jbrowse-plugin-mafviewer 1.4.3 → 1.4.6

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 @@
+{"version":3,"file":"colToGenomePos.js","sourceRoot":"","sources":["../../src/MafSequenceWidget/colToGenomePos.ts"],"names":[],"mappings":"AAEA;;;GAGG;AACH,MAAM,UAAU,kBAAkB,CAChC,OAA6B,EAC7B,YAAgC;IAEhC,IAAI,CAAC,OAAO,IAAI,CAAC,YAAY,EAAE,CAAC;QAC9B,OAAO,CAAC,CAAA;IACV,CAAC;IACD,MAAM,GAAG,GAAG,OAAO,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,YAAY,CAAC,CAAA;IACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;AAC7B,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,mBAAmB,CACjC,WAAmB,EACnB,WAAmB;IAEnB,MAAM,OAAO,GAA2B,EAAE,CAAA;IAC1C,IAAI,SAAS,GAAG,WAAW,CAAA;IAE3B,KAAK,MAAM,IAAI,IAAI,WAAW,EAAE,CAAC;QAC/B,IAAI,IAAI,KAAK,GAAG,EAAE,CAAC;YACjB,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;QACzB,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;YACvB,SAAS,EAAE,CAAA;QACb,CAAC;IACH,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC"}

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 @@
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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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package/dist/MafTabixAdapter/MafTabixAdapter.js

@@ -2,10 +2,11 @@ import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter
 import { SimpleFeature, updateStatus, } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { getSnapshot } from 'mobx-state-tree';
+import { getSnapshot } from '@jbrowse/mobx-state-tree';
 import { firstValueFrom, toArray } from 'rxjs';
 import parseNewick from '../parseNewick';
 import { normalize } from '../util';
+import { parseAssemblyAndChr, selectReferenceSequence, } from '../util/parseAssemblyName';
 export default class MafTabixAdapter extends BaseFeatureDataAdapter {
     setupP;
     async setupPre() {
@@ -62,38 +63,7 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
                         if (!assemblyAndChr || !seq) {
                             continue;
                         }
-                        // Optimized assembly name parsing with simplified logic
-                        let assemblyName;
-                        let chr;
-                        const firstDotIndex = assemblyAndChr.indexOf('.');
-                        if (firstDotIndex === -1) {
-                            // No dot found, entire string is assembly name
-                            assemblyName = assemblyAndChr;
-                            chr = '';
-                        }
-                        else {
-                            const secondDotIndex = assemblyAndChr.indexOf('.', firstDotIndex + 1);
-                            if (secondDotIndex === -1) {
-                                // Only one dot: assembly.chr
-                                assemblyName = assemblyAndChr.slice(0, Math.max(0, firstDotIndex));
-                                chr = assemblyAndChr.slice(Math.max(0, firstDotIndex + 1));
-                            }
-                            else {
-                                // Multiple dots: check if second part is numeric (version number)
-                                const secondPart = assemblyAndChr.slice(firstDotIndex + 1, secondDotIndex);
-                                const isNumeric = secondPart.length > 0 && !Number.isNaN(+secondPart);
-                                if (isNumeric) {
-                                    // assembly.version.chr format
-                                    assemblyName = assemblyAndChr.slice(0, Math.max(0, secondDotIndex));
-                                    chr = assemblyAndChr.slice(Math.max(0, secondDotIndex + 1));
-                                }
-                                else {
-                                    // assembly.chr.more format
-                                    assemblyName = assemblyAndChr.slice(0, Math.max(0, firstDotIndex));
-                                    chr = assemblyAndChr.slice(Math.max(0, firstDotIndex + 1));
-                                }
-                            }
-                        }
+                        const { assemblyName, chr } = parseAssemblyAndChr(assemblyAndChr);
                         if (assemblyName) {
                             // Set first assembly name found (only once)
                             if (!firstAssemblyNameFound) {
@@ -119,8 +89,7 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
                             name: feature.get('name'),
                             score: feature.get('score'),
                             alignments,
-                            seq: alignments[refAssemblyName || query.assemblyName]?.seq ||
-                                alignments[firstAssemblyNameFound]?.seq,
+                            seq: selectReferenceSequence(alignments, refAssemblyName, query.assemblyName, firstAssemblyNameFound),
                         },
                     }));
                 }

package/dist/MafTabixAdapter/MafTabixAdapter.js.map

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package/dist/MafTabixAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const configSchema: import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
     /**
      * #slot
      */
@@ -24,7 +24,7 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
         type: string;
         defaultValue: string;
     };
-    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    index: import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
         /**
          * #slot index.location
          */
@@ -41,7 +41,7 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
             type: string;
             defaultValue: string;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     /**
      * #slot
      */
@@ -53,5 +53,5 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
             locationType: string;
         };
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/dist/MafTrack/configSchema.d.ts

@@ -1,5 +1,5 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
     name: {
         description: string;
         type: string;
@@ -25,8 +25,13 @@ export default function configSchemaF(pluginManager: PluginManager): import("@jb
         description: string;
         defaultValue: {};
     };
-    adapter: import("mobx-state-tree").IAnyModelType;
-    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    rpcDriverName: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    adapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
+    textSearching: import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
         indexingAttributes: {
             type: string;
             description: string;
@@ -37,10 +42,10 @@ export default function configSchemaF(pluginManager: PluginManager): import("@jb
             description: string;
             defaultValue: string[];
         };
-        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        textSearchAdapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
+    }, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
+    formatDetails: import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
         feature: {
             type: string;
             description: string;
@@ -63,8 +68,8 @@ export default function configSchemaF(pluginManager: PluginManager): import("@jb
             defaultValue: number;
             description: string;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    }, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
         config: {
             type: string;
             description: string;
@@ -75,5 +80,5 @@ export default function configSchemaF(pluginManager: PluginManager): import("@jb
             type: string;
             defaultValue: boolean;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, "trackId">>;
+    }, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, "trackId">>;

package/dist/index.js

@@ -6,6 +6,7 @@ import LinearMafRendererF from './LinearMafRenderer';
 import MafAddTrackWorkflowF from './MafAddTrackWorkflow';
 import MafGetSamplesF from './MafGetSamples';
 import MafGetSequencesF from './MafGetSequences';
+import MafSequenceWidgetF from './MafSequenceWidget';
 import MafTabixAdapterF from './MafTabixAdapter';
 import MafTrackF from './MafTrack';
 export default class MafViewerPlugin extends Plugin {
@@ -20,6 +21,7 @@ export default class MafViewerPlugin extends Plugin {
         MafAddTrackWorkflowF(pluginManager);
         MafGetSequencesF(pluginManager);
         MafGetSamplesF(pluginManager);
+        MafSequenceWidgetF(pluginManager);
     }
     configure(_pluginManager) { }
 }

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAGzC,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AACzC,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,iBAAiB,MAAM,oBAAoB,CAAA;AAClD,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,SAAS,MAAM,YAAY,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,eAAgB,SAAQ,MAAM;IACjD,IAAI,GAAG,iBAAiB,CAAA;IACxB,OAAO,GAAG,OAAO,CAAA;IAEjB,OAAO,CAAC,aAA4B;QAClC,cAAc,CAAC,aAAa,CAAC,CAAA;QAC7B,SAAS,CAAC,aAAa,CAAC,CAAA;QACxB,iBAAiB,CAAC,aAAa,CAAC,CAAA;QAChC,kBAAkB,CAAC,aAAa,CAAC,CAAA;QACjC,gBAAgB,CAAC,aAAa,CAAC,CAAA;QAC/B,oBAAoB,CAAC,aAAa,CAAC,CAAA;QACnC,gBAAgB,CAAC,aAAa,CAAC,CAAA;QAC/B,cAAc,CAAC,aAAa,CAAC,CAAA;QAC7B,kBAAkB,CAAC,aAAa,CAAC,CAAA;IACnC,CAAC;IAED,SAAS,CAAC,cAA6B,IAAG,CAAC;CAC5C"}