react-msaview 8.2.0 → 8.4.0

package/dist/blockFasta.d.ts

@@ -0,0 +1,6 @@
+/**
+ * FASTA for a block of the alignment: each row's letters from column `start`
+ * to `end`, 1-based and inclusive, under its name. Gaps stay in, and a row that
+ * ends before `end` is padded with gaps, so every record is the block's width.
+ */
+export declare function blockFasta(rows: readonly (readonly [string, string])[], start: number, end: number): string;

package/dist/blockFasta.js

@@ -0,0 +1,12 @@
+/**
+ * FASTA for a block of the alignment: each row's letters from column `start`
+ * to `end`, 1-based and inclusive, under its name. Gaps stay in, and a row that
+ * ends before `end` is padded with gaps, so every record is the block's width.
+ */
+export function blockFasta(rows, start, end) {
+    const width = Math.max(0, end - start + 1);
+    return rows
+        .map(([name, seq]) => `>${name}\n${seq.slice(start - 1, end).padEnd(width, '-')}\n`)
+        .join('');
+}
+//# sourceMappingURL=blockFasta.js.map

package/dist/blockFasta.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"blockFasta.js","sourceRoot":"","sources":["../src/blockFasta.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,MAAM,UAAU,UAAU,CACxB,IAA4C,EAC5C,KAAa,EACb,GAAW;IAEX,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,GAAG,GAAG,KAAK,GAAG,CAAC,CAAC,CAAA;IAC1C,OAAO,IAAI;SACR,GAAG,CACF,CAAC,CAAC,IAAI,EAAE,GAAG,CAAC,EAAE,EAAE,CACd,IAAI,IAAI,KAAK,GAAG,CAAC,KAAK,CAAC,KAAK,GAAG,CAAC,EAAE,GAAG,CAAC,CAAC,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,CAChE;SACA,IAAI,CAAC,EAAE,CAAC,CAAA;AACb,CAAC"}

package/dist/colorSchemes.d.ts

@@ -2,3 +2,10 @@ declare const _default: {
     [k: string]: Record<string, string>;
 };
 export default _default;
+/**
+ * A letter map as the renderer looks letters up. The model upper-cases every
+ * row before coloring it, so a table keys its letters in upper case and a map
+ * may key them in either. The table is cached per map, so its identity is
+ * stable enough for the raster cache to key on.
+ */
+export declare function letterColorTable(map: Record<string, string>): Record<string, string>;

package/dist/colorSchemes.js

@@ -343,4 +343,19 @@ export default transform(colorSchemes, ([key, val]) => [
     key,
     transform(val, ([letter, color]) => [letter, colord(color).toHex()]),
 ]);
+const letterTables = new WeakMap();
+/**
+ * A letter map as the renderer looks letters up. The model upper-cases every
+ * row before coloring it, so a table keys its letters in upper case and a map
+ * may key them in either. The table is cached per map, so its identity is
+ * stable enough for the raster cache to key on.
+ */
+export function letterColorTable(map) {
+    let table = letterTables.get(map);
+    if (!table) {
+        table = transform(map, ([letter, color]) => [letter.toUpperCase(), color]);
+        letterTables.set(map, table);
+    }
+    return table;
+}
 //# sourceMappingURL=colorSchemes.js.map

package/dist/colorSchemes.js.map

@@ -1 +1 @@
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+{"version":3,"file":"colorSchemes.js","sourceRoot":"","sources":["../src/colorSchemes.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,sBAAsB,CAAA;AAC/D,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AACvC,OAAO,WAAW,MAAM,sBAAsB,CAAA;AAE9C,OAAO,EAAE,SAAS,EAAE,MAAM,WAAW,CAAA;AAErC,MAAM,CAAC,CAAC,WAAW,CAAC,CAAC,CAAA;AAErB,8EAA8E;AAC9E,eAAe;AACf,MAAM,GAAG,GAAG;IACV,CAAC,EAAE,KAAK,CAAC,GAAG,CAAC;IACb,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC;IACZ,CAAC,EAAE,MAAM,CAAC,GAAG,CAAC;IACd,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC;IACX,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC;CACZ,CAAA;AAED,gEAAgE;AAChE,MAAM,YAAY,GAA2C;IAC3D,IAAI,EAAE,EAAE;IACR,UAAU,EAAE,GAAG;IACf,OAAO,EAAE;QACP,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;KACX;IACD,IAAI,EAAE;QACJ,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;KACV;IACD,QAAQ,EAAE;QACR,CAAC,EAAE,YAAY;QACf,CAAC,EAAE,YAAY;QACf,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,UAAU;QACb,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,KAAK;KACT;IAED,wBAAwB,EAAE,EAAE;IAC5B,+IAA+I;IAC/I,MAAM,EAAE;QACN,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IACD,WAAW,EAAE;QACX,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,yJAAyJ;IACzJ,gBAAgB,EAAE;QAChB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,4BAA4B;IAC5B,wBAAwB,EAAE,EAAE;IAE5B,YAAY,EAAE;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IACD,WAAW,EAAE,GAAG;IAChB,cAAc,EAAE;QACd,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,sBAAsB,EAAE;QACtB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,iBAAiB,EAAE;QACjB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,kBAAkB,EAAE;QAClB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,gBAAgB,EAAE;QAChB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CA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package/dist/columnCounts.d.ts

@@ -5,6 +5,7 @@ export declare class ColumnCounts {
     readonly totals: Uint32Array;
     private readonly slotTotals;
     constructor(numColumns: number);
+    /** tallies a row, counting the columns past a short row's end as gaps */
     addRow(row: string): void;
     add(col: number, letter: string): void;
     total(col: number): number;
@@ -32,10 +33,10 @@ export declare function residueSlotOfLetter(letter: string): number;
 export declare const numResidueSlots = 32;
 /**
  * Tally counts from alignment rows (gapped sequence strings, one per row). The
- * column count follows the longest row, matching what a per-column tally of
- * ragged input produces.
+ * column count defaults to the longest row, and a shorter row counts as gapped
+ * to the end.
  */
-export declare function columnCountsFromRows(rows: string[]): ColumnCounts;
+export declare function columnCountsFromRows(rows: string[], numColumns?: number): ColumnCounts;
 /**
  * Tally counts from column strings (one string per column, listing that
  * column's residues top to bottom). Convenient for tests and for callers that

package/dist/columnCounts.js

@@ -52,15 +52,21 @@ export class ColumnCounts {
         this.counts = new Uint32Array(numColumns * SLOTS);
         this.totals = new Uint32Array(numColumns);
     }
+    /** tallies a row, counting the columns past a short row's end as gaps */
     addRow(row) {
-        const { counts, totals, slotTotals } = this;
-        const n = Math.min(row.length, this.numColumns);
+        const { counts, totals, slotTotals, numColumns } = this;
+        const n = Math.min(row.length, numColumns);
         for (let col = 0; col < n; col++) {
             const slot = slotOf(row.charCodeAt(col));
             counts[col * SLOTS + slot]++;
             totals[col]++;
             slotTotals[slot]++;
         }
+        for (let col = n; col < numColumns; col++) {
+            counts[col * SLOTS + DASH]++;
+            totals[col]++;
+        }
+        slotTotals[DASH] += numColumns - n;
     }
     add(col, letter) {
         const slot = slotOf(letter.charCodeAt(0));
@@ -138,11 +144,10 @@ export function residueSlotOfLetter(letter) {
 export const numResidueSlots = SLOTS;
 /**
  * Tally counts from alignment rows (gapped sequence strings, one per row). The
- * column count follows the longest row, matching what a per-column tally of
- * ragged input produces.
+ * column count defaults to the longest row, and a shorter row counts as gapped
+ * to the end.
  */
-export function columnCountsFromRows(rows) {
-    const numColumns = rows.reduce((max, row) => Math.max(max, row.length), 0);
+export function columnCountsFromRows(rows, numColumns = rows.reduce((max, row) => Math.max(max, row.length), 0)) {
     const counts = new ColumnCounts(numColumns);
     for (const row of rows) {
         counts.addRow(row);

package/dist/columnCounts.js.map

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

@@ -4,6 +4,6 @@ import React from 'react';
  * cleared on unmount, since these live in dialogs the copy itself often closes.
  */
 export default function CopyButton({ text, label, }: {
-    text: string;
+    text: string | (() => string);
     label?: string;
 }): React.JSX.Element;

package/dist/components/CopyButton.js

@@ -12,7 +12,7 @@ export default function CopyButton({ text, label = 'Copy to clipboard', }) {
         clearTimeout(timer.current);
     }, []);
     return (React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
-            copy(text);
+            copy(typeof text === 'string' ? text : text());
             setCopied(true);
             clearTimeout(timer.current);
             timer.current = setTimeout(() => {

package/dist/components/CopyButton.js.map

@@ -1 +1 @@
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package/dist/components/DragHandle.js

@@ -2,6 +2,9 @@ import React, { useState } from 'react';
 import { useTheme } from '@mui/material';
 import { useDragScroll } from '../useDragScroll.js';
 export const scrollbarThumbFill = 'rgba(66,119,127,0.3)';
+// the model's resizeHandleWidth feeds the layout, so a divider keeps its drawn
+// width and widens its target with this much invisible margin each side
+const hitSlop = 4;
 // 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
@@ -38,7 +41,10 @@ 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: () => {
+    return (React.createElement("div", { ...(variant === 'resizer' && {
+            role: 'separator',
+            'aria-orientation': axis === 'x' ? 'vertical' : 'horizontal',
+        }), onMouseEnter: () => {
             setHovered(true);
         }, onMouseLeave: () => {
             setHovered(false);
@@ -50,6 +56,12 @@ export default function DragHandle({ axis, variant, getStart, onDrag, style, })
             cursor: cursor(axis),
             background: hovered ? fillHovered(theme) : fill(theme),
             ...style,
-        } }));
+        } }, variant === 'resizer' ? (React.createElement("div", { style: {
+            position: 'absolute',
+            zIndex: 101,
+            ...(axis === 'x'
+                ? { top: 0, bottom: 0, left: -hitSlop, right: -hitSlop }
+                : { left: 0, right: 0, top: -hitSlop, bottom: -hitSlop }),
+        } })) : null));
 }
 //# sourceMappingURL=DragHandle.js.map

package/dist/components/DragHandle.js.map

@@ -1 +1 @@
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package/dist/components/Loading.js

@@ -1,17 +1,11 @@
 import React from 'react';
 import { ErrorMessage } from '@jbrowse/core/ui';
 import { ErrorBoundary } from '@jbrowse/core/ui/ErrorBoundary';
-import { Button, CircularProgress, Typography } from '@mui/material';
+import { Button } from '@mui/material';
 import { observer } from 'mobx-react';
 import MSAView from './MSAView.js';
+import StatusMessage from './StatusMessage.js';
 import ImportForm from './import/ImportForm.js';
-const LoadingSpinner = observer(function ({ model }) {
-    const { status } = model;
-    return (React.createElement("div", { style: { display: 'flex', alignItems: 'center', gap: 12, padding: 20 } },
-        React.createElement(CircularProgress, { size: 24 }),
-        React.createElement(Typography, { variant: "h6" }, status?.msg ?? 'Loading...'),
-        status?.onCancel ? (React.createElement(Button, { variant: "outlined", size: "small", onClick: () => status.onCancel?.() }, "Cancel")) : null));
-});
 const Reset = observer(function ({ model, error, }) {
     return (React.createElement("div", null,
         React.createElement(ErrorMessage, { error: error }),
@@ -20,9 +14,14 @@ const Reset = observer(function ({ model, error, }) {
             } }, "Return to import form")));
 });
 const Loading = observer(function ({ model }) {
-    const { isLoading, dataInitialized, error, resetCount, msaFilehandle, treeFilehandle, } = model;
-    const hasPendingFilehandle = !!(msaFilehandle || treeFilehandle);
-    return (React.createElement("div", null, React.createElement(ErrorBoundary, { key: resetCount, 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 })))));
+    const { isLoading, dataInitialized, data, error, resetCount, msaFilehandle, treeFilehandle, } = model;
+    const hasData = !!(data.msa || data.tree);
+    // a failed load keeps its filehandle, so the error outranks the spinner
+    const loading = !error && !!(msaFilehandle || treeFilehandle || isLoading);
+    return (React.createElement("div", null, React.createElement(ErrorBoundary, { key: resetCount, FallbackComponent: e => React.createElement(Reset, { model: model, error: e.error }) }, dataInitialized ? (isLoading ? (React.createElement(StatusMessage, { model: model, variant: "page" })) : (React.createElement(MSAView, { model: model }))) : hasData ? (React.createElement(Reset, { model: model, error: error })) : (React.createElement(React.Fragment, null,
+        loading ? React.createElement(StatusMessage, { model: model, variant: "page" }) : null,
+        React.createElement("div", { style: { display: loading ? 'none' : undefined } },
+            React.createElement(ImportForm, { model: model })))))));
 });
 export default Loading;
 //# sourceMappingURL=Loading.js.map

package/dist/components/Loading.js.map

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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,MAAM,eAAe,CAAA;AACtC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,OAAO,MAAM,cAAe,CAAA;AACnC,OAAO,aAAa,MAAM,oBAAqB,CAAA;AAC/C,OAAO,UAAU,MAAM,wBAAyB,CAAA;AAIhD,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,EACJ,SAAS,EACT,eAAe,EACf,IAAI,EACJ,KAAK,EACL,UAAU,EACV,aAAa,EACb,cAAc,GACf,GAAG,KAAK,CAAA;IACT,MAAM,OAAO,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,IAAI,IAAI,CAAC,IAAI,CAAC,CAAA;IACzC,wEAAwE;IACxE,MAAM,OAAO,GAAG,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,aAAa,IAAI,cAAc,IAAI,SAAS,CAAC,CAAA;IAE1E,OAAO,CACL,iCAIE,oBAAC,aAAa,IACZ,GAAG,EAAE,UAAU,EACf,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,aAAa,IAAC,KAAK,EAAE,KAAK,EAAE,OAAO,EAAC,MAAM,GAAG,CAC/C,CAAC,CAAC,CAAC,CACF,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACF,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CACZ,oBAAC,KAAK,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI,CACtC,CAAC,CAAC,CAAC,CACF;QACG,OAAO,CAAC,CAAC,CAAC,oBAAC,aAAa,IAAC,KAAK,EAAE,KAAK,EAAE,OAAO,EAAC,MAAM,GAAG,CAAC,CAAC,CAAC,IAAI;QAChE,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,EAAE;YACnD,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CACxB,CACL,CACJ,CACa,CACZ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}

package/dist/components/MSAView.js

@@ -6,7 +6,7 @@ import VerticalScrollbar from './VerticalScrollbar.js';
 import Header from './header/Header.js';
 import Minimap from './minimap/Minimap.js';
 import MSAPanel from './msa/MSAPanel.js';
-import { clickColor, hoverColor } from './overlayColors.js';
+import { clickColor, hoverColor, selectionFill } from './overlayColors.js';
 import RowPanelHeaders from './rowpanels/RowPanelHeaders.js';
 import RowPanels from './rowpanels/RowPanels.js';
 import TreeOverview from './tree/TreeOverview.js';
@@ -26,11 +26,17 @@ const TopArea = observer(function ({ model }) {
         showHorizontalScrollbar ? React.createElement(Minimap, { model: model }) : null));
 });
 const TrackColumnIndicator = observer(function ({ model, }) {
-    const { mouseCol, mouseClickCol, colWidth, scrollX, treeAreaWidth, rowPanelsWidth, resizeHandleWidth, totalTrackAreaHeight, msaCanvasWidth, } = model;
-    // hovered column, then the pinned one, matching the alignment's own overlay
+    const { mouseCol, mouseClickCol, colWidth, scrollX, treeAreaWidth, rowPanelsWidth, resizeHandleWidth, totalTrackAreaHeight, msaCanvasWidth, resolvedSelection, } = model;
+    // the selected columns, the hovered column, then the pinned one, matching
+    // the alignment's own overlay
     const bands = [
-        { col: mouseCol, color: hoverColor },
-        { col: mouseClickCol, color: clickColor },
+        {
+            start: resolvedSelection?.startCol,
+            end: resolvedSelection?.endCol,
+            color: selectionFill,
+        },
+        { start: mouseCol, end: mouseCol, color: hoverColor },
+        { start: mouseClickCol, end: mouseClickCol, color: clickColor },
     ];
     return (React.createElement("div", { style: {
             position: 'absolute',
@@ -40,11 +46,11 @@ const TrackColumnIndicator = observer(function ({ model, }) {
             height: totalTrackAreaHeight,
             overflow: 'hidden',
             pointerEvents: 'none',
-        } }, bands.map(({ col, color }) => col === undefined ? null : (React.createElement("div", { key: color, style: {
+        } }, bands.map(({ start, end, color }) => start === undefined || end === undefined ? null : (React.createElement("div", { key: color, style: {
             position: 'absolute',
-            left: col * colWidth + scrollX,
+            left: start * colWidth + scrollX,
             top: 0,
-            width: colWidth,
+            width: (end - start + 1) * colWidth,
             height: totalTrackAreaHeight,
             backgroundColor: color,
             zIndex: 100,
@@ -77,7 +83,7 @@ const View = observer(function ({ model }) {
 const MSAView = observer(function ({ model }) {
     const { height, hideHeader, viewInitialized, DialogComponent, DialogProps } = model;
     return (React.createElement("div", null, viewInitialized ? (React.createElement(React.Fragment, null,
-        React.createElement("div", { style: { height, overflow: 'hidden' } },
+        React.createElement("div", { style: { height, overflow: 'clip' } },
             hideHeader ? null : React.createElement(Header, { model: model }),
             React.createElement(View, { model: model })),
         React.createElement(HorizontalResizeHandle, { model: model }),

package/dist/components/MSAView.js.map

@@ -1 +1 @@
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+{"version":3,"file":"MSAView.js","sourceRoot":"","sources":["../../src/components/MSAView.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EACL,sBAAsB,EACtB,oBAAoB,GACrB,MAAM,oBAAqB,CAAA;AAC5B,OAAO,KAAK,MAAM,YAAa,CAAA;AAC/B,OAAO,iBAAiB,MAAM,wBAAyB,CAAA;AACvD,OAAO,MAAM,MAAM,oBAAqB,CAAA;AACxC,OAAO,OAAO,MAAM,sBAAuB,CAAA;AAC3C,OAAO,QAAQ,MAAM,mBAAoB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,UAAU,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA;AAC1E,OAAO,eAAe,MAAM,gCAAiC,CAAA;AAC7D,OAAO,SAAS,MAAM,0BAA2B,CAAA;AACjD,OAAO,YAAY,MAAM,wBAAyB,CAAA;AAClD,OAAO,SAAS,MAAM,qBAAsB,CAAA;AAC5C,OAAO,SAAS,MAAM,qBAAsB,CAAA;AAI5C,wEAAwE;AACxE,4EAA4E;AAC5E,gFAAgF;AAChF,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,uBAAuB,EAAE,gBAAgB,EAAE,iBAAiB,EAAE,GAAG,KAAK,CAAA;IAC9E,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QAC7B,6BAAK,KAAK,EAAE,EAAE,UAAU,EAAE,CAAC,EAAE;YAC1B,gBAAgB,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YACzD,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI,CACvB;QACN,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QACjC,6BAAK,KAAK,EAAE,EAAE,KAAK,EAAE,iBAAiB,EAAE,UAAU,EAAE,CAAC,EAAE,GAAI;QAC1D,uBAAuB,CAAC,CAAC,CAAC,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI,CACvD,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,oBAAoB,GAAG,QAAQ,CAAC,UAAU,EAC9C,KAAK,GAGN;IACC,MAAM,EACJ,QAAQ,EACR,aAAa,EACb,QAAQ,EACR,OAAO,EACP,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,oBAAoB,EACpB,cAAc,EACd,iBAAiB,GAClB,GAAG,KAAK,CAAA;IAET,0EAA0E;IAC1E,8BAA8B;IAC9B,MAAM,KAAK,GAAG;QACZ;YACE,KAAK,EAAE,iBAAiB,EAAE,QAAQ;YAClC,GAAG,EAAE,iBAAiB,EAAE,MAAM;YAC9B,KAAK,EAAE,aAAa;SACrB;QACD,EAAE,KAAK,EAAE,QAAQ,EAAE,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,UAAU,EAAE;QACrD,EAAE,KAAK,EAAE,aAAa,EAAE,GAAG,EAAE,aAAa,EAAE,KAAK,EAAE,UAAU,EAAE;KAChE,CAAA;IAED,OAAO,CACL,6BACE,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,IAAI,EAAE,aAAa,GAAG,cAAc,GAAG,iBAAiB;YACxD,GAAG,EAAE,CAAC;YACN,KAAK,EAAE,cAAc;YACrB,MAAM,EAAE,oBAAoB;YAC5B,QAAQ,EAAE,QAAQ;YAClB,aAAa,EAAE,MAAM;SACtB,IAEA,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,EAAE,CACnC,KAAK,KAAK,SAAS,IAAI,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAChD,6BACE,GAAG,EAAE,KAAK,EACV,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,IAAI,EAAE,KAAK,GAAG,QAAQ,GAAG,OAAO;YAChC,GAAG,EAAE,CAAC;YACN,KAAK,EAAE,CAAC,GAAG,GAAG,KAAK,GAAG,CAAC,CAAC,GAAG,QAAQ;YACnC,MAAM,EAAE,oBAAoB;YAC5B,eAAe,EAAE,KAAK;YACtB,MAAM,EAAE,GAAG;SACZ,GACD,CACH,CACF,CACG,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,SAAS,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACrE,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAChC,IAAI,cAAc,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAChC,OAAO,IAAI,CAAA;IACb,CAAC;IACD,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAClC,oBAAC,oBAAoB,IAAC,KAAK,EAAE,KAAK,GAAI;QACrC,cAAc,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAC3B,oBAAC,KAAK,IAAC,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI,CAC3D,CAAC,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACpE,MAAM,EAAE,qBAAqB,EAAE,GAAG,KAAK,CAAA;IAEvC,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QAC7B,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,oBAAC,oBAAoB,IAAC,KAAK,EAAE,KAAK,GAAI;QACtC,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI;QACzB,qBAAqB,CAAC,CAAC,CAAC,oBAAC,iBAAiB,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI,CAC/D,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,IAAI,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAChE,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAClC,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI;QACzB,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI,CACtB,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,eAAe,EAAE,eAAe,EAAE,WAAW,EAAE,GACzE,KAAK,CAAA;IAEP,OAAO,CACL,iCACG,eAAe,CAAC,CAAC,CAAC,CACjB;QACE,6BAAK,KAAK,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE;YACrC,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,oBAAC,MAAM,IAAC,KAAK,EAAE,KAAK,GAAI;YAC7C,oBAAC,IAAI,IAAC,KAAK,EAAE,KAAK,GAAI,CAClB;QACN,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI;QAEvC,eAAe,CAAC,CAAC,CAAC,CACjB,oBAAC,QAAQ,IAAC,QAAQ,EAAE,IAAI;YACtB,oBAAC,eAAe,OAAK,WAAW,GAAI,CAC3B,CACZ,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}

package/dist/components/MSAViewer.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
 import type { MsaViewModel } from '../model.ts';
-import type { Cell, Clade, ColumnTrackSpec, Encoding, Highlight, Region, ResidueEncoding, ResidueMapping, RowPanelSpec, Viewport } from '../types.ts';
+import type { Cell, Clade, ColorScheme, ColumnTrackSpec, Encoding, Feature, Highlight, MsaSelection, Region, ResidueEncoding, ResidueMapping, RowDataInput, RowPanelSpec, TreeOrder, TreeRoot, Viewport } from '../types.ts';
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
 import type { ThemeOptions } from '@mui/material/styles';
 export interface MSAViewerProps {
@@ -10,7 +10,11 @@ export interface MSAViewerProps {
     msaFilehandle?: FileLocationType;
     treeFilehandle?: FileLocationType;
     gffFilehandle?: FileLocationType;
-    colorScheme?: string;
+    /**
+     * a scheme name from the built-in table, or `{map}`, a color per residue
+     * letter that leaves every other letter uncolored
+     */
+    colorScheme?: ColorScheme;
     height?: number;
     /** initial per-column pixel width (zoom level) */
     colWidth?: number;
@@ -28,6 +32,13 @@ export interface MSAViewerProps {
      * for whole rows, each with an optional `label` and `color`
      */
     highlights?: Highlight[];
+    /**
+     * features on the rows as data, drawn with the GFF's: `{row, start, end}` in
+     * residues of that row, 1-based and inclusive, with an optional `name`,
+     * `description`, `type`, `strand` and `color`, and any other field an
+     * encoding reads (see docs/layers.md)
+     */
+    features?: Feature[];
     /**
      * clades of the tree with a mark drawn over them: `{mrca, tips, mark}` or
      * `{range, tips, mark}`, where `mark` is `highlight`, `bracket`, `collapse`
@@ -41,7 +52,7 @@ export interface MSAViewerProps {
     /** which residue of which structure each row's residues are (see docs/layers.md) */
     residueMappings?: ResidueMapping[];
     /** extra fields per row name, such as a lineage or a host (see docs/layers.md) */
-    rowData?: Record<string, Record<string, string>>;
+    rowData?: RowDataInput;
     /**
      * what the viewer's marks read from a table: `{channel, field, scale?}`,
      * where `channel` is `tipLabel`, `rowTint` or `branch` over `rowData`, or
@@ -62,6 +73,17 @@ export interface MSAViewerProps {
     autoTreeAreaWidth?: boolean;
     /** draw branch lengths (default true); false draws a cladogram */
     showBranchLen?: boolean;
+    /**
+     * the order each node's children draw in: `branchLength` (default,
+     * shortest first), `input` (as the file gives them), `ladderize` (fewest
+     * tips first) or `ladderizeReverse` (most tips first)
+     */
+    treeOrder?: TreeOrder;
+    /**
+     * reroot the tree: `midpoint`, or `{outgroup: [tip names]}` on the branch
+     * above those tips' common ancestor
+     */
+    treeRoot?: TreeRoot;
     /**
      * which channel `colorScheme` paints: `fill` (default) colors the background
      * of the cell a residue sits in, `color` colors the letter itself and leaves
@@ -75,6 +97,11 @@ export interface MSAViewerProps {
      * in columns, 1-based and inclusive
      */
     region?: Region;
+    /**
+     * the selected block: `{start, end}` columns of the file, 1-based and
+     * inclusive, and `rows` by name, every row where absent
+     */
+    selection?: MsaSelection;
     /** leave out the toolbar, for a page drawing its own controls */
     hideHeader?: boolean;
     /**
@@ -88,15 +115,20 @@ export interface MSAViewerProps {
     onCellClick?: (cell: Cell | undefined) => void;
     /** the alignment columns on screen, after every scroll, zoom and resize */
     onViewportChange?: (viewport: Viewport | undefined) => void;
+    /**
+     * the selected block, after each change a drag, the header menu, Escape or
+     * the `selection` prop makes, or undefined when it clears
+     */
+    onSelectionChange?: (selection: MsaSelection | undefined) => void;
     /**
      * the model the viewer built, for the model API; called again with the new
-     * model when msa, tree, gff or a filehandle changes
+     * model when msa, tree, msaFilehandle or treeFilehandle changes
      */
     onModel?: (model: MsaViewModel) => void;
 }
 /**
- * A new alignment, tree or annotation file needs a new model, so the viewer
- * remounts when one of those props changes and keeps its model across every
- * other change.
+ * A new alignment or tree needs a new model, so the viewer remounts when one
+ * of those props changes and keeps its model across every other change,
+ * including a new annotation file.
  */
 export default function MSAViewer(props: MSAViewerProps): React.JSX.Element;