jbrowse-plugin-mafviewer 1.4.5 → 1.4.6

package/dist/MafSequenceWidget/SequenceDisplay.js

@@ -0,0 +1,117 @@
+import React, { useCallback, useEffect, useMemo, useRef } from 'react';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import LabelsCanvas from './LabelsCanvas';
+import SequenceCanvas from './SequenceCanvas';
+import SequenceTooltip from './SequenceTooltip';
+import { buildColToGenomePos, findRefSampleIndex } from './colToGenomePos';
+const useStyles = makeStyles()(theme => ({
+    container: {
+        border: `1px solid ${theme.palette.divider}`,
+        borderRadius: theme.shape.borderRadius,
+        maxHeight: 400,
+        backgroundColor: theme.palette.background.paper,
+        display: 'flex',
+        overflow: 'hidden',
+        position: 'relative',
+    },
+    labelsContainer: {
+        flexShrink: 0,
+        borderRight: `1px solid ${theme.palette.divider}`,
+        backgroundColor: theme.palette.background.paper,
+        overflowY: 'auto',
+        scrollbarWidth: 'none',
+        '&::-webkit-scrollbar': {
+            display: 'none',
+        },
+    },
+    sequenceContainer: {
+        flex: 1,
+        overflow: 'auto',
+    },
+}));
+const SequenceDisplay = observer(function SequenceDisplay({ model, sequences, colorBackground, showSampleNames, }) {
+    const { classes } = useStyles();
+    const labelsContainerRef = useRef(null);
+    const seqContainerRef = useRef(null);
+    const { samples, regions } = model;
+    const [hoveredCol, setHoveredCol] = React.useState();
+    const [hoveredRow, setHoveredRow] = React.useState();
+    const [tooltipPos, setTooltipPos] = React.useState();
+    const maxLabelLength = useMemo(() => samples ? Math.max(...samples.map(s => (s.label ?? s.id).length)) : 0, [samples]);
+    const colToGenomePos = useMemo(() => {
+        if (!regions) {
+            return [];
+        }
+        const region = regions[0];
+        if (!region) {
+            return [];
+        }
+        const refIdx = findRefSampleIndex(samples, region.assemblyName);
+        const refSequence = sequences[refIdx] || '';
+        return buildColToGenomePos(refSequence, region.start);
+    }, [sequences, regions, samples]);
+    // Sync vertical scroll between labels and sequences
+    useEffect(() => {
+        const labelsContainer = labelsContainerRef.current;
+        const seqContainer = seqContainerRef.current;
+        if (!labelsContainer || !seqContainer) {
+            return;
+        }
+        const handleSeqScroll = () => {
+            labelsContainer.scrollTop = seqContainer.scrollTop;
+        };
+        seqContainer.addEventListener('scroll', handleSeqScroll);
+        return () => {
+            seqContainer.removeEventListener('scroll', handleSeqScroll);
+        };
+    }, []);
+    const handleHover = useCallback((col, row, clientX, clientY) => {
+        if (!regions) {
+            return;
+        }
+        setHoveredCol(col);
+        setHoveredRow(row);
+        setTooltipPos({ x: clientX, y: clientY });
+        if (col !== undefined) {
+            const genomicPos = colToGenomePos[col];
+            const region = regions[0];
+            if (genomicPos !== undefined && region) {
+                model.setHoverHighlight({
+                    refName: region.refName,
+                    start: genomicPos,
+                    end: genomicPos + 1,
+                    assemblyName: region.assemblyName,
+                });
+            }
+            else {
+                model.setHoverHighlight(undefined);
+            }
+        }
+        else {
+            model.setHoverHighlight(undefined);
+        }
+    }, [colToGenomePos, model, regions]);
+    const handleLeave = useCallback(() => {
+        setHoveredCol(undefined);
+        setHoveredRow(undefined);
+        setTooltipPos(undefined);
+        model.setHoverHighlight(undefined);
+    }, [model]);
+    if (!samples || !regions || sequences.length === 0) {
+        return React.createElement("div", null, "No sequence data");
+    }
+    const hoveredSample = hoveredRow !== undefined ? samples[hoveredRow] : undefined;
+    const hoveredChar = hoveredRow !== undefined && hoveredCol !== undefined
+        ? sequences[hoveredRow]?.[hoveredCol]
+        : undefined;
+    const genomicPos = hoveredCol !== undefined ? colToGenomePos[hoveredCol] : undefined;
+    return (React.createElement("div", { className: classes.container },
+        showSampleNames && (React.createElement("div", { ref: labelsContainerRef, className: classes.labelsContainer },
+            React.createElement(LabelsCanvas, { samples: samples, maxLabelLength: maxLabelLength }))),
+        React.createElement("div", { ref: seqContainerRef, className: classes.sequenceContainer },
+            React.createElement(SequenceCanvas, { samples: samples, sequences: sequences, colorBackground: colorBackground, hoveredCol: hoveredCol, onHover: handleHover, onLeave: handleLeave })),
+        tooltipPos && hoveredSample && (React.createElement(SequenceTooltip, { x: tooltipPos.x, y: tooltipPos.y, sample: hoveredSample, base: hoveredChar, genomicPos: genomicPos }))));
+});
+export default SequenceDisplay;
+//# sourceMappingURL=SequenceDisplay.js.map

package/dist/MafSequenceWidget/SequenceDisplay.js.map

@@ -0,0 +1 @@
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package/dist/MafSequenceWidget/SequenceTooltip.d.ts

@@ -0,0 +1,11 @@
+import React from 'react';
+import type { Sample } from '../LinearMafDisplay/types';
+interface SequenceTooltipProps {
+    x: number;
+    y: number;
+    sample: Sample;
+    base?: string;
+    genomicPos?: number;
+}
+export default function SequenceTooltip({ x, y, sample, base, genomicPos, }: SequenceTooltipProps): React.JSX.Element;
+export {};

package/dist/MafSequenceWidget/SequenceTooltip.js

@@ -0,0 +1,39 @@
+import React from 'react';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()(theme => ({
+    tooltip: {
+        position: 'fixed',
+        pointerEvents: 'none',
+        zIndex: 1000,
+        backgroundColor: theme.palette.grey[800],
+        color: theme.palette.common.white,
+        padding: '4px 8px',
+        borderRadius: 4,
+        fontSize: 12,
+        whiteSpace: 'nowrap',
+    },
+    insertion: {
+        color: theme.palette.warning.light,
+        fontStyle: 'italic',
+    },
+}));
+export default function SequenceTooltip({ x, y, sample, base, genomicPos, }) {
+    const { classes } = useStyles();
+    // An insertion is when we have a base but no genomic position
+    // (the reference has a gap at this column)
+    const isInsertion = base !== undefined && genomicPos === undefined;
+    return (React.createElement("div", { className: classes.tooltip, style: {
+            left: x + 12,
+            top: y + 12,
+        } },
+        React.createElement("div", null,
+            React.createElement("strong", null, sample.label)),
+        base && (React.createElement("div", null,
+            "Base: ",
+            base,
+            genomicPos !== undefined
+                ? ` | Pos: ${(genomicPos + 1).toLocaleString('en-US')}`
+                : null)),
+        isInsertion && (React.createElement("div", { className: classes.insertion }, "Insertion (not in reference)"))));
+}
+//# sourceMappingURL=SequenceTooltip.js.map

package/dist/MafSequenceWidget/SequenceTooltip.js.map

@@ -0,0 +1 @@
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package/dist/MafSequenceWidget/baseColors.d.ts

@@ -0,0 +1,3 @@
+import type { Theme } from '@mui/material';
+export declare function getBaseColor(base: string, theme: Theme): string;
+export declare function getContrastText(base: string, theme: Theme): string;

package/dist/MafSequenceWidget/baseColors.js

@@ -0,0 +1,64 @@
+function getBases(theme) {
+    return theme.palette.bases;
+}
+export function getBaseColor(base, theme) {
+    const bases = getBases(theme);
+    if (!bases) {
+        switch (base.toUpperCase()) {
+            case 'A':
+                return '#6dbf6d';
+            case 'C':
+                return '#6c6cff';
+            case 'G':
+                return '#ffb347';
+            case 'T':
+            case 'U':
+                return '#ff6b6b';
+            default:
+                return theme.palette.grey[500];
+        }
+    }
+    switch (base.toUpperCase()) {
+        case 'A':
+            return bases.A.main;
+        case 'C':
+            return bases.C.main;
+        case 'G':
+            return bases.G.main;
+        case 'T':
+        case 'U':
+            return bases.T.main;
+        default:
+            return theme.palette.grey[500];
+    }
+}
+export function getContrastText(base, theme) {
+    const bases = getBases(theme);
+    if (!bases) {
+        switch (base.toUpperCase()) {
+            case 'A':
+            case 'C':
+            case 'T':
+            case 'U':
+                return '#fff';
+            case 'G':
+                return '#000';
+            default:
+                return theme.palette.common.white;
+        }
+    }
+    switch (base.toUpperCase()) {
+        case 'A':
+            return bases.A.contrastText;
+        case 'C':
+            return bases.C.contrastText;
+        case 'G':
+            return bases.G.contrastText;
+        case 'T':
+        case 'U':
+            return bases.T.contrastText;
+        default:
+            return theme.palette.common.white;
+    }
+}
+//# sourceMappingURL=baseColors.js.map

package/dist/MafSequenceWidget/baseColors.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"baseColors.js","sourceRoot":"","sources":["../../src/MafSequenceWidget/baseColors.ts"],"names":[],"mappings":"AASA,SAAS,QAAQ,CAAC,KAAY;IAC5B,OAAQ,KAAK,CAAC,OAAe,CAAC,KAAgC,CAAA;AAChE,CAAC;AAED,MAAM,UAAU,YAAY,CAAC,IAAY,EAAE,KAAY;IACrD,MAAM,KAAK,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC7B,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,QAAQ,IAAI,CAAC,WAAW,EAAE,EAAE,CAAC;YAC3B,KAAK,GAAG;gBACN,OAAO,SAAS,CAAA;YAClB,KAAK,GAAG;gBACN,OAAO,SAAS,CAAA;YAClB,KAAK,GAAG;gBACN,OAAO,SAAS,CAAA;YAClB,KAAK,GAAG,CAAC;YACT,KAAK,GAAG;gBACN,OAAO,SAAS,CAAA;YAClB;gBACE,OAAO,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAClC,CAAC;IACH,CAAC;IAED,QAAQ,IAAI,CAAC,WAAW,EAAE,EAAE,CAAC;QAC3B,KAAK,GAAG;YACN,OAAO,KAAK,CAAC,CAAC,CAAC,IAAI,CAAA;QACrB,KAAK,GAAG;YACN,OAAO,KAAK,CAAC,CAAC,CAAC,IAAI,CAAA;QACrB,KAAK,GAAG;YACN,OAAO,KAAK,CAAC,CAAC,CAAC,IAAI,CAAA;QACrB,KAAK,GAAG,CAAC;QACT,KAAK,GAAG;YACN,OAAO,KAAK,CAAC,CAAC,CAAC,IAAI,CAAA;QACrB;YACE,OAAO,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IAClC,CAAC;AACH,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,IAAY,EAAE,KAAY;IACxD,MAAM,KAAK,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC7B,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,QAAQ,IAAI,CAAC,WAAW,EAAE,EAAE,CAAC;YAC3B,KAAK,GAAG,CAAC;YACT,KAAK,GAAG,CAAC;YACT,KAAK,GAAG,CAAC;YACT,KAAK,GAAG;gBACN,OAAO,MAAM,CAAA;YACf,KAAK,GAAG;gBACN,OAAO,MAAM,CAAA;YACf;gBACE,OAAO,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,KAAK,CAAA;QACrC,CAAC;IACH,CAAC;IAED,QAAQ,IAAI,CAAC,WAAW,EAAE,EAAE,CAAC;QAC3B,KAAK,GAAG;YACN,OAAO,KAAK,CAAC,CAAC,CAAC,YAAY,CAAA;QAC7B,KAAK,GAAG;YACN,OAAO,KAAK,CAAC,CAAC,CAAC,YAAY,CAAA;QAC7B,KAAK,GAAG;YACN,OAAO,KAAK,CAAC,CAAC,CAAC,YAAY,CAAA;QAC7B,KAAK,GAAG,CAAC;QACT,KAAK,GAAG;YACN,OAAO,KAAK,CAAC,CAAC,CAAC,YAAY,CAAA;QAC7B;YACE,OAAO,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,KAAK,CAAA;IACrC,CAAC;AACH,CAAC"}

package/dist/MafSequenceWidget/colToGenomePos.d.ts

@@ -0,0 +1,13 @@
+import type { Sample } from '../LinearMafDisplay/types';
+/**
+ * Find the index of the reference sample (matching the assembly name from the region)
+ * Falls back to 0 if no match is found
+ */
+export declare function findRefSampleIndex(samples: Sample[] | undefined, assemblyName: string | undefined): number;
+/**
+ * Build a mapping from display column index to genomic position.
+ * Only the reference sequence determines genomic positions - gaps in the
+ * reference map to undefined (no genomic position), while gaps in other
+ * samples don't affect the mapping.
+ */
+export declare function buildColToGenomePos(refSequence: string, regionStart: number): (number | undefined)[];

package/dist/MafSequenceWidget/colToGenomePos.js

@@ -0,0 +1,32 @@
+/**
+ * Find the index of the reference sample (matching the assembly name from the region)
+ * Falls back to 0 if no match is found
+ */
+export function findRefSampleIndex(samples, assemblyName) {
+    if (!samples || !assemblyName) {
+        return 0;
+    }
+    const idx = samples.findIndex(s => s.id === assemblyName);
+    return idx === -1 ? 0 : idx;
+}
+/**
+ * Build a mapping from display column index to genomic position.
+ * Only the reference sequence determines genomic positions - gaps in the
+ * reference map to undefined (no genomic position), while gaps in other
+ * samples don't affect the mapping.
+ */
+export function buildColToGenomePos(refSequence, regionStart) {
+    const mapping = [];
+    let genomePos = regionStart;
+    for (const char of refSequence) {
+        if (char === '-') {
+            mapping.push(undefined);
+        }
+        else {
+            mapping.push(genomePos);
+            genomePos++;
+        }
+    }
+    return mapping;
+}
+//# sourceMappingURL=colToGenomePos.js.map

package/dist/MafSequenceWidget/colToGenomePos.js.map

@@ -0,0 +1 @@
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package/dist/MafSequenceWidget/colToGenomePos.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/MafSequenceWidget/colToGenomePos.test.js

@@ -0,0 +1,136 @@
+import { describe, expect, test } from 'vitest';
+import { buildColToGenomePos, findRefSampleIndex } from './colToGenomePos';
+describe('findRefSampleIndex', () => {
+    const samples = [
+        { id: 'mm10', label: 'Mouse' },
+        { id: 'hg38', label: 'Human' },
+        { id: 'panTro6', label: 'Chimp' },
+    ];
+    test('returns index of sample matching assemblyName', () => {
+        expect(findRefSampleIndex(samples, 'hg38')).toBe(1);
+        expect(findRefSampleIndex(samples, 'mm10')).toBe(0);
+        expect(findRefSampleIndex(samples, 'panTro6')).toBe(2);
+    });
+    test('returns 0 when no match found', () => {
+        expect(findRefSampleIndex(samples, 'galGal6')).toBe(0);
+    });
+    test('returns 0 when samples is undefined', () => {
+        expect(findRefSampleIndex(undefined, 'hg38')).toBe(0);
+    });
+    test('returns 0 when assemblyName is undefined', () => {
+        expect(findRefSampleIndex(samples, undefined)).toBe(0);
+    });
+    test('returns 0 when both are undefined', () => {
+        expect(findRefSampleIndex(undefined, undefined)).toBe(0);
+    });
+    test('returns 0 for empty samples array', () => {
+        expect(findRefSampleIndex([], 'hg38')).toBe(0);
+    });
+});
+describe('buildColToGenomePos', () => {
+    test('maps non-gap characters to sequential genomic positions', () => {
+        const result = buildColToGenomePos('ACGT', 100);
+        expect(result).toEqual([100, 101, 102, 103]);
+    });
+    test('maps gaps to undefined', () => {
+        const result = buildColToGenomePos('AC-GT', 100);
+        expect(result).toEqual([100, 101, undefined, 102, 103]);
+    });
+    test('handles multiple consecutive gaps', () => {
+        const result = buildColToGenomePos('A--G', 100);
+        expect(result).toEqual([100, undefined, undefined, 101]);
+    });
+    test('handles gaps at start', () => {
+        const result = buildColToGenomePos('--ACG', 100);
+        expect(result).toEqual([undefined, undefined, 100, 101, 102]);
+    });
+    test('handles gaps at end', () => {
+        const result = buildColToGenomePos('ACG--', 100);
+        expect(result).toEqual([100, 101, 102, undefined, undefined]);
+    });
+    test('handles all gaps', () => {
+        const result = buildColToGenomePos('----', 100);
+        expect(result).toEqual([undefined, undefined, undefined, undefined]);
+    });
+    test('handles empty sequence', () => {
+        const result = buildColToGenomePos('', 100);
+        expect(result).toEqual([]);
+    });
+    test('works with different start positions', () => {
+        const result = buildColToGenomePos('AC-T', 50000);
+        expect(result).toEqual([50000, 50001, undefined, 50002]);
+    });
+});
+describe('integration: hover highlight with gaps', () => {
+    const samples = [
+        { id: 'mm10', label: 'Mouse' },
+        { id: 'hg38', label: 'Human' },
+        { id: 'panTro6', label: 'Chimp' },
+    ];
+    test('gap in non-reference sample does not affect mapping', () => {
+        // Reference is hg38 (index 1)
+        // mm10 (index 0) has a gap, but hg38 does not
+        const sequences = [
+            'A-GT', // mm10 - has gap at position 1
+            'ACGT', // hg38 - no gap (this is the reference)
+            'ACGT', // panTro6
+        ];
+        const refIdx = findRefSampleIndex(samples, 'hg38');
+        expect(refIdx).toBe(1);
+        const mapping = buildColToGenomePos(sequences[refIdx], 100);
+        // All positions should map to genomic coordinates since reference has no gaps
+        expect(mapping).toEqual([100, 101, 102, 103]);
+    });
+    test('gap in reference sample maps to undefined', () => {
+        // Reference is hg38 (index 1)
+        // hg38 has a gap (insertion in other species)
+        const sequences = [
+            'ACGT', // mm10
+            'A-GT', // hg38 - has gap (this is the reference)
+            'ATGT', // panTro6 - has T where hg38 has gap
+        ];
+        const refIdx = findRefSampleIndex(samples, 'hg38');
+        const mapping = buildColToGenomePos(sequences[refIdx], 100);
+        // Position 1 should be undefined because reference has gap there
+        expect(mapping).toEqual([100, undefined, 101, 102]);
+    });
+    test('correctly handles reference as first sample', () => {
+        // Reference is mm10 (index 0)
+        const sequences = [
+            'ACGT', // mm10 - reference
+            'A-GT', // hg38 - has gap
+            'ACGT', // panTro6
+        ];
+        const refIdx = findRefSampleIndex(samples, 'mm10');
+        expect(refIdx).toBe(0);
+        const mapping = buildColToGenomePos(sequences[refIdx], 100);
+        // All positions map because reference (mm10) has no gaps
+        expect(mapping).toEqual([100, 101, 102, 103]);
+    });
+    test('correctly handles reference as last sample', () => {
+        // Reference is panTro6 (index 2)
+        const sequences = [
+            'A-GT', // mm10 - has gap
+            'A-GT', // hg38 - has gap
+            'ACGT', // panTro6 - no gap (this is the reference)
+        ];
+        const refIdx = findRefSampleIndex(samples, 'panTro6');
+        expect(refIdx).toBe(2);
+        const mapping = buildColToGenomePos(sequences[refIdx], 100);
+        // All positions map because reference (panTro6) has no gaps
+        expect(mapping).toEqual([100, 101, 102, 103]);
+    });
+    test('falls back to first sample when assembly not found', () => {
+        // Reference is galGal6 which doesn't exist in samples
+        const sequences = [
+            'ACGT', // mm10
+            'A-GT', // hg38
+            'ACGT', // panTro6
+        ];
+        const refIdx = findRefSampleIndex(samples, 'galGal6');
+        expect(refIdx).toBe(0); // Falls back to first sample
+        const mapping = buildColToGenomePos(sequences[refIdx], 100);
+        expect(mapping).toEqual([100, 101, 102, 103]);
+    });
+});
+//# sourceMappingURL=colToGenomePos.test.js.map

package/dist/MafSequenceWidget/colToGenomePos.test.js.map

@@ -0,0 +1 @@
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package/dist/MafSequenceWidget/configSchema.d.ts

@@ -0,0 +1 @@
+export declare const configSchema: import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;

package/dist/MafSequenceWidget/configSchema.js

@@ -0,0 +1,3 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export const configSchema = ConfigurationSchema('MafSequenceWidget', {});
+//# sourceMappingURL=configSchema.js.map

package/dist/MafSequenceWidget/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/MafSequenceWidget/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,MAAM,CAAC,MAAM,YAAY,GAAG,mBAAmB,CAAC,mBAAmB,EAAE,EAAE,CAAC,CAAA"}

package/dist/MafSequenceWidget/constants.d.ts

@@ -0,0 +1,4 @@
+export declare const CHAR_WIDTH = 12;
+export declare const ROW_HEIGHT = 16;
+export declare const FONT = "bold 12px monospace";
+export declare const LABEL_PADDING = 10;

package/dist/MafSequenceWidget/constants.js

@@ -0,0 +1,5 @@
+export const CHAR_WIDTH = 12;
+export const ROW_HEIGHT = 16;
+export const FONT = 'bold 12px monospace';
+export const LABEL_PADDING = 10;
+//# sourceMappingURL=constants.js.map

package/dist/MafSequenceWidget/constants.js.map

@@ -0,0 +1 @@
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package/dist/MafSequenceWidget/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function MafSequenceWidgetF(pluginManager: PluginManager): void;

package/dist/MafSequenceWidget/index.js

@@ -0,0 +1,16 @@
+import { lazy } from 'react';
+import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType';
+import MafSequenceHoverHighlightExtensionF from './MafSequenceHoverHighlightExtension';
+import { configSchema } from './configSchema';
+import { stateModelFactory } from './stateModelFactory';
+export default function MafSequenceWidgetF(pluginManager) {
+    pluginManager.addWidgetType(() => new WidgetType({
+        name: 'MafSequenceWidget',
+        heading: 'MAF Sequence',
+        configSchema: configSchema,
+        stateModel: stateModelFactory(),
+        ReactComponent: lazy(() => import('./MafSequenceWidget')),
+    }));
+    MafSequenceHoverHighlightExtensionF(pluginManager);
+}
+//# sourceMappingURL=index.js.map

package/dist/MafSequenceWidget/index.js.map

@@ -0,0 +1 @@
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package/dist/MafSequenceWidget/stateModelFactory.d.ts

@@ -0,0 +1,67 @@
+import type { Sample } from '../LinearMafDisplay/types';
+import type { Instance } from '@jbrowse/mobx-state-tree';
+export interface HoverHighlight {
+    refName: string;
+    start: number;
+    end: number;
+    assemblyName: string;
+}
+export declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelType<{
+    id: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"MafSequenceWidget">;
+    adapterConfig: import("@jbrowse/mobx-state-tree").IType<({
+        [x: string]: any;
+    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | null | undefined, ({
+        [x: string]: any;
+    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | undefined, ({
+        [x: string]: any;
+    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | undefined>;
+    samples: import("@jbrowse/mobx-state-tree").IType<Sample[] | null | undefined, Sample[] | undefined, Sample[] | undefined>;
+    regions: import("@jbrowse/mobx-state-tree").IType<{
+        refName: string;
+        start: number;
+        end: number;
+        assemblyName: string;
+    }[] | null | undefined, {
+        refName: string;
+        start: number;
+        end: number;
+        assemblyName: string;
+    }[] | undefined, {
+        refName: string;
+        start: number;
+        end: number;
+        assemblyName: string;
+    }[] | undefined>;
+    connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+}, {
+    hoverHighlight: HoverHighlight | undefined;
+} & {
+    setHoverHighlight(highlight: HoverHighlight | undefined): void;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
+export type MafSequenceWidgetStateModel = ReturnType<typeof stateModelFactory>;
+export type MafSequenceWidgetModel = Instance<MafSequenceWidgetStateModel>;

package/dist/MafSequenceWidget/stateModelFactory.js

@@ -0,0 +1,21 @@
+import { types } from '@jbrowse/mobx-state-tree';
+export function stateModelFactory() {
+    return types
+        .model('MafSequenceWidget', {
+        id: types.identifier,
+        type: types.literal('MafSequenceWidget'),
+        adapterConfig: types.frozen(undefined),
+        samples: types.frozen(undefined),
+        regions: types.frozen(undefined),
+        connectedViewId: types.maybe(types.string),
+    })
+        .volatile(() => ({
+        hoverHighlight: undefined,
+    }))
+        .actions(self => ({
+        setHoverHighlight(highlight) {
+            self.hoverHighlight = highlight;
+        },
+    }));
+}
+//# sourceMappingURL=stateModelFactory.js.map

package/dist/MafSequenceWidget/stateModelFactory.js.map

@@ -0,0 +1 @@
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