@jbrowse/plugin-sequence 2.1.6 → 2.2.0

package/esm/IndexedFastaAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,qBAAqB,EACrB;IACE,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,iBAAiB,EAAE,YAAY,EAAE,aAAa,EAAE;KACtE;IACD,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,qBAAqB,EAAE,YAAY,EAAE,aAAa,EAAE;KAC1E;IACD,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"}
+{"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"}

package/esm/LinearReferenceSequenceDisplay/configSchema.js

@@ -1,4 +1,13 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { default as divSequenceRendererConfigSchema } from '../DivSequenceRenderer/configSchema';
-export const configSchema = ConfigurationSchema('LinearReferenceSequenceDisplay', { renderer: divSequenceRendererConfigSchema }, { explicitIdentifier: 'displayId', explicitlyTyped: true });
+/**
+ * #config LinearReferenceSequenceDisplay
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+export const configSchema = ConfigurationSchema('LinearReferenceSequenceDisplay', {
+    /**
+     * #slot
+     */
+    renderer: divSequenceRendererConfigSchema,
+}, { explicitIdentifier: 'displayId', explicitlyTyped: true });
 //# sourceMappingURL=configSchema.js.map

package/esm/LinearReferenceSequenceDisplay/configSchema.js.map

@@ -1 +1 @@
-{"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,EAAE,QAAQ,EAAE,+BAA+B,EAAE,EAC7C,EAAE,kBAAkB,EAAE,WAAW,EAAE,eAAe,EAAE,IAAI,EAAE,CAC3D,CAAA"}
+{"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"}

package/esm/LinearReferenceSequenceDisplay/model.d.ts

@@ -182,7 +182,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     }[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").ExportSvgOptions & {
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
         overrideHeight: number;
     }): Promise<JSX.Element>;
 } & {
@@ -202,8 +202,8 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     }[];
 }, import("mobx-state-tree")._NotCustomized, {
     type: string;
-    height: number;
     id: string;
+    height: number;
     rpcDriverName: string | undefined;
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;

package/esm/ReferenceSequenceTrack/configSchema.js

@@ -1,32 +1,55 @@
 /* eslint-disable @typescript-eslint/no-explicit-any */
 import { types } from 'mobx-state-tree';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/*
-Note: this is primarily a copy of createBaseTrackConfig, except with a subset
-of the config slots, to avoid including fields that don't make sense for the
-ReferenceSequenceTrack
-*/
+// Note: this is primarily a copy of createBaseTrackConfig, except with a
+// subset of the config slots, to avoid including fields that don't make sense
+// for the ReferenceSequenceTrack
+/**
+ * #config ReferenceSequenceTrack
+ * used to display base level DNA sequence tracks
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 export function createReferenceSeqTrackConfig(pluginManager) {
     return ConfigurationSchema('ReferenceSequenceTrack', {
+        /**
+         * #slot
+         * configuration for track adapter
+         */
         adapter: pluginManager.pluggableConfigSchemaType('adapter'),
+        /**
+         * #slot
+         * configuration for the displays e.g. LinearReferenceSequenceDisplay
+         */
         displays: types.array(pluginManager.pluggableConfigSchemaType('display')),
+        /**
+         * #slot
+         */
         name: {
             type: 'string',
-            description: 'optional track name',
+            description: 'optional track name, otherwise uses the "Reference sequence (assemblyName)"',
             defaultValue: '',
         },
+        /**
+         * #slot
+         */
         metadata: {
             type: 'frozen',
             description: 'anything to add about this track',
             defaultValue: {},
         },
         formatAbout: ConfigurationSchema('FormatAbout', {
+            /**
+             * #slot formatAbout.config
+             */
             config: {
                 type: 'frozen',
                 description: 'formats configuration in about dialog',
                 defaultValue: {},
                 contextVariable: ['config'],
             },
+            /**
+             * #slot formatAbout.hideUris
+             */
             hideUris: {
                 type: 'boolean',
                 defaultValue: false,
@@ -54,6 +77,10 @@ export function createReferenceSeqTrackConfig(pluginManager) {
             }
             return { ...snap, displays };
         },
+        /**
+         * #identifier
+         * all tracks have a globally unique 'trackId'
+         */
         explicitIdentifier: 'trackId',
         explicitlyTyped: true,
         actions: (self) => ({

package/esm/ReferenceSequenceTrack/configSchema.js.map

@@ -1 +1 @@
-{"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;;;;EAIE;AACF,MAAM,UAAU,6BAA6B,CAAC,aAA4B;IACxE,OAAO,mBAAmB,CACxB,wBAAwB,EACxB;QACE,OAAO,EAAE,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC;QAC3D,QAAQ,EAAE,KAAK,CAAC,KAAK,CAAC,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC,CAAC;QACzE,IAAI,EAAE;YACJ,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,EAAE;SACjB;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,kCAAkC;YAC/C,YAAY,EAAE,EAAE;SACjB;QAED,WAAW,EAAE,mBAAmB,CAAC,aAAa,EAAE;YAC9C,MAAM,EAAE;gBACN,IAAI,EAAE,QAAQ;gBACd,WAAW,EAAE,uCAAuC;gBACpD,YAAY,EAAE,EAAE;gBAChB,eAAe,EAAE,CAAC,QAAQ,CAAC;aAC5B;YACD,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,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"}
+{"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"}

package/esm/SequenceSearchAdapter/configSchema.js

@@ -1,22 +1,41 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config SequenceSearchAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 const configSchema = ConfigurationSchema('SequenceSearchAdapter', {
+    /**
+     * #slot
+     */
     search: {
         type: 'string',
         defaultValue: '',
         description: 'Search string or regex to search for',
     },
+    /**
+     * #slot
+     */
     sequenceAdapter: {
         type: 'frozen',
         defaultValue: null,
     },
+    /**
+     * #slot
+     */
     searchForward: {
         type: 'boolean',
         defaultValue: true,
     },
+    /**
+     * #slot
+     */
     searchReverse: {
         type: 'boolean',
         defaultValue: true,
     },
+    /**
+     * #slot
+     */
     caseInsensitive: {
         type: 'boolean',
         defaultValue: true,

package/esm/SequenceSearchAdapter/configSchema.js.map

@@ -1 +1 @@
-{"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"}
+{"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"}

package/esm/TwoBitAdapter/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const TwoBitAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default TwoBitAdapter;

package/esm/TwoBitAdapter/configSchema.js

@@ -1,9 +1,19 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-export default ConfigurationSchema('TwoBitAdapter', {
+/**
+ * #config TwoBitAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const TwoBitAdapter = ConfigurationSchema('TwoBitAdapter', {
+    /**
+     * #slot
+     */
     twoBitLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.2bit', locationType: 'UriLocation' },
     },
+    /**
+     * #slot
+     */
     chromSizesLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -13,4 +23,5 @@ export default ConfigurationSchema('TwoBitAdapter', {
         description: 'An optional chrom.sizes file can be supplied to speed up loading since parsing the twobit file can take time',
     },
 }, { explicitlyTyped: true });
+export default TwoBitAdapter;
 //# sourceMappingURL=configSchema.js.map

package/esm/TwoBitAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,eAAe,EACf;IACE,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,kBAAkB,EAAE,YAAY,EAAE,aAAa,EAAE;KACvE;IACD,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"}
+{"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

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "2.1.6",
+  "version": "2.2.0",
   "description": "JBrowse 2 sequence adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -59,5 +59,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "df810d2a4f057adcd8f5345d54972508fba007a7"
+  "gitHead": "cf31db8d833117f8822510340664fb3f045975cb"
 }

package/src/BgzipFastaAdapter/configSchema.ts

@@ -1,12 +1,22 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
+/**
+ * #config BgzipFastaAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
 
-export default ConfigurationSchema(
+const BgzipFastaAdapter = ConfigurationSchema(
   'BgzipFastaAdapter',
   {
+    /**
+     * #slot
+     */
     fastaLocation: {
       type: 'fileLocation',
       defaultValue: { uri: '/path/to/seq.fa.gz', locationType: 'UriLocation' },
     },
+    /**
+     * #slot
+     */
     faiLocation: {
       type: 'fileLocation',
       defaultValue: {
@@ -14,6 +24,9 @@ export default ConfigurationSchema(
         locationType: 'UriLocation',
       },
     },
+    /**
+     * #slot
+     */
     metadataLocation: {
       description: 'Optional metadata file',
       type: 'fileLocation',
@@ -22,6 +35,9 @@ export default ConfigurationSchema(
         locationType: 'UriLocation',
       },
     },
+    /**
+     * #slot
+     */
     gziLocation: {
       type: 'fileLocation',
       defaultValue: {
@@ -32,3 +48,4 @@ export default ConfigurationSchema(
   },
   { explicitlyTyped: true },
 )
+export default BgzipFastaAdapter

package/src/ChromSizesAdapter/configSchema.ts

@@ -1,8 +1,16 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
-export default ConfigurationSchema(
+/**
+ * #config ChromSizesAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const ChromSizesAdapter = ConfigurationSchema(
   'ChromSizesAdapter',
   {
+    /**
+     * #slot
+     */
     chromSizesLocation: {
       type: 'fileLocation',
       defaultValue: {
@@ -13,3 +21,5 @@ export default ConfigurationSchema(
   },
   { explicitlyTyped: true },
 )
+
+export default ChromSizesAdapter

package/src/DivSequenceRenderer/configSchema.ts

@@ -1,8 +1,16 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
-export default ConfigurationSchema(
+/**
+ * #config DivSequenceRenderer
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const DivSequenceRenderer = ConfigurationSchema(
   'DivSequenceRenderer',
   {
+    /**
+     * #slot
+     */
     height: {
       type: 'number',
       description: 'height in pixels of each line of sequence',
@@ -11,3 +19,5 @@ export default ConfigurationSchema(
   },
   { explicitlyTyped: true },
 )
+
+export default DivSequenceRenderer

package/src/GCContentAdapter/configSchema.ts

@@ -1,12 +1,22 @@
 import PluginManager from '@jbrowse/core/PluginManager'
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
-export default (pluginManager: PluginManager) => {
+/**
+ * #config GCContentAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const GCContentAdapterF = (pluginManager: PluginManager) => {
   return ConfigurationSchema(
     'GCContentAdapter',
     {
+      /**
+       * #slot
+       */
       sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
     },
     { explicitlyTyped: true },
   )
 }
+
+export default GCContentAdapterF

package/src/IndexedFastaAdapter/configSchema.ts

@@ -1,16 +1,30 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
-export default ConfigurationSchema(
+/**
+ * #config IndexedFastaAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const IndexedFastaAdapter = ConfigurationSchema(
   'IndexedFastaAdapter',
   {
+    /**
+     * #slot
+     */
     fastaLocation: {
       type: 'fileLocation',
       defaultValue: { uri: '/path/to/seq.fa', locationType: 'UriLocation' },
     },
+    /**
+     * #slot
+     */
     faiLocation: {
       type: 'fileLocation',
       defaultValue: { uri: '/path/to/seq.fa.fai', locationType: 'UriLocation' },
     },
+    /**
+     * #slot
+     */
     metadataLocation: {
       description: 'Optional metadata file',
       type: 'fileLocation',
@@ -22,3 +36,4 @@ export default ConfigurationSchema(
   },
   { explicitlyTyped: true },
 )
+export default IndexedFastaAdapter

package/src/LinearReferenceSequenceDisplay/configSchema.ts

@@ -1,8 +1,18 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import { default as divSequenceRendererConfigSchema } from '../DivSequenceRenderer/configSchema'
 
+/**
+ * #config LinearReferenceSequenceDisplay
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
 export const configSchema = ConfigurationSchema(
   'LinearReferenceSequenceDisplay',
-  { renderer: divSequenceRendererConfigSchema },
+  {
+    /**
+     * #slot
+     */
+    renderer: divSequenceRendererConfigSchema,
+  },
   { explicitIdentifier: 'displayId', explicitlyTyped: true },
 )

package/src/ReferenceSequenceTrack/configSchema.ts

@@ -3,22 +3,45 @@ import { types } from 'mobx-state-tree'
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import PluginManager from '@jbrowse/core/PluginManager'
 
-/*
-Note: this is primarily a copy of createBaseTrackConfig, except with a subset
-of the config slots, to avoid including fields that don't make sense for the
-ReferenceSequenceTrack
-*/
+// Note: this is primarily a copy of createBaseTrackConfig, except with a
+// subset of the config slots, to avoid including fields that don't make sense
+// for the ReferenceSequenceTrack
+
+/**
+ * #config ReferenceSequenceTrack
+ * used to display base level DNA sequence tracks
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
 export function createReferenceSeqTrackConfig(pluginManager: PluginManager) {
   return ConfigurationSchema(
     'ReferenceSequenceTrack',
     {
+      /**
+       * #slot
+       * configuration for track adapter
+       */
       adapter: pluginManager.pluggableConfigSchemaType('adapter'),
+
+      /**
+       * #slot
+       * configuration for the displays e.g. LinearReferenceSequenceDisplay
+       */
       displays: types.array(pluginManager.pluggableConfigSchemaType('display')),
+
+      /**
+       * #slot
+       */
       name: {
         type: 'string',
-        description: 'optional track name',
+        description:
+          'optional track name, otherwise uses the "Reference sequence (assemblyName)"',
         defaultValue: '',
       },
+
+      /**
+       * #slot
+       */
       metadata: {
         type: 'frozen',
         description: 'anything to add about this track',
@@ -26,12 +49,19 @@ export function createReferenceSeqTrackConfig(pluginManager: PluginManager) {
       },
 
       formatAbout: ConfigurationSchema('FormatAbout', {
+        /**
+         * #slot formatAbout.config
+         */
         config: {
           type: 'frozen',
           description: 'formats configuration in about dialog',
           defaultValue: {},
           contextVariable: ['config'],
         },
+
+        /**
+         * #slot formatAbout.hideUris
+         */
         hideUris: {
           type: 'boolean',
           defaultValue: false,
@@ -60,6 +90,10 @@ export function createReferenceSeqTrackConfig(pluginManager: PluginManager) {
         }
         return { ...snap, displays }
       },
+      /**
+       * #identifier
+       * all tracks have a globally unique 'trackId'
+       */
       explicitIdentifier: 'trackId',
       explicitlyTyped: true,
       actions: (self: any) => ({

package/src/SequenceSearchAdapter/configSchema.ts

@@ -1,25 +1,45 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
+/**
+ * #config SequenceSearchAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
 const configSchema = ConfigurationSchema(
   'SequenceSearchAdapter',
   {
+    /**
+     * #slot
+     */
     search: {
       type: 'string',
       defaultValue: '',
       description: 'Search string or regex to search for',
     },
+    /**
+     * #slot
+     */
     sequenceAdapter: {
       type: 'frozen',
       defaultValue: null,
     },
+    /**
+     * #slot
+     */
     searchForward: {
       type: 'boolean',
       defaultValue: true,
     },
+    /**
+     * #slot
+     */
     searchReverse: {
       type: 'boolean',
       defaultValue: true,
     },
+    /**
+     * #slot
+     */
     caseInsensitive: {
       type: 'boolean',
       defaultValue: true,

package/src/TwoBitAdapter/configSchema.ts

@@ -1,12 +1,23 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
-export default ConfigurationSchema(
+/**
+ * #config TwoBitAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const TwoBitAdapter = ConfigurationSchema(
   'TwoBitAdapter',
   {
+    /**
+     * #slot
+     */
     twoBitLocation: {
       type: 'fileLocation',
       defaultValue: { uri: '/path/to/my.2bit', locationType: 'UriLocation' },
     },
+    /**
+     * #slot
+     */
     chromSizesLocation: {
       type: 'fileLocation',
       defaultValue: {
@@ -19,3 +30,5 @@ export default ConfigurationSchema(
   },
   { explicitlyTyped: true },
 )
+
+export default TwoBitAdapter