jbrowse-plugin-mafviewer 1.0.8 → 1.1.2

package/dist/BigMafAdapter/BigMafAdapter.js.map

@@ -1 +1 @@
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package/dist/BigMafAdapter/configSchema.d.ts

@@ -17,5 +17,16 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
             locationType: string;
         };
     };
+    /**
+     * #slot
+     */
+    nhLocation: {
+        type: string;
+        description: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/dist/BigMafAdapter/configSchema.js

@@ -23,6 +23,17 @@ const configSchema = ConfigurationSchema('BigMafAdapter', {
             locationType: 'UriLocation',
         },
     },
+    /**
+     * #slot
+     */
+    nhLocation: {
+        type: 'fileLocation',
+        description: 'newick tree',
+        defaultValue: {
+            uri: '/path/to/my.nh',
+            locationType: 'UriLocation',
+        },
+    },
 }, { explicitlyTyped: true });
 export default configSchema;
 //# sourceMappingURL=configSchema.js.map

package/dist/BigMafAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BigMafAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,mBAAmB,CACtC,eAAe,EACf;IACE;;OAEG;IACH,OAAO,EAAE;QACP,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,sDAAsD;QACnE,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,gBAAgB;YACrB,YAAY,EAAE,aAAa;SAC5B;KACF;IACD;;OAEG;IACH,UAAU,EAAE;QACV,IAAI,EAAE,cAAc;QACpB,WAAW,EAAE,aAAa;QAC1B,YAAY,EAAE;YACZ,GAAG,EAAE,gBAAgB;YACrB,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,YAAY,CAAA"}

package/dist/BigMafAdapter/index.js

@@ -1,6 +1,6 @@
 import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
-import configSchema from './configSchema';
 import BigMafAdapter from './BigMafAdapter';
+import configSchema from './configSchema';
 export default function BigMafAdapterF(pluginManager) {
     return pluginManager.addAdapterType(() => new AdapterType({
         name: 'BigMafAdapter',

package/dist/BigMafAdapter/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BigMafAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAA;AAEjE,OAAO,aAAa,MAAM,iBAAiB,CAAA;AAC3C,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,aAA4B;IACjE,OAAO,aAAa,CAAC,cAAc,CACjC,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,eAAe;QACrB,YAAY,EAAE,aAAa;QAC3B,YAAY;KACb,CAAC,CACL,CAAA;AACH,CAAC"}

package/dist/LinearMafDisplay/components/ColorLegend.js

@@ -1,15 +1,19 @@
 import React from 'react';
 import { observer } from 'mobx-react';
 import RectBg from './RectBg';
+import Tree from './Tree';
 const ColorLegend = observer(function ({ model, labelWidth, svgFontSize, }) {
-    const { samples, rowHeight } = model;
-    const canDisplayLabel = rowHeight >= 10;
+    const { totalHeight, treeWidth, samples, rowHeight } = model;
+    const canDisplayLabel = rowHeight >= 8;
     const boxHeight = Math.min(20, rowHeight);
     return (React.createElement(React.Fragment, null,
-        samples.map((sample, idx) => (React.createElement(RectBg, { key: `${sample.id}-${idx}`, y: idx * rowHeight, x: 0, width: labelWidth + 5, height: boxHeight, color: sample.color }))),
-        canDisplayLabel
-            ? samples.map((sample, idx) => (React.createElement("text", { key: `${sample.id}-${idx}`, y: idx * rowHeight + rowHeight / 2, dominantBaseline: "middle", x: 2, fontSize: svgFontSize }, sample.label)))
-            : null));
+        React.createElement(RectBg, { y: 0, x: 0, width: labelWidth + 5 + treeWidth, height: totalHeight }),
+        React.createElement(Tree, { model: model }),
+        React.createElement("g", { transform: `translate(${treeWidth + 5},0)` },
+            samples.map((sample, idx) => (React.createElement(RectBg, { key: `${sample.id}-${idx}`, y: idx * rowHeight, x: 0, width: labelWidth + 5, height: boxHeight, color: sample.color }))),
+            canDisplayLabel
+                ? samples.map((sample, idx) => (React.createElement("text", { key: `${sample.id}-${idx}`, y: idx * rowHeight + rowHeight / 2, dominantBaseline: "middle", x: 2, fontSize: svgFontSize }, sample.label)))
+                : null)));
 });
 export default ColorLegend;
 //# sourceMappingURL=ColorLegend.js.map

package/dist/LinearMafDisplay/components/ColorLegend.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ColorLegend.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/ColorLegend.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,OAAO,MAAM,MAAM,UAAU,CAAA;AAC7B,OAAO,IAAI,MAAM,QAAQ,CAAA;AAEzB,MAAM,WAAW,GAAG,QAAQ,CAAC,UAAU,EACrC,KAAK,EACL,UAAU,EACV,WAAW,GAKZ;IACC,MAAM,EAAE,WAAW,EAAE,SAAS,EAAE,OAAO,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IAC5D,MAAM,eAAe,GAAG,SAAS,IAAI,CAAC,CAAA;IACtC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,SAAS,CAAC,CAAA;IAEzC,OAAO,CACL;QACE,oBAAC,MAAM,IACL,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,UAAU,GAAG,CAAC,GAAG,SAAS,EACjC,MAAM,EAAE,WAAW,GACnB;QACF,oBAAC,IAAI,IAAC,KAAK,EAAE,KAAK,GAAI;QACtB,2BAAG,SAAS,EAAE,aAAa,SAAS,GAAG,CAAC,KAAK;YAC1C,OAAO,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,GAAG,EAAE,EAAE,CAAC,CAC5B,oBAAC,MAAM,IACL,GAAG,EAAE,GAAG,MAAM,CAAC,EAAE,IAAI,GAAG,EAAE,EAC1B,CAAC,EAAE,GAAG,GAAG,SAAS,EAClB,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,UAAU,GAAG,CAAC,EACrB,MAAM,EAAE,SAAS,EACjB,KAAK,EAAE,MAAM,CAAC,KAAK,GACnB,CACH,CAAC;YACD,eAAe;gBACd,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,GAAG,EAAE,EAAE,CAAC,CAC3B,8BACE,GAAG,EAAE,GAAG,MAAM,CAAC,EAAE,IAAI,GAAG,EAAE,EAC1B,CAAC,EAAE,GAAG,GAAG,SAAS,GAAG,SAAS,GAAG,CAAC,EAClC,gBAAgB,EAAC,QAAQ,EACzB,CAAC,EAAE,CAAC,EACJ,QAAQ,EAAE,WAAW,IAEpB,MAAM,CAAC,KAAK,CACR,CACR,CAAC;gBACJ,CAAC,CAAC,IAAI,CACN,CACH,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,WAAW,CAAA"}

package/dist/LinearMafDisplay/components/ReactComponent.js

@@ -1,15 +1,50 @@
-import React from 'react';
-import { getEnv } from '@jbrowse/core/util';
+import React, { useRef, useState } from 'react';
+import BaseTooltip from '@jbrowse/core/ui/BaseTooltip';
+import SanitizedHTML from '@jbrowse/core/ui/SanitizedHTML';
+import { getContainingView, getEnv } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
 import YScaleBars from './YScaleBars';
+const useStyles = makeStyles()({
+    cursor: {
+        pointerEvents: 'none',
+    },
+});
 const LinearMafDisplay = observer(function (props) {
     const { model } = props;
+    const { classes } = useStyles();
     const { pluginManager } = getEnv(model);
+    const { rowHeight, height, scrollTop, samples: sources } = model;
+    const ref = useRef(null);
     const LinearGenomePlugin = pluginManager.getPlugin('LinearGenomeViewPlugin');
     const { BaseLinearDisplayComponent } = LinearGenomePlugin.exports;
-    return (React.createElement("div", null,
+    const [mouseY, setMouseY] = useState();
+    const [mouseX, setMouseX] = useState();
+    const { width } = getContainingView(model);
+    return (React.createElement("div", { ref: ref, onMouseMove: event => {
+            const rect = ref.current?.getBoundingClientRect();
+            const top = rect?.top || 0;
+            const left = rect?.left || 0;
+            setMouseY(event.clientY - top);
+            setMouseX(event.clientX - left);
+        }, onMouseLeave: () => {
+            setMouseY(undefined);
+            setMouseX(undefined);
+        } },
         React.createElement(BaseLinearDisplayComponent, { ...props }),
-        React.createElement(YScaleBars, { model: model })));
+        React.createElement(YScaleBars, { model: model }),
+        mouseY ? (React.createElement("div", { style: { position: 'relative' } },
+            React.createElement("svg", { className: classes.cursor, width: width, height: height, style: {
+                    position: 'absolute',
+                    top: scrollTop,
+                } },
+                React.createElement("line", { x1: 0, x2: width, y1: mouseY - scrollTop, y2: mouseY - scrollTop, stroke: "black" }),
+                React.createElement("line", { x1: mouseX, x2: mouseX, y1: 0, y2: height, stroke: "black" })),
+            React.createElement(BaseTooltip, null,
+                React.createElement(SanitizedHTML, { html: Object.entries(sources[Math.floor(mouseY / rowHeight)] || {})
+                        .filter(([key]) => key !== 'color' && key !== 'id')
+                        .map(([key, value]) => `${key}:${value}`)
+                        .join('\n') })))) : null));
 });
 export default LinearMafDisplay;
 //# sourceMappingURL=ReactComponent.js.map

package/dist/LinearMafDisplay/components/ReactComponent.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ReactComponent.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/ReactComponent.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAE/C,OAAO,WAAW,MAAM,8BAA8B,CAAA;AACtD,OAAO,aAAa,MAAM,gCAAgC,CAAA;AAC1D,OAAO,EAAE,iBAAiB,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAA;AAC9D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,UAAU,MAAM,cAAc,CAAA;AAKrC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,MAAM,EAAE;QACN,aAAa,EAAE,MAAM;KACtB;CACF,CAAC,CAAA;AAEF,MAAM,gBAAgB,GAAG,QAAQ,CAAC,UAAU,KAE3C;IACC,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IACvC,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,SAAS,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAChE,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IAExC,MAAM,kBAAkB,GAAG,aAAa,CAAC,SAAS,CAChD,wBAAwB,CAC+B,CAAA;IACzD,MAAM,EAAE,0BAA0B,EAAE,GAAG,kBAAkB,CAAC,OAAO,CAAA;IAEjE,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,EAAU,CAAA;IAC9C,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,EAAU,CAAA;IAC9C,MAAM,EAAE,KAAK,EAAE,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAEnE,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,EACR,WAAW,EAAE,KAAK,CAAC,EAAE;YACnB,MAAM,IAAI,GAAG,GAAG,CAAC,OAAO,EAAE,qBAAqB,EAAE,CAAA;YACjD,MAAM,GAAG,GAAG,IAAI,EAAE,GAAG,IAAI,CAAC,CAAA;YAC1B,MAAM,IAAI,GAAG,IAAI,EAAE,IAAI,IAAI,CAAC,CAAA;YAC5B,SAAS,CAAC,KAAK,CAAC,OAAO,GAAG,GAAG,CAAC,CAAA;YAC9B,SAAS,CAAC,KAAK,CAAC,OAAO,GAAG,IAAI,CAAC,CAAA;QACjC,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;YACjB,SAAS,CAAC,SAAS,CAAC,CAAA;YACpB,SAAS,CAAC,SAAS,CAAC,CAAA;QACtB,CAAC;QAED,oBAAC,0BAA0B,OAAK,KAAK,GAAI;QACzC,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,MAAM,CAAC,CAAC,CAAC,CACR,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;YAClC,6BACE,SAAS,EAAE,OAAO,CAAC,MAAM,EACzB,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;oBACL,QAAQ,EAAE,UAAU;oBACpB,GAAG,EAAE,SAAS;iBACf;gBAED,8BACE,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,KAAK,EACT,EAAE,EAAE,MAAM,GAAG,SAAS,EACtB,EAAE,EAAE,MAAM,GAAG,SAAS,EACtB,MAAM,EAAC,OAAO,GACd;gBACF,8BAAM,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,EAAC,OAAO,GAAG,CAC9D;YACN,oBAAC,WAAW;gBACV,oBAAC,aAAa,IACZ,IAAI,EAAE,MAAM,CAAC,OAAO,CAClB,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,SAAS,CAAC,CAAC,IAAI,EAAE,CAC9C;yBACE,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,GAAG,KAAK,OAAO,IAAI,GAAG,KAAK,IAAI,CAAC;yBAClD,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG,IAAI,KAAK,EAAE,CAAC;yBACxC,IAAI,CAAC,IAAI,CAAC,GACb,CACU,CACV,CACP,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}

package/dist/LinearMafDisplay/components/SetRowHeight.js

@@ -1,7 +1,7 @@
 import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
 import { Dialog } from '@jbrowse/core/ui';
+import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
+import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()({
     root: {
@@ -13,15 +13,15 @@ const SetRowHeightDialog = observer(function (props) {
     const { classes } = useStyles();
     const [rowHeight, setRowHeight] = useState(`${model.rowHeight}`);
     const [rowProportion, setRowProportion] = useState(`${model.rowProportion}`);
-    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Filter options" },
+    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Set row height" },
         React.createElement(DialogContent, { className: classes.root },
             React.createElement(Typography, null, "Set row height and the proportion of the row height to use for drawing each row"),
-            React.createElement(TextField, { value: rowHeight, onChange: event => {
+            React.createElement(TextField, { value: rowHeight, helperText: "Enter row height", onChange: event => {
                     setRowHeight(event.target.value);
-                }, placeholder: "Enter row height" }),
-            React.createElement(TextField, { value: rowProportion, onChange: event => {
+                } }),
+            React.createElement(TextField, { value: rowProportion, helperText: "Enter row proportion", onChange: event => {
                     setRowProportion(event.target.value);
-                }, placeholder: "Enter row proportion" }),
+                } }),
             React.createElement(DialogActions, null,
                 React.createElement(Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: () => {
                         model.setRowProportion(+rowProportion);

package/dist/LinearMafDisplay/components/SetRowHeight.js.map

@@ -1 +1 @@
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+{"version":3,"file":"SetRowHeight.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/SetRowHeight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,IAAI,EAAE;QACJ,KAAK,EAAE,GAAG;KACX;CACF,CAAC,CAAA;AAEF,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,KAQ7C;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,CAAC,GAAG,KAAK,CAAC,SAAS,EAAE,CAAC,CAAA;IAChE,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,GAAG,KAAK,CAAC,aAAa,EAAE,CAAC,CAAA;IAE5E,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI;YACpC,oBAAC,UAAU,0FAGE;YACb,oBAAC,SAAS,IACR,KAAK,EAAE,SAAS,EAChB,UAAU,EAAC,kBAAkB,EAC7B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,YAAY,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAClC,CAAC,GACD;YACF,oBAAC,SAAS,IACR,KAAK,EAAE,aAAa,EACpB,UAAU,EAAC,sBAAsB,EACjC,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,gBAAgB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBACtC,CAAC,GACD;YACF,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,gBAAgB,CAAC,CAAC,aAAa,CAAC,CAAA;wBACtC,KAAK,CAAC,YAAY,CAAC,CAAC,SAAS,CAAC,CAAA;wBAC9B,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE;wBACZ,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AACF,eAAe,kBAAkB,CAAA"}

package/dist/LinearMafDisplay/components/SvgWrapper.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { LinearMafDisplayModel } from '../stateModel';
+declare const SvgWrapper: ({ children, model, exportSVG, }: {
+    model: LinearMafDisplayModel;
+    children: React.ReactNode;
+    exportSVG?: boolean;
+}) => React.JSX.Element;
+export default SvgWrapper;

package/dist/LinearMafDisplay/components/SvgWrapper.js

@@ -0,0 +1,21 @@
+import React from 'react';
+import { getContainingView } from '@jbrowse/core/util';
+import { observer } from 'mobx-react';
+const SvgWrapper = observer(function ({ children, model, exportSVG, }) {
+    if (exportSVG) {
+        return React.createElement(React.Fragment, null, children);
+    }
+    else {
+        const { rowHeight, samples } = model;
+        return (React.createElement("svg", { style: {
+                position: 'absolute',
+                top: 0,
+                left: 0,
+                pointerEvents: 'none',
+                height: samples.length * rowHeight,
+                width: getContainingView(model).width,
+            } }, children));
+    }
+});
+export default SvgWrapper;
+//# sourceMappingURL=SvgWrapper.js.map

package/dist/LinearMafDisplay/components/SvgWrapper.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SvgWrapper.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/SvgWrapper.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AACtD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAKrC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EACpC,QAAQ,EACR,KAAK,EACL,SAAS,GAKV;IACC,IAAI,SAAS,EAAE,CAAC;QACd,OAAO,0CAAG,QAAQ,CAAI,CAAA;IACxB,CAAC;SAAM,CAAC;QACN,MAAM,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;QACpC,OAAO,CACL,6BACE,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,CAAC;gBACN,IAAI,EAAE,CAAC;gBACP,aAAa,EAAE,MAAM;gBACrB,MAAM,EAAE,OAAO,CAAC,MAAM,GAAG,SAAS;gBAClC,KAAK,EAAE,iBAAiB,CAAC,KAAK,CAAC,CAAC,KAAK;aACtC,IAEA,QAAQ,CACL,CACP,CAAA;IACH,CAAC;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/LinearMafDisplay/components/Tree.d.ts

@@ -0,0 +1,5 @@
+import React from 'react';
+declare const Tree: ({ model }: {
+    model: any;
+}) => React.JSX.Element;
+export default Tree;

package/dist/LinearMafDisplay/components/Tree.js

@@ -0,0 +1,22 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+const Tree = observer(function ({ model }) {
+    const { hierarchy, showBranchLen } = model;
+    return (React.createElement(React.Fragment, null, hierarchy
+        ? [...hierarchy.links()].map(link => {
+            const { source, target } = link;
+            const sy = source.x;
+            const ty = target.x;
+            const tx = showBranchLen ? target.len : target.y;
+            const sx = showBranchLen ? source.len : source.y;
+            // 1d line intersection to check if line crosses block at all, this is
+            // an optimization that allows us to skip drawing most tree links
+            // outside the block
+            return (React.createElement(React.Fragment, { key: [sy, ty, tx, sx].join('-') },
+                React.createElement("line", { stroke: "black", x1: sx, y1: sy, x2: sx, y2: ty }),
+                React.createElement("line", { stroke: "black", x1: sx, y1: ty, x2: tx, y2: ty })));
+        })
+        : null));
+});
+export default Tree;
+//# sourceMappingURL=Tree.js.map

package/dist/LinearMafDisplay/components/Tree.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"Tree.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/Tree.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,MAAM,IAAI,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAAkB;IACvD,MAAM,EAAE,SAAS,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAE1C,OAAO,CACL,0CACG,SAAS;QACR,CAAC,CAAC,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;YAChC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;YAC/B,MAAM,EAAE,GAAG,MAAM,CAAC,CAAE,CAAA;YACpB,MAAM,EAAE,GAAG,MAAM,CAAC,CAAE,CAAA;YACpB,MAAM,EAAE,GAAG,aAAa,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAA;YAChD,MAAM,EAAE,GAAG,aAAa,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAA;YAEhD,sEAAsE;YACtE,iEAAiE;YACjE,oBAAoB;YACpB,OAAO,CACL,oBAAC,KAAK,CAAC,QAAQ,IAAC,GAAG,EAAE,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC;gBAC7C,8BAAM,MAAM,EAAC,OAAO,EAAC,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,GAAI;gBACvD,8BAAM,MAAM,EAAC,OAAO,EAAC,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,GAAI,CACxC,CAClB,CAAA;QACH,CAAC,CAAC;QACJ,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,IAAI,CAAA"}

package/dist/LinearMafDisplay/components/YScaleBars.d.ts

@@ -1,6 +1,5 @@
 import React from 'react';
 import { LinearMafDisplayModel } from '../stateModel';
-export declare function max(arr: number[], init?: number): number;
 export declare const YScaleBars: (props: {
     model: LinearMafDisplayModel;
     orientation?: string;

package/dist/LinearMafDisplay/components/YScaleBars.js

@@ -1,40 +1,19 @@
 import React from 'react';
-import { measureText, getContainingView } from '@jbrowse/core/util';
+import { measureText } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import ColorLegend from './ColorLegend';
-const Wrapper = observer(function ({ children, model, exportSVG, }) {
-    if (exportSVG) {
-        return React.createElement(React.Fragment, null, children);
-    }
-    else {
-        const { rowHeight, samples } = model;
-        return (React.createElement("svg", { style: {
-                position: 'absolute',
-                top: 0,
-                left: 0,
-                pointerEvents: 'none',
-                height: samples.length * rowHeight,
-                width: getContainingView(model).width,
-            } }, children));
-    }
-});
-export function max(arr, init = Number.NEGATIVE_INFINITY) {
-    let max = init;
-    for (const entry of arr) {
-        max = Math.max(entry, max);
-    }
-    return max;
-}
+import SvgWrapper from './SvgWrapper';
+import { max } from './util';
 export const YScaleBars = observer(function (props) {
     const { model } = props;
     const { rowHeight, samples } = model;
-    const svgFontSize = Math.min(Math.max(rowHeight, 10), 14);
-    const canDisplayLabel = rowHeight >= 10;
+    const svgFontSize = Math.min(Math.max(rowHeight, 8), 14);
+    const canDisplayLabel = rowHeight >= 8;
     const minWidth = 20;
     const labelWidth = max(samples
         .map(s => measureText(s.label, svgFontSize))
         .map(width => (canDisplayLabel ? width : minWidth)));
-    return (React.createElement(Wrapper, { ...props },
+    return (React.createElement(SvgWrapper, { ...props },
         React.createElement(ColorLegend, { model: model, labelWidth: labelWidth, svgFontSize: svgFontSize })));
 });
 export default YScaleBars;

package/dist/LinearMafDisplay/components/YScaleBars.js.map

@@ -1 +1 @@
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+{"version":3,"file":"YScaleBars.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/YScaleBars.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAA;AAChD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,OAAO,WAAW,MAAM,eAAe,CAAA;AACvC,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,EAAE,GAAG,EAAE,MAAM,QAAQ,CAAA;AAE5B,MAAM,CAAC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,KAI5C;IACC,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAA;IACxD,MAAM,eAAe,GAAG,SAAS,IAAI,CAAC,CAAA;IACtC,MAAM,QAAQ,GAAG,EAAE,CAAA;IAEnB,MAAM,UAAU,GAAG,GAAG,CACpB,OAAO;SACJ,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,EAAE,WAAW,CAAC,CAAC;SAC3C,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CACtD,CAAA;IAED,OAAO,CACL,oBAAC,UAAU,OAAK,KAAK;QACnB,oBAAC,WAAW,IACV,KAAK,EAAE,KAAK,EACZ,UAAU,EAAE,UAAU,EACtB,WAAW,EAAE,WAAW,GACxB,CACS,CACd,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/LinearMafDisplay/components/util.d.ts

@@ -0,0 +1 @@
+export declare function max(arr: number[], init?: number): number;

package/dist/LinearMafDisplay/components/util.js

@@ -0,0 +1,8 @@
+export function max(arr, init = Number.NEGATIVE_INFINITY) {
+    let max = init;
+    for (const entry of arr) {
+        max = Math.max(entry, max);
+    }
+    return max;
+}
+//# sourceMappingURL=util.js.map

package/dist/LinearMafDisplay/components/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/util.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,GAAG,CAAC,GAAa,EAAE,IAAI,GAAG,MAAM,CAAC,iBAAiB;IAChE,IAAI,GAAG,GAAG,IAAI,CAAA;IACd,KAAK,MAAM,KAAK,IAAI,GAAG,EAAE,CAAC;QACxB,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;IAC5B,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}

package/dist/LinearMafDisplay/index.js

@@ -1,7 +1,7 @@
 import { DisplayType } from '@jbrowse/core/pluggableElementTypes';
+import ReactComponent from './components/ReactComponent';
 import configSchemaF from './configSchema';
 import stateModelFactory from './stateModel';
-import ReactComponent from './components/ReactComponent';
 export default function LinearMafDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaF(pluginManager);

package/dist/LinearMafDisplay/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearMafDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAA;AACjE,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAC1C,OAAO,iBAAiB,MAAM,cAAc,CAAA;AAC5C,OAAO,cAAc,MAAM,6BAA6B,CAAA;AAExD,MAAM,CAAC,OAAO,UAAU,iBAAiB,CAAC,aAA4B;IACpE,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,aAAa,CAAC,aAAa,CAAC,CAAA;QACjD,MAAM,UAAU,GAAG,iBAAiB,CAAC,YAAY,EAAE,aAAa,CAAC,CAAA;QACjE,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,kBAAkB;YACxB,YAAY;YACZ,UAAU;YACV,cAAc;YACd,QAAQ,EAAE,kBAAkB;YAC5B,SAAS,EAAE,UAAU;YACrB,WAAW,EAAE,aAAa;SAC3B,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearMafDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAA;AAEjE,OAAO,cAAc,MAAM,6BAA6B,CAAA;AACxD,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAC1C,OAAO,iBAAiB,MAAM,cAAc,CAAA;AAE5C,MAAM,CAAC,OAAO,UAAU,iBAAiB,CAAC,aAA4B;IACpE,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,aAAa,CAAC,aAAa,CAAC,CAAA;QACjD,MAAM,UAAU,GAAG,iBAAiB,CAAC,YAAY,EAAE,aAAa,CAAC,CAAA;QACjE,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,kBAAkB;YACxB,YAAY;YACZ,UAAU;YACV,cAAc;YACd,QAAQ,EAAE,kBAAkB;YAC5B,SAAS,EAAE,UAAU;YACrB,WAAW,EAAE,aAAa;SAC3B,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/dist/LinearMafDisplay/renderSvg.js

@@ -1,5 +1,6 @@
 import React from 'react';
 import { getContainingView } from '@jbrowse/core/util';
+// locals
 import YScaleBars from './components/YScaleBars';
 export async function renderSvg(self, opts, superRenderSvg) {
     const { height, id } = self;

package/dist/LinearMafDisplay/renderSvg.js.map

@@ -1 +1 @@
-{"version":3,"file":"renderSvg.js","sourceRoot":"","sources":["../../src/LinearMafDisplay/renderSvg.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AAQtD,OAAO,UAAU,MAAM,yBAAyB,CAAA;AAEhD,MAAM,CAAC,KAAK,UAAU,SAAS,CAC7B,IAA2B,EAC3B,IAA6B,EAC7B,cAA2E;IAE3E,MAAM,EAAE,MAAM,EAAE,EAAE,EAAE,GAAG,IAAI,CAAA;IAC3B,MAAM,EAAE,QAAQ,EAAE,KAAK,EAAE,GAAG,iBAAiB,CAAC,IAAI,CAA0B,CAAA;IAC5E,MAAM,MAAM,GAAG,WAAW,EAAE,EAAE,CAAA;IAC9B,OAAO,CACL;QACE;YACE,kCAAU,EAAE,EAAE,MAAM;gBAClB,8BAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,GAAI,CACzC,CACN;QACP,2BAAG,QAAQ,EAAE,QAAQ,MAAM,GAAG;YAC5B,2BAAG,EAAE,EAAC,QAAQ,IAAE,MAAM,cAAc,CAAC,IAAI,CAAC,CAAK;YAC/C,2BAAG,SAAS,EAAE,aAAa,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,GAAG;gBAClD,oBAAC,UAAU,IAAC,KAAK,EAAE,IAAI,EAAE,WAAW,EAAC,MAAM,EAAC,SAAS,SAAG,CACtD,CACF,CACH,CACJ,CAAA;AACH,CAAC"}
+{"version":3,"file":"renderSvg.js","sourceRoot":"","sources":["../../src/LinearMafDisplay/renderSvg.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AAMtD,SAAS;AACT,OAAO,UAAU,MAAM,yBAAyB,CAAA;AAGhD,MAAM,CAAC,KAAK,UAAU,SAAS,CAC7B,IAA2B,EAC3B,IAA6B,EAC7B,cAA2E;IAE3E,MAAM,EAAE,MAAM,EAAE,EAAE,EAAE,GAAG,IAAI,CAAA;IAC3B,MAAM,EAAE,QAAQ,EAAE,KAAK,EAAE,GAAG,iBAAiB,CAAC,IAAI,CAA0B,CAAA;IAC5E,MAAM,MAAM,GAAG,WAAW,EAAE,EAAE,CAAA;IAC9B,OAAO,CACL;QACE;YACE,kCAAU,EAAE,EAAE,MAAM;gBAClB,8BAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,GAAI,CACzC,CACN;QACP,2BAAG,QAAQ,EAAE,QAAQ,MAAM,GAAG;YAC5B,2BAAG,EAAE,EAAC,QAAQ,IAAE,MAAM,cAAc,CAAC,IAAI,CAAC,CAAK;YAC/C,2BAAG,SAAS,EAAE,aAAa,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,GAAG;gBAClD,oBAAC,UAAU,IAAC,KAAK,EAAE,IAAI,EAAE,WAAW,EAAC,MAAM,EAAC,SAAS,SAAG,CACtD,CACF,CACH,CACJ,CAAA;AACH,CAAC"}

package/dist/LinearMafDisplay/stateModel.d.ts

@@ -1,7 +1,14 @@
-import { Instance } from 'mobx-state-tree';
-import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
+import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
+import { type HierarchyNode } from 'd3-hierarchy';
+import { Instance } from 'mobx-state-tree';
+import { NodeWithIdsAndLength } from './types';
+interface Sample {
+    id: string;
+    label: string;
+    color?: string;
+}
 /**
  * #stateModel LinearMafDisplay
  * extends LinearBasicDisplay
@@ -18,7 +25,9 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
+        region: import("mobx-state-tree" /**
+         * #property
+         */).IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -41,7 +50,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
@@ -49,7 +58,9 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         setStatus(message: string): void;
         setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: import("@jbrowse/plugin-linear-genome-view/dist/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/dist/BaseLinearDisplay/models/serverSideRenderedBlock" /**
+         * #getter
+         */).RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -89,6 +100,8 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     rowProportion: import("mobx-state-tree").IType<number | undefined, number, number>;
     showAllLetters: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     mismatchRendering: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    showBranchLen: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    treeAreaWidth: import("mobx-state-tree").IType<number | undefined, number, number>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -104,7 +117,9 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             error: unknown;
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree" /**
+             * #getter
+             */).ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
@@ -115,7 +130,9 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
-    readonly DisplayBlurb: React.FC<{
+    readonly DisplayBlurb: React.FC /**
+     * #method
+     */<{
         model: {
             id: string;
             type: string;
@@ -180,13 +197,13 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
-    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -213,13 +230,21 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/dist/BaseLinearDisplay").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/dist/BaseLinearDisplay").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
     afterAttach(): void;
 } & {
     /**
      * #volatile
      */
     prefersOffset: boolean;
+    /**
+     * #volatile
+     */
+    volatileSamples: Sample[];
+    /**
+     * #volatile
+     */
+    tree: any;
 } & {
     /**
      * #action
@@ -237,7 +262,33 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
      * #action
      */
     setMismatchRendering(f: boolean): void;
+    /**
+     * #action
+     */
+    setSamples({ samples, tree }: {
+        samples: Sample[];
+        tree: unknown;
+    }): void;
+} & {
+    /**
+     * #getter
+     */
+    readonly rendererTypeName: string;
+    /**
+     * #getter
+     */
+    readonly rendererConfig: AnyConfigurationModel;
 } & {
+    /**
+     * #getter
+     */
+    readonly root: HierarchyNode<any> | undefined;
+} & {
+    /**
+     * #getter
+     * generates a new tree that is clustered with x,y positions
+     */
+    readonly hierarchy: HierarchyNode<NodeWithIdsAndLength> | undefined;
     /**
      * #getter
      */
@@ -249,12 +300,20 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     /**
      * #getter
      */
-    readonly rendererTypeName: string;
+    readonly totalHeight: number;
     /**
      * #getter
      */
-    readonly rendererConfig: AnyConfigurationModel;
+    readonly leaves: HierarchyNode<any>[] | undefined;
+    /**
+     * #getter
+     */
+    readonly rowNames: string[] | undefined;
 } & {
+    /**
+     * #getter
+     */
+    readonly treeWidth: number;
     /**
      * #method
      */
@@ -268,6 +327,8 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         checked: boolean;
         onClick: () => void;
     })[];
+} & {
+    afterCreate(): void;
 } & {
     /**
      * #action
@@ -310,7 +371,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
@@ -362,3 +423,4 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & import("mobx-state-tree")._NotCustomized>;
 export type LinearMafDisplayStateModel = ReturnType<typeof stateModelFactory>;
 export type LinearMafDisplayModel = Instance<LinearMafDisplayStateModel>;
+export {};