npm - jbrowse-plugin-mafviewer - Versions diffs - 1.4.2 → 1.4.5 - Mend

jbrowse-plugin-mafviewer 1.4.2 → 1.4.5

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (100) hide show

package/README.md CHANGED Viewed

@@ -9,7 +9,7 @@ JBrowse 2
 ## Demo
-https://jbrowse.org/code/jb2/main/?config=%2Fdemos%2Fmaf%2Fhg38%2Fdistconfig.json&session=share-2v5qIkvufP&password=uYpiC
+https://jbrowse.org/code/jb2/main/?config=%2Fdemos%2Fmaf%2Fhg38%2Fdistconfig.json&session=share-bJXbDiWcc9&password=87GhV
 ## GUI usage (e.g. in JBrowse Desktop)

package/dist/LinearMafDisplay/components/InsertionSequenceDialog/InsertionSequenceDialog.d.ts ADDED Viewed

@@ -0,0 +1,14 @@
+import React from 'react';
+declare const InsertionSequenceDialog: ({ onClose, model, insertionData, }: {
+    onClose: () => void;
+    model: {
+        showAsUpperCase: boolean;
+    };
+    insertionData: {
+        sequence: string;
+        sampleLabel: string;
+        chr: string;
+        pos: number;
+    };
+}) => React.JSX.Element;
+export default InsertionSequenceDialog;

package/dist/LinearMafDisplay/components/InsertionSequenceDialog/InsertionSequenceDialog.js ADDED Viewed

@@ -0,0 +1,69 @@
+import React, { useState } from 'react';
+import { Dialog } from '@jbrowse/core/ui';
+import { Button, DialogActions, DialogContent, TextField } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()({
+    dialogContent: {
+        width: '60em',
+    },
+    textAreaInput: {
+        fontFamily: 'monospace',
+        whiteSpace: 'pre',
+        overflowX: 'auto',
+    },
+});
+const InsertionSequenceDialog = observer(function ({ onClose, model, insertionData, }) {
+    const { classes } = useStyles();
+    const [copied, setCopied] = useState(false);
+    const { sequence, sampleLabel, chr, pos } = insertionData;
+    const { showAsUpperCase } = model;
+    const displaySequence = showAsUpperCase
+        ? sequence.toUpperCase()
+        : sequence.toLowerCase();
+    return (React.createElement(Dialog, { open: true, onClose: onClose, title: `Insertion Sequence (${sequence.length}bp)`, maxWidth: "lg" },
+        React.createElement(DialogContent, null,
+            React.createElement("div", { style: { marginBottom: 16 } },
+                React.createElement("strong", null, "Sample:"),
+                " ",
+                sampleLabel,
+                React.createElement("br", null),
+                React.createElement("strong", null, "Position:"),
+                " ",
+                chr,
+                ":",
+                pos.toLocaleString('en-US'),
+                React.createElement("br", null),
+                React.createElement("strong", null, "Length:"),
+                " ",
+                sequence.length,
+                "bp"),
+            React.createElement(TextField, { variant: "outlined", multiline: true, minRows: 3, maxRows: 10, className: classes.dialogContent, fullWidth: true, value: displaySequence, slotProps: {
+                    input: {
+                        readOnly: true,
+                        classes: {
+                            input: classes.textAreaInput,
+                        },
+                    },
+                } })),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
+                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+                    ;
+                    (async () => {
+                        try {
+                            await navigator.clipboard.writeText(displaySequence);
+                            setCopied(true);
+                            setTimeout(() => {
+                                setCopied(false);
+                            }, 1000);
+                        }
+                        catch (e) {
+                            console.error(e);
+                        }
+                    })();
+                } }, copied ? 'Copied!' : 'Copy to Clipboard'),
+            React.createElement(Button, { color: "secondary", variant: "contained", onClick: onClose }, "Close"))));
+});
+export default InsertionSequenceDialog;
+//# sourceMappingURL=InsertionSequenceDialog.js.map

package/dist/LinearMafDisplay/components/InsertionSequenceDialog/InsertionSequenceDialog.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"InsertionSequenceDialog.js","sourceRoot":"","sources":["../../../../src/LinearMafDisplay/components/InsertionSequenceDialog/InsertionSequenceDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAC/E,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,aAAa,EAAE;QACb,UAAU,EAAE,WAAW;QACvB,UAAU,EAAE,KAAK;QACjB,SAAS,EAAE,MAAM;KAClB;CACF,CAAC,CAAA;AAEF,MAAM,uBAAuB,GAAG,QAAQ,CAAC,UAAU,EACjD,OAAO,EACP,KAAK,EACL,aAAa,GAYd;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC3C,MAAM,EAAE,QAAQ,EAAE,WAAW,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,aAAa,CAAA;IACzD,MAAM,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IACjC,MAAM,eAAe,GAAG,eAAe;QACrC,CAAC,CAAC,QAAQ,CAAC,WAAW,EAAE;QACxB,CAAC,CAAC,QAAQ,CAAC,WAAW,EAAE,CAAA;IAE1B,OAAO,CACL,oBAAC,MAAM,IACL,IAAI,QACJ,OAAO,EAAE,OAAO,EAChB,KAAK,EAAE,uBAAuB,QAAQ,CAAC,MAAM,KAAK,EAClD,QAAQ,EAAC,IAAI;QAEb,oBAAC,aAAa;YACZ,6BAAK,KAAK,EAAE,EAAE,YAAY,EAAE,EAAE,EAAE;gBAC9B,8CAAwB;;gBAAE,WAAW;gBACrC,+BAAM;gBACN,gDAA0B;;gBAAE,GAAG;;gBAAG,GAAG,CAAC,cAAc,CAAC,OAAO,CAAC;gBAC7D,+BAAM;gBACN,8CAAwB;;gBAAE,QAAQ,CAAC,MAAM;qBACrC;YACN,oBAAC,SAAS,IACR,OAAO,EAAC,UAAU,EAClB,SAAS,QACT,OAAO,EAAE,CAAC,EACV,OAAO,EAAE,EAAE,EACX,SAAS,EAAE,OAAO,CAAC,aAAa,EAChC,SAAS,QACT,KAAK,EAAE,eAAe,EACtB,SAAS,EAAE;oBACT,KAAK,EAAE;wBACL,QAAQ,EAAE,IAAI;wBACd,OAAO,EAAE;4BACP,KAAK,EAAE,OAAO,CAAC,aAAa;yBAC7B;qBACF;iBACF,GACD,CACY;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;oBACZ,mEAAmE;oBACnE,CAAC;oBAAA,CAAC,KAAK,IAAI,EAAE;wBACX,IAAI,CAAC;4BACH,MAAM,SAAS,CAAC,SAAS,CAAC,SAAS,CAAC,eAAe,CAAC,CAAA;4BACpD,SAAS,CAAC,IAAI,CAAC,CAAA;4BACf,UAAU,CAAC,GAAG,EAAE;gCACd,SAAS,CAAC,KAAK,CAAC,CAAA;4BAClB,CAAC,EAAE,IAAI,CAAC,CAAA;wBACV,CAAC;wBAAC,OAAO,CAAC,EAAE,CAAC;4BACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAClB,CAAC;oBACH,CAAC,CAAC,EAAE,CAAA;gBACN,CAAC,IAEA,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,mBAAmB,CAClC;YACT,oBAAC,MAAM,IAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAC,WAAW,EAAC,OAAO,EAAE,OAAO,YAErD,CACK,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,uBAAuB,CAAA"}

package/dist/LinearMafDisplay/components/LinearMafDisplayComponent.js CHANGED Viewed

@@ -1,4 +1,4 @@
-import React, { useEffect, useRef, useState } from 'react';
+import React, { useCallback, useEffect, useRef, useState } from 'react';
 import { Menu } from '@jbrowse/core/ui';
 import { getContainingView, getEnv } from '@jbrowse/core/util';
 import { useTheme } from '@mui/material';
@@ -71,11 +71,11 @@ const LinearMafDisplay = observer(function (props) {
         setIsDragging(false);
     };
     // Function to clear the selection box
-    const clearSelectionBox = () => {
+    const clearSelectionBox = useCallback(() => {
         setShowSelectionBox(false);
         setDragStartX(undefined);
         setDragEndX(undefined);
-    };
+    }, []);
     // Add keydown event handler to clear selection box when Escape key is pressed
     useEffect(() => {
         const handleKeyDown = (event) => {
@@ -109,7 +109,7 @@ const LinearMafDisplay = observer(function (props) {
             setIsDragging(false);
         } },
         React.createElement(BaseLinearDisplayComponent, { ...props }),
-        React.createElement(YScaleBars, { model: model }),
+        model.showSidebar ? React.createElement(YScaleBars, { model: model }) : null,
         mouseY && mouseX && sources && !contextCoord && !showSequenceDialog ? (React.createElement("div", { style: { position: 'relative' } },
             React.createElement(Crosshairs, { width: width, height: height, scrollTop: scrollTop, mouseX: mouseX, mouseY: mouseY }),
             React.createElement(MAFTooltip, { model: model, mouseX: mouseX, mouseY: mouseY, origMouseX: dragStartX, rowHeight: rowHeight, sources: sources }))) : null,

package/dist/LinearMafDisplay/components/LinearMafDisplayComponent.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/LinearMafDisplay/components/Sidebar/ColorLegend.js CHANGED Viewed

@@ -3,10 +3,10 @@ import { observer } from 'mobx-react';
 import RectBg from './RectBg';
 import Tree from './Tree';
 const ColorLegend = observer(function ({ model, }) {
-    const { labelWidth, canDisplayLabel, totalHeight, treeWidth, samples = [], rowHeight, svgFontSize, } = model;
+    const { labelWidth, canDisplayLabel, totalHeight, treeWidth, sidebarWidth, samples = [], rowHeight, svgFontSize, } = model;
     const boxHeight = Math.min(20, rowHeight);
     return (React.createElement(React.Fragment, null,
-        React.createElement(RectBg, { y: 0, x: 0, width: labelWidth + 5 + treeWidth, height: totalHeight }),
+        React.createElement(RectBg, { y: 0, x: 0, width: sidebarWidth, 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 }))),

package/dist/LinearMafDisplay/components/Sidebar/ColorLegend.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"ColorLegend.js","sourceRoot":"","sources":["../../../../src/LinearMafDisplay/components/Sidebar/ColorLegend.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,MAAM,MAAM,UAAU,CAAA;AAC7B,OAAO,IAAI,MAAM,QAAQ,CAAA;AAIzB,MAAM,WAAW,GAAG,QAAQ,CAAC,UAAU,EACrC,KAAK,GAGN;IACC,MAAM,EACJ,UAAU,EACV,eAAe,EACf,WAAW,EACX,SAAS,EACT,OAAO,GAAG,EAAE,EACZ,SAAS,EACT,WAAW,GACZ,GAAG,KAAK,CAAA;IACT,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,gBAAgB,EAAC,QAAQ,EACzB,QAAQ,EAAE,WAAW,EACrB,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,GAAG,GAAG,SAAS,GAAG,SAAS,GAAG,CAAC,IAEjC,MAAM,CAAC,KAAK,CACR,CACR,CAAC;gBACJ,CAAC,CAAC,IAAI,CACN,CACH,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,WAAW,CAAA"}
1	+ {"version":3,"file":"ColorLegend.js","sourceRoot":"","sources":["../../../../src/LinearMafDisplay/components/Sidebar/ColorLegend.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,MAAM,MAAM,UAAU,CAAA;AAC7B,OAAO,IAAI,MAAM,QAAQ,CAAA;AAIzB,MAAM,WAAW,GAAG,QAAQ,CAAC,UAAU,EACrC,KAAK,GAGN;IACC,MAAM,EACJ,UAAU,EACV,eAAe,EACf,WAAW,EACX,SAAS,EACT,YAAY,EACZ,OAAO,GAAG,EAAE,EACZ,SAAS,EACT,WAAW,GACZ,GAAG,KAAK,CAAA;IACT,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,SAAS,CAAC,CAAA;IAEzC,OAAO,CACL;QACE,oBAAC,MAAM,IAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,YAAY,EAAE,MAAM,EAAE,WAAW,GAAI;QAChE,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,gBAAgB,EAAC,QAAQ,EACzB,QAAQ,EAAE,WAAW,EACrB,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,GAAG,GAAG,SAAS,GAAG,SAAS,GAAG,CAAC,IAEjC,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/Sidebar/RectBg.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 import React from 'react';
-declare const RectBg: (props: {
+declare const RectBg: ({ x, y, width, height, color, }: {
     x: number;
     y: number;
     width: number;

package/dist/LinearMafDisplay/components/Sidebar/RectBg.js CHANGED Viewed

@@ -1,7 +1,6 @@
 import React from 'react';
-const RectBg = (props) => {
-    const { color = 'rgb(255,255,255,0.5)' } = props;
-    return React.createElement("rect", { ...props, fill: color });
+const RectBg = ({ x, y, width, height, color = 'rgb(255,255,255,0.5)', }) => {
+    return React.createElement("rect", { x: x, y: y, width: width, height: height, fill: color });
 };
 export default RectBg;
 //# sourceMappingURL=RectBg.js.map

package/dist/LinearMafDisplay/components/Sidebar/RectBg.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"RectBg.js","sourceRoot":"","sources":["../../../../src/LinearMafDisplay/components/Sidebar/RectBg.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,MAAM,MAAM,GAAG,CAAC,EACd,CAAC,EACD,CAAC,EACD,KAAK,EACL,MAAM,EACN,KAAK,GAAG,sBAAsB,GAO/B,EAAE,EAAE;IACH,OAAO,8BAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,GAAI,CAAA;AACxE,CAAC,CAAA;AAED,eAAe,MAAM,CAAA"}

package/dist/LinearMafDisplay/components/Sidebar/SvgWrapper.js CHANGED Viewed

@@ -1,22 +1,92 @@
-import React from 'react';
+import React, { useEffect, useRef } from 'react';
+import { ResizeHandle } from '@jbrowse/core/ui';
 import { getContainingView } from '@jbrowse/core/util';
+import { autorun } from 'mobx';
 import { observer } from 'mobx-react';
+import { isAlive } from 'mobx-state-tree';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()({
+    resizeHandle: {
+        position: 'absolute',
+        top: 0,
+        height: '100%',
+        width: 4,
+        zIndex: 1001,
+        background: 'transparent',
+        cursor: 'col-resize',
+        '&:hover': {
+            background: 'rgba(0,0,0,0.2)',
+        },
+    },
+});
 const SvgWrapper = observer(function ({ children, model, exportSVG, }) {
+    const { classes } = useStyles();
+    const mouseoverRef = useRef(null);
+    useEffect(() => {
+        const ctx = mouseoverRef.current?.getContext('2d');
+        return ctx
+            ? autorun(() => {
+                if (isAlive(model)) {
+                    const { totalHeight, leafMap, rowHeight, highlightedRowNames, hoveredTreeNode, } = model;
+                    const { width: viewWidth } = getContainingView(model);
+                    ctx.resetTransform();
+                    ctx.clearRect(0, 0, viewWidth, totalHeight);
+                    if (highlightedRowNames) {
+                        ctx.fillStyle = 'rgba(255,165,0,0.2)';
+                        const halfRowHeight = rowHeight / 2;
+                        for (const name of highlightedRowNames) {
+                            const leaf = leafMap.get(name);
+                            if (leaf) {
+                                ctx.fillRect(0, leaf.x - halfRowHeight, viewWidth, rowHeight);
+                            }
+                        }
+                        // Draw orange dot at hovered tree node
+                        if (hoveredTreeNode) {
+                            ctx.fillStyle = 'rgba(255,165,0,0.8)';
+                            ctx.beginPath();
+                            ctx.arc(hoveredTreeNode.y, hoveredTreeNode.x, 4, 0, 2 * Math.PI);
+                            ctx.fill();
+                            ctx.strokeStyle = 'rgba(255,140,0,1)';
+                            ctx.lineWidth = 1;
+                            ctx.stroke();
+                        }
+                    }
+                }
+            })
+            : undefined;
+    }, [model]);
     if (exportSVG) {
         return React.createElement(React.Fragment, null, children);
     }
     else {
-        const { totalHeight } = model;
+        const { totalHeight, treeWidth, hierarchy } = model;
         const { width } = getContainingView(model);
-        return (React.createElement("svg", { style: {
-                position: 'absolute',
-                userSelect: 'none',
-                top: 0,
-                left: 0,
-                pointerEvents: 'none',
-                height: totalHeight,
-                width,
-            } }, children));
+        return (React.createElement(React.Fragment, null,
+            React.createElement("svg", { style: {
+                    position: 'absolute',
+                    userSelect: 'none',
+                    top: 0,
+                    left: 0,
+                    pointerEvents: 'none',
+                    height: totalHeight,
+                    width,
+                } }, children),
+            React.createElement("canvas", { ref: mouseoverRef, width: width, height: totalHeight, style: {
+                    position: 'absolute',
+                    top: 0,
+                    left: 0,
+                    width,
+                    height: totalHeight,
+                    zIndex: 1000,
+                    pointerEvents: 'none',
+                } }),
+            hierarchy ? (React.createElement("div", { onMouseDown: e => {
+                    e.stopPropagation();
+                } },
+                React.createElement(ResizeHandle, { onDrag: distance => {
+                        model.setTreeAreaWidth(Math.max(20, model.treeAreaWidth + distance));
+                        return undefined;
+                    }, className: classes.resizeHandle, style: { left: treeWidth }, vertical: true }))) : null));
     }
 });
 export default SvgWrapper;

package/dist/LinearMafDisplay/components/Sidebar/SvgWrapper.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"SvgWrapper.js","sourceRoot":"","sources":["../../../../src/LinearMafDisplay/components/Sidebar/SvgWrapper.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,MAAM,OAAO,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AACtD,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAK1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,YAAY,EAAE;QACZ,QAAQ,EAAE,UAAU;QACpB,GAAG,EAAE,CAAC;QACN,MAAM,EAAE,MAAM;QACd,KAAK,EAAE,CAAC;QACR,MAAM,EAAE,IAAI;QACZ,UAAU,EAAE,aAAa;QACzB,MAAM,EAAE,YAAY;QACpB,SAAS,EAAE;YACT,UAAU,EAAE,iBAAiB;SAC9B;KACF;CACF,CAAC,CAAA;AAEF,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EACpC,QAAQ,EACR,KAAK,EACL,SAAS,GAKV;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,YAAY,GAAG,MAAM,CAAoB,IAAI,CAAC,CAAA;IAEpD,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,GAAG,GAAG,YAAY,CAAC,OAAO,EAAE,UAAU,CAAC,IAAI,CAAC,CAAA;QAClD,OAAO,GAAG;YACR,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE;gBACX,IAAI,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC;oBACnB,MAAM,EACJ,WAAW,EACX,OAAO,EACP,SAAS,EACT,mBAAmB,EACnB,eAAe,GAChB,GAAG,KAAK,CAAA;oBACT,MAAM,EAAE,KAAK,EAAE,SAAS,EAAE,GAAG,iBAAiB,CAC5C,KAAK,CACmB,CAAA;oBAE1B,GAAG,CAAC,cAAc,EAAE,CAAA;oBACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,SAAS,EAAE,WAAW,CAAC,CAAA;oBAE3C,IAAI,mBAAmB,EAAE,CAAC;wBACxB,GAAG,CAAC,SAAS,GAAG,qBAAqB,CAAA;wBACrC,MAAM,aAAa,GAAG,SAAS,GAAG,CAAC,CAAA;wBACnC,KAAK,MAAM,IAAI,IAAI,mBAAmB,EAAE,CAAC;4BACvC,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;4BAC9B,IAAI,IAAI,EAAE,CAAC;gCACT,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAE,GAAG,aAAa,EAAE,SAAS,EAAE,SAAS,CAAC,CAAA;4BAChE,CAAC;wBACH,CAAC;wBAED,uCAAuC;wBACvC,IAAI,eAAe,EAAE,CAAC;4BACpB,GAAG,CAAC,SAAS,GAAG,qBAAqB,CAAA;4BACrC,GAAG,CAAC,SAAS,EAAE,CAAA;4BACf,GAAG,CAAC,GAAG,CAAC,eAAe,CAAC,CAAC,EAAE,eAAe,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,EAAE,CAAC,CAAA;4BAChE,GAAG,CAAC,IAAI,EAAE,CAAA;4BACV,GAAG,CAAC,WAAW,GAAG,mBAAmB,CAAA;4BACrC,GAAG,CAAC,SAAS,GAAG,CAAC,CAAA;4BACjB,GAAG,CAAC,MAAM,EAAE,CAAA;wBACd,CAAC;oBACH,CAAC;gBACH,CAAC;YACH,CAAC,CAAC;YACJ,CAAC,CAAC,SAAS,CAAA;IACf,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAA;IAEX,IAAI,SAAS,EAAE,CAAC;QACd,OAAO,0CAAG,QAAQ,CAAI,CAAA;IACxB,CAAC;SAAM,CAAC;QACN,MAAM,EAAE,WAAW,EAAE,SAAS,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;QACnD,MAAM,EAAE,KAAK,EAAE,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;QACnE,OAAO,CACL;YACE,6BACE,KAAK,EAAE;oBACL,QAAQ,EAAE,UAAU;oBACpB,UAAU,EAAE,MAAM;oBAClB,GAAG,EAAE,CAAC;oBACN,IAAI,EAAE,CAAC;oBACP,aAAa,EAAE,MAAM;oBACrB,MAAM,EAAE,WAAW;oBACnB,KAAK;iBACN,IAEA,QAAQ,CACL;YACN,gCACE,GAAG,EAAE,YAAY,EACjB,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,WAAW,EACnB,KAAK,EAAE;oBACL,QAAQ,EAAE,UAAU;oBACpB,GAAG,EAAE,CAAC;oBACN,IAAI,EAAE,CAAC;oBACP,KAAK;oBACL,MAAM,EAAE,WAAW;oBACnB,MAAM,EAAE,IAAI;oBACZ,aAAa,EAAE,MAAM;iBACtB,GACD;YACD,SAAS,CAAC,CAAC,CAAC,CACX,6BACE,WAAW,EAAE,CAAC,CAAC,EAAE;oBACf,CAAC,CAAC,eAAe,EAAE,CAAA;gBACrB,CAAC;gBAED,oBAAC,YAAY,IACX,MAAM,EAAE,QAAQ,CAAC,EAAE;wBACjB,KAAK,CAAC,gBAAgB,CACpB,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,KAAK,CAAC,aAAa,GAAG,QAAQ,CAAC,CAC7C,CAAA;wBACD,OAAO,SAAS,CAAA;oBAClB,CAAC,EACD,SAAS,EAAE,OAAO,CAAC,YAAY,EAC/B,KAAK,EAAE,EAAE,IAAI,EAAE,SAAS,EAAE,EAC1B,QAAQ,SACR,CACE,CACP,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;IACH,CAAC;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/LinearMafDisplay/components/Sidebar/Tree.js CHANGED Viewed

@@ -1,11 +1,33 @@
-import React from 'react';
+import React, { useCallback, useMemo } from 'react';
 import { observer } from 'mobx-react';
+const hitboxStyle = {
+    pointerEvents: 'all',
+    cursor: 'pointer',
+    strokeWidth: 8,
+    stroke: 'transparent',
+};
 const Tree = observer(function ({ model }) {
     const {
-    // this is needed for redrawing after zoom change, similar to react-msaview
-    // renderTreeCanvas
+    // rowHeight is needed for redrawing after zoom change
     // eslint-disable-next-line  @typescript-eslint/no-unused-vars
-    rowHeight: _rowHeight, hierarchy, showBranchLen, } = model;
+    rowHeight: _rowHeight, treeAreaWidth, hierarchy, showBranchLen, nodeDescendantNames, } = model;
+    const clearHighlight = useCallback(() => {
+        model.setHighlightedRowNames(undefined);
+    }, [model]);
+    const nodeHandlers = useMemo(() => {
+        const handlers = new Map();
+        if (hierarchy) {
+            for (const node of hierarchy.descendants()) {
+                handlers.set(node, () => {
+                    model.setHighlightedRowNames(nodeDescendantNames.get(node), {
+                        x: node.x,
+                        y: node.y,
+                    });
+                });
+            }
+        }
+        return handlers;
+    }, [model, hierarchy, nodeDescendantNames, treeAreaWidth]);
     return (React.createElement(React.Fragment, null, hierarchy
         ? [...hierarchy.links()].map(link => {
             const { source, target } = link;
@@ -15,12 +37,11 @@ const Tree = observer(function ({ model }) {
             const tx = showBranchLen ? target.len : target.y;
             // @ts-expect-error
             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('-') },
+            return (React.createElement(React.Fragment, { key: `${treeAreaWidth}-${sy}-${ty}-${tx}-${sx}` },
                 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 })));
+                React.createElement("line", { stroke: "black", x1: sx, y1: ty, x2: tx, y2: ty }),
+                React.createElement("line", { x1: sx, y1: sy, x2: sx, y2: ty, style: hitboxStyle, onMouseEnter: nodeHandlers.get(source), onMouseLeave: clearHighlight }),
+                React.createElement("line", { x1: sx, y1: ty, x2: tx, y2: ty, style: hitboxStyle, onMouseEnter: nodeHandlers.get(target), onMouseLeave: clearHighlight })));
         })
         : null));
 });

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	@@ -1 +1 @@
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package/dist/LinearMafDisplay/components/Sidebar/YScaleBars.d.ts CHANGED Viewed

@@ -2,7 +2,6 @@ import React from 'react';
 import type { LinearMafDisplayModel } from '../../stateModel';
 export declare const YScaleBars: (props: {
     model: LinearMafDisplayModel;
-    orientation?: string;
     exportSVG?: boolean;
 }) => React.JSX.Element;
 export default YScaleBars;

package/dist/LinearMafDisplay/components/Sidebar/YScaleBars.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"YScaleBars.js","sourceRoot":"","sources":["../../../../src/LinearMafDisplay/components/Sidebar/YScaleBars.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,WAAW,MAAM,eAAe,CAAA;AACvC,OAAO,UAAU,MAAM,cAAc,CAAA;AAIrC,MAAM,CAAC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,~~KAI5C~~;IACC,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,OAAO,CACL,oBAAC,UAAU,OAAK,KAAK;QACnB,oBAAC,WAAW,IAAC,KAAK,EAAE,KAAK,GAAI,CAClB,CACd,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}
1	+ {"version":3,"file":"YScaleBars.js","sourceRoot":"","sources":["../../../../src/LinearMafDisplay/components/Sidebar/YScaleBars.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,WAAW,MAAM,eAAe,CAAA;AACvC,OAAO,UAAU,MAAM,cAAc,CAAA;AAIrC,MAAM,CAAC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,KAG5C;IACC,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,OAAO,CACL,oBAAC,UAAU,OAAK,KAAK;QACnB,oBAAC,WAAW,IAAC,KAAK,EAAE,KAAK,GAAI,CAClB,CACd,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/LinearMafDisplay/renderSvg.js CHANGED Viewed

@@ -12,6 +12,6 @@ export async function renderSvg(self, opts, superRenderSvg) {
         React.createElement("g", { clipPath: `url(#${clipid})` },
             React.createElement("g", { id: "snpcov" }, await superRenderSvg(opts)),
             React.createElement("g", { transform: `translate(${Math.max(-offsetPx, 0)})` },
-                React.createElement(YScaleBars, { model: self, orientation: "left", exportSVG: true })))));
+                React.createElement(YScaleBars, { model: self, exportSVG: true })))));
 }
 //# sourceMappingURL=renderSvg.js.map

package/dist/LinearMafDisplay/renderSvg.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"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;AAEtD,OAAO,UAAU,MAAM,iCAAiC,CAAA;AAQxD,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,SAAS,SAAG,CACnC,CACF,CACH,CACJ,CAAA;AACH,CAAC"}

package/dist/LinearMafDisplay/stateModel.d.ts CHANGED Viewed

@@ -36,7 +36,9 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
             model: {
-                error?: unknown;
+                error? /**
+                 * #property
+                 */: unknown;
                 reload: () => void;
                 message: React.ReactNode;
                 filled?: boolean;
@@ -94,6 +96,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     showBranchLen: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     treeAreaWidth: import("mobx-state-tree").IType<number | undefined, number, number>;
     showAsUpperCase: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    showSidebar: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -187,6 +190,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
+    mouseoverExtraInformation: string | undefined;
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
@@ -201,9 +205,22 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]>;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
+    searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
@@ -212,6 +229,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
+    setMouseoverExtraInformation(extra?: string): void;
 } & {
     reload(): Promise<void>;
 } & {
@@ -238,6 +256,17 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
      * #volatile
      */
     volatileTree: any;
+    /**
+     * #volatile
+     */
+    highlightedRowNames: string[] | undefined;
+    /**
+     * #volatile
+     */
+    hoveredTreeNode: {
+        x: number;
+        y: number;
+    } | undefined;
 } & {
     /**
      * #action
@@ -270,6 +299,30 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
      * #action
      */
     setShowAsUpperCase(arg: boolean): void;
+    /**
+     * #action
+     */
+    setTreeAreaWidth(width: number): void;
+    /**
+     * #action
+     */
+    setShowSidebar(arg: boolean): void;
+    /**
+     * #action
+     */
+    setHighlightedRowNames(names?: string[], nodePosition?: {
+        x: number;
+        y: number;
+    }): void;
+    /**
+     * #action
+     */
+    showInsertionSequenceDialog(insertionData: {
+        sequence: string;
+        sampleLabel: string;
+        chr: string;
+        pos: number;
+    }): void;
 } & {
     /**
      * #getter
@@ -302,6 +355,15 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
      * #getter
      */
     readonly leaves: HierarchyNode<any>[] | undefined;
+    /**
+     * #getter
+     */
+    readonly leafMap: Map<any, HierarchyNode<any>>;
+    /**
+     * #getter
+     * Precomputed map from hierarchy node to its descendant leaf names
+     */
+    readonly nodeDescendantNames: Map<unknown, string[]>;
     /**
      * #getter
      */
@@ -347,6 +409,10 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
      * #getter
      */
     readonly labelWidth: number;
+    /**
+     * #getter
+     */
+    readonly sidebarWidth: number;
 } & {
     afterCreate(): void;
 } & {