react-msaview 7.0.0 → 8.1.0

package/dist/components/tree/TreeCanvasBlock.js

@@ -2,32 +2,18 @@ import React, { useState } from 'react';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
-import { createPortal } from 'react-dom';
 import { useCanvasAutorun } from '../../useCanvasAutorun.js';
+import PortalTooltip from '../PortalTooltip.js';
 import TreeBranchMenu from './TreeBranchMenu.js';
 import TreeNodeMenu from './TreeNodeMenu.js';
 import { renderTreeCanvas } from './renderTreeCanvas.js';
 import { useTreeHover } from './useTreeHover.js';
 const useStyles = makeStyles()(theme => ({
-    tooltip: {
-        position: 'fixed',
-        pointerEvents: 'none',
-        zIndex: 10000,
-        backgroundColor: theme.palette.grey[700],
-        color: theme.palette.common.white,
-        padding: '4px 8px',
-        borderRadius: 4,
-        fontSize: 12,
-        whiteSpace: 'nowrap',
-        maxWidth: 300,
-        overflow: 'hidden',
-        textOverflow: 'ellipsis',
-    },
     hover: {
         position: 'absolute',
         pointerEvents: 'none',
         zIndex: 100,
-        background: 'rgba(0,0,0,0.1)',
+        background: theme.palette.action.hover,
     },
 }));
 const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
@@ -37,8 +23,7 @@ const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
     const [nodeMenu, setNodeMenu] = useState();
     const { clickMap, hovered, hitTest, onMouseMove, onMouseLeave } = useTreeHover({ model, offsetY });
     const { treeAreaWidth, blockSize, highResScaleFactor } = model;
-    // TreePanel clips to treeAreaWidth, so anything wider is backing store the
-    // viewer never sees -- it was 600px of it per block, at dpr squared
+    // TreePanel clips to treeAreaWidth, so a wider canvas is wasted backing store
     const width = treeAreaWidth;
     const height = blockSize;
     const canvasWidth = width * highResScaleFactor;
@@ -100,9 +85,7 @@ const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
                 width: hovered.maxX - hovered.minX,
                 height: hovered.maxY - hovered.minY,
             } })) : null,
-        hovered
-            ? createPortal(React.createElement("div", { className: classes.tooltip, style: { left: hovered.clientX + 12, top: hovered.clientY + 12 } }, hovered.name), document.body)
-            : null));
+        hovered ? (React.createElement(PortalTooltip, { clientX: hovered.clientX, clientY: hovered.clientY }, hovered.name)) : null));
 });
 export default TreeCanvasBlock;
 //# sourceMappingURL=TreeCanvasBlock.js.map

package/dist/components/tree/TreeCanvasBlock.js.map

@@ -1 +1 @@
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+{"version":3,"file":"TreeCanvasBlock.js","sourceRoot":"","sources":["../../../src/components/tree/TreeCanvasBlock.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAC5D,OAAO,aAAa,MAAM,qBAAsB,CAAA;AAChD,OAAO,cAAc,MAAM,qBAAsB,CAAA;AACjD,OAAO,YAAY,MAAM,mBAAoB,CAAA;AAC7C,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACxD,OAAO,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAA;AAIhD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,QAAQ,EAAE,UAAU;QACpB,aAAa,EAAE,MAAM;QACrB,MAAM,EAAE,GAAG;QACX,UAAU,EAAE,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,KAAK;KACvC;CACF,CAAC,CAAC,CAAA;AASH,MAAM,eAAe,GAAG,QAAQ,CAAC,UAAU,EACzC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,EAAY,CAAA;IACxD,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAY,CAAA;IACpD,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,OAAO,EAAE,WAAW,EAAE,YAAY,EAAE,GAC7D,YAAY,CAAC,EAAE,KAAK,EAAE,OAAO,EAAE,CAAC,CAAA;IAElC,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IAC9D,8EAA8E;IAC9E,MAAM,KAAK,GAAG,aAAa,CAAA;IAC3B,MAAM,MAAM,GAAG,SAAS,CAAA;IAExB,MAAM,WAAW,GAAG,KAAK,GAAG,kBAAkB,CAAA;IAC9C,MAAM,YAAY,GAAG,MAAM,GAAG,kBAAkB,CAAA;IAChD,MAAM,GAAG,GAAG,gBAAgB,CAAC;QAC3B,IAAI,EAAE,GAAG,CAAC,EAAE;YACV,GAAG,CAAC,cAAc,EAAE,CAAA;YACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,WAAW,EAAE,YAAY,CAAC,CAAA;YAC9C,gBAAgB,CAAC;gBACf,GAAG;gBACH,KAAK;gBACL,OAAO;gBACP,QAAQ;gBACR,KAAK;aACN,CAAC,CAAA;QACJ,CAAC;QACD,KAAK,EAAE,WAAW;QAClB,MAAM,EAAE,YAAY;QACpB,IAAI,EAAE,CAAC,KAAK,EAAE,QAAQ,EAAE,OAAO,EAAE,KAAK,CAAC;KACxC,CAAC,CAAA;IAEF,MAAM,KAAK,GAAG;QACZ,KAAK;QACL,MAAM;QACN,GAAG,EAAE,OAAO;QACZ,IAAI,EAAE,CAAC;QACP,QAAQ,EAAE,UAAU;KACZ,CAAA;IAEV,OAAO,CACL;QACG,UAAU,CAAC,CAAC,CAAC,CACZ,oBAAC,cAAc,IACb,IAAI,EAAE,UAAU,EAChB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,aAAa,CAAC,SAAS,CAAC,CAAA;YAC1B,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI;QAEP,QAAQ,CAAC,CAAC,CAAC,CACV,oBAAC,YAAY,IACX,IAAI,EAAE,QAAQ,EACd,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,WAAW,CAAC,SAAS,CAAC,CAAA;YACxB,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI;QAER,gCACE,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,YAAY,EACpB,KAAK,EAAE,EAAE,GAAG,KAAK,EAAE,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,EAAE,EAC5D,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,WAAW,CAAC,KAAK,CAAC,CAAA;YACpB,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;gBACjB,YAAY,EAAE,CAAA;YAChB,CAAC,EACD,OAAO,EAAE,KAAK,CAAC,EAAE;gBACf,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;gBAC5B,IAAI,KAAK,EAAE,CAAC;oBACV,MAAM,IAAI,GAAG;wBACX,CAAC,EAAE,KAAK,CAAC,OAAO;wBAChB,CAAC,EAAE,KAAK,CAAC,OAAO;wBAChB,EAAE,EAAE,KAAK,CAAC,EAAE;wBACZ,IAAI,EAAE,KAAK,CAAC,IAAI;qBACjB,CAAA;oBACD,IAAI,KAAK,CAAC,MAAM,EAAE,CAAC;wBACjB,aAAa,CAAC,IAAI,CAAC,CAAA;oBACrB,CAAC;yBAAM,CAAC;wBACN,WAAW,CAAC,IAAI,CAAC,CAAA;oBACnB,CAAC;gBACH,CAAC;YACH,CAAC,GACD;QAGD,OAAO,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAC5B,6BACE,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE;gBACL,IAAI,EAAE,OAAO,CAAC,IAAI;gBAClB,GAAG,EAAE,OAAO,CAAC,IAAI;gBACjB,KAAK,EAAE,OAAO,CAAC,IAAI,GAAG,OAAO,CAAC,IAAI;gBAClC,MAAM,EAAE,OAAO,CAAC,IAAI,GAAG,OAAO,CAAC,IAAI;aACpC,GACD,CACH,CAAC,CAAC,CAAC,IAAI;QAEP,OAAO,CAAC,CAAC,CAAC,CACT,oBAAC,aAAa,IAAC,OAAO,EAAE,OAAO,CAAC,OAAO,EAAE,OAAO,EAAE,OAAO,CAAC,OAAO,IAC9D,OAAO,CAAC,IAAI,CACC,CACjB,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,eAAe,CAAA"}

package/dist/components/tree/TreeNodeMenu.js

@@ -10,7 +10,7 @@ const TreeMenu = observer(function ({ node, onClose, model, }) {
     return (React.createElement(Menu, { anchorReference: "anchorPosition", anchorPosition: {
             top: node.y,
             left: node.x,
-        }, transitionDuration: 0, keepMounted: true, open: Boolean(node), onClose: onClose },
+        }, transitionDuration: 0, open: true, onClose: onClose },
         React.createElement(MenuItem, { dense: true, disabled: true }, name),
         React.createElement(MenuItem, { dense: true, onClick: () => {
                 model.queueDialog(onClose => [

package/dist/components/tree/TreeNodeMenu.js.map

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package/dist/components/tree/TreeOverview.d.ts

@@ -0,0 +1,14 @@
+import React from 'react';
+import type { MsaViewModel } from '../../model.ts';
+/**
+ * The brush on the row scale: the whole tree drawn small above the tree panel,
+ * with the focused subtree boxed. A click focuses the subtree under the
+ * pointer, and a click inside the box clears the focus.
+ *
+ * The tree itself comes off a cached offscreen canvas, so the frames a pointer
+ * moving across it costs are a blit and two boxes.
+ */
+declare const TreeOverview: ({ model }: {
+    model: MsaViewModel;
+}) => React.JSX.Element;
+export default TreeOverview;

package/dist/components/tree/TreeOverview.js

@@ -0,0 +1,75 @@
+import React, { useState } from 'react';
+import { useTheme } from '@mui/material';
+import { observer } from 'mobx-react';
+import { useCanvasAutorun } from '../../useCanvasAutorun.js';
+import { drawTreeOverview, drawTreeOverviewBox, treeOverviewImage, } from './renderTreeOverview.js';
+/**
+ * The brush on the row scale: the whole tree drawn small above the tree panel,
+ * with the focused subtree boxed. A click focuses the subtree under the
+ * pointer, and a click inside the box clears the focus.
+ *
+ * The tree itself comes off a cached offscreen canvas, so the frames a pointer
+ * moving across it costs are a blit and two boxes.
+ */
+const TreeOverview = observer(function ({ model }) {
+    const { treeAreaWidth, overviewHeight, highResScaleFactor } = model;
+    const theme = useTheme();
+    const [hover, setHover] = useState();
+    const width = Math.round(treeAreaWidth * highResScaleFactor);
+    const height = Math.round(overviewHeight * highResScaleFactor);
+    const ref = useCanvasAutorun({
+        draw: ctx => {
+            ctx.resetTransform();
+            ctx.clearRect(0, 0, width, height);
+            const image = treeOverviewImage({
+                model,
+                theme,
+                width: treeAreaWidth,
+                height: overviewHeight,
+                scale: highResScaleFactor,
+            });
+            ctx.scale(highResScaleFactor, highResScaleFactor);
+            const box = { model, ctx, width: treeAreaWidth, height: overviewHeight };
+            if (image) {
+                ctx.drawImage(image, 0, 0, image.width, image.height, 0, 0, box.width, box.height);
+            }
+            else {
+                drawTreeOverview({ ...box, theme });
+            }
+            if (hover) {
+                drawTreeOverviewBox({
+                    ...box,
+                    rows: hover.rows,
+                    color: theme.palette.text.secondary,
+                });
+            }
+            const focus = model.treeOverviewFocusRows;
+            if (focus) {
+                drawTreeOverviewBox({
+                    ...box,
+                    rows: focus,
+                    color: theme.palette.text.primary,
+                });
+            }
+        },
+        width,
+        height,
+        deps: [model, theme, hover],
+    });
+    return (React.createElement("canvas", { "data-testid": "tree_overview", ref: ref, width: width, height: height, style: {
+            display: 'block',
+            flexShrink: 0,
+            cursor: 'pointer',
+            width: treeAreaWidth,
+            height: overviewHeight,
+        }, onMouseMove: event => {
+            const hit = model.treeOverviewHit(event.nativeEvent.offsetY);
+            setHover(prev => (prev?.id === hit?.id ? prev : hit));
+        }, onMouseLeave: () => {
+            setHover(undefined);
+        }, onClick: event => {
+            model.treeOverviewClick(event.nativeEvent.offsetY);
+        } }));
+});
+export default TreeOverview;
+//# sourceMappingURL=TreeOverview.js.map

package/dist/components/tree/TreeOverview.js.map

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package/dist/components/tree/TreeRuler.js

@@ -1,21 +1,17 @@
 import React from 'react';
 import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
-import { scaleBarLength } from './scaleBar.js';
-const BAR_HEIGHT = 22;
-// The gutter above the tree panel. It spans the resize handle too, so whatever
-// follows it in the top row starts exactly where the alignment canvas does --
-// MainArea has TreePanel + VerticalResizeHandle before the alignment. A
-// phylogram fills it with a scale bar: without one the branch lengths are drawn
-// to a scale nothing states.
+import { treeScaleBarHeight as h } from '../../constants.js';
+// The gutter above the tree panel, the width of the tree area, so the strip
+// headers beside it start where the strips do. A phylogram fills it with a
+// scale bar: without one the branch lengths are drawn to a scale nothing
+// states.
 const TreeRuler = observer(({ model }) => {
-    const { treeAreaWidth, resizeHandleWidth, marginLeft, pxPerBranchLength } = model;
+    const { treeAreaWidth, marginLeft, treeScaleBar: bar } = model;
     const theme = useTheme();
-    const width = treeAreaWidth + resizeHandleWidth;
-    const bar = scaleBarLength(pxPerBranchLength, treeAreaWidth - marginLeft * 2);
-    return (React.createElement("div", { style: { flexShrink: 0, width } }, bar ? (React.createElement("svg", { width: width, height: BAR_HEIGHT, style: { display: 'block' }, color: theme.palette.text.primary },
-        React.createElement("text", { x: marginLeft, y: BAR_HEIGHT - 9, fontSize: 10, fill: "currentColor" }, bar.label),
-        React.createElement("path", { d: `M${marginLeft} ${BAR_HEIGHT - 7} v6 h${bar.px} v-6`, fill: "none", stroke: "currentColor" }))) : null));
+    return (React.createElement("div", { style: { flexShrink: 0, width: treeAreaWidth } }, bar ? (React.createElement("svg", { width: treeAreaWidth, height: h, style: { display: 'block' }, color: theme.palette.text.primary },
+        React.createElement("text", { x: marginLeft, y: h - 9, fontSize: 10, fill: "currentColor" }, bar.label),
+        React.createElement("path", { d: `M${marginLeft} ${h - 7} v6 h${bar.px} v-6`, fill: "none", stroke: "currentColor" }))) : null));
 });
 export default TreeRuler;
 //# sourceMappingURL=TreeRuler.js.map

package/dist/components/tree/TreeRuler.js.map

@@ -1 +1 @@
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package/dist/components/tree/cladeBrackets.d.ts

@@ -0,0 +1,25 @@
+import type { ResolvedClade } from '../../types.ts';
+export declare const bracketBarWidth = 3;
+export declare const bracketGap = 4;
+export declare const maxCladeGutterWidth = 140;
+/** whether a clade draws in the gutter: a bracket, or a highlight with a label */
+export declare function cladeInGutter(clade: ResolvedClade): boolean;
+/** the pixel height of the rows a clade covers */
+export declare function cladeHeight(clade: ResolvedClade, rowHeight: number): number;
+/**
+ * Whether a label reads across the rows. It does where they are taller than the
+ * font, and runs up the bar where they are not.
+ */
+export declare function cladeLabelHorizontal(clade: ResolvedClade, rowHeight: number, fontSize: number): boolean;
+/** the px between the left edge of the gutter and the label's own column */
+export declare function cladeLabelOffset(clade: ResolvedClade): number;
+/**
+ * The gutter the bracket mark needs at the right of the tree area: the bar plus
+ * the widest label at the tree font, zero where no clade draws there, and at
+ * most maxCladeGutterWidth.
+ */
+export declare function cladeGutterWidth({ clades, rowHeight, fontSize, }: {
+    clades: ResolvedClade[];
+    rowHeight: number;
+    fontSize: number;
+}): number;

package/dist/components/tree/cladeBrackets.js

@@ -0,0 +1,51 @@
+import { measureTextCanvas } from '../../measureTextCanvas.js';
+// The bar of the bracket mark and the space around it, in px.
+export const bracketBarWidth = 3;
+export const bracketGap = 4;
+// The widest gutter the bracket mark takes. A longer label is clipped, so one
+// long name cannot squeeze the tree it annotates.
+export const maxCladeGutterWidth = 140;
+/** whether a clade draws in the gutter: a bracket, or a highlight with a label */
+export function cladeInGutter(clade) {
+    return (clade.mark === 'bracket' || (clade.mark === 'highlight' && !!clade.label));
+}
+/** the pixel height of the rows a clade covers */
+export function cladeHeight(clade, rowHeight) {
+    return (clade.rows[1] - clade.rows[0] + 1) * rowHeight;
+}
+/**
+ * Whether a label reads across the rows. It does where they are taller than the
+ * font, and runs up the bar where they are not.
+ */
+export function cladeLabelHorizontal(clade, rowHeight, fontSize) {
+    return cladeHeight(clade, rowHeight) >= fontSize;
+}
+/** the px between the left edge of the gutter and the label's own column */
+export function cladeLabelOffset(clade) {
+    return clade.mark === 'bracket'
+        ? bracketGap + bracketBarWidth + bracketGap
+        : bracketGap;
+}
+/**
+ * The gutter the bracket mark needs at the right of the tree area: the bar plus
+ * the widest label at the tree font, zero where no clade draws there, and at
+ * most maxCladeGutterWidth.
+ */
+export function cladeGutterWidth({ clades, rowHeight, fontSize, }) {
+    let widest = 0;
+    for (const clade of clades) {
+        if (!cladeInGutter(clade)) {
+            continue;
+        }
+        const text = clade.label
+            ? cladeLabelHorizontal(clade, rowHeight, fontSize)
+                ? measureTextCanvas(clade.label, fontSize)
+                : fontSize
+            : 0;
+        widest = Math.max(widest, cladeLabelOffset(clade) + text + bracketGap);
+    }
+    // a whole pixel, so the room the renderers measure against covers the label
+    // the measurement here sized the gutter for
+    return Math.min(maxCladeGutterWidth, Math.ceil(widest));
+}
+//# sourceMappingURL=cladeBrackets.js.map

package/dist/components/tree/cladeBrackets.js.map

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package/dist/components/tree/dialogs/TreeNodeInfoDialog.js

@@ -6,8 +6,8 @@ import { DialogContent } from '@mui/material';
 import { observer } from 'mobx-react';
 import SequenceTextArea from '../../SequenceTextArea.js';
 const TreeNodeInfoDialog = observer(function ({ info, model, nodeName, onClose, }) {
-    const { treeMetadata, rows } = model;
-    const metadata = treeMetadata[nodeName];
+    const { rows } = model;
+    const metadata = model.rowDataOf(nodeName);
     const res = rows.find(f => f[0] === nodeName);
     return (React.createElement(Dialog, { onClose: () => {
             onClose();

package/dist/components/tree/dialogs/TreeNodeInfoDialog.js.map

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