react-msaview 7.0.0 → 8.1.0

package/dist/calculateBlocks.js

@@ -1,11 +1,13 @@
 // Returns the block offsets (in pixels) needed to cover the viewport along one
 // axis. mapSize/viewportPos/viewportSize are all in pixels. The clamp pins the
-// block set to the content edge so an over-scroll past the end still fills the
-// viewport rather than leaving a gap.
+// block set to the content edge, so an over-scroll past the end still fills
+// the viewport, and content smaller than the viewport mounts only the blocks
+// it covers: none for a tree-only figure with zero columns.
 export function calculateBlocks({ mapSize, blockSize, viewportPos, viewportSize, }) {
     const clamped = Math.max(0, Math.min(viewportPos, mapSize - viewportSize));
+    const end = Math.min(clamped + viewportSize, mapSize);
     const minTile = Math.floor(clamped / blockSize);
-    const maxTile = Math.floor((clamped + viewportSize - 1) / blockSize);
+    const maxTile = Math.ceil(end / blockSize) - 1;
     const blocks = [];
     for (let tile = minTile; tile <= maxTile; tile++) {
         blocks.push(tile * blockSize);

package/dist/calculateBlocks.js.map

@@ -1 +1 @@
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+{"version":3,"file":"calculateBlocks.js","sourceRoot":"","sources":["../src/calculateBlocks.ts"],"names":[],"mappings":"AAAA,+EAA+E;AAC/E,+EAA+E;AAC/E,4EAA4E;AAC5E,6EAA6E;AAC7E,4DAA4D;AAC5D,MAAM,UAAU,eAAe,CAAC,EAC9B,OAAO,EACP,SAAS,EACT,WAAW,EACX,YAAY,GAMb;IACC,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,WAAW,EAAE,OAAO,GAAG,YAAY,CAAC,CAAC,CAAA;IAC1E,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,GAAG,YAAY,EAAE,OAAO,CAAC,CAAA;IACrD,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,GAAG,SAAS,CAAC,CAAA;IAC/C,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,GAAG,SAAS,CAAC,GAAG,CAAC,CAAA;IAE9C,MAAM,MAAM,GAAG,EAAE,CAAA;IACjB,KAAK,IAAI,IAAI,GAAG,OAAO,EAAE,IAAI,IAAI,OAAO,EAAE,IAAI,EAAE,EAAE,CAAC;QACjD,MAAM,CAAC,IAAI,CAAC,IAAI,GAAG,SAAS,CAAC,CAAA;IAC/B,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC"}

package/dist/colorSchemes.js

@@ -12,8 +12,7 @@ const dna = {
     T: red[500],
     U: red[500],
 };
-// annotated rather than asserted: the wide type is what lets a free-string
-// scheme name index this, and an annotation still checks the literal against it
+// Record<string, ...> so a free-string scheme name can index it
 const colorSchemes = {
     none: {},
     nucleotide: dna,

package/dist/colorSchemes.js.map

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

@@ -0,0 +1,28 @@
+import type { ColumnCounts } from './columnCounts.ts';
+export interface ColumnStats {
+    col: number;
+    total: number;
+    gaps: number;
+    gapFraction: number;
+    conservation: number;
+    propertyConservation: number | undefined;
+    consensusLetter: string;
+    consensusCount: number;
+    consensusFraction: number;
+    distribution: [string, number][];
+}
+/**
+ * Summarize one column: consensus residue and its identity fraction, the two
+ * conservation scores, gap fraction, and the non-gap residue distribution
+ * sorted by count. undefined past the end of the alignment or for a column with
+ * no sequences.
+ *
+ * A module-level function: a getter that reached the method through `this` made
+ * TypeScript infer the whole views object to type it, and fell back to `any`.
+ */
+export declare function columnStats({ col, colStats, conservation, propertyConservation, }: {
+    col: number;
+    colStats: ColumnCounts;
+    conservation: number[];
+    propertyConservation: number[];
+}): ColumnStats | undefined;

package/dist/columnStats.js

@@ -0,0 +1,34 @@
+/**
+ * Summarize one column: consensus residue and its identity fraction, the two
+ * conservation scores, gap fraction, and the non-gap residue distribution
+ * sorted by count. undefined past the end of the alignment or for a column with
+ * no sequences.
+ *
+ * A module-level function: a getter that reached the method through `this` made
+ * TypeScript infer the whole views object to type it, and fell back to `any`.
+ */
+export function columnStats({ col, colStats, conservation, propertyConservation, }) {
+    if (col >= colStats.numColumns) {
+        return undefined;
+    }
+    const total = colStats.total(col);
+    if (!total) {
+        return undefined;
+    }
+    const gaps = colStats.gapCount(col);
+    const distribution = colStats.residueEntries(col).sort((a, b) => b[1] - a[1]);
+    const consensus = distribution[0];
+    return {
+        col,
+        total,
+        gaps,
+        gapFraction: gaps / total,
+        conservation: conservation[col] ?? 0,
+        propertyConservation: propertyConservation[col],
+        consensusLetter: consensus?.[0] ?? '',
+        consensusCount: consensus?.[1] ?? 0,
+        consensusFraction: consensus ? consensus[1] / total : 0,
+        distribution,
+    };
+}
+//# sourceMappingURL=columnStats.js.map

package/dist/columnStats.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"columnStats.js","sourceRoot":"","sources":["../src/columnStats.ts"],"names":[],"mappings":"AAeA;;;;;;;;GAQG;AACH,MAAM,UAAU,WAAW,CAAC,EAC1B,GAAG,EACH,QAAQ,EACR,YAAY,EACZ,oBAAoB,GAMrB;IACC,IAAI,GAAG,IAAI,QAAQ,CAAC,UAAU,EAAE,CAAC;QAC/B,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,KAAK,GAAG,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IACjC,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,IAAI,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;IACnC,MAAM,YAAY,GAAG,QAAQ,CAAC,cAAc,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC7E,MAAM,SAAS,GAAG,YAAY,CAAC,CAAC,CAAC,CAAA;IACjC,OAAO;QACL,GAAG;QACH,KAAK;QACL,IAAI;QACJ,WAAW,EAAE,IAAI,GAAG,KAAK;QACzB,YAAY,EAAE,YAAY,CAAC,GAAG,CAAC,IAAI,CAAC;QACpC,oBAAoB,EAAE,oBAAoB,CAAC,GAAG,CAAC;QAC/C,eAAe,EAAE,SAAS,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE;QACrC,cAAc,EAAE,SAAS,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC;QACnC,iBAAiB,EAAE,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC;QACvD,YAAY;KACb,CAAA;AACH,CAAC"}

package/dist/components/DragHandle.d.ts

@@ -1,8 +1,9 @@
 import React from 'react';
+import type { Theme } from '@mui/material';
 export declare const scrollbarThumbFill = "rgba(66,119,127,0.3)";
 declare const variants: Record<'thumb' | 'resizer', {
-    fill: string;
-    fillHovered: string;
+    fill: (theme: Theme) => string;
+    fillHovered: (theme: Theme) => string;
     cursor: (axis: 'x' | 'y') => string;
     position: React.CSSProperties['position'];
     zIndex?: number;

package/dist/components/DragHandle.js

@@ -1,4 +1,5 @@
 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 scroll thumbs (minimap, vertical scrollbar) and the resize dividers are
@@ -7,15 +8,19 @@ export const scrollbarThumbFill = 'rgba(66,119,127,0.3)';
 // difference rather than a second copy of the drag wiring.
 const variants = {
     thumb: {
-        fill: scrollbarThumbFill,
-        fillHovered: 'rgba(66,119,127,0.6)',
+        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)',
+        fill: theme => theme.palette.mode === 'dark'
+            ? theme.palette.grey[800]
+            : 'rgba(200,200,200)',
+        fillHovered: theme => theme.palette.mode === 'dark'
+            ? theme.palette.grey[600]
+            : 'rgba(150,150,150)',
         cursor: axis => (axis === 'x' ? 'ew-resize' : 'ns-resize'),
         position: 'relative',
     },
@@ -29,6 +34,7 @@ const variants = {
  * on every render.
  */
 export default function DragHandle({ axis, variant, getStart, onDrag, style, }) {
+    const theme = useTheme();
     const [hovered, setHovered] = useState(false);
     const { startDrag } = useDragScroll(axis, onDrag);
     const { fill, fillHovered, cursor, position, zIndex } = variants[variant];
@@ -42,7 +48,7 @@ export default function DragHandle({ axis, variant, getStart, onDrag, style, })
             position,
             zIndex,
             cursor: cursor(axis),
-            background: hovered ? fillHovered : fill,
+            background: hovered ? fillHovered(theme) : fill(theme),
             ...style,
         } }));
 }

package/dist/components/DragHandle.js.map

@@ -1 +1 @@
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+{"version":3,"file":"DragHandle.js","sourceRoot":"","sources":["../../src/components/DragHandle.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAExC,OAAO,EAAE,aAAa,EAAE,MAAM,qBAAqB,CAAA;AAInD,MAAM,CAAC,MAAM,kBAAkB,GAAG,sBAAsB,CAAA;AAExD,8EAA8E;AAC9E,+EAA+E;AAC/E,wEAAwE;AACxE,2DAA2D;AAC3D,MAAM,QAAQ,GASV;IACF,KAAK,EAAE;QACL,IAAI,EAAE,GAAG,EAAE,CAAC,kBAAkB;QAC9B,WAAW,EAAE,GAAG,EAAE,CAAC,sBAAsB;QACzC,MAAM,EAAE,GAAG,EAAE,CAAC,SAAS;QACvB,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,GAAG;KACZ;IACD,OAAO,EAAE;QACP,IAAI,EAAE,KAAK,CAAC,EAAE,CACZ,KAAK,CAAC,OAAO,CAAC,IAAI,KAAK,MAAM;YAC3B,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;YACzB,CAAC,CAAC,mBAAmB;QACzB,WAAW,EAAE,KAAK,CAAC,EAAE,CACnB,KAAK,CAAC,OAAO,CAAC,IAAI,KAAK,MAAM;YAC3B,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;YACzB,CAAC,CAAC,mBAAmB;QACzB,MAAM,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,IAAI,KAAK,GAAG,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,WAAW,CAAC;QAC1D,QAAQ,EAAE,UAAU;KACrB;CACF,CAAA;AAED;;;;;;;GAOG;AACH,MAAM,CAAC,OAAO,UAAU,UAAU,CAAC,EACjC,IAAI,EACJ,OAAO,EACP,QAAQ,EACR,MAAM,EACN,KAAK,GAON;IACC,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,EAAE,SAAS,EAAE,GAAG,aAAa,CAAC,IAAI,EAAE,MAAM,CAAC,CAAA;IACjD,MAAM,EAAE,IAAI,EAAE,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAA;IAEzE,OAAO,CACL,6BACE,YAAY,EAAE,GAAG,EAAE;YACjB,UAAU,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;YACjB,UAAU,CAAC,KAAK,CAAC,CAAA;QACnB,CAAC,EACD,WAAW,EAAE,KAAK,CAAC,EAAE;YACnB,SAAS,CAAC,KAAK,EAAE,QAAQ,EAAE,CAAC,CAAA;QAC9B,CAAC,EACD,KAAK,EAAE;YACL,QAAQ;YACR,MAAM;YACN,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC;YACpB,UAAU,EAAE,OAAO,CAAC,CAAC,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC;YACtD,GAAG,KAAK;SACT,GACD,CACH,CAAA;AACH,CAAC"}

package/dist/components/Loading.js

@@ -1,20 +1,14 @@
 import React from 'react';
 import { ErrorMessage } from '@jbrowse/core/ui';
 import { ErrorBoundary } from '@jbrowse/core/ui/ErrorBoundary';
-import { Button, Typography } from '@mui/material';
+import { Button, CircularProgress, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
 import MSAView from './MSAView.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("svg", { width: "24", height: "24", viewBox: "0 0 24 24", xmlns: "http://www.w3.org/2000/svg" },
-            React.createElement("style", null, `@keyframes spinner { to { transform: rotate(360deg); } }`),
-            React.createElement("circle", { cx: "12", cy: "12", r: "10", stroke: "#ccc", strokeWidth: "3", fill: "none" }),
-            React.createElement("path", { d: "M12 2a10 10 0 0 1 10 10", stroke: "#1976d2", strokeWidth: "3", fill: "none", strokeLinecap: "round", style: {
-                    animation: 'spinner 1s linear infinite',
-                    transformOrigin: 'center',
-                } })),
+        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));
 });

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,gBAAgB,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AACpE,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,oBAAC,gBAAgB,IAAC,IAAI,EAAE,EAAE,GAAI;QAC9B,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,EACJ,SAAS,EACT,eAAe,EACf,KAAK,EACL,UAAU,EACV,aAAa,EACb,cAAc,GACf,GAAG,KAAK,CAAA;IACT,MAAM,oBAAoB,GAAG,CAAC,CAAC,CAAC,aAAa,IAAI,cAAc,CAAC,CAAA;IAEhE,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,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,CAGV,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

@@ -7,16 +7,26 @@ 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 RowPanelHeaders from './rowpanels/RowPanelHeaders.js';
+import RowPanels from './rowpanels/RowPanels.js';
+import TreeOverview from './tree/TreeOverview.js';
 import TreePanel from './tree/TreePanel.js';
 import TreeRuler from './tree/TreeRuler.js';
+// The band above the panels: the tree overview and scale bar, the strip
+// headers, and the minimap over the alignment. The spacer stands in for the
+// resize handle, so the minimap starts exactly where the alignment canvas does.
 const TopArea = observer(function ({ model }) {
-    const { showHorizontalScrollbar } = model;
+    const { showHorizontalScrollbar, showTreeOverview, resizeHandleWidth } = model;
     return (React.createElement("div", { style: { display: 'flex' } },
-        React.createElement(TreeRuler, { model: model }),
+        React.createElement("div", { style: { flexShrink: 0 } },
+            showTreeOverview ? React.createElement(TreeOverview, { model: model }) : null,
+            React.createElement(TreeRuler, { model: model })),
+        React.createElement(RowPanelHeaders, { model: model }),
+        React.createElement("div", { style: { width: resizeHandleWidth, flexShrink: 0 } }),
         showHorizontalScrollbar ? React.createElement(Minimap, { model: model }) : null));
 });
 const TrackColumnIndicator = observer(function ({ model, }) {
-    const { mouseCol, mouseClickCol, colWidth, scrollX, treeAreaWidth, resizeHandleWidth, totalTrackAreaHeight, msaCanvasWidth, } = 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 bands = [
         { col: mouseCol, color: hoverColor },
@@ -24,7 +34,7 @@ const TrackColumnIndicator = observer(function ({ model, }) {
     ];
     return (React.createElement("div", { style: {
             position: 'absolute',
-            left: treeAreaWidth + resizeHandleWidth,
+            left: treeAreaWidth + rowPanelsWidth + resizeHandleWidth,
             top: 0,
             width: msaCanvasWidth,
             height: totalTrackAreaHeight,
@@ -53,6 +63,7 @@ const MainArea = observer(function ({ model }) {
     const { showVerticalScrollbar } = model;
     return (React.createElement("div", { style: { display: 'flex' } },
         React.createElement(TreePanel, { model: model }),
+        React.createElement(RowPanels, { model: model }),
         React.createElement(VerticalResizeHandle, { model: model }),
         React.createElement(MSAPanel, { model: model }),
         showVerticalScrollbar ? React.createElement(VerticalScrollbar, { model: model }) : null));
@@ -64,10 +75,10 @@ const View = observer(function ({ model }) {
         React.createElement(MainArea, { model: model })));
 });
 const MSAView = observer(function ({ model }) {
-    const { height, viewInitialized, DialogComponent, DialogProps } = 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(Header, { model: model }),
+            hideHeader ? null : React.createElement(Header, { model: model }),
             React.createElement(View, { model: model })),
         React.createElement(HorizontalResizeHandle, { model: model }),
         DialogComponent ? (React.createElement(Suspense, { fallback: null },

package/dist/components/MSAView.js.map

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

@@ -1,7 +1,9 @@
 import React from 'react';
-import type { ColumnTrackSpec, Highlight, ResidueMapping } from '../types.ts';
+import type { MsaViewModel } from '../model.ts';
+import type { Cell, Clade, ColumnTrackSpec, Encoding, Highlight, Region, ResidueEncoding, ResidueMapping, RowPanelSpec, Viewport } from '../types.ts';
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
-interface MSAViewerProps {
+import type { ThemeOptions } from '@mui/material/styles';
+export interface MSAViewerProps {
     msa?: string;
     tree?: string;
     gff?: string;
@@ -15,9 +17,7 @@ interface MSAViewerProps {
     /** initial per-row pixel height */
     rowHeight?: number;
     /**
-     * hide columns at least this percent gaps (default 100, i.e. hide nothing).
-     * A deep family's alignment is mostly insertions carried by a few members;
-     * dropping those columns is what makes the rest readable
+     * hide columns at least this percent gaps (default 100, i.e. hide nothing)
      */
     allowedGappyness?: number;
     /** alignment columns (0-based) to highlight with a persistent overlay */
@@ -28,18 +28,75 @@ interface MSAViewerProps {
      * for whole rows, each with an optional `label` and `color`
      */
     highlights?: Highlight[];
+    /**
+     * clades of the tree with a mark drawn over them: `{mrca, tips, mark}` or
+     * `{range, tips, mark}`, where `mark` is `highlight`, `bracket`, `collapse`
+     * or `focus` (see docs/layers.md)
+     */
+    clades?: Clade[];
     /** row name to diff every other row against (matches render as ".") */
     relativeTo?: string;
     /** tracks supplied as data: per-column bar values or a text row (see docs/layers.md) */
     columnTracks?: ColumnTrackSpec[];
     /** 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>>;
+    /**
+     * what the viewer's marks read from a table: `{channel, field, scale?}`,
+     * where `channel` is `tipLabel`, `rowTint` or `branch` over `rowData`, or
+     * `featureFill` or `featureLabel` over the annotations (see docs/layers.md)
+     */
+    encodings?: Encoding[];
+    /**
+     * panels between the tree and the alignment, one cell per row:
+     * `{kind: 'strip', field, scale?, width?, header?}` colors each row by a
+     * `rowData` field (see docs/layers.md)
+     */
+    rowPanels?: RowPanelSpec[];
     /** draw the phylogenetic tree (default true); false leaves a labels-only gutter */
     drawTree?: boolean;
     /** fixed width (px) of the tree/label area */
     treeAreaWidth?: number;
     /** auto-size the tree/label area to the labels (used when drawTree is false) */
     autoTreeAreaWidth?: boolean;
+    /** draw branch lengths (default true); false draws a cladogram */
+    showBranchLen?: boolean;
+    /**
+     * which channel `colorScheme` paints: `fill` (default) colors the background
+     * of the cell a residue sits in, `color` colors the letter itself and leaves
+     * the background plain, which lets a domain overlay mark each span with a bar
+     * under the row and the residue colors show through
+     */
+    residueEncoding?: ResidueEncoding;
+    /**
+     * a span to zoom and scroll to once the alignment loads, and again whenever
+     * it changes: `{row, start, end}` in residues of that row, or `{start, end}`
+     * in columns, 1-based and inclusive
+     */
+    region?: Region;
+    /** leave out the toolbar, for a page drawing its own controls */
+    hideHeader?: boolean;
+    /**
+     * 'light' (default), 'dark', or MUI theme options (palette, typography)
+     * merged over the JBrowse theme
+     */
+    theme?: 'light' | 'dark' | ThemeOptions;
+    /** the cell under the pointer, or undefined when it leaves the alignment */
+    onCellHover?: (cell: Cell | undefined) => void;
+    /** the cell a click pinned, or undefined when a click clears it */
+    onCellClick?: (cell: Cell | undefined) => void;
+    /** the alignment columns on screen, after every scroll, zoom and resize */
+    onViewportChange?: (viewport: Viewport | 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
+     */
+    onModel?: (model: MsaViewModel) => void;
 }
-export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, colWidth, rowHeight, allowedGappyness, highlightColumns, highlights, relativeTo, columnTracks, residueMappings, drawTree, treeAreaWidth, autoTreeAreaWidth, }: MSAViewerProps): React.JSX.Element;
-export {};
+/**
+ * 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.
+ */
+export default function MSAViewer(props: MSAViewerProps): React.JSX.Element;