react-msaview 9.0.0 → 9.1.1

package/dist/components/tree/CladeLabels.js

@@ -1,7 +1,7 @@
 import React from 'react';
 import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
-import { bracketGap, cladeHeight, cladeInGutter, cladeLabelHorizontal, cladeLabelOffset, } from './cladeBrackets.js';
+import { cladeLabelBoxes } from './cladeBrackets.js';
 /**
  * The label of each bracket, in the gutter beside its bar, where the canvas
  * draws the bar itself. The text is DOM text, turned on its side for a clade
@@ -9,40 +9,28 @@ import { bracketGap, cladeHeight, cladeInGutter, cladeLabelHorizontal, cladeLabe
  * the same labels with a `rotate(-90)`.
  */
 const CladeLabels = observer(function ({ model }) {
-    const { resolvedClades, cladeGutterWidth, rowHeight, effectiveTreeAreaWidth, fontSize, } = model;
     const theme = useTheme();
-    if (cladeGutterWidth === 0) {
-        return null;
-    }
-    const gutterLeft = effectiveTreeAreaWidth - cladeGutterWidth;
-    return (React.createElement(React.Fragment, null, resolvedClades.map((clade, index) => {
-        const { label, markColor, rows } = clade;
-        if (!label || !cladeInGutter(clade)) {
-            return null;
-        }
-        const left = gutterLeft + cladeLabelOffset(clade);
-        const horizontal = cladeLabelHorizontal(clade, rowHeight, fontSize);
-        return (React.createElement("div", { key: `${rows[0]}-${rows[1]}-${index}`, title: label, style: {
-                position: 'absolute',
-                left,
-                top: rows[0] * rowHeight,
-                width: effectiveTreeAreaWidth - left - bracketGap,
-                height: cladeHeight(clade, rowHeight),
-                display: 'flex',
-                alignItems: 'center',
-                color: markColor ?? theme.palette.text.primary,
-                fontSize,
-                overflow: 'hidden',
-                textOverflow: 'ellipsis',
-                whiteSpace: 'nowrap',
-                pointerEvents: 'none',
-                // vertical-rl reads top to bottom, and the half turn makes it
-                // read upwards, which is what rotate(-90) exports
-                ...(horizontal
-                    ? {}
-                    : { writingMode: 'vertical-rl', transform: 'rotate(180deg)' }),
-            } }, label));
-    })));
+    const { fontSize } = model;
+    return (React.createElement(React.Fragment, null, cladeLabelBoxes(model).map(box => (React.createElement("div", { key: box.key, title: box.label, style: {
+            position: 'absolute',
+            left: box.left,
+            top: box.top,
+            width: box.width,
+            height: box.height,
+            display: 'flex',
+            alignItems: 'center',
+            color: box.color ?? theme.palette.text.primary,
+            fontSize,
+            overflow: 'hidden',
+            textOverflow: 'ellipsis',
+            whiteSpace: 'nowrap',
+            pointerEvents: 'none',
+            // vertical-rl reads top to bottom, and the half turn makes it
+            // read upwards, which is what rotate(-90) exports
+            ...(box.horizontal
+                ? {}
+                : { writingMode: 'vertical-rl', transform: 'rotate(180deg)' }),
+        } }, box.label)))));
 });
 export default CladeLabels;
 //# sourceMappingURL=CladeLabels.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"CladeLabels.js","sourceRoot":"","sources":["../../../src/components/tree/CladeLabels.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAA;AAIpD;;;;;GAKG;AACH,MAAM,WAAW,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACvE,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,OAAO,CACL,0CACG,eAAe,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CACjC,6BACE,GAAG,EAAE,GAAG,CAAC,GAAG,EACZ,KAAK,EAAE,GAAG,CAAC,KAAK,EAChB,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,IAAI,EAAE,GAAG,CAAC,IAAI;YACd,GAAG,EAAE,GAAG,CAAC,GAAG;YACZ,KAAK,EAAE,GAAG,CAAC,KAAK;YAChB,MAAM,EAAE,GAAG,CAAC,MAAM;YAClB,OAAO,EAAE,MAAM;YACf,UAAU,EAAE,QAAQ;YACpB,KAAK,EAAE,GAAG,CAAC,KAAK,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO;YAC9C,QAAQ;YACR,QAAQ,EAAE,QAAQ;YAClB,YAAY,EAAE,UAAU;YACxB,UAAU,EAAE,QAAQ;YACpB,aAAa,EAAE,MAAM;YACrB,8DAA8D;YAC9D,kDAAkD;YAClD,GAAG,CAAC,GAAG,CAAC,UAAU;gBAChB,CAAC,CAAC,EAAE;gBACJ,CAAC,CAAC,EAAE,WAAW,EAAE,aAAa,EAAE,SAAS,EAAE,gBAAgB,EAAE,CAAC;SACjE,IAEA,GAAG,CAAC,KAAK,CACN,CACP,CAAC,CACD,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,WAAW,CAAA"}

package/dist/components/tree/TreeCanvasBlock.js

@@ -1,8 +1,8 @@
 import React, { useState } from 'react';
 import BaseTooltip from '@jbrowse/core/ui/BaseTooltip';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
-import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
+import { useCanvasTheme } from '../../darkReader.js';
 import { useCanvasAutorun } from '../../useCanvasAutorun.js';
 import TreeMenu from './TreeMenu.js';
 import { renderTreeCanvas } from './renderTreeCanvas.js';
@@ -17,7 +17,7 @@ const useStyles = makeStyles()(theme => ({
 }));
 const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
     const { classes } = useStyles();
-    const theme = useTheme();
+    const theme = useCanvasTheme();
     const [menu, setMenu] = useState();
     const { clickMap, anchor, hitTest, onMouseMove, onMouseLeave } = useTreeHover({ model, offsetY });
     const hovered = anchor?.value;

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

@@ -1 +1 @@
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package/dist/components/tree/TreeMenu.js

@@ -7,7 +7,7 @@ const TreeMenu = observer(function ({ node, model, onClose, }) {
     const { name, id, leaf } = node;
     const isCollapsed = collapsed.includes(id);
     const isRoot = id === model.tree.id;
-    const noun = leaf ? 'subtree' : 'this node';
+    const noun = leaf ? 'subtree' : 'clade';
     return (React.createElement(Menu, { anchorReference: "anchorPosition", anchorPosition: { left: node.x, top: node.y }, transitionDuration: 0, open: true, onClose: onClose },
         React.createElement(MenuItem, { dense: true, disabled: true }, name),
         leaf ? (React.createElement(MenuItem, { dense: true, onClick: () => {
@@ -24,13 +24,11 @@ const TreeMenu = observer(function ({ node, model, onClose, }) {
         leaf ? null : (React.createElement(MenuItem, { dense: true, onClick: () => {
                 model.setShowOnly(showOnly === id ? undefined : id);
                 onClose();
-            } }, showOnly === id
-            ? 'Disable show only this node'
-            : 'Show only this node')),
+            } }, showOnly === id ? 'Show all rows' : 'Show only this clade')),
         leaf || isCollapsed ? null : (React.createElement(MenuItem, { dense: true, onClick: () => {
                 model.toggleRotated(id);
                 onClose();
-            } }, "Rotate this node")),
+            } }, "Rotate clade")),
         isRoot ? null : (React.createElement(MenuItem, { dense: true, onClick: () => {
                 model.rerootAt(id);
                 onClose();
@@ -38,7 +36,7 @@ const TreeMenu = observer(function ({ node, model, onClose, }) {
         leaf ? (React.createElement(MenuItem, { dense: true, onClick: () => {
                 model.drawRelativeTo(name);
                 onClose();
-            } }, "Indicate differences from this row")) : null,
+            } }, "Use as reference row")) : null,
         leaf && relativeTo ? (React.createElement(MenuItem, { dense: true, onClick: () => {
                 model.drawRelativeTo(undefined);
                 onClose();

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

@@ -1 +1 @@
-{"version":3,"file":"TreeMenu.js","sourceRoot":"","sources":["../../../src/components/tree/TreeMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAEnC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,kBAAkB,GAAG,IAAI,CAC7B,GAAG,EAAE,CAAC,MAAM,CAAC,iCAAkC,CAAC,CACjD,CAAA;AAUD,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,EAClC,IAAI,EACJ,KAAK,EACL,OAAO,GAKR;IACC,MAAM,EAAE,SAAS,EAAE,QAAQ,EAAE,UAAU,EAAE,GAAG,KAAK,CAAA;IACjD,MAAM,EAAE,IAAI,EAAE,EAAE,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;IAC/B,MAAM,WAAW,GAAG,SAAS,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAA;IAC1C,MAAM,MAAM,GAAG,EAAE,KAAK,KAAK,CAAC,IAAI,CAAC,EAAE,CAAA;IACnC,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,WAAW,CAAA;IAC3C,OAAO,CACL,oBAAC,IAAI,IACH,eAAe,EAAC,gBAAgB,EAChC,cAAc,EAAE,EAAE,IAAI,EAAE,IAAI,CAAC,CAAC,EAAE,GAAG,EAAE,IAAI,CAAC,CAAC,EAAE,EAC7C,kBAAkB,EAAE,CAAC,EACrB,IAAI,QACJ,OAAO,EAAE,OAAO;QAEhB,oBAAC,QAAQ,IAAC,KAAK,QAAC,QAAQ,UACrB,IAAI,CACI;QACV,IAAI,CAAC,CAAC,CAAC,CACN,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;oBAC3B,kBAAkB;oBAClB,EAAE,IAAI,EAAE,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,QAAQ,EAAE,IAAI,EAAE,OAAO,EAAE;iBACjE,CAAC,CAAA;gBACF,OAAO,EAAE,CAAA;YACX,CAAC,mBAGQ,CACZ,CAAC,CAAC,CAAC,IAAI;QACR,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,eAAe,CAAC,EAAE,CAAC,CAAA;gBACzB,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,WAAW,CAAC,CAAC,CAAC,UAAU,IAAI,EAAE,CAAC,CAAC,CAAC,YAAY,IAAI,EAAE,CAC3C;QACV,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CACb,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,QAAQ,KAAK,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAA;gBACnD,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,QAAQ,KAAK,EAAE;YACd,CAAC,CAAC,6BAA6B;YAC/B,CAAC,CAAC,qBAAqB,CAChB,CACZ;QACA,IAAI,IAAI,WAAW,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAC5B,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,aAAa,CAAC,EAAE,CAAC,CAAA;gBACvB,OAAO,EAAE,CAAA;YACX,CAAC,uBAGQ,CACZ;QACA,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CACf,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAA;gBAClB,OAAO,EAAE,CAAA;YACX,CAAC,kBAGQ,CACZ;QACA,IAAI,CAAC,CAAC,CAAC,CACN,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;gBAC1B,OAAO,EAAE,CAAA;YACX,CAAC,yCAGQ,CACZ,CAAC,CAAC,CAAC,IAAI;QACP,IAAI,IAAI,UAAU,CAAC,CAAC,CAAC,CACpB,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;gBAC/B,OAAO,EAAE,CAAA;YACX,CAAC,0BAGQ,CACZ,CAAC,CAAC,CAAC,IAAI,CACH,CACR,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}
+{"version":3,"file":"TreeMenu.js","sourceRoot":"","sources":["../../../src/components/tree/TreeMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAEnC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,kBAAkB,GAAG,IAAI,CAC7B,GAAG,EAAE,CAAC,MAAM,CAAC,iCAAkC,CAAC,CACjD,CAAA;AAUD,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,EAClC,IAAI,EACJ,KAAK,EACL,OAAO,GAKR;IACC,MAAM,EAAE,SAAS,EAAE,QAAQ,EAAE,UAAU,EAAE,GAAG,KAAK,CAAA;IACjD,MAAM,EAAE,IAAI,EAAE,EAAE,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;IAC/B,MAAM,WAAW,GAAG,SAAS,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAA;IAC1C,MAAM,MAAM,GAAG,EAAE,KAAK,KAAK,CAAC,IAAI,CAAC,EAAE,CAAA;IACnC,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,OAAO,CAAA;IACvC,OAAO,CACL,oBAAC,IAAI,IACH,eAAe,EAAC,gBAAgB,EAChC,cAAc,EAAE,EAAE,IAAI,EAAE,IAAI,CAAC,CAAC,EAAE,GAAG,EAAE,IAAI,CAAC,CAAC,EAAE,EAC7C,kBAAkB,EAAE,CAAC,EACrB,IAAI,QACJ,OAAO,EAAE,OAAO;QAEhB,oBAAC,QAAQ,IAAC,KAAK,QAAC,QAAQ,UACrB,IAAI,CACI;QACV,IAAI,CAAC,CAAC,CAAC,CACN,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;oBAC3B,kBAAkB;oBAClB,EAAE,IAAI,EAAE,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,QAAQ,EAAE,IAAI,EAAE,OAAO,EAAE;iBACjE,CAAC,CAAA;gBACF,OAAO,EAAE,CAAA;YACX,CAAC,mBAGQ,CACZ,CAAC,CAAC,CAAC,IAAI;QACR,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,eAAe,CAAC,EAAE,CAAC,CAAA;gBACzB,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,WAAW,CAAC,CAAC,CAAC,UAAU,IAAI,EAAE,CAAC,CAAC,CAAC,YAAY,IAAI,EAAE,CAC3C;QACV,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CACb,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,QAAQ,KAAK,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAA;gBACnD,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,QAAQ,KAAK,EAAE,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,sBAAsB,CAClD,CACZ;QACA,IAAI,IAAI,WAAW,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAC5B,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,aAAa,CAAC,EAAE,CAAC,CAAA;gBACvB,OAAO,EAAE,CAAA;YACX,CAAC,mBAGQ,CACZ;QACA,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CACf,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAA;gBAClB,OAAO,EAAE,CAAA;YACX,CAAC,kBAGQ,CACZ;QACA,IAAI,CAAC,CAAC,CAAC,CACN,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;gBAC1B,OAAO,EAAE,CAAA;YACX,CAAC,2BAGQ,CACZ,CAAC,CAAC,CAAC,IAAI;QACP,IAAI,IAAI,UAAU,CAAC,CAAC,CAAC,CACpB,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;gBAC/B,OAAO,EAAE,CAAA;YACX,CAAC,0BAGQ,CACZ,CAAC,CAAC,CAAC,IAAI,CACH,CACR,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}

package/dist/components/tree/TreeOverview.js

@@ -1,6 +1,6 @@
 import React, { useState } from 'react';
-import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
+import { useCanvasTheme } from '../../darkReader.js';
 import { useCanvasAutorun } from '../../useCanvasAutorun.js';
 import { drawTreeOverview, drawTreeOverviewBox, treeOverviewImage, } from './renderTreeOverview.js';
 /**
@@ -13,7 +13,7 @@ import { drawTreeOverview, drawTreeOverviewBox, treeOverviewImage, } from './ren
  */
 const TreeOverview = observer(function ({ model }) {
     const { effectiveTreeAreaWidth, overviewHeight, highResScaleFactor } = model;
-    const theme = useTheme();
+    const theme = useCanvasTheme();
     const [hover, setHover] = useState();
     const width = Math.round(effectiveTreeAreaWidth * highResScaleFactor);
     const height = Math.round(overviewHeight * highResScaleFactor);

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

@@ -1 +1 @@
-{"version":3,"file":"TreeOverview.js","sourceRoot":"","sources":["../../../src/components/tree/TreeOverview.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,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,EACL,gBAAgB,EAChB,mBAAmB,EACnB,iBAAiB,GAClB,MAAM,yBAAyB,CAAA;AAIhC;;;;;;;GAOG;AACH,MAAM,YAAY,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACxE,MAAM,EAAE,sBAAsB,EAAE,cAAc,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IAC5E,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAA0C,CAAA;IAC5E,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,sBAAsB,GAAG,kBAAkB,CAAC,CAAA;IACrE,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,cAAc,GAAG,kBAAkB,CAAC,CAAA;IAE9D,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,KAAK,EAAE,MAAM,CAAC,CAAA;YAClC,MAAM,KAAK,GAAG,iBAAiB,CAAC;gBAC9B,KAAK;gBACL,KAAK;gBACL,KAAK,EAAE,sBAAsB;gBAC7B,MAAM,EAAE,cAAc;gBACtB,KAAK,EAAE,kBAAkB;aAC1B,CAAC,CAAA;YACF,GAAG,CAAC,KAAK,CAAC,kBAAkB,EAAE,kBAAkB,CAAC,CAAA;YACjD,MAAM,GAAG,GAAG;gBACV,KAAK;gBACL,GAAG;gBACH,KAAK,EAAE,sBAAsB;gBAC7B,MAAM,EAAE,cAAc;aACvB,CAAA;YACD,IAAI,KAAK,EAAE,CAAC;gBACV,GAAG,CAAC,SAAS,CACX,KAAK,EACL,CAAC,EACD,CAAC,EACD,KAAK,CAAC,KAAK,EACX,KAAK,CAAC,MAAM,EACZ,CAAC,EACD,CAAC,EACD,GAAG,CAAC,KAAK,EACT,GAAG,CAAC,MAAM,CACX,CAAA;YACH,CAAC;iBAAM,CAAC;gBACN,gBAAgB,CAAC,EAAE,GAAG,GAAG,EAAE,KAAK,EAAE,CAAC,CAAA;YACrC,CAAC;YACD,IAAI,KAAK,EAAE,CAAC;gBACV,mBAAmB,CAAC;oBAClB,GAAG,GAAG;oBACN,IAAI,EAAE,KAAK,CAAC,IAAI;oBAChB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS;iBACpC,CAAC,CAAA;YACJ,CAAC;YACD,MAAM,KAAK,GAAG,KAAK,CAAC,qBAAqB,CAAA;YACzC,IAAI,KAAK,EAAE,CAAC;gBACV,mBAAmB,CAAC;oBAClB,GAAG,GAAG;oBACN,IAAI,EAAE,KAAK;oBACX,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO;iBAClC,CAAC,CAAA;YACJ,CAAC;QACH,CAAC;QACD,KAAK;QACL,MAAM;QACN,IAAI,EAAE,CAAC,KAAK,EAAE,KAAK,EAAE,KAAK,CAAC;KAC5B,CAAC,CAAA;IAEF,OAAO,CACL,+CACc,eAAe,EAC3B,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;YACL,OAAO,EAAE,OAAO;YAChB,UAAU,EAAE,CAAC;YACb,MAAM,EAAE,SAAS;YACjB,KAAK,EAAE,sBAAsB;YAC7B,MAAM,EAAE,cAAc;SACvB,EACD,WAAW,EAAE,KAAK,CAAC,EAAE;YACnB,MAAM,GAAG,GAAG,KAAK,CAAC,eAAe,CAAC,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC5D,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,IAAI,EAAE,EAAE,KAAK,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;QACvD,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;YACjB,QAAQ,CAAC,SAAS,CAAC,CAAA;QACrB,CAAC,EACD,OAAO,EAAE,KAAK,CAAC,EAAE;YACf,KAAK,CAAC,iBAAiB,CAAC,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QACpD,CAAC,GACD,CACH,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}
+{"version":3,"file":"TreeOverview.js","sourceRoot":"","sources":["../../../src/components/tree/TreeOverview.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAC5D,OAAO,EACL,gBAAgB,EAChB,mBAAmB,EACnB,iBAAiB,GAClB,MAAM,yBAAyB,CAAA;AAIhC;;;;;;;GAOG;AACH,MAAM,YAAY,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACxE,MAAM,EAAE,sBAAsB,EAAE,cAAc,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IAC5E,MAAM,KAAK,GAAG,cAAc,EAAE,CAAA;IAC9B,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAA0C,CAAA;IAC5E,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,sBAAsB,GAAG,kBAAkB,CAAC,CAAA;IACrE,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,cAAc,GAAG,kBAAkB,CAAC,CAAA;IAE9D,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,KAAK,EAAE,MAAM,CAAC,CAAA;YAClC,MAAM,KAAK,GAAG,iBAAiB,CAAC;gBAC9B,KAAK;gBACL,KAAK;gBACL,KAAK,EAAE,sBAAsB;gBAC7B,MAAM,EAAE,cAAc;gBACtB,KAAK,EAAE,kBAAkB;aAC1B,CAAC,CAAA;YACF,GAAG,CAAC,KAAK,CAAC,kBAAkB,EAAE,kBAAkB,CAAC,CAAA;YACjD,MAAM,GAAG,GAAG;gBACV,KAAK;gBACL,GAAG;gBACH,KAAK,EAAE,sBAAsB;gBAC7B,MAAM,EAAE,cAAc;aACvB,CAAA;YACD,IAAI,KAAK,EAAE,CAAC;gBACV,GAAG,CAAC,SAAS,CACX,KAAK,EACL,CAAC,EACD,CAAC,EACD,KAAK,CAAC,KAAK,EACX,KAAK,CAAC,MAAM,EACZ,CAAC,EACD,CAAC,EACD,GAAG,CAAC,KAAK,EACT,GAAG,CAAC,MAAM,CACX,CAAA;YACH,CAAC;iBAAM,CAAC;gBACN,gBAAgB,CAAC,EAAE,GAAG,GAAG,EAAE,KAAK,EAAE,CAAC,CAAA;YACrC,CAAC;YACD,IAAI,KAAK,EAAE,CAAC;gBACV,mBAAmB,CAAC;oBAClB,GAAG,GAAG;oBACN,IAAI,EAAE,KAAK,CAAC,IAAI;oBAChB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS;iBACpC,CAAC,CAAA;YACJ,CAAC;YACD,MAAM,KAAK,GAAG,KAAK,CAAC,qBAAqB,CAAA;YACzC,IAAI,KAAK,EAAE,CAAC;gBACV,mBAAmB,CAAC;oBAClB,GAAG,GAAG;oBACN,IAAI,EAAE,KAAK;oBACX,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO;iBAClC,CAAC,CAAA;YACJ,CAAC;QACH,CAAC;QACD,KAAK;QACL,MAAM;QACN,IAAI,EAAE,CAAC,KAAK,EAAE,KAAK,EAAE,KAAK,CAAC;KAC5B,CAAC,CAAA;IAEF,OAAO,CACL,+CACc,eAAe,EAC3B,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;YACL,OAAO,EAAE,OAAO;YAChB,UAAU,EAAE,CAAC;YACb,MAAM,EAAE,SAAS;YACjB,KAAK,EAAE,sBAAsB;YAC7B,MAAM,EAAE,cAAc;SACvB,EACD,WAAW,EAAE,KAAK,CAAC,EAAE;YACnB,MAAM,GAAG,GAAG,KAAK,CAAC,eAAe,CAAC,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC5D,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,IAAI,EAAE,EAAE,KAAK,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;QACvD,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;YACjB,QAAQ,CAAC,SAAS,CAAC,CAAA;QACrB,CAAC,EACD,OAAO,EAAE,KAAK,CAAC,EAAE;YACf,KAAK,CAAC,iBAAiB,CAAC,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QACpD,CAAC,GACD,CACH,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}

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

@@ -1,18 +1,10 @@
-import type { Clade, ResolvedClade } from '../../types.ts';
+import type { MsaViewModel } from '../../model.ts';
+import type { Clade } 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: Pick<Clade, 'mark' | 'label'>): 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: Pick<Clade, 'mark'>): number;
 /**
  * The gutter the bracket mark needs at the right of the tree area: the bar plus
  * the widest label read across at labelFitFontSize, zero where no clade draws
@@ -21,3 +13,18 @@ export declare function cladeLabelOffset(clade: Pick<Clade, 'mark'>): number;
  * outgrows it.
  */
 export declare function cladeGutterWidth(clades: Pick<Clade, 'mark' | 'label'>[]): number;
+/**
+ * The box each gutter label takes, in unscrolled tree-area px: from the
+ * label's column to the right edge of the gutter, across the clade's rows. The
+ * live view sets DOM text in it, and the SVG export a `<text>`.
+ */
+export declare function cladeLabelBoxes(model: Pick<MsaViewModel, 'resolvedClades' | 'cladeGutterWidth' | 'rowHeight' | 'effectiveTreeAreaWidth' | 'fontSize'>): {
+    key: string;
+    label: string;
+    color: string | undefined;
+    left: number;
+    top: number;
+    width: number;
+    height: number;
+    horizontal: boolean;
+}[];

package/dist/components/tree/cladeBrackets.js

@@ -11,18 +11,18 @@ 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) {
+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) {
+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) {
+function cladeLabelOffset(clade) {
     return clade.mark === 'bracket'
         ? bracketGap + bracketBarWidth + bracketGap
         : bracketGap;
@@ -49,4 +49,34 @@ export function cladeGutterWidth(clades) {
     // the measurement here sized the gutter for
     return Math.min(maxCladeGutterWidth, Math.ceil(widest));
 }
+/**
+ * The box each gutter label takes, in unscrolled tree-area px: from the
+ * label's column to the right edge of the gutter, across the clade's rows. The
+ * live view sets DOM text in it, and the SVG export a `<text>`.
+ */
+export function cladeLabelBoxes(model) {
+    const { resolvedClades, cladeGutterWidth, rowHeight, effectiveTreeAreaWidth, fontSize, } = model;
+    const gutterLeft = effectiveTreeAreaWidth - cladeGutterWidth;
+    return cladeGutterWidth === 0
+        ? []
+        : resolvedClades.flatMap((clade, index) => {
+            const { label, markColor, rows } = clade;
+            if (!label || !cladeInGutter(clade)) {
+                return [];
+            }
+            const left = gutterLeft + cladeLabelOffset(clade);
+            return [
+                {
+                    key: `${rows[0]}-${rows[1]}-${index}`,
+                    label,
+                    color: markColor,
+                    left,
+                    top: rows[0] * rowHeight,
+                    width: effectiveTreeAreaWidth - left - bracketGap,
+                    height: cladeHeight(clade, rowHeight),
+                    horizontal: cladeLabelHorizontal(clade, rowHeight, fontSize),
+                },
+            ];
+        });
+}
 //# sourceMappingURL=cladeBrackets.js.map

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

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package/dist/components/tree/renderTreeCanvas.js

@@ -21,7 +21,7 @@ function inYBlock(y, offsetY, by, pad) {
 /**
  * Every node whose subtree reaches into the block, skipping the subtrees that
  * do not. A subtree's leaves are one contiguous run of rows, recorded by
- * clusterLayout as xMin/xMax, so a block of a 200k-tip tree visits a few dozen
+ * layoutTree as xMin/xMax, so a block of a 200k-tip tree visits a few dozen
  * nodes.
  *
  * A link out of a visited node is drawn even when its child is pruned, so a
@@ -428,13 +428,7 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
     setFontSize(ctx, fontSize);
     // memoized on the model and shared across the tree/bubble/label passes (and
     // across all tree blocks) rather than re-traversing the hierarchy in each
-    const { maxBranchLength, maxDepthToLeaf, showBranchLenEffective, effectiveTreeWidth, } = model;
-    // pixel x of the tips. A phylogram scales branch lengths so the longest
-    // root-to-tip path lands at maxBranchLength; a cladogram ignores lengths and
-    // spreads topological depth across the whole tree area instead. Reusing
-    // maxBranchLength for the cladogram would pin every node to x=0 for a tree
-    // with no branch lengths -- which is exactly what forces cladogram mode.
-    const tipX = showBranchLenEffective ? maxBranchLength : effectiveTreeWidth;
+    const { maxDepthToLeaf, effectiveTreeWidth: tipX } = model;
     // built once for all three passes: each of them asks about a different node on
     // every block of every redraw, and `collapsed` is a list
     const collapsedSet = new Set(model.collapsed);

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

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package/dist/components/tree/renderTreeOverview.js

@@ -1,4 +1,5 @@
 import { descendants } from '../../hierarchy.js';
+import { makeOffscreenCanvas } from '../msa/msaRaster.js';
 import { getNodeX } from './renderTreeCanvas.js';
 // the tree draws this far inside the band, so a box around the first or the
 // last row keeps both of its edges
@@ -100,16 +101,8 @@ function overviewKeys({ model, theme, width, height, scale, }) {
         theme.palette.text.primary,
     ];
 }
-function makeCanvas(width, height) {
-    const canvas = typeof OffscreenCanvas !== 'undefined'
-        ? new OffscreenCanvas(width, height)
-        : typeof document !== 'undefined'
-            ? Object.assign(document.createElement('canvas'), { width, height })
-            : undefined;
-    const ctx = canvas?.getContext('2d');
-    return ctx && typeof ctx.stroke === 'function'
-        ? { canvas: canvas, ctx: ctx }
-        : undefined;
+function canStroke(ctx) {
+    return typeof ctx?.stroke === 'function';
 }
 /**
  * The tree and its clade highlights on an offscreen canvas, drawn once per
@@ -126,7 +119,7 @@ export function treeOverviewImage({ model, theme, width, height, scale, }) {
     if (prev && keys.every((key, i) => key === prev.keys[i])) {
         return prev.canvas;
     }
-    const made = makeCanvas(Math.max(1, Math.round(width * scale)), Math.max(1, Math.round(height * scale)));
+    const made = makeOffscreenCanvas(Math.max(1, Math.round(width * scale)), Math.max(1, Math.round(height * scale)), canStroke);
     if (made) {
         made.ctx.scale(scale, scale);
         drawTreeOverview({ model, ctx: made.ctx, theme, width, height });

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

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

@@ -21,12 +21,14 @@ export type ScrollZoomAxis = (typeof scrollZoomAxes)[number];
 export declare const defaultScrollZoomAxis: ScrollZoomAxis;
 export declare const minLetterRowHeight = 8;
 export declare const minLetterColWidth = 5;
+export declare const zoomFrameMaxLetters = 2000;
 export declare const minFeatureLabelHeight = 9;
 export declare function fontSizeFor(rowHeight: number): number;
 export declare const labelFitFontSize: number;
 export declare const minColWidth = 0.2;
-export declare const minRowHeight = 1;
+export declare const minRowHeight = 0.2;
 export declare const maxCellSize = 80;
+export declare const settingsPanelWidth = 280;
 export declare const defaultBgColor = true;
 export declare const defaultColorSchemeName = "maeditor";
 export declare const defaultShowColumnStats = true;
@@ -43,6 +45,7 @@ export declare const defaultDrawTree = true;
 export declare const defaultDrawNodeBubbles = true;
 export declare const defaultDrawNodeLabels = false;
 export declare const defaultShowTreeOverview = false;
+export declare const defaultShowTreeScaleBar = false;
 export declare const defaultOverviewHeight = 120;
 export declare const maxNeighborJoiningRows = 500;
 export declare const rowTintAlpha = 0.25;

package/dist/constants.js

@@ -42,6 +42,9 @@ export const defaultScrollZoomAxis = 'both';
 // frame. A sprite atlas measured slower.
 export const minLetterRowHeight = 8;
 export const minLetterColWidth = 5;
+// A wheel-zoom frame draws a block's letters only when the block holds at most
+// this many cells; the settle redraw after the gesture draws the rest
+export const zoomFrameMaxLetters = 2000;
 // A feature span draws its label at two pixels under its height, capped at 11,
 // so a span shorter than this holds no readable text: an underline bar, a
 // sub-row band or a features panel over small rows
@@ -57,8 +60,10 @@ export const labelFitFontSize = fontSizeFor(defaultRowHeight);
 // zoom-in buttons (which otherwise grow unbounded). minColWidth/minRowHeight are
 // the smooth-zoom floors.
 export const minColWidth = 0.2;
-export const minRowHeight = 1;
+export const minRowHeight = 0.2;
 export const maxCellSize = 80;
+// the settings panel's width, which it takes out of the view's
+export const settingsPanelWidth = 280;
 // MSA model defaults
 export const defaultBgColor = true;
 export const defaultColorSchemeName = 'maeditor';
@@ -86,6 +91,7 @@ export const defaultDrawTree = true;
 export const defaultDrawNodeBubbles = true;
 export const defaultDrawNodeLabels = false;
 export const defaultShowTreeOverview = false;
+export const defaultShowTreeScaleBar = false;
 export const defaultOverviewHeight = 120;
 // Neighbor joining does not run above this many rows. The distance matrix is
 // O(n^2*L) and the join loop O(n^3), both on the main thread with no progress

package/dist/constants.js.map

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

@@ -0,0 +1,7 @@
+import type { Theme } from '@mui/material';
+/**
+ * The theme a canvas draws in: the surrounding MUI theme, or a dark one while
+ * Dark Reader darkens a light page. The DOM keeps the surrounding theme, which
+ * Dark Reader restyles itself, and the SVG export keeps it too.
+ */
+export declare function useCanvasTheme(): Theme;

package/dist/darkReader.js

@@ -0,0 +1,42 @@
+import { useSyncExternalStore } from 'react';
+import { createJBrowseTheme } from '@jbrowse/core/ui/theme';
+import { useTheme } from '@mui/material';
+// Dark Reader's Dynamic mode rewrites the page's CSS and leaves canvas pixels
+// alone, so a light theme's black letters land on the dark page it paints.
+// Inlined from @jbrowse/core/util/systemColorScheme, which an older host core
+// lacks (see CLAUDE.md on externals).
+const DARK_READER_ATTRIBUTE = 'data-darkreader-scheme';
+function darkReaderIsDark() {
+    return (typeof document !== 'undefined' &&
+        document.documentElement.getAttribute(DARK_READER_ATTRIBUTE) === 'dark');
+}
+function onDarkReaderChange(listener) {
+    if (typeof MutationObserver !== 'function' ||
+        typeof document === 'undefined') {
+        return () => { };
+    }
+    const observer = new MutationObserver(listener);
+    observer.observe(document.documentElement, {
+        attributes: true,
+        attributeFilter: [DARK_READER_ATTRIBUTE],
+    });
+    return () => {
+        observer.disconnect();
+    };
+}
+let darkTheme;
+/**
+ * The theme a canvas draws in: the surrounding MUI theme, or a dark one while
+ * Dark Reader darkens a light page. The DOM keeps the surrounding theme, which
+ * Dark Reader restyles itself, and the SVG export keeps it too.
+ */
+export function useCanvasTheme() {
+    const theme = useTheme();
+    const darkReader = useSyncExternalStore(onDarkReaderChange, darkReaderIsDark, () => false);
+    if (darkReader && theme.palette.mode !== 'dark') {
+        darkTheme ??= createJBrowseTheme({ palette: { mode: 'dark' } });
+        return darkTheme;
+    }
+    return theme;
+}
+//# sourceMappingURL=darkReader.js.map