jbrowse-plugin-mafviewer 1.2.3 → 1.3.0

package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.d.ts

@@ -20,7 +20,7 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
     getSamples(_query: Region): Promise<{
         samples: {
             id: string;
-            label: string;
+            label?: string;
             color?: string;
         }[];
         tree: Record<string, any> | undefined;

package/dist/BigMafAdapter/BigMafAdapter.d.ts

@@ -17,7 +17,7 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
     getSamples(_query: Region): Promise<{
         samples: {
             id: string;
-            label: string;
+            label?: string;
             color?: string;
         }[];
         tree: Record<string, any> | undefined;

package/dist/BigMafAdapter/BigMafAdapter.js

@@ -12,12 +12,11 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
         if (!this.getSubAdapter) {
             throw new Error('no getSubAdapter available');
         }
-        const adapter = await this.getSubAdapter({
-            ...getSnapshot(this.config),
-            type: 'BigBedAdapter',
-        });
         return {
-            adapter: adapter.dataAdapter,
+            adapter: (await this.getSubAdapter({
+                ...getSnapshot(this.config),
+                type: 'BigBedAdapter',
+            })).dataAdapter,
         };
     }
     async setupPre() {
@@ -41,53 +40,55 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
         const { statusCallback = () => { } } = opts || {};
         return ObservableCreate(async (observer) => {
             const { adapter } = await this.setup();
-            const features = await updateStatus('Downloading alignment', statusCallback, () => firstValueFrom(adapter.getFeatures(query).pipe(toArray())));
-            for (const feature of features) {
-                const maf = feature.get('mafBlock');
-                const blocks = maf.split(';');
-                let aln;
-                const alns = [];
-                const alignments = {};
-                const blocks2 = [];
-                for (const block of blocks) {
-                    if (block.startsWith('s')) {
-                        if (aln) {
-                            alns.push(block.split(/ +/)[6]);
-                            blocks2.push(block);
-                        }
-                        else {
-                            aln = block.split(/ +/)[6];
-                            alns.push(aln);
-                            blocks2.push(block);
+            const features = await updateStatus('Downloading alignments', statusCallback, () => firstValueFrom(adapter.getFeatures(query).pipe(toArray())));
+            await updateStatus('Processing alignments', statusCallback, () => {
+                for (const feature of features) {
+                    const maf = feature.get('mafBlock');
+                    const blocks = maf.split(';');
+                    let aln;
+                    const alns = [];
+                    const alignments = {};
+                    const blocks2 = [];
+                    for (const block of blocks) {
+                        if (block.startsWith('s')) {
+                            if (aln) {
+                                alns.push(block.split(/ +/)[6]);
+                                blocks2.push(block);
+                            }
+                            else {
+                                aln = block.split(/ +/)[6];
+                                alns.push(aln);
+                                blocks2.push(block);
+                            }
                         }
                     }
+                    for (let i = 0; i < blocks2.length; i++) {
+                        const elt = blocks2[i];
+                        const ad = elt.split(/ +/);
+                        const y = ad[1].split('.');
+                        const org = y[0];
+                        const chr = y[1];
+                        alignments[org] = {
+                            chr: chr,
+                            start: +ad[1],
+                            srcSize: +ad[2],
+                            strand: ad[3] === '+' ? 1 : -1,
+                            unknown: +ad[4],
+                            data: alns[i],
+                        };
+                    }
+                    observer.next(new SimpleFeature({
+                        id: feature.id(),
+                        data: {
+                            start: feature.get('start'),
+                            end: feature.get('end'),
+                            refName: feature.get('refName'),
+                            seq: alns[0],
+                            alignments: alignments,
+                        },
+                    }));
                 }
-                for (let i = 0; i < blocks2.length; i++) {
-                    const elt = blocks2[i];
-                    const ad = elt.split(/ +/);
-                    const y = ad[1].split('.');
-                    const org = y[0];
-                    const chr = y[1];
-                    alignments[org] = {
-                        chr: chr,
-                        start: +ad[1],
-                        srcSize: +ad[2],
-                        strand: ad[3] === '+' ? 1 : -1,
-                        unknown: +ad[4],
-                        data: alns[i],
-                    };
-                }
-                observer.next(new SimpleFeature({
-                    id: feature.id(),
-                    data: {
-                        start: feature.get('start'),
-                        end: feature.get('end'),
-                        refName: feature.get('refName'),
-                        seq: alns[0],
-                        alignments: alignments,
-                    },
-                }));
-            }
+            });
             observer.complete();
         });
     }

package/dist/BigMafAdapter/BigMafAdapter.js.map

@@ -1 +1 @@
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package/dist/LinearMafDisplay/components/Crosshairs.d.ts

@@ -0,0 +1,10 @@
+import React from 'react';
+interface CrosshairsProps {
+    width: number;
+    height: number;
+    scrollTop: number;
+    mouseX?: number;
+    mouseY: number;
+}
+declare const Crosshairs: ({ width, height, scrollTop, mouseX, mouseY, }: CrosshairsProps) => React.JSX.Element;
+export default Crosshairs;

package/dist/LinearMafDisplay/components/Crosshairs.js

@@ -0,0 +1,18 @@
+import React from 'react';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()({
+    cursor: {
+        pointerEvents: 'none',
+    },
+});
+const Crosshairs = ({ width, height, scrollTop, mouseX, mouseY, }) => {
+    const { classes } = useStyles();
+    return (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" })));
+};
+export default Crosshairs;
+//# sourceMappingURL=Crosshairs.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"Crosshairs.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/Crosshairs.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,MAAM,EAAE;QACN,aAAa,EAAE,MAAM;KACtB;CACF,CAAC,CAAA;AAUF,MAAM,UAAU,GAAG,CAAC,EAClB,KAAK,EACL,MAAM,EACN,SAAS,EACT,MAAM,EACN,MAAM,GACU,EAAE,EAAE;IACpB,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAE/B,OAAO,CACL,6BACE,SAAS,EAAE,OAAO,CAAC,MAAM,EACzB,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,GAAG,EAAE,SAAS;SACf;QAED,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;QACF,8BAAM,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,EAAC,OAAO,GAAG,CAC9D,CACP,CAAA;AACH,CAAC,CAAA;AAED,eAAe,UAAU,CAAA"}

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

@@ -0,0 +1,11 @@
+import React from 'react';
+import type { LinearMafDisplayModel } from '../../stateModel';
+declare const GetSequenceDialog: ({ onClose, model, selectionCoords, }: {
+    onClose: () => void;
+    model: LinearMafDisplayModel;
+    selectionCoords?: {
+        dragStartX: number;
+        dragEndX: number;
+    };
+}) => React.JSX.Element;
+export default GetSequenceDialog;

package/dist/LinearMafDisplay/components/GetSequenceDialog/GetSequenceDialog.js

@@ -0,0 +1,97 @@
+import React, { useState } from 'react';
+import { Dialog, ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
+import { getSession } from '@jbrowse/core/util';
+import { Button, DialogActions, DialogContent, TextField, ToggleButton, ToggleButtonGroup, } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import { useSequences } from '../../../util/useSequences';
+const useStyles = makeStyles()({
+    dialogContent: {
+        width: '80em',
+    },
+    textAreaInput: {
+        fontFamily: 'monospace',
+        whiteSpace: 'pre',
+        overflowX: 'auto',
+    },
+    ml: {
+        marginLeft: 10,
+    },
+});
+const GetSequenceDialog = observer(function ({ onClose, model, selectionCoords, }) {
+    const [showAllLetters, setShowAllLetters] = useState(true);
+    const { classes } = useStyles();
+    const { sequence, loading, error } = useSequences({
+        model,
+        selectionCoords,
+        showAllLetters,
+    });
+    const sequenceTooLarge = sequence ? sequence.length > 1_000_000 : false;
+    return (React.createElement(Dialog, { open: true, onClose: onClose, title: "Subsequence Data", maxWidth: "xl" },
+        React.createElement(DialogContent, null,
+            React.createElement("div", { style: {
+                    display: 'flex',
+                    alignItems: 'center',
+                    marginBottom: '16px',
+                } },
+                React.createElement(ToggleButtonGroup, { value: showAllLetters, exclusive: true, size: "small", onChange: (_event, newDisplayMode) => {
+                        if (newDisplayMode !== null) {
+                            setShowAllLetters(newDisplayMode);
+                        }
+                    } },
+                    React.createElement(ToggleButton, { value: true }, "Show All Letters"),
+                    React.createElement(ToggleButton, { value: false }, "Show Only Differences")),
+                React.createElement("div", { style: { flexGrow: 1 } }),
+                React.createElement(Button, { variant: "contained", color: "primary", disabled: loading || !sequence, onClick: () => {
+                        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+                        ;
+                        (async () => {
+                            try {
+                                await navigator.clipboard.writeText(sequence);
+                                getSession(model).notify('Sequence copied to clipboard', 'info');
+                            }
+                            catch (e) {
+                                console.error(e);
+                                getSession(model).notifyError(`${e}`, e);
+                            }
+                        })();
+                    } }, "Copy to Clipboard"),
+                React.createElement(Button, { variant: "contained", color: "secondary", disabled: loading || !sequence, onClick: () => {
+                        try {
+                            const url = URL.createObjectURL(new Blob([sequence], { type: 'text/plain' }));
+                            // Create a temporary anchor element
+                            const a = document.createElement('a');
+                            a.href = url;
+                            a.download = 'sequence.fasta';
+                            // Trigger the download
+                            document.body.append(a);
+                            a.click();
+                            // Clean up
+                            a.remove();
+                            URL.revokeObjectURL(url);
+                            getSession(model).notify('Sequence downloaded', 'info');
+                        }
+                        catch (e) {
+                            console.error(e);
+                            getSession(model).notifyError(`${e}`, e);
+                        }
+                    } }, "Download")),
+            error ? (React.createElement(ErrorMessage, { error: error })) : (React.createElement(React.Fragment, null,
+                loading ? React.createElement(LoadingEllipses, null) : null,
+                React.createElement(TextField, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, disabled: sequenceTooLarge, className: classes.dialogContent, fullWidth: true, value: loading
+                        ? 'Loading...'
+                        : sequenceTooLarge
+                            ? 'Reference sequence too large to display, use the download FASTA button'
+                            : sequence, slotProps: {
+                        input: {
+                            readOnly: true,
+                            classes: {
+                                input: classes.textAreaInput,
+                            },
+                        },
+                    } })))),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { color: "primary", variant: "outlined", onClick: onClose }, "Close"))));
+});
+export default GetSequenceDialog;
+//# sourceMappingURL=GetSequenceDialog.js.map

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

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package/dist/LinearMafDisplay/components/{ReactComponent.d.ts → LinearMafDisplayComponent.d.ts}

@@ -1,5 +1,5 @@
 import React from 'react';
-import { LinearMafDisplayModel } from '../stateModel';
+import type { LinearMafDisplayModel } from '../stateModel';
 declare const LinearMafDisplay: (props: {
     model: LinearMafDisplayModel;
 }) => React.JSX.Element;

package/dist/LinearMafDisplay/components/LinearMafDisplayComponent.js

@@ -0,0 +1,168 @@
+import React, { useEffect, useRef, useState } from 'react';
+import { Menu } from '@jbrowse/core/ui';
+import { getContainingView, getEnv } from '@jbrowse/core/util';
+import { useTheme } from '@mui/material';
+import { observer } from 'mobx-react';
+import Crosshairs from './Crosshairs';
+import SequenceDialog from './GetSequenceDialog/GetSequenceDialog';
+import MAFTooltip from './MAFTooltip';
+import YScaleBars from './Sidebar/YScaleBars';
+const LinearMafDisplay = observer(function (props) {
+    const { model } = props;
+    const { pluginManager } = getEnv(model);
+    const { rowHeight, height, scrollTop, samples: sources } = model;
+    const ref = useRef(null);
+    const theme = useTheme();
+    const LinearGenomePlugin = pluginManager.getPlugin('LinearGenomeViewPlugin');
+    const { BaseLinearDisplayComponent } = LinearGenomePlugin.exports;
+    const [mouseY, setMouseY] = useState();
+    const [mouseX, setMouseX] = useState();
+    const [isDragging, setIsDragging] = useState(false);
+    const [dragStartX, setDragStartX] = useState();
+    const [dragEndX, setDragEndX] = useState();
+    const [showSelectionBox, setShowSelectionBox] = useState(false);
+    const [contextCoord, setContextCoord] = useState();
+    const [showSequenceDialog, setShowSequenceDialog] = useState(false);
+    const [selectionCoords, setSelectionCoords] = useState();
+    const { width } = getContainingView(model);
+    const handleMouseDown = (event) => {
+        const rect = ref.current?.getBoundingClientRect();
+        const left = rect?.left || 0;
+        const clientX = event.clientX - left;
+        // Clear the previous selection box when starting a new drag
+        setShowSelectionBox(false);
+        setIsDragging(true);
+        setDragStartX(clientX);
+        setDragEndX(clientX);
+        event.stopPropagation();
+    };
+    const handleMouseMove = (event) => {
+        const rect = ref.current?.getBoundingClientRect();
+        const top = rect?.top || 0;
+        const left = rect?.left || 0;
+        const clientX = event.clientX - left;
+        const clientY = event.clientY - top;
+        setMouseY(clientY);
+        setMouseX(clientX);
+        if (isDragging) {
+            setDragEndX(clientX);
+        }
+    };
+    const handleMouseUp = (event) => {
+        if (isDragging && dragStartX !== undefined && dragEndX !== undefined) {
+            // Calculate the drag distance
+            const dragDistanceX = Math.abs(dragEndX - dragStartX);
+            // Only show context menu if the drag distance is at least 2 pixels in either direction
+            if (dragDistanceX >= 2) {
+                setContextCoord({
+                    coord: [event.clientX, event.clientY],
+                    dragEndX: event.clientX,
+                    dragStartX: dragStartX,
+                });
+                // Set showSelectionBox to true to keep the selection visible
+                setShowSelectionBox(true);
+            }
+            else {
+                // For very small drags (less than 2px), don't show selection box or context menu
+                clearSelectionBox();
+            }
+        }
+        // Only set isDragging to false, but keep the coordinates
+        setIsDragging(false);
+    };
+    // Function to clear the selection box
+    const clearSelectionBox = () => {
+        setShowSelectionBox(false);
+        setDragStartX(undefined);
+        setDragEndX(undefined);
+    };
+    // Add keydown event handler to clear selection box when Escape key is pressed
+    useEffect(() => {
+        const handleKeyDown = (event) => {
+            if (event.key === 'Escape' && showSelectionBox) {
+                clearSelectionBox();
+            }
+        };
+        // Add click handler to clear selection box when clicking outside of it
+        const handleClickOutside = (event) => {
+            if (ref.current &&
+                !ref.current.contains(event.target) &&
+                showSelectionBox) {
+                clearSelectionBox();
+            }
+        };
+        document.addEventListener('keydown', handleKeyDown);
+        document.addEventListener('click', handleClickOutside);
+        return () => {
+            document.removeEventListener('keydown', handleKeyDown);
+            document.removeEventListener('click', handleClickOutside);
+        };
+    }, [showSelectionBox, clearSelectionBox]);
+    return (React.createElement("div", { ref: ref, onMouseDown: handleMouseDown, onMouseMove: handleMouseMove, onMouseUp: handleMouseUp, onDoubleClick: () => {
+            // Clear selection box on double click
+            if (showSelectionBox) {
+                clearSelectionBox();
+            }
+        }, onMouseLeave: () => {
+            setMouseY(undefined);
+            setMouseX(undefined);
+            setIsDragging(false);
+        } },
+        React.createElement(BaseLinearDisplayComponent, { ...props }),
+        React.createElement(YScaleBars, { model: model }),
+        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,
+        (isDragging || showSelectionBox) &&
+            dragStartX !== undefined &&
+            dragEndX !== undefined ? (React.createElement("div", { style: {
+                position: 'absolute',
+                left: Math.min(dragStartX, dragEndX),
+                top: 0,
+                width: Math.abs(dragEndX - dragStartX),
+                height,
+                backgroundColor: 'rgba(0, 0, 255, 0.2)',
+                border: '1px solid rgba(0, 0, 255, 0.5)',
+                pointerEvents: 'none',
+            } })) : null,
+        React.createElement(Menu, { open: Boolean(contextCoord), onMenuItemClick: (_, callback) => {
+                callback();
+                setContextCoord(undefined);
+            }, onClose: () => {
+                setContextCoord(undefined);
+            }, slotProps: {
+                transition: {
+                    onExit: () => {
+                        setContextCoord(undefined);
+                    },
+                },
+            }, anchorReference: "anchorPosition", anchorPosition: contextCoord
+                ? { top: contextCoord.coord[1], left: contextCoord.coord[0] }
+                : undefined, style: {
+                zIndex: theme.zIndex.tooltip,
+            }, menuItems: [
+                {
+                    label: 'View subsequence',
+                    onClick: () => {
+                        if (!contextCoord) {
+                            return;
+                        }
+                        // Store the selection coordinates for the SequenceDialog to use
+                        setSelectionCoords({
+                            dragStartX: contextCoord.dragStartX,
+                            dragEndX: contextCoord.dragEndX,
+                        });
+                        // Show the dialog
+                        setShowSequenceDialog(true);
+                        // Close the context menu
+                        setContextCoord(undefined);
+                    },
+                },
+            ] }),
+        showSequenceDialog ? (React.createElement(SequenceDialog, { model: model, selectionCoords: selectionCoords, onClose: () => {
+                setShowSequenceDialog(false);
+                setSelectionCoords(undefined);
+            } })) : null));
+});
+export default LinearMafDisplay;
+//# sourceMappingURL=LinearMafDisplayComponent.js.map

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

@@ -0,0 +1 @@
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package/dist/LinearMafDisplay/components/MAFTooltip.d.ts

@@ -0,0 +1,12 @@
+import React from 'react';
+import type { LinearMafDisplayModel } from '../stateModel';
+interface MAFTooltipProps {
+    mouseY: number;
+    mouseX: number;
+    rowHeight: number;
+    sources: Record<string, any>[];
+    model: LinearMafDisplayModel;
+    origMouseX?: number;
+}
+declare const MAFTooltip: ({ model, mouseY, mouseX, origMouseX, rowHeight, sources, }: MAFTooltipProps) => React.JSX.Element | null;
+export default MAFTooltip;

package/dist/LinearMafDisplay/components/MAFTooltip.js

@@ -0,0 +1,29 @@
+import React from 'react';
+import { SanitizedHTML } from '@jbrowse/core/ui';
+import BaseTooltip from '@jbrowse/core/ui/BaseTooltip';
+import { getBpDisplayStr, getContainingView, toLocale, } from '@jbrowse/core/util';
+import { observer } from 'mobx-react';
+const MAFTooltip = observer(function ({ model, mouseY, mouseX, origMouseX, rowHeight, sources, }) {
+    const view = getContainingView(model);
+    const ret = Object.entries(sources[Math.floor(mouseY / rowHeight)] || {})
+        .filter(([key]) => key !== 'color' && key !== 'id')
+        .map(([key, value]) => `${key}:${value}`)
+        .join('\n');
+    const p1 = origMouseX ? view.pxToBp(origMouseX) : undefined;
+    const p2 = view.pxToBp(mouseX);
+    return ret ? (React.createElement(BaseTooltip, null,
+        React.createElement(SanitizedHTML, { html: [
+                ret,
+                ...(p1
+                    ? [
+                        `Start: ${p1.refName}:${toLocale(p1.coord)}`,
+                        `End: ${p2.refName}:${toLocale(p2.coord)}`,
+                        `Length: ${getBpDisplayStr(Math.abs(p1.coord - p2.coord))}`,
+                    ]
+                    : [`${p2.refName}:${toLocale(p2.coord)}`]),
+            ]
+                .filter(f => !!f)
+                .join('<br/>') }))) : null;
+});
+export default MAFTooltip;
+//# sourceMappingURL=MAFTooltip.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"MAFTooltip.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/MAFTooltip.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAA;AAChD,OAAO,WAAW,MAAM,8BAA8B,CAAA;AACtD,OAAO,EACL,eAAe,EACf,iBAAiB,EACjB,QAAQ,GACT,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAcrC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EACpC,KAAK,EACL,MAAM,EACN,MAAM,EACN,UAAU,EACV,SAAS,EACT,OAAO,GACS;IAChB,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,GAAG,GAAG,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,SAAS,CAAC,CAAC,IAAI,EAAE,CAAC;SACtE,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,GAAG,KAAK,OAAO,IAAI,GAAG,KAAK,IAAI,CAAC;SAClD,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG,IAAI,KAAK,EAAE,CAAC;SACxC,IAAI,CAAC,IAAI,CAAC,CAAA;IACb,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IAC3D,MAAM,EAAE,GAAG,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;IAC9B,OAAO,GAAG,CAAC,CAAC,CAAC,CACX,oBAAC,WAAW;QACV,oBAAC,aAAa,IACZ,IAAI,EAAE;gBACJ,GAAG;gBACH,GAAG,CAAC,EAAE;oBACJ,CAAC,CAAC;wBACE,UAAU,EAAE,CAAC,OAAO,IAAI,QAAQ,CAAC,EAAE,CAAC,KAAK,CAAC,EAAE;wBAC5C,QAAQ,EAAE,CAAC,OAAO,IAAI,QAAQ,CAAC,EAAE,CAAC,KAAK,CAAC,EAAE;wBAC1C,WAAW,eAAe,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,GAAG,EAAE,CAAC,KAAK,CAAC,CAAC,EAAE;qBAC5D;oBACH,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,OAAO,IAAI,QAAQ,CAAC,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;aAC7C;iBACE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;iBAChB,IAAI,CAAC,OAAO,CAAC,GAChB,CACU,CACf,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/LinearMafDisplay/components/SetRowHeightDialog/SetRowHeightDialog.js

@@ -0,0 +1,38 @@
+import React, { useState } from 'react';
+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: {
+        width: 500,
+    },
+});
+const SetRowHeightDialog = observer(function (props) {
+    const { model, handleClose } = 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: "Set row height" },
+        React.createElement("form", { onSubmit: event => {
+                event.preventDefault();
+                model.setRowProportion(+rowProportion);
+                model.setRowHeight(+rowHeight);
+                handleClose();
+            } },
+            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, helperText: "Enter row height", autoFocus: true, onChange: event => {
+                        setRowHeight(event.target.value);
+                    } }),
+                React.createElement(TextField, { value: rowProportion, helperText: "Enter row proportion", onChange: event => {
+                        setRowProportion(event.target.value);
+                    } }),
+                React.createElement(DialogActions, null,
+                    React.createElement(Button, { variant: "contained", color: "primary", type: "submit" }, "Submit"),
+                    React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
+                            handleClose();
+                        } }, "Cancel"))))));
+});
+export default SetRowHeightDialog;
+//# sourceMappingURL=SetRowHeightDialog.js.map

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

@@ -0,0 +1 @@
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package/dist/LinearMafDisplay/components/Sidebar/ColorLegend.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import type { LinearMafDisplayModel } from '../../stateModel';
+declare const ColorLegend: ({ model, }: {
+    model: LinearMafDisplayModel;
+}) => React.JSX.Element;
+export default ColorLegend;

package/dist/LinearMafDisplay/components/{ColorLegend.js → Sidebar/ColorLegend.js}

@@ -2,9 +2,8 @@ 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 { totalHeight, treeWidth, samples = [], rowHeight } = model;
-    const canDisplayLabel = rowHeight >= 8;
+const ColorLegend = observer(function ({ model, }) {
+    const { labelWidth, canDisplayLabel, totalHeight, treeWidth, 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 }),

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

@@ -0,0 +1 @@
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package/dist/LinearMafDisplay/components/Sidebar/RectBg.js.map

@@ -0,0 +1 @@
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