26, 179, 179)';
  */
 export function clustalXColumnColors(counts, col) {
     const total = counts.total(col);
-    const n = (letter) => counts.count(col, letter);
-    const W = n('W');
-    const L = n('L');
-    const V = n('V');
-    const I = n('I');
-    const M = n('M');
-    const A = n('A');
-    const F = n('F');
-    const C = n('C');
-    const H = n('H');
-    const P = n('P');
-    const R = n('R');
-    const K = n('K');
-    const Q = n('Q');
-    const E = n('E');
-    const D = n('D');
-    const T = n('T');
-    const S = n('S');
-    const G = n('G');
-    const Y = n('Y');
-    const N = n('N');
+    const count = (letter) => counts.count(col, letter);
+    const W = count('W');
+    const L = count('L');
+    const V = count('V');
+    const I = count('I');
+    const M = count('M');
+    const A = count('A');
+    const F = count('F');
+    const C = count('C');
+    const H = count('H');
+    const P = count('P');
+    const R = count('R');
+    const K = count('K');
+    const Q = count('Q');
+    const E = count('E');
+    const D = count('D');
+    const T = count('T');
+    const S = count('S');
+    const G = count('G');
+    const Y = count('Y');
+    const N = count('N');
     const hydrophobic = W + L + V + I + M + A + F + C + H + P + Y;
     const KR = K + R;
     const QE = Q + E;
     const ED = E + D;
     const TS = T + S;
-    const p = (n) => n / total;
+    const p = (subtotal) => subtotal / total;
     const colors = {};
     if (p(hydrophobic) > 0.6) {
         colors.W = BLUE;

package/dist/clustalX.js.map

@@ -1 +1 @@
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+{"version":3,"file":"clustalX.js","sourceRoot":"","sources":["../src/clustalX.ts"],"names":[],"mappings":"AAAA,+BAA+B;AAC/B,kEAAkE;AAIlE,MAAM,IAAI,GAAG,kBAAkB,CAAA;AAC/B,MAAM,GAAG,GAAG,MAAM,CAAA;AAClB,MAAM,SAAS,GAAG,mBAAmB,CAAA;AACrC,MAAM,SAAS,GAAG,mBAAmB,CAAA;AACrC,MAAM,KAAK,GAAG,MAAM,CAAA;AACpB,MAAM,QAAQ,GAAG,gBAAgB,CAAA;AACjC,MAAM,IAAI,GAAG,oBAAoB,CAAA;AACjC,MAAM,MAAM,GAAG,mBAAmB,CAAA;AAClC,MAAM,MAAM,GAAG,kBAAkB,CAAA;AACjC,MAAM,IAAI,GAAG,mBAAmB,CAAA;AAEhC;;;GAGG;AACH,MAAM,UAAU,oBAAoB,CAAC,MAAoB,EAAE,GAAW;IACpE,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IAC/B,MAAM,KAAK,GAAG,CAAC,MAAc,EAAE,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,EAAE,MAAM,CAAC,CAAA;IAC3D,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACpB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACpB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACpB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACpB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACpB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACpB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACpB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACpB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACpB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACpB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACpB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACpB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACpB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACpB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACpB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACpB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACpB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACpB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACpB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IAEpB,MAAM,WAAW,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;IAC7D,MAAM,EAAE,GAAG,CAAC,GAAG,CAAC,CAAA;IAChB,MAAM,EAAE,GAAG,CAAC,GAAG,CAAC,CAAA;IAChB,MAAM,EAAE,GAAG,CAAC,GAAG,CAAC,CAAA;IAChB,MAAM,EAAE,GAAG,CAAC,GAAG,CAAC,CAAA;IAChB,MAAM,CAAC,GAAG,CAAC,QAAgB,EAAE,EAAE,CAAC,QAAQ,GAAG,KAAK,CAAA;IAEhD,MAAM,MAAM,GAA2B,EAAE,CAAA;IAEzC,IAAI,CAAC,CAAC,WAAW,CAAC,GAAG,GAAG,EAAE,CAAC;QACzB,MAAM,CAAC,CAAC,GAAG,IAAI,CAAA;QACf,MAAM,CAAC,CAAC,GAAG,IAAI,CAAA;QACf,MAAM,CAAC,CAAC,GAAG,IAAI,CAAA;QACf,MAAM,CAAC,CAAC,GAAG,IAAI,CAAA;QACf,MAAM,CAAC,CAAC,GAAG,IAAI,CAAA;QACf,MAAM,CAAC,CAAC,GAAG,IAAI,CAAA;QACf,MAAM,CAAC,CAAC,GAAG,IAAI,CAAA;QACf,MAAM,CAAC,CAAC,GAAG,IAAI,CAAA;IACjB,CAAC;IAED,IAAI,CAAC,CAAC,EAAE,CAAC,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,EAAE,CAAC;QAC1D,MAAM,CAAC,CAAC,GAAG,GAAG,CAAA;QACd,MAAM,CAAC,CAAC,GAAG,GAAG,CAAA;IAChB,CAAC;IAED,IAAI,CAAC,CAAC,EAAE,CAAC,GAAG,GAAG,IAAI,CAAC,CAAC,EAAE,CAAC,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,EAAE,CAAC;QACzE,MAAM,CAAC,CAAC,GAAG,SAAS,CAAA;IACtB,CAAC;IAED,IAAI,CAAC,CAAC,EAAE,CAAC,GAAG,GAAG,IAAI,CAAC,CAAC,EAAE,CAAC,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,EAAE,CAAC;QACzE,MAAM,CAAC,CAAC,GAAG,SAAS,CAAA;IACtB,CAAC;IAED,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,EAAE,CAAC;QAC9B,MAAM,CAAC,CAAC,GAAG,KAAK,CAAA;IAClB,CAAC;IAED,IACE,CAAC,CAAC,EAAE,CAAC,GAAG,GAAG;QACX,CAAC,CAAC,EAAE,CAAC,GAAG,GAAG;QACX,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI;QACX,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI;QACX,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI;QACX,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,EACX,CAAC;QACD,MAAM,CAAC,CAAC,GAAG,KAAK,CAAA;IAClB,CAAC;IAED,IAAI,CAAC,CAAC,WAAW,CAAC,GAAG,GAAG,IAAI,CAAC,CAAC,EAAE,CAAC,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,EAAE,CAAC;QACtE,MAAM,CAAC,CAAC,GAAG,QAAQ,CAAA;QACnB,MAAM,CAAC,CAAC,GAAG,QAAQ,CAAA;IACrB,CAAC;IAED,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,EAAE,CAAC;QAChB,MAAM,CAAC,CAAC,GAAG,IAAI,CAAA;IACjB,CAAC;IAED,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;QACV,MAAM,CAAC,CAAC,GAAG,MAAM,CAAA;IACnB,CAAC;IAED,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;QACV,MAAM,CAAC,CAAC,GAAG,MAAM,CAAA;IACnB,CAAC;IAED,IACE,CAAC,CAAC,WAAW,CAAC,GAAG,GAAG;QACpB,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI;QACX,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI;QACX,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI;QACX,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI;QACX,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI;QACX,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI;QACX,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI;QACX,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI;QACX,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI;QACX,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI;QACX,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI;QACX,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,EACX,CAAC;QACD,MAAM,CAAC,CAAC,GAAG,IAAI,CAAA;QACf,MAAM,CAAC,CAAC,GAAG,IAAI,CAAA;IACjB,CAAC;IAED,OAAO,MAAM,CAAA;AACf,CAAC"}

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/CopyButton.d.ts

@@ -0,0 +1,9 @@
+import React from 'react';
+/**
+ * Copy-to-clipboard button that confirms on the label for a moment. The timer is
+ * cleared on unmount, since these live in dialogs the copy itself often closes.
+ */
+export default function CopyButton({ text, label, }: {
+    text: string;
+    label?: string;
+}): React.JSX.Element;

package/dist/components/CopyButton.js

@@ -0,0 +1,23 @@
+import React, { useEffect, useRef, useState } from 'react';
+import { Button } from '@mui/material';
+import copy from '../vendor/copyToClipboard.js';
+/**
+ * Copy-to-clipboard button that confirms on the label for a moment. The timer is
+ * cleared on unmount, since these live in dialogs the copy itself often closes.
+ */
+export default function CopyButton({ text, label = 'Copy to clipboard', }) {
+    const [copied, setCopied] = useState(false);
+    const timer = useRef(undefined);
+    useEffect(() => () => {
+        clearTimeout(timer.current);
+    }, []);
+    return (React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
+            copy(text);
+            setCopied(true);
+            clearTimeout(timer.current);
+            timer.current = setTimeout(() => {
+                setCopied(false);
+            }, 500);
+        } }, copied ? 'Copied!' : label));
+}
+//# sourceMappingURL=CopyButton.js.map

package/dist/components/CopyButton.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"CopyButton.js","sourceRoot":"","sources":["../../src/components/CopyButton.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAE1D,OAAO,EAAE,MAAM,EAAE,MAAM,eAAe,CAAA;AAEtC,OAAO,IAAI,MAAM,8BAA8B,CAAA;AAE/C;;;GAGG;AACH,MAAM,CAAC,OAAO,UAAU,UAAU,CAAC,EACjC,IAAI,EACJ,KAAK,GAAG,mBAAmB,GAI5B;IACC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC3C,MAAM,KAAK,GAAG,MAAM,CAAgC,SAAS,CAAC,CAAA;IAE9D,SAAS,CACP,GAAG,EAAE,CAAC,GAAG,EAAE;QACT,YAAY,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IAC7B,CAAC,EACD,EAAE,CACH,CAAA;IAED,OAAO,CACL,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;YACZ,IAAI,CAAC,IAAI,CAAC,CAAA;YACV,SAAS,CAAC,IAAI,CAAC,CAAA;YACf,YAAY,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;YAC3B,KAAK,CAAC,OAAO,GAAG,UAAU,CAAC,GAAG,EAAE;gBAC9B,SAAS,CAAC,KAAK,CAAC,CAAA;YAClB,CAAC,EAAE,GAAG,CAAC,CAAA;QACT,CAAC,IAEA,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,KAAK,CACpB,CACV,CAAA;AACH,CAAC"}

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/Loading.js

@@ -26,9 +26,9 @@ const Reset = observer(function ({ model, error, }) {
             } }, "Return to import form")));
 });
 const Loading = observer(function ({ model }) {
-    const { isLoading, dataInitialized, msaFilehandle, treeFilehandle } = model;
+    const { isLoading, dataInitialized, error, msaFilehandle, treeFilehandle } = model;
     const hasPendingFilehandle = !!(msaFilehandle || treeFilehandle);
-    return (React.createElement("div", null, React.createElement(ErrorBoundary, { FallbackComponent: e => React.createElement(Reset, { model: model, error: e.error }) }, dataInitialized ? (isLoading ? (React.createElement(LoadingSpinner, { model: model })) : (React.createElement(MSAView, { model: model }))) : hasPendingFilehandle || isLoading ? (React.createElement(LoadingSpinner, { model: model })) : (React.createElement(ImportForm, { model: model })))));
+    return (React.createElement("div", null, React.createElement(ErrorBoundary, { FallbackComponent: e => React.createElement(Reset, { model: model, error: e.error }) }, dataInitialized ? (isLoading ? (React.createElement(LoadingSpinner, { model: model })) : (React.createElement(MSAView, { model: model }))) : error ? (React.createElement(Reset, { model: model, error: error })) : hasPendingFilehandle || isLoading ? (React.createElement(LoadingSpinner, { model: model })) : (React.createElement(ImportForm, { model: model })))));
 });
 export default Loading;
 //# sourceMappingURL=Loading.js.map

package/dist/components/Loading.js.map

@@ -1 +1 @@
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+{"version":3,"file":"Loading.js","sourceRoot":"","sources":["../../src/components/Loading.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAAE,aAAa,EAAE,MAAM,gCAAgC,CAAA;AAC9D,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,OAAO,MAAM,cAAe,CAAA;AACnC,OAAO,UAAU,MAAM,wBAAyB,CAAA;AAIhD,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAC1E,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IACxB,OAAO,CACL,6BACE,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,GAAG,EAAE,EAAE,EAAE,OAAO,EAAE,EAAE,EAAE;QAEtE,6BACE,KAAK,EAAC,IAAI,EACV,MAAM,EAAC,IAAI,EACX,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,4BAA4B;YAElC,mCACG,0DAA0D,CACrD;YACR,gCACE,EAAE,EAAC,IAAI,EACP,EAAE,EAAC,IAAI,EACP,CAAC,EAAC,IAAI,EACN,MAAM,EAAC,MAAM,EACb,WAAW,EAAC,GAAG,EACf,IAAI,EAAC,MAAM,GACX;YACF,8BACE,CAAC,EAAC,yBAAyB,EAC3B,MAAM,EAAC,SAAS,EAChB,WAAW,EAAC,GAAG,EACf,IAAI,EAAC,MAAM,EACX,aAAa,EAAC,OAAO,EACrB,KAAK,EAAE;oBACL,SAAS,EAAE,4BAA4B;oBACvC,eAAe,EAAE,QAAQ;iBAC1B,GACD,CACE;QACN,oBAAC,UAAU,IAAC,OAAO,EAAC,IAAI,IAAE,MAAM,EAAE,GAAG,IAAI,YAAY,CAAc;QAClE,MAAM,EAAE,QAAQ,CAAC,CAAC,CAAC,CAClB,oBAAC,MAAM,IACL,OAAO,EAAC,UAAU,EAClB,IAAI,EAAC,OAAO,EACZ,OAAO,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,QAAQ,EAAE,EAAE,aAG3B,CACV,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,KAAK,GAAG,QAAQ,CAAC,UAAU,EAC/B,KAAK,EACL,KAAK,GAIN;IACC,OAAO,CACL;QACE,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC9B,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,KAAK,EAAE,CAAA;YACf,CAAC,4BAGM,CACL,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,SAAS,EAAE,eAAe,EAAE,KAAK,EAAE,aAAa,EAAE,cAAc,EAAE,GACxE,KAAK,CAAA;IACP,MAAM,oBAAoB,GAAG,CAAC,CAAC,CAAC,aAAa,IAAI,cAAc,CAAC,CAAA;IAEhE,OAAO,CACL,iCACE,oBAAC,aAAa,IACZ,iBAAiB,EAAE,CAAC,CAAC,EAAE,CAAC,oBAAC,KAAK,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,GAAI,IAE9D,eAAe,CAAC,CAAC,CAAC,CACjB,SAAS,CAAC,CAAC,CAAC,CACV,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI,CACjC,CAAC,CAAC,CAAC,CACF,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACF,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAOV,oBAAC,KAAK,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI,CACtC,CAAC,CAAC,CAAC,oBAAoB,IAAI,SAAS,CAAC,CAAC,CAAC,CACtC,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI,CACjC,CAAC,CAAC,CAAC,CACF,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CAC7B,CACa,CACZ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}

package/dist/components/MSAView.js

@@ -16,7 +16,7 @@ const TopArea = observer(function ({ model }) {
         showHorizontalScrollbar ? React.createElement(Minimap, { model: model }) : null));
 });
 const TrackColumnIndicator = observer(function ({ model, }) {
-    const { mouseCol, mouseClickCol, colWidth, scrollX, treeAreaWidth, resizeHandleWidth, totalTrackAreaHeight, msaAreaWidth, verticalScrollbarWidth, } = model;
+    const { mouseCol, mouseClickCol, colWidth, scrollX, treeAreaWidth, resizeHandleWidth, totalTrackAreaHeight, msaCanvasWidth, } = model;
     // hovered column, then the pinned one, matching the alignment's own overlay
     const bands = [
         { col: mouseCol, color: hoverColor },
@@ -26,7 +26,7 @@ const TrackColumnIndicator = observer(function ({ model, }) {
             position: 'absolute',
             left: treeAreaWidth + resizeHandleWidth,
             top: 0,
-            width: msaAreaWidth - verticalScrollbarWidth,
+            width: msaCanvasWidth,
             height: totalTrackAreaHeight,
             overflow: 'hidden',
             pointerEvents: 'none',

package/dist/components/MSAView.js.map

@@ -1 +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

@@ -1,68 +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)';
+import DragHandle from './DragHandle.js';
 export const VerticalResizeHandle = observer(function ({ model, }) {
-    const { resizeHandleWidth } = model;
-    const [hovered, setHovered] = useState(false);
-    const { startDrag } = useDragScroll('x', useCallback((delta, startWidth) => {
+    const onDrag = useCallback((delta, startWidth) => {
         model.setTreeAreaWidth(startWidth + delta);
-    }, [model]));
-    return (React.createElement("div", { onMouseDown: event => {
-            startDrag(event, model.treeAreaWidth);
-        }, onMouseEnter: () => {
-            setHovered(true);
-        }, onMouseLeave: () => {
-            setHovered(false);
-        }, style: {
-            cursor: 'ew-resize',
-            width: resizeHandleWidth,
-            background: hovered ? handleBgHover : handleBg,
-            position: 'relative',
-        } }));
+    }, [model]);
+    return (React.createElement(DragHandle, { axis: "x", variant: "resizer", getStart: () => model.treeAreaWidth, onDrag: onDrag, style: { width: model.resizeHandleWidth } }));
 });
 export const HorizontalResizeHandle = observer(function ({ model, }) {
-    const { resizeHandleWidth } = model;
-    const [hovered, setHovered] = useState(false);
-    const { startDrag } = useDragScroll('y', useCallback((delta, startHeight) => {
+    const onDrag = useCallback((delta, startHeight) => {
         model.setHeight(startHeight + delta);
-    }, [model]));
-    return (React.createElement("div", { onMouseDown: event => {
-            startDrag(event, model.height);
-        }, onMouseEnter: () => {
-            setHovered(true);
-        }, onMouseLeave: () => {
-            setHovered(false);
-        }, style: {
-            cursor: 'ns-resize',
-            width: '100%',
-            height: resizeHandleWidth,
-            background: hovered ? handleBgHover : handleBg,
-            position: 'relative',
-        } }));
+    }, [model]);
+    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, }) {
-    const { resizeHandleWidth } = model;
-    const [hovered, setHovered] = useState(false);
-    const { startDrag } = useDragScroll('y', useCallback((delta, startHeight) => {
-        model.setConservationTrackHeight(Math.max(10, startHeight + delta));
-    }, [model]));
-    return (React.createElement("div", { onMouseDown: event => {
-            startDrag(event, model.conservationTrackHeight);
-        }, onMouseEnter: () => {
-            setHovered(true);
-        }, onMouseLeave: () => {
-            setHovered(false);
-        }, style: {
+// 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) => {
+        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,
-            cursor: 'ns-resize',
             width: '100%',
-            height: resizeHandleWidth,
+            height: model.resizeHandleWidth,
             zIndex: 1,
-            background: hovered ? handleBgHover : handleBg,
-        } }));
+        } })) : null;
 });
 //# sourceMappingURL=ResizeHandles.js.map

package/dist/components/ResizeHandles.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ResizeHandles.js","sourceRoot":"","sources":["../../src/components/ResizeHandles.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,WAAW,EAAE,MAAM,OAAO,CAAA;AAE1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,UAAU,MAAM,iBAAkB,CAAA;AAKzC,MAAM,CAAC,MAAM,oBAAoB,GAAG,QAAQ,CAAC,UAAU,EACrD,KAAK,GAGN;IACC,MAAM,MAAM,GAAG,WAAW,CACxB,CAAC,KAAa,EAAE,UAAkB,EAAE,EAAE;QACpC,KAAK,CAAC,gBAAgB,CAAC,UAAU,GAAG,KAAK,CAAC,CAAA;IAC5C,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,OAAO,CACL,oBAAC,UAAU,IACT,IAAI,EAAC,GAAG,EACR,OAAO,EAAC,SAAS,EACjB,QAAQ,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,aAAa,EACnC,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,iBAAiB,EAAE,GACzC,CACH,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,CAAC,MAAM,sBAAsB,GAAG,QAAQ,CAAC,UAAU,EACvD,KAAK,GAGN;IACC,MAAM,MAAM,GAAG,WAAW,CACxB,CAAC,KAAa,EAAE,WAAmB,EAAE,EAAE;QACrC,KAAK,CAAC,SAAS,CAAC,WAAW,GAAG,KAAK,CAAC,CAAA;IACtC,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,OAAO,CACL,oBAAC,UAAU,IACT,IAAI,EAAC,GAAG,EACR,OAAO,EAAC,SAAS,EACjB,QAAQ,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,MAAM,EAC5B,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,KAAK,CAAC,iBAAiB,EAAE,GACzD,CACH,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,+EAA+E;AAC/E,+EAA+E;AAC/E,+EAA+E;AAC/E,6EAA6E;AAC7E,QAAQ;AACR,MAAM,YAAY,GAQd;IACF,GAAG,EAAE;QACH,GAAG,EAAE,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,uBAAuB;QAC3C,GAAG,EAAE,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE;YACrB,KAAK,CAAC,0BAA0B,CAAC,MAAM,CAAC,CAAA;QAC1C,CAAC;KACF;IACD,IAAI,EAAE;QACJ,GAAG,EAAE,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,uBAAuB;QAC3C,GAAG,EAAE,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE;YACrB,KAAK,CAAC,0BAA0B,CAAC,MAAM,CAAC,CAAA;QAC1C,CAAC;KACF;CACF,CAAA;AAED,MAAM,CAAC,MAAM,iBAAiB,GAAG,QAAQ,CAAC,UAAU,EAClD,KAAK,EACL,IAAI,GAIL;IACC,MAAM,MAAM,GAAG,YAAY,CAAC,IAAI,CAAC,CAAA;IACjC,MAAM,MAAM,GAAG,WAAW,CACxB,CAAC,KAAa,EAAE,WAAmB,EAAE,EAAE;QACrC,MAAM,EAAE,GAAG,CAAC,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,WAAW,GAAG,KAAK,CAAC,CAAC,CAAA;IACvD,CAAC,EACD,CAAC,KAAK,EAAE,MAAM,CAAC,CAChB,CAAA;IACD,OAAO,MAAM,CAAC,CAAC,CAAC,CACd,oBAAC,UAAU,IACT,IAAI,EAAC,GAAG,EACR,OAAO,EAAC,SAAS,EACjB,QAAQ,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,EACjC,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,MAAM,EAAE,CAAC;YACT,IAAI,EAAE,CAAC;YACP,KAAK,EAAE,MAAM;YACb,MAAM,EAAE,KAAK,CAAC,iBAAiB;YAC/B,MAAM,EAAE,CAAC;SACV,GACD,CACH,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA"}

package/dist/components/SequenceTextArea.js

@@ -1,9 +1,9 @@
 import React, { useState } from 'react';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
-import { Button, TextField } from '@mui/material';
+import { TextField } from '@mui/material';
 import { getUngappedSequence } from 'msa-parsers';
-import copy from '../vendor/copyToClipboard.js';
 import Checkbox2 from './Checkbox2.js';
+import CopyButton from './CopyButton.js';
 const useStyles = makeStyles()({
     textAreaFont: {
         fontFamily: 'Courier New',
@@ -17,7 +17,6 @@ const useStyles = makeStyles()({
 });
 export default function SequenceTextArea({ str }) {
     const { classes } = useStyles();
-    const [copied, setCopied] = useState(false);
     const [showGaps, setShowGaps] = useState(false);
     const [showEmpty, setShowEmpty] = useState(false);
     const disp = str
@@ -26,13 +25,7 @@ export default function SequenceTextArea({ str }) {
         .map(([s1, s2]) => `>${s1}\n${s2}`)
         .join('\n');
     return (React.createElement(React.Fragment, null,
-        React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
-                copy(disp);
-                setCopied(true);
-                setTimeout(() => {
-                    setCopied(false);
-                }, 500);
-            } }, copied ? 'Copied!' : 'Copy to clipboard'),
+        React.createElement(CopyButton, { text: disp }),
         React.createElement(Checkbox2, { label: "Show gaps", checked: showGaps, onChange: () => {
                 setShowGaps(!showGaps);
             } }),

package/dist/components/SequenceTextArea.js.map

@@ -1 +1 @@
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+{"version":3,"file":"SequenceTextArea.js","sourceRoot":"","sources":["../../src/components/SequenceTextArea.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AACzC,OAAO,EAAE,mBAAmB,EAAE,MAAM,aAAa,CAAA;AAEjD,OAAO,SAAS,MAAM,gBAAiB,CAAA;AACvC,OAAO,UAAU,MAAM,iBAAkB,CAAA;AAEzC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;QACzB,QAAQ,EAAE,YAAY;KACvB;IACD,aAAa,EAAE;QACb,UAAU,EAAE,WAAW;QACvB,MAAM,EAAE,CAAC;QACT,QAAQ,EAAE,MAAM;KACjB;CACF,CAAC,CAAA;AAEF,MAAM,CAAC,OAAO,UAAU,gBAAgB,CAAC,EAAE,GAAG,EAA+B;IAC3E,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC/C,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAEjD,MAAM,IAAI,GAAG,GAAG;SACb,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,mBAAmB,CAAC,EAAE,CAAC,CAAU,CAAC;SACzE,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,SAAS,IAAI,CAAC,CAAC,EAAE,CAAC;SACrC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC;SAClC,IAAI,CAAC,IAAI,CAAC,CAAA;IACb,OAAO,CACL;QACE,oBAAC,UAAU,IAAC,IAAI,EAAE,IAAI,GAAI;QAC1B,oBAAC,SAAS,IACR,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,QAAQ,EACjB,QAAQ,EAAE,GAAG,EAAE;gBACb,WAAW,CAAC,CAAC,QAAQ,CAAC,CAAA;YACxB,CAAC,GACD;QACF,oBAAC,SAAS,IACR,KAAK,EAAC,YAAY,EAClB,OAAO,EAAE,SAAS,EAClB,QAAQ,EAAE,GAAG,EAAE;gBACb,YAAY,CAAC,CAAC,SAAS,CAAC,CAAA;YAC1B,CAAC,GACD;QACF,oBAAC,SAAS,IACR,OAAO,EAAC,UAAU,EAClB,SAAS,QACT,SAAS,EAAE,OAAO,CAAC,aAAa,EAChC,OAAO,EAAE,CAAC,EACV,OAAO,EAAE,EAAE,EACX,SAAS,QACT,KAAK,EAAE,IAAI,EACX,SAAS,EAAE;gBACT,KAAK,EAAE;oBACL,QAAQ,EAAE,IAAI;oBACd,SAAS,EAAE,OAAO,CAAC,YAAY;iBAChC;aACF,GACD,CACD,CACJ,CAAA;AACH,CAAC"}

package/dist/components/VerticalScrollbar.js

@@ -1,43 +1,29 @@
-import React, { useCallback, useState } from 'react';
-import { clamp } from '@jbrowse/core/util';
+import React, { useCallback } from 'react';
 import { observer } from 'mobx-react';
-import { useDragScroll } from '../useDragScroll.js';
+import DragHandle from './DragHandle.js';
+const width = 20;
 const VerticalScrollbar = observer(({ model }) => {
     const { msaAreaHeight, scrollY, totalHeight } = model;
-    const [hovered, setHovered] = useState(false);
-    const fill = 'rgba(66, 119, 127, 0.3)';
     const unit = msaAreaHeight / totalHeight;
-    const top = -scrollY;
-    const bottom = top + msaAreaHeight;
-    const t = top * unit;
-    const b = bottom * unit;
-    const { startDrag } = useDragScroll('y', useCallback((delta, startScroll) => {
-        model.setScrollY(clamp(startScroll - delta / unit, model.maxScrollY, 0));
-    }, [model, unit]));
+    const t = -scrollY * unit;
+    const b = (-scrollY + msaAreaHeight) * unit;
+    const onDrag = useCallback((delta, startScroll) => {
+        model.setScrollY(startScroll - delta / unit);
+    }, [model, unit]);
     return (React.createElement("div", { style: {
             position: 'relative',
-            width: 20,
+            width,
             height: msaAreaHeight,
             borderLeft: '1px solid #555',
             borderTop: '1px solid #555',
             boxSizing: 'border-box',
         } },
-        React.createElement("div", { style: {
-                position: 'absolute',
+        React.createElement(DragHandle, { axis: "y", variant: "thumb", getStart: () => model.scrollY, onDrag: onDrag, style: {
                 top: Math.max(0, t),
                 left: 0,
-                background: hovered ? 'rgba(66,119,127,0.6)' : fill,
-                cursor: 'pointer',
                 boxSizing: 'border-box',
-                width: 20,
+                width,
                 height: Math.max(b - t, 20),
-                zIndex: 100,
-            }, onMouseOver: () => {
-                setHovered(true);
-            }, onMouseOut: () => {
-                setHovered(false);
-            }, onMouseDown: event => {
-                startDrag(event, model.scrollY);
             } })));
 });
 export default VerticalScrollbar;

package/dist/components/VerticalScrollbar.js.map

@@ -1 +1 @@
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package/dist/components/dialogs/FeatureDialog.js

@@ -17,9 +17,9 @@ const Toggles = observer(function ({ model }) {
             } }, "Toggle all off")));
 });
 const FeatureTable = observer(function ({ model }) {
-    const { tidyInterProAnnotationTypes, tidyInterProAnnotations, fillPalette } = model;
+    const { annotationTypes, annotations, fillPalette } = model;
     const counts = new Map();
-    for (const annot of tidyInterProAnnotations) {
+    for (const annot of annotations) {
         counts.set(annot.accession, (counts.get(annot.accession) ?? 0) + 1);
     }
     return (React.createElement(React.Fragment, null,
@@ -33,7 +33,7 @@ const FeatureTable = observer(function ({ model }) {
                     React.createElement(TableCell, null, "name"),
                     React.createElement(TableCell, null, "count"),
                     React.createElement(TableCell, null, "description"))),
-            React.createElement(TableBody, null, [...tidyInterProAnnotationTypes.values()].map(({ accession, name, description }) => (React.createElement(TableRow, { key: accession },
+            React.createElement(TableBody, null, [...annotationTypes.values()].map(({ accession, name, description }) => (React.createElement(TableRow, { key: accession },
                 React.createElement(TableCell, { padding: "checkbox" },
                     React.createElement(Checkbox, { checked: model.featureFilters.get(accession) ?? false, onChange: () => {
                             model.setFilter(accession, !model.featureFilters.get(accession));