@jbrowse/plugin-linear-genome-view 5.0.0-beta.17 → 5.0.0-beta.19

package/esm/FeatureTrack/configSchema.d.ts

@@ -1,217 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #config FeatureTrack
- * #category track
- * Holds gene and other feature annotations, such as a GFF3 or BED file, which
- * `LinearBasicDisplay` usually draws.
- *
- * #example
- * A minimal hand-authored entry in the top-level `tracks` array — `adapter`
- * points at the data file, and the track opens with a `LinearBasicDisplay`:
- * ```js
- * {
- *   type: 'FeatureTrack',
- *   trackId: 'genes',
- *   name: 'Genes',
- *   assemblyNames: ['hg38'],
- *   adapter: {
- *     type: 'Gff3TabixAdapter',
- *     uri: 'https://example.com/genes.sorted.gff.gz',
- *   },
- * }
- * ```
- *
- * #example
- * The same track, colored. Rather than writing out the full `displays` array,
- * you can put appearance settings in a `displayDefaults` object — JBrowse works
- * out which display they belong to and applies them for you (here, the track's
- * `LinearBasicDisplay`), so you don't have to know display names. A `jexl:`
- * value gives per-feature coloring:
- * ```js
- * {
- *   type: 'FeatureTrack',
- *   trackId: 'genes',
- *   name: 'Genes',
- *   assemblyNames: ['hg38'],
- *   adapter: {
- *     type: 'Gff3TabixAdapter',
- *     uri: 'https://example.com/genes.sorted.gff.gz',
- *   },
- *   displayDefaults: { color: "jexl:feature.type=='CDS'?'red':'blue'" },
- * }
- * ```
- */
-declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
-    assemblyNames: {
-        type: "stringArray";
-    } & {
-        defaultValue: unknown;
-    };
-    category: {
-        type: "stringArray";
-    } & {
-        defaultValue: unknown;
-    };
-    description: {
-        type: "string";
-    } & {
-        defaultValue: string;
-    };
-    displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
-    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        readonly config: {
-            type: "frozen";
-        } & {
-            defaultValue: unknown;
-        };
-        readonly hideUris: {
-            type: "boolean";
-        } & {
-            defaultValue: boolean;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
-    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        readonly feature: {
-            type: "frozen";
-        } & {
-            defaultValue: unknown;
-        };
-        readonly subfeatures: {
-            type: "frozen";
-        } & {
-            defaultValue: unknown;
-        };
-        readonly depth: {
-            type: "maybeNumber";
-        };
-        readonly maxDepth: {
-            type: "maybeNumber";
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
-    metadata: {
-        type: "frozen";
-    } & {
-        defaultValue: unknown;
-    };
-    name: {
-        type: "string";
-    } & {
-        defaultValue: string;
-    };
-    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        readonly indexingAttributes: {
-            type: "stringArray";
-        } & {
-            defaultValue: unknown;
-        };
-        readonly indexingFeatureTypesToExclude: {
-            type: "stringArray";
-        } & {
-            defaultValue: unknown;
-        };
-        readonly indexingFeatureTypesToInclude: {
-            type: "stringArray";
-        } & {
-            defaultValue: unknown;
-        };
-        readonly textSearchAdapter: import("@jbrowse/mobx-state-tree").ITypeUnion<any, any, import("@jbrowse/core/configuration").PluggableConfigNode | undefined>;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
-    trackId: {
-        type: "string";
-    } & {
-        defaultValue: string;
-    };
-    type: {
-        type: "string";
-    } & {
-        defaultValue: string;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    readonly name: {
-        type: "string";
-    } & {
-        defaultValue: string;
-    };
-    readonly assemblyNames: {
-        type: "stringArray";
-    } & {
-        defaultValue: unknown;
-    };
-    readonly description: {
-        type: "string";
-    } & {
-        defaultValue: string;
-    };
-    readonly category: {
-        type: "stringArray";
-    } & {
-        defaultValue: unknown;
-    };
-    readonly metadata: {
-        type: "frozen";
-    } & {
-        defaultValue: unknown;
-    };
-    readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
-    readonly textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        readonly indexingAttributes: {
-            type: "stringArray";
-        } & {
-            defaultValue: unknown;
-        };
-        readonly indexingFeatureTypesToExclude: {
-            type: "stringArray";
-        } & {
-            defaultValue: unknown;
-        };
-        readonly indexingFeatureTypesToInclude: {
-            type: "stringArray";
-        } & {
-            defaultValue: unknown;
-        };
-        readonly textSearchAdapter: import("@jbrowse/mobx-state-tree").ITypeUnion<any, any, import("@jbrowse/core/configuration").PluggableConfigNode | undefined>;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
-    readonly displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
-    readonly formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        readonly feature: {
-            type: "frozen";
-        } & {
-            defaultValue: unknown;
-        };
-        readonly subfeatures: {
-            type: "frozen";
-        } & {
-            defaultValue: unknown;
-        };
-        readonly depth: {
-            type: "maybeNumber";
-        };
-        readonly maxDepth: {
-            type: "maybeNumber";
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
-    readonly formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        readonly config: {
-            type: "frozen";
-        } & {
-            defaultValue: unknown;
-        };
-        readonly hideUris: {
-            type: "boolean";
-        } & {
-            defaultValue: boolean;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
-    type: {
-        type: "string";
-    } & {
-        defaultValue: string;
-    };
-    trackId: {
-        type: "string";
-    } & {
-        defaultValue: string;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId", true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>, "trackId", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
-export default configSchema;

package/esm/FeatureTrack/configSchema.js

@@ -1,55 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
-/**
- * #config FeatureTrack
- * #category track
- * Holds gene and other feature annotations, such as a GFF3 or BED file, which
- * `LinearBasicDisplay` usually draws.
- *
- * #example
- * A minimal hand-authored entry in the top-level `tracks` array — `adapter`
- * points at the data file, and the track opens with a `LinearBasicDisplay`:
- * ```js
- * {
- *   type: 'FeatureTrack',
- *   trackId: 'genes',
- *   name: 'Genes',
- *   assemblyNames: ['hg38'],
- *   adapter: {
- *     type: 'Gff3TabixAdapter',
- *     uri: 'https://example.com/genes.sorted.gff.gz',
- *   },
- * }
- * ```
- *
- * #example
- * The same track, colored. Rather than writing out the full `displays` array,
- * you can put appearance settings in a `displayDefaults` object — JBrowse works
- * out which display they belong to and applies them for you (here, the track's
- * `LinearBasicDisplay`), so you don't have to know display names. A `jexl:`
- * value gives per-feature coloring:
- * ```js
- * {
- *   type: 'FeatureTrack',
- *   trackId: 'genes',
- *   name: 'Genes',
- *   assemblyNames: ['hg38'],
- *   adapter: {
- *     type: 'Gff3TabixAdapter',
- *     uri: 'https://example.com/genes.sorted.gff.gz',
- *   },
- *   displayDefaults: { color: "jexl:feature.type=='CDS'?'red':'blue'" },
- * }
- * ```
- */
-const configSchema = (pluginManager) => ConfigurationSchema('FeatureTrack', {}, {
-    /**
-     * #baseConfiguration
-     */
-    baseConfiguration: createBaseTrackConfig(pluginManager),
-    /**
-     * #identifier
-     */
-    explicitIdentifier: 'trackId',
-});
-export default configSchema;

package/esm/FeatureTrack/index.d.ts

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

package/esm/FeatureTrack/index.js

@@ -1,13 +0,0 @@
-import { TrackType, createBaseTrackModel, } from '@jbrowse/core/pluggableElementTypes';
-import configSchemaF from './configSchema.js';
-export default function FeatureTrackF(pm) {
-    pm.addTrackType(() => {
-        const configSchema = configSchemaF(pm);
-        return new TrackType({
-            name: 'FeatureTrack',
-            displayName: 'Feature track',
-            configSchema,
-            stateModel: createBaseTrackModel(pm, 'FeatureTrack', configSchema),
-        });
-    });
-}