@jbrowse/plugin-sequence 2.1.7 → 2.2.0
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.
- package/dist/BgzipFastaAdapter/configSchema.d.ts +2 -2
- package/dist/BgzipFastaAdapter/configSchema.js +18 -1
- package/dist/BgzipFastaAdapter/configSchema.js.map +1 -1
- package/dist/ChromSizesAdapter/configSchema.d.ts +2 -2
- package/dist/ChromSizesAdapter/configSchema.js +9 -1
- package/dist/ChromSizesAdapter/configSchema.js.map +1 -1
- package/dist/DivSequenceRenderer/configSchema.d.ts +2 -2
- package/dist/DivSequenceRenderer/configSchema.js +9 -1
- package/dist/DivSequenceRenderer/configSchema.js.map +1 -1
- package/dist/GCContentAdapter/configSchema.d.ts +2 -2
- package/dist/GCContentAdapter/configSchema.js +9 -1
- package/dist/GCContentAdapter/configSchema.js.map +1 -1
- package/dist/IndexedFastaAdapter/configSchema.d.ts +2 -2
- package/dist/IndexedFastaAdapter/configSchema.js +15 -1
- package/dist/IndexedFastaAdapter/configSchema.js.map +1 -1
- package/dist/LinearReferenceSequenceDisplay/configSchema.js +10 -1
- package/dist/LinearReferenceSequenceDisplay/configSchema.js.map +1 -1
- package/dist/LinearReferenceSequenceDisplay/model.d.ts +2 -2
- package/dist/ReferenceSequenceTrack/configSchema.js +33 -6
- package/dist/ReferenceSequenceTrack/configSchema.js.map +1 -1
- package/dist/SequenceSearchAdapter/configSchema.js +19 -0
- package/dist/SequenceSearchAdapter/configSchema.js.map +1 -1
- package/dist/TwoBitAdapter/configSchema.d.ts +2 -2
- package/dist/TwoBitAdapter/configSchema.js +12 -1
- package/dist/TwoBitAdapter/configSchema.js.map +1 -1
- package/esm/BgzipFastaAdapter/configSchema.d.ts +2 -2
- package/esm/BgzipFastaAdapter/configSchema.js +18 -1
- package/esm/BgzipFastaAdapter/configSchema.js.map +1 -1
- package/esm/ChromSizesAdapter/configSchema.d.ts +2 -2
- package/esm/ChromSizesAdapter/configSchema.js +9 -1
- package/esm/ChromSizesAdapter/configSchema.js.map +1 -1
- package/esm/DivSequenceRenderer/configSchema.d.ts +2 -2
- package/esm/DivSequenceRenderer/configSchema.js +9 -1
- package/esm/DivSequenceRenderer/configSchema.js.map +1 -1
- package/esm/GCContentAdapter/configSchema.d.ts +2 -2
- package/esm/GCContentAdapter/configSchema.js +9 -1
- package/esm/GCContentAdapter/configSchema.js.map +1 -1
- package/esm/IndexedFastaAdapter/configSchema.d.ts +2 -2
- package/esm/IndexedFastaAdapter/configSchema.js +15 -1
- package/esm/IndexedFastaAdapter/configSchema.js.map +1 -1
- package/esm/LinearReferenceSequenceDisplay/configSchema.js +10 -1
- package/esm/LinearReferenceSequenceDisplay/configSchema.js.map +1 -1
- package/esm/LinearReferenceSequenceDisplay/model.d.ts +2 -2
- package/esm/ReferenceSequenceTrack/configSchema.js +33 -6
- package/esm/ReferenceSequenceTrack/configSchema.js.map +1 -1
- package/esm/SequenceSearchAdapter/configSchema.js +19 -0
- package/esm/SequenceSearchAdapter/configSchema.js.map +1 -1
- package/esm/TwoBitAdapter/configSchema.d.ts +2 -2
- package/esm/TwoBitAdapter/configSchema.js +12 -1
- package/esm/TwoBitAdapter/configSchema.js.map +1 -1
- package/package.json +2 -2
- package/src/BgzipFastaAdapter/configSchema.ts +18 -1
- package/src/ChromSizesAdapter/configSchema.ts +11 -1
- package/src/DivSequenceRenderer/configSchema.ts +11 -1
- package/src/GCContentAdapter/configSchema.ts +11 -1
- package/src/IndexedFastaAdapter/configSchema.ts +16 -1
- package/src/LinearReferenceSequenceDisplay/configSchema.ts +11 -1
- package/src/ReferenceSequenceTrack/configSchema.ts +40 -6
- package/src/SequenceSearchAdapter/configSchema.ts +20 -0
- package/src/TwoBitAdapter/configSchema.ts +14 -1
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@@ -1 +1 @@
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-
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,
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{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,mBAAmB,CAC7C,qBAAqB,EACrB;IACE;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,iBAAiB,EAAE,YAAY,EAAE,aAAa,EAAE;KACtE;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,qBAAqB,EAAE,YAAY,EAAE,aAAa,EAAE;KAC1E;IACD;;OAEG;IACH,gBAAgB,EAAE;QAChB,WAAW,EAAE,wBAAwB;QACrC,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,2BAA2B;YAChC,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,eAAe,mBAAmB,CAAA"}
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@@ -1,4 +1,13 @@
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import { ConfigurationSchema } from '@jbrowse/core/configuration';
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import { default as divSequenceRendererConfigSchema } from '../DivSequenceRenderer/configSchema';
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/**
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* #config LinearReferenceSequenceDisplay
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*/
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function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
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export const configSchema = ConfigurationSchema('LinearReferenceSequenceDisplay', {
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/**
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* #slot
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*/
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renderer: divSequenceRendererConfigSchema,
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}, { explicitIdentifier: 'displayId', explicitlyTyped: true });
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//# sourceMappingURL=configSchema.js.map
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{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,OAAO,IAAI,+BAA+B,EAAE,MAAM,qCAAqC,CAAA;AAEhG,MAAM,CAAC,MAAM,YAAY,GAAG,mBAAmB,CAC7C,gCAAgC,EAChC,
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{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,OAAO,IAAI,+BAA+B,EAAE,MAAM,qCAAqC,CAAA;AAEhG;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,CAAC,MAAM,YAAY,GAAG,mBAAmB,CAC7C,gCAAgC,EAChC;IACE;;OAEG;IACH,QAAQ,EAAE,+BAA+B;CAC1C,EACD,EAAE,kBAAkB,EAAE,WAAW,EAAE,eAAe,EAAE,IAAI,EAAE,CAC3D,CAAA"}
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@@ -182,7 +182,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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}[];
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renderProps(): any;
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} & {
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renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/
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renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
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overrideHeight: number;
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}): Promise<JSX.Element>;
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} & {
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@@ -202,8 +202,8 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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}[];
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}, import("mobx-state-tree")._NotCustomized, {
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type: string;
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height: number;
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id: string;
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height: number;
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rpcDriverName: string | undefined;
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userBpPerPxLimit: number | undefined;
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userByteSizeLimit: number | undefined;
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/* eslint-disable @typescript-eslint/no-explicit-any */
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import { types } from 'mobx-state-tree';
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import { ConfigurationSchema } from '@jbrowse/core/configuration';
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// Note: this is primarily a copy of createBaseTrackConfig, except with a
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// subset of the config slots, to avoid including fields that don't make sense
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// for the ReferenceSequenceTrack
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/**
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* #config ReferenceSequenceTrack
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* used to display base level DNA sequence tracks
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*/
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function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
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export function createReferenceSeqTrackConfig(pluginManager) {
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return ConfigurationSchema('ReferenceSequenceTrack', {
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/**
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* #slot
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* configuration for track adapter
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*/
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adapter: pluginManager.pluggableConfigSchemaType('adapter'),
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/**
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* #slot
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* configuration for the displays e.g. LinearReferenceSequenceDisplay
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*/
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displays: types.array(pluginManager.pluggableConfigSchemaType('display')),
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/**
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* #slot
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*/
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name: {
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type: 'string',
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description: 'optional track name',
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description: 'optional track name, otherwise uses the "Reference sequence (assemblyName)"',
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defaultValue: '',
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},
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/**
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* #slot
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*/
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metadata: {
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type: 'frozen',
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description: 'anything to add about this track',
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defaultValue: {},
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},
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formatAbout: ConfigurationSchema('FormatAbout', {
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/**
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* #slot formatAbout.config
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*/
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config: {
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type: 'frozen',
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description: 'formats configuration in about dialog',
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defaultValue: {},
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contextVariable: ['config'],
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},
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/**
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* #slot formatAbout.hideUris
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*/
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hideUris: {
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type: 'boolean',
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defaultValue: false,
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}
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return { ...snap, displays };
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},
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/**
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* #identifier
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* all tracks have a globally unique 'trackId'
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*/
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explicitIdentifier: 'trackId',
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actions: (self) => ({
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{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/ReferenceSequenceTrack/configSchema.ts"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACvC,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAGjE
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{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/ReferenceSequenceTrack/configSchema.ts"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACvC,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAGjE,yEAAyE;AACzE,8EAA8E;AAC9E,iCAAiC;AAEjC;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,UAAU,6BAA6B,CAAC,aAA4B;IACxE,OAAO,mBAAmB,CACxB,wBAAwB,EACxB;QACE;;;WAGG;QACH,OAAO,EAAE,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC;QAE3D;;;WAGG;QACH,QAAQ,EAAE,KAAK,CAAC,KAAK,CAAC,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC,CAAC;QAEzE;;WAEG;QACH,IAAI,EAAE;YACJ,IAAI,EAAE,QAAQ;YACd,WAAW,EACT,6EAA6E;YAC/E,YAAY,EAAE,EAAE;SACjB;QAED;;WAEG;QACH,QAAQ,EAAE;YACR,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,kCAAkC;YAC/C,YAAY,EAAE,EAAE;SACjB;QAED,WAAW,EAAE,mBAAmB,CAAC,aAAa,EAAE;YAC9C;;eAEG;YACH,MAAM,EAAE;gBACN,IAAI,EAAE,QAAQ;gBACd,WAAW,EAAE,uCAAuC;gBACpD,YAAY,EAAE,EAAE;gBAChB,eAAe,EAAE,CAAC,QAAQ,CAAC;aAC5B;YAED;;eAEG;YACH,QAAQ,EAAE;gBACR,IAAI,EAAE,SAAS;gBACf,YAAY,EAAE,KAAK;aACpB;SACF,CAAC;KACH,EACD;QACE,kBAAkB,EAAE,CAAC,CAAC,EAAE;YACtB,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAA;YAC1C,MAAM,YAAY,GAAG,IAAI,GAAG,EAAE,CAAA;YAC9B,MAAM,EAAE,QAAQ,GAAG,EAAE,EAAE,GAAG,IAAI,CAAA;YAC9B,IAAI,IAAI,CAAC,OAAO,KAAK,eAAe,EAAE;gBACpC,oEAAoE;gBACpE,oEAAoE;gBACpE,WAAW;gBACX,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAM,EAAE,EAAE,CAAC,CAAC,IAAI,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;gBAC3D,MAAM,SAAS,GAAG,aAAa,CAAC,YAAY,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACvD,SAAS,CAAC,YAAY,CAAC,OAAO,CAAC,WAAW,CAAC,EAAE;oBAC3C,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,WAAW,CAAC,IAAI,CAAC,EAAE;wBACvC,QAAQ,CAAC,IAAI,CAAC;4BACZ,SAAS,EAAE,GAAG,IAAI,CAAC,OAAO,IAAI,WAAW,CAAC,IAAI,EAAE;4BAChD,IAAI,EAAE,WAAW,CAAC,IAAI;yBACvB,CAAC,CAAA;qBACH;gBACH,CAAC,CAAC,CAAA;aACH;YACD,OAAO,EAAE,GAAG,IAAI,EAAE,QAAQ,EAAE,CAAA;QAC9B,CAAC;QACD;;;WAGG;QACH,kBAAkB,EAAE,SAAS;QAC7B,eAAe,EAAE,IAAI;QACrB,OAAO,EAAE,CAAC,IAAS,EAAE,EAAE,CAAC,CAAC;YACvB,cAAc,CAAC,WAAgD;gBAC7D,MAAM,EAAE,IAAI,EAAE,GAAG,WAAW,CAAA;gBAC5B,IAAI,CAAC,IAAI,EAAE;oBACT,MAAM,IAAI,KAAK,CAAC,wBAAwB,IAAI,EAAE,CAAC,CAAA;iBAChD;gBACD,MAAM,OAAO,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAChC,CAAC,CAAM,EAAE,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,SAAS,KAAK,WAAW,CAAC,SAAS,CACvD,CAAA;gBACD,IAAI,OAAO,EAAE;oBACX,OAAO,OAAO,CAAA;iBACf;gBACD,MAAM,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,CAAC,CAAA;gBAC9C,OAAO,IAAI,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;YAClC,CAAC;SACF,CAAC;KACH,CACF,CAAA;AACH,CAAC"}
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* #config SequenceSearchAdapter
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function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
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const configSchema = ConfigurationSchema('SequenceSearchAdapter', {
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search: {
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description: 'Search string or regex to search for',
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*/
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sequenceAdapter: {
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searchForward: {
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searchReverse: {
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caseInsensitive: {
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{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SequenceSearchAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,MAAM,YAAY,GAAG,mBAAmB,CACtC,uBAAuB,EACvB;IACE,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,sCAAsC;KACpD;IACD,eAAe,EAAE;QACf,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,IAAI;KACnB;IACD,aAAa,EAAE;QACb,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,IAAI;KACnB;IACD,aAAa,EAAE;QACb,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,IAAI;KACnB;IACD,eAAe,EAAE;QACf,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,YAAY,CAAA"}
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+
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SequenceSearchAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,mBAAmB,CACtC,uBAAuB,EACvB;IACE;;OAEG;IACH,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,sCAAsC;KACpD;IACD;;OAEG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,IAAI;KACnB;IACD;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,IAAI;KACnB;IACD;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,IAAI;KACnB;IACD;;OAEG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,YAAY,CAAA"}
|
|
@@ -1,2 +1,2 @@
|
|
|
1
|
-
declare const
|
|
2
|
-
export default
|
|
1
|
+
declare const TwoBitAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
|
|
2
|
+
export default TwoBitAdapter;
|
|
@@ -1,9 +1,19 @@
|
|
|
1
1
|
import { ConfigurationSchema } from '@jbrowse/core/configuration';
|
|
2
|
-
|
|
2
|
+
/**
|
|
3
|
+
* #config TwoBitAdapter
|
|
4
|
+
*/
|
|
5
|
+
function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
|
|
6
|
+
const TwoBitAdapter = ConfigurationSchema('TwoBitAdapter', {
|
|
7
|
+
/**
|
|
8
|
+
* #slot
|
|
9
|
+
*/
|
|
3
10
|
twoBitLocation: {
|
|
4
11
|
type: 'fileLocation',
|
|
5
12
|
defaultValue: { uri: '/path/to/my.2bit', locationType: 'UriLocation' },
|
|
6
13
|
},
|
|
14
|
+
/**
|
|
15
|
+
* #slot
|
|
16
|
+
*/
|
|
7
17
|
chromSizesLocation: {
|
|
8
18
|
type: 'fileLocation',
|
|
9
19
|
defaultValue: {
|
|
@@ -13,4 +23,5 @@ export default ConfigurationSchema('TwoBitAdapter', {
|
|
|
13
23
|
description: 'An optional chrom.sizes file can be supplied to speed up loading since parsing the twobit file can take time',
|
|
14
24
|
},
|
|
15
25
|
}, { explicitlyTyped: true });
|
|
26
|
+
export default TwoBitAdapter;
|
|
16
27
|
//# sourceMappingURL=configSchema.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,
|
|
1
|
+
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,aAAa,GAAG,mBAAmB,CACvC,eAAe,EACf;IACE;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,kBAAkB,EAAE,YAAY,EAAE,aAAa,EAAE;KACvE;IACD;;OAEG;IACH,kBAAkB,EAAE;QAClB,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,8BAA8B;YACnC,YAAY,EAAE,aAAa;SAC5B;QACD,WAAW,EACT,8GAA8G;KACjH;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,aAAa,CAAA"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-sequence",
|
|
3
|
-
"version": "2.
|
|
3
|
+
"version": "2.2.0",
|
|
4
4
|
"description": "JBrowse 2 sequence adapters, tracks, etc.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -59,5 +59,5 @@
|
|
|
59
59
|
"distModule": "esm/index.js",
|
|
60
60
|
"srcModule": "src/index.ts",
|
|
61
61
|
"module": "esm/index.js",
|
|
62
|
-
"gitHead": "
|
|
62
|
+
"gitHead": "cf31db8d833117f8822510340664fb3f045975cb"
|
|
63
63
|
}
|
|
@@ -1,12 +1,22 @@
|
|
|
1
1
|
import { ConfigurationSchema } from '@jbrowse/core/configuration'
|
|
2
|
+
/**
|
|
3
|
+
* #config BgzipFastaAdapter
|
|
4
|
+
*/
|
|
5
|
+
function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
|
|
2
6
|
|
|
3
|
-
|
|
7
|
+
const BgzipFastaAdapter = ConfigurationSchema(
|
|
4
8
|
'BgzipFastaAdapter',
|
|
5
9
|
{
|
|
10
|
+
/**
|
|
11
|
+
* #slot
|
|
12
|
+
*/
|
|
6
13
|
fastaLocation: {
|
|
7
14
|
type: 'fileLocation',
|
|
8
15
|
defaultValue: { uri: '/path/to/seq.fa.gz', locationType: 'UriLocation' },
|
|
9
16
|
},
|
|
17
|
+
/**
|
|
18
|
+
* #slot
|
|
19
|
+
*/
|
|
10
20
|
faiLocation: {
|
|
11
21
|
type: 'fileLocation',
|
|
12
22
|
defaultValue: {
|
|
@@ -14,6 +24,9 @@ export default ConfigurationSchema(
|
|
|
14
24
|
locationType: 'UriLocation',
|
|
15
25
|
},
|
|
16
26
|
},
|
|
27
|
+
/**
|
|
28
|
+
* #slot
|
|
29
|
+
*/
|
|
17
30
|
metadataLocation: {
|
|
18
31
|
description: 'Optional metadata file',
|
|
19
32
|
type: 'fileLocation',
|
|
@@ -22,6 +35,9 @@ export default ConfigurationSchema(
|
|
|
22
35
|
locationType: 'UriLocation',
|
|
23
36
|
},
|
|
24
37
|
},
|
|
38
|
+
/**
|
|
39
|
+
* #slot
|
|
40
|
+
*/
|
|
25
41
|
gziLocation: {
|
|
26
42
|
type: 'fileLocation',
|
|
27
43
|
defaultValue: {
|
|
@@ -32,3 +48,4 @@ export default ConfigurationSchema(
|
|
|
32
48
|
},
|
|
33
49
|
{ explicitlyTyped: true },
|
|
34
50
|
)
|
|
51
|
+
export default BgzipFastaAdapter
|
|
@@ -1,8 +1,16 @@
|
|
|
1
1
|
import { ConfigurationSchema } from '@jbrowse/core/configuration'
|
|
2
2
|
|
|
3
|
-
|
|
3
|
+
/**
|
|
4
|
+
* #config ChromSizesAdapter
|
|
5
|
+
*/
|
|
6
|
+
function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
|
|
7
|
+
|
|
8
|
+
const ChromSizesAdapter = ConfigurationSchema(
|
|
4
9
|
'ChromSizesAdapter',
|
|
5
10
|
{
|
|
11
|
+
/**
|
|
12
|
+
* #slot
|
|
13
|
+
*/
|
|
6
14
|
chromSizesLocation: {
|
|
7
15
|
type: 'fileLocation',
|
|
8
16
|
defaultValue: {
|
|
@@ -13,3 +21,5 @@ export default ConfigurationSchema(
|
|
|
13
21
|
},
|
|
14
22
|
{ explicitlyTyped: true },
|
|
15
23
|
)
|
|
24
|
+
|
|
25
|
+
export default ChromSizesAdapter
|
|
@@ -1,8 +1,16 @@
|
|
|
1
1
|
import { ConfigurationSchema } from '@jbrowse/core/configuration'
|
|
2
2
|
|
|
3
|
-
|
|
3
|
+
/**
|
|
4
|
+
* #config DivSequenceRenderer
|
|
5
|
+
*/
|
|
6
|
+
function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
|
|
7
|
+
|
|
8
|
+
const DivSequenceRenderer = ConfigurationSchema(
|
|
4
9
|
'DivSequenceRenderer',
|
|
5
10
|
{
|
|
11
|
+
/**
|
|
12
|
+
* #slot
|
|
13
|
+
*/
|
|
6
14
|
height: {
|
|
7
15
|
type: 'number',
|
|
8
16
|
description: 'height in pixels of each line of sequence',
|
|
@@ -11,3 +19,5 @@ export default ConfigurationSchema(
|
|
|
11
19
|
},
|
|
12
20
|
{ explicitlyTyped: true },
|
|
13
21
|
)
|
|
22
|
+
|
|
23
|
+
export default DivSequenceRenderer
|
|
@@ -1,12 +1,22 @@
|
|
|
1
1
|
import PluginManager from '@jbrowse/core/PluginManager'
|
|
2
2
|
import { ConfigurationSchema } from '@jbrowse/core/configuration'
|
|
3
3
|
|
|
4
|
-
|
|
4
|
+
/**
|
|
5
|
+
* #config GCContentAdapter
|
|
6
|
+
*/
|
|
7
|
+
function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
|
|
8
|
+
|
|
9
|
+
const GCContentAdapterF = (pluginManager: PluginManager) => {
|
|
5
10
|
return ConfigurationSchema(
|
|
6
11
|
'GCContentAdapter',
|
|
7
12
|
{
|
|
13
|
+
/**
|
|
14
|
+
* #slot
|
|
15
|
+
*/
|
|
8
16
|
sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
|
|
9
17
|
},
|
|
10
18
|
{ explicitlyTyped: true },
|
|
11
19
|
)
|
|
12
20
|
}
|
|
21
|
+
|
|
22
|
+
export default GCContentAdapterF
|
|
@@ -1,16 +1,30 @@
|
|
|
1
1
|
import { ConfigurationSchema } from '@jbrowse/core/configuration'
|
|
2
2
|
|
|
3
|
-
|
|
3
|
+
/**
|
|
4
|
+
* #config IndexedFastaAdapter
|
|
5
|
+
*/
|
|
6
|
+
function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
|
|
7
|
+
|
|
8
|
+
const IndexedFastaAdapter = ConfigurationSchema(
|
|
4
9
|
'IndexedFastaAdapter',
|
|
5
10
|
{
|
|
11
|
+
/**
|
|
12
|
+
* #slot
|
|
13
|
+
*/
|
|
6
14
|
fastaLocation: {
|
|
7
15
|
type: 'fileLocation',
|
|
8
16
|
defaultValue: { uri: '/path/to/seq.fa', locationType: 'UriLocation' },
|
|
9
17
|
},
|
|
18
|
+
/**
|
|
19
|
+
* #slot
|
|
20
|
+
*/
|
|
10
21
|
faiLocation: {
|
|
11
22
|
type: 'fileLocation',
|
|
12
23
|
defaultValue: { uri: '/path/to/seq.fa.fai', locationType: 'UriLocation' },
|
|
13
24
|
},
|
|
25
|
+
/**
|
|
26
|
+
* #slot
|
|
27
|
+
*/
|
|
14
28
|
metadataLocation: {
|
|
15
29
|
description: 'Optional metadata file',
|
|
16
30
|
type: 'fileLocation',
|
|
@@ -22,3 +36,4 @@ export default ConfigurationSchema(
|
|
|
22
36
|
},
|
|
23
37
|
{ explicitlyTyped: true },
|
|
24
38
|
)
|
|
39
|
+
export default IndexedFastaAdapter
|
|
@@ -1,8 +1,18 @@
|
|
|
1
1
|
import { ConfigurationSchema } from '@jbrowse/core/configuration'
|
|
2
2
|
import { default as divSequenceRendererConfigSchema } from '../DivSequenceRenderer/configSchema'
|
|
3
3
|
|
|
4
|
+
/**
|
|
5
|
+
* #config LinearReferenceSequenceDisplay
|
|
6
|
+
*/
|
|
7
|
+
function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
|
|
8
|
+
|
|
4
9
|
export const configSchema = ConfigurationSchema(
|
|
5
10
|
'LinearReferenceSequenceDisplay',
|
|
6
|
-
{
|
|
11
|
+
{
|
|
12
|
+
/**
|
|
13
|
+
* #slot
|
|
14
|
+
*/
|
|
15
|
+
renderer: divSequenceRendererConfigSchema,
|
|
16
|
+
},
|
|
7
17
|
{ explicitIdentifier: 'displayId', explicitlyTyped: true },
|
|
8
18
|
)
|
|
@@ -3,22 +3,45 @@ import { types } from 'mobx-state-tree'
|
|
|
3
3
|
import { ConfigurationSchema } from '@jbrowse/core/configuration'
|
|
4
4
|
import PluginManager from '@jbrowse/core/PluginManager'
|
|
5
5
|
|
|
6
|
-
|
|
7
|
-
|
|
8
|
-
|
|
9
|
-
|
|
10
|
-
|
|
6
|
+
// Note: this is primarily a copy of createBaseTrackConfig, except with a
|
|
7
|
+
// subset of the config slots, to avoid including fields that don't make sense
|
|
8
|
+
// for the ReferenceSequenceTrack
|
|
9
|
+
|
|
10
|
+
/**
|
|
11
|
+
* #config ReferenceSequenceTrack
|
|
12
|
+
* used to display base level DNA sequence tracks
|
|
13
|
+
*/
|
|
14
|
+
function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
|
|
15
|
+
|
|
11
16
|
export function createReferenceSeqTrackConfig(pluginManager: PluginManager) {
|
|
12
17
|
return ConfigurationSchema(
|
|
13
18
|
'ReferenceSequenceTrack',
|
|
14
19
|
{
|
|
20
|
+
/**
|
|
21
|
+
* #slot
|
|
22
|
+
* configuration for track adapter
|
|
23
|
+
*/
|
|
15
24
|
adapter: pluginManager.pluggableConfigSchemaType('adapter'),
|
|
25
|
+
|
|
26
|
+
/**
|
|
27
|
+
* #slot
|
|
28
|
+
* configuration for the displays e.g. LinearReferenceSequenceDisplay
|
|
29
|
+
*/
|
|
16
30
|
displays: types.array(pluginManager.pluggableConfigSchemaType('display')),
|
|
31
|
+
|
|
32
|
+
/**
|
|
33
|
+
* #slot
|
|
34
|
+
*/
|
|
17
35
|
name: {
|
|
18
36
|
type: 'string',
|
|
19
|
-
description:
|
|
37
|
+
description:
|
|
38
|
+
'optional track name, otherwise uses the "Reference sequence (assemblyName)"',
|
|
20
39
|
defaultValue: '',
|
|
21
40
|
},
|
|
41
|
+
|
|
42
|
+
/**
|
|
43
|
+
* #slot
|
|
44
|
+
*/
|
|
22
45
|
metadata: {
|
|
23
46
|
type: 'frozen',
|
|
24
47
|
description: 'anything to add about this track',
|
|
@@ -26,12 +49,19 @@ export function createReferenceSeqTrackConfig(pluginManager: PluginManager) {
|
|
|
26
49
|
},
|
|
27
50
|
|
|
28
51
|
formatAbout: ConfigurationSchema('FormatAbout', {
|
|
52
|
+
/**
|
|
53
|
+
* #slot formatAbout.config
|
|
54
|
+
*/
|
|
29
55
|
config: {
|
|
30
56
|
type: 'frozen',
|
|
31
57
|
description: 'formats configuration in about dialog',
|
|
32
58
|
defaultValue: {},
|
|
33
59
|
contextVariable: ['config'],
|
|
34
60
|
},
|
|
61
|
+
|
|
62
|
+
/**
|
|
63
|
+
* #slot formatAbout.hideUris
|
|
64
|
+
*/
|
|
35
65
|
hideUris: {
|
|
36
66
|
type: 'boolean',
|
|
37
67
|
defaultValue: false,
|
|
@@ -60,6 +90,10 @@ export function createReferenceSeqTrackConfig(pluginManager: PluginManager) {
|
|
|
60
90
|
}
|
|
61
91
|
return { ...snap, displays }
|
|
62
92
|
},
|
|
93
|
+
/**
|
|
94
|
+
* #identifier
|
|
95
|
+
* all tracks have a globally unique 'trackId'
|
|
96
|
+
*/
|
|
63
97
|
explicitIdentifier: 'trackId',
|
|
64
98
|
explicitlyTyped: true,
|
|
65
99
|
actions: (self: any) => ({
|
|
@@ -1,25 +1,45 @@
|
|
|
1
1
|
import { ConfigurationSchema } from '@jbrowse/core/configuration'
|
|
2
2
|
|
|
3
|
+
/**
|
|
4
|
+
* #config SequenceSearchAdapter
|
|
5
|
+
*/
|
|
6
|
+
function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
|
|
7
|
+
|
|
3
8
|
const configSchema = ConfigurationSchema(
|
|
4
9
|
'SequenceSearchAdapter',
|
|
5
10
|
{
|
|
11
|
+
/**
|
|
12
|
+
* #slot
|
|
13
|
+
*/
|
|
6
14
|
search: {
|
|
7
15
|
type: 'string',
|
|
8
16
|
defaultValue: '',
|
|
9
17
|
description: 'Search string or regex to search for',
|
|
10
18
|
},
|
|
19
|
+
/**
|
|
20
|
+
* #slot
|
|
21
|
+
*/
|
|
11
22
|
sequenceAdapter: {
|
|
12
23
|
type: 'frozen',
|
|
13
24
|
defaultValue: null,
|
|
14
25
|
},
|
|
26
|
+
/**
|
|
27
|
+
* #slot
|
|
28
|
+
*/
|
|
15
29
|
searchForward: {
|
|
16
30
|
type: 'boolean',
|
|
17
31
|
defaultValue: true,
|
|
18
32
|
},
|
|
33
|
+
/**
|
|
34
|
+
* #slot
|
|
35
|
+
*/
|
|
19
36
|
searchReverse: {
|
|
20
37
|
type: 'boolean',
|
|
21
38
|
defaultValue: true,
|
|
22
39
|
},
|
|
40
|
+
/**
|
|
41
|
+
* #slot
|
|
42
|
+
*/
|
|
23
43
|
caseInsensitive: {
|
|
24
44
|
type: 'boolean',
|
|
25
45
|
defaultValue: true,
|
|
@@ -1,12 +1,23 @@
|
|
|
1
1
|
import { ConfigurationSchema } from '@jbrowse/core/configuration'
|
|
2
2
|
|
|
3
|
-
|
|
3
|
+
/**
|
|
4
|
+
* #config TwoBitAdapter
|
|
5
|
+
*/
|
|
6
|
+
function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
|
|
7
|
+
|
|
8
|
+
const TwoBitAdapter = ConfigurationSchema(
|
|
4
9
|
'TwoBitAdapter',
|
|
5
10
|
{
|
|
11
|
+
/**
|
|
12
|
+
* #slot
|
|
13
|
+
*/
|
|
6
14
|
twoBitLocation: {
|
|
7
15
|
type: 'fileLocation',
|
|
8
16
|
defaultValue: { uri: '/path/to/my.2bit', locationType: 'UriLocation' },
|
|
9
17
|
},
|
|
18
|
+
/**
|
|
19
|
+
* #slot
|
|
20
|
+
*/
|
|
10
21
|
chromSizesLocation: {
|
|
11
22
|
type: 'fileLocation',
|
|
12
23
|
defaultValue: {
|
|
@@ -19,3 +30,5 @@ export default ConfigurationSchema(
|
|
|
19
30
|
},
|
|
20
31
|
{ explicitlyTyped: true },
|
|
21
32
|
)
|
|
33
|
+
|
|
34
|
+
export default TwoBitAdapter
|