@jbrowse/plugin-alignments 2.1.6 → 2.2.0

package/esm/CramAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/CramAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,mBAAmB,CACtC,aAAa,EACb;IACE;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,4FAA4F;QAC9F,YAAY,EAAE,OAAS;KACxB;IAED;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,kBAAkB;YACvB,YAAY,EAAE,aAAa;SAC5B;KACF;IAED;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,uBAAuB;YAC5B,YAAY,EAAE,aAAa;SAC5B;KACF;IAED;;;;OAIG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,8EAA8E;QAChF,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,eAAe,YAAY,CAAA"}

package/esm/CramAdapter/index.js

@@ -1,10 +1,10 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 // locals
-import configSchemaF from './configSchema';
+import configSchema from './configSchema';
 export default (pluginManager) => {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'CramAdapter',
-        configSchema: pluginManager.load(configSchemaF),
+        configSchema,
         getAdapterClass: () => import('./CramAdapter').then(r => r.default),
     }));
 };

package/esm/CramAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/CramAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,SAAS;AACT,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAE1C,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,aAAa,CAAC,IAAI,CAAC,aAAa,CAAC;QAC/C,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,eAAe,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACpE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/CramAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,SAAS;AACT,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,aAAa;QACnB,YAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,eAAe,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACpE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/HtsgetBamAdapter/HtsgetBamAdapter.d.ts

@@ -2,8 +2,11 @@ import { BamFile } from '@gmod/bam';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import BamAdapter from '../BamAdapter/BamAdapter';
 export default class HtsgetBamAdapter extends BamAdapter {
-    protected configure(): Promise<{
+    protected configurePre(): Promise<{
         bam: BamFile;
-        sequenceAdapter?: BaseFeatureDataAdapter | undefined;
+        sequenceAdapter: BaseFeatureDataAdapter;
+    } | {
+        bam: BamFile;
+        sequenceAdapter?: undefined;
     }>;
 }

package/esm/HtsgetBamAdapter/HtsgetBamAdapter.js

@@ -1,27 +1,22 @@
 import { HtsgetFile } from '@gmod/bam';
-import { readConfObject } from '@jbrowse/core/configuration';
 import BamAdapter from '../BamAdapter/BamAdapter';
 export default class HtsgetBamAdapter extends BamAdapter {
-    async configure() {
-        if (!this.configured) {
-            const htsgetBase = readConfObject(this.config, 'htsgetBase');
-            const htsgetTrackId = readConfObject(this.config, 'htsgetTrackId');
-            const bam = new HtsgetFile({
-                baseUrl: htsgetBase,
-                trackId: htsgetTrackId,
-            });
-            const adapterConfig = readConfObject(this.config, 'sequenceAdapter');
-            if (adapterConfig && this.getSubAdapter) {
-                this.configured = this.getSubAdapter(adapterConfig).then(({ dataAdapter }) => {
-                    return {
-                        bam,
-                        sequenceAdapter: dataAdapter,
-                    };
-                });
-            }
-            this.configured = Promise.resolve({ bam });
+    async configurePre() {
+        const htsgetBase = this.getConf('htsgetBase');
+        const htsgetTrackId = this.getConf('htsgetTrackId');
+        const bam = new HtsgetFile({
+            baseUrl: htsgetBase,
+            trackId: htsgetTrackId,
+        });
+        const adapterConfig = this.getConf('sequenceAdapter');
+        if (adapterConfig && this.getSubAdapter) {
+            const adapter = await this.getSubAdapter(adapterConfig);
+            return {
+                bam,
+                sequenceAdapter: adapter.dataAdapter,
+            };
         }
-        return this.configured;
+        return { bam };
     }
 }
 //# sourceMappingURL=HtsgetBamAdapter.js.map

package/esm/HtsgetBamAdapter/HtsgetBamAdapter.js.map

@@ -1 +1 @@
-{"version":3,"file":"HtsgetBamAdapter.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/HtsgetBamAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAW,UAAU,EAAE,MAAM,WAAW,CAAA;AAC/C,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAE5D,OAAO,UAAU,MAAM,0BAA0B,CAAA;AAEjD,MAAM,CAAC,OAAO,OAAO,gBAAiB,SAAQ,UAAU;IAC5C,KAAK,CAAC,SAAS;QACvB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,MAAM,UAAU,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,YAAY,CAAC,CAAA;YAC5D,MAAM,aAAa,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;YAClE,MAAM,GAAG,GAAG,IAAI,UAAU,CAAC;gBACzB,OAAO,EAAE,UAAU;gBACnB,OAAO,EAAE,aAAa;aACvB,CAAuB,CAAA;YAExB,MAAM,aAAa,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,iBAAiB,CAAC,CAAA;YACpE,IAAI,aAAa,IAAI,IAAI,CAAC,aAAa,EAAE;gBACvC,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,aAAa,CAAC,aAAa,CAAC,CAAC,IAAI,CACtD,CAAC,EAAE,WAAW,EAAE,EAAE,EAAE;oBAClB,OAAO;wBACL,GAAG;wBACH,eAAe,EAAE,WAAqC;qBACvD,CAAA;gBACH,CAAC,CACF,CAAA;aACF;YACD,IAAI,CAAC,UAAU,GAAG,OAAO,CAAC,OAAO,CAAC,EAAE,GAAG,EAAE,CAAC,CAAA;SAC3C;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;CACF"}
+{"version":3,"file":"HtsgetBamAdapter.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/HtsgetBamAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAW,UAAU,EAAE,MAAM,WAAW,CAAA;AAE/C,OAAO,UAAU,MAAM,0BAA0B,CAAA;AAEjD,MAAM,CAAC,OAAO,OAAO,gBAAiB,SAAQ,UAAU;IAC5C,KAAK,CAAC,YAAY;QAC1B,MAAM,UAAU,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QAC7C,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAA;QACnD,MAAM,GAAG,GAAG,IAAI,UAAU,CAAC;YACzB,OAAO,EAAE,UAAU;YACnB,OAAO,EAAE,aAAa;SACvB,CAAuB,CAAA;QAExB,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;QACrD,IAAI,aAAa,IAAI,IAAI,CAAC,aAAa,EAAE;YACvC,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC,aAAa,CAAC,CAAA;YACvD,OAAO;gBACL,GAAG;gBACH,eAAe,EAAE,OAAO,CAAC,WAAqC;aAC/D,CAAA;SACF;QACD,OAAO,EAAE,GAAG,EAAE,CAAA;IAChB,CAAC;CACF"}

package/esm/HtsgetBamAdapter/configSchema.d.ts

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

package/esm/HtsgetBamAdapter/configSchema.js

@@ -1,17 +1,34 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { types } from 'mobx-state-tree';
-export default types.late(() => ConfigurationSchema('HtsgetBamAdapter', {
+/**
+ * #config HtsgetBamAdapter
+ * Used to fetch data from Htsget endpoints in BAM format, using the gmod/bam library
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const HtsgetBamAdapter = ConfigurationSchema('HtsgetBamAdapter', {
+    /**
+     * #slot
+     */
     htsgetBase: {
         type: 'string',
+        description: 'the base URL to fetch from',
         defaultValue: '',
     },
+    /**
+     * #slot
+     */
     htsgetTrackId: {
         type: 'string',
+        description: 'the trackId, which is appended to the base URL',
         defaultValue: '',
     },
+    /**
+     * #slot
+     */
     sequenceAdapter: {
         type: 'frozen',
+        description: 'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
         defaultValue: null,
     },
-}, { explicitlyTyped: true }));
+}, { explicitlyTyped: true });
+export default HtsgetBamAdapter;
 //# sourceMappingURL=configSchema.js.map

package/esm/HtsgetBamAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,eAAe,KAAK,CAAC,IAAI,CAAC,GAAG,EAAE,CAC7B,mBAAmB,CACjB,kBAAkB,EAClB;IACE,UAAU,EAAE;QACV,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD,eAAe,EAAE;QACf,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CACF,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,gBAAgB,GAAG,mBAAmB,CAC1C,kBAAkB,EAClB;IACE;;OAEG;IACH,UAAU,EAAE;QACV,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,4BAA4B;QACzC,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,gDAAgD;QAC7D,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,8EAA8E;QAChF,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,gBAAgB,CAAA"}

package/esm/LinearAlignmentsDisplay/models/configSchema.d.ts

@@ -1,4 +1,4 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const configModelFactory: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configModelFactory: (pm: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
 export declare type AlignmentsConfigModel = ReturnType<typeof configModelFactory>;
 export default configModelFactory;

package/esm/LinearAlignmentsDisplay/models/configSchema.js

@@ -1,12 +1,29 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view';
-const configModelFactory = (pluginManager) => {
-    const PileupDisplayConfigSchema = pluginManager.getDisplayType('LinearPileupDisplay').configSchema;
-    const SNPCoverageDisplayConfigSchema = pluginManager.getDisplayType('LinearSNPCoverageDisplay').configSchema;
+/**
+ * #config LinearAlignmentsDisplay
+ * has a "pileup" sub-display, where you can see individual reads and a
+ * quantitative "snpcoverage" sub-display track showing SNP frequencies
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const configModelFactory = (pm) => {
     return ConfigurationSchema('LinearAlignmentsDisplay', {
-        pileupDisplay: PileupDisplayConfigSchema,
-        snpCoverageDisplay: SNPCoverageDisplayConfigSchema,
-    }, { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true });
+        /**
+         * #slot
+         */
+        pileupDisplay: pm.getDisplayType('LinearPileupDisplay').configSchema,
+        /**
+         * #slot
+         */
+        snpCoverageDisplay: pm.getDisplayType('LinearSNPCoverageDisplay')
+            .configSchema,
+    }, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: baseLinearDisplayConfigSchema,
+        explicitlyTyped: true,
+    });
 };
 export default configModelFactory;
 //# sourceMappingURL=configSchema.js.map

package/esm/LinearAlignmentsDisplay/models/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/models/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,6BAA6B,EAAE,MAAM,oCAAoC,CAAA;AAGlF,MAAM,kBAAkB,GAAG,CAAC,aAA4B,EAAE,EAAE;IAC1D,MAAM,yBAAyB,GAAG,aAAa,CAAC,cAAc,CAC5D,qBAAqB,CACtB,CAAC,YAAY,CAAA;IACd,MAAM,8BAA8B,GAAG,aAAa,CAAC,cAAc,CACjE,0BAA0B,CAC3B,CAAC,YAAY,CAAA;IAEd,OAAO,mBAAmB,CACxB,yBAAyB,EACzB;QACE,aAAa,EAAE,yBAAyB;QACxC,kBAAkB,EAAE,8BAA8B;KACnD,EACD,EAAE,iBAAiB,EAAE,6BAA6B,EAAE,eAAe,EAAE,IAAI,EAAE,CAC5E,CAAA;AACH,CAAC,CAAA;AAGD,eAAe,kBAAkB,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/models/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,6BAA6B,EAAE,MAAM,oCAAoC,CAAA;AAGlF;;;;GAIG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,kBAAkB,GAAG,CAAC,EAAiB,EAAE,EAAE;IAC/C,OAAO,mBAAmB,CACxB,yBAAyB,EACzB;QACE;;WAEG;QACH,aAAa,EAAE,EAAE,CAAC,cAAc,CAAC,qBAAqB,CAAC,CAAC,YAAY;QACpE;;WAEG;QACH,kBAAkB,EAAE,EAAE,CAAC,cAAc,CAAC,0BAA0B,CAAC;aAC9D,YAAY;KAChB,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,6BAA6B;QAChD,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC,CAAA;AAGD,eAAe,kBAAkB,CAAA"}

package/esm/LinearAlignmentsDisplay/models/model.d.ts

@@ -1,10 +1,13 @@
 import React from 'react';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { MenuItem } from '@jbrowse/core/ui';
 import { Instance } from 'mobx-state-tree';
-import { AlignmentsConfigModel } from './configSchema';
-declare const stateModelFactory: (pluginManager: PluginManager, configSchema: AlignmentsConfigModel) => import("mobx-state-tree").IModelType<{
+/**
+ * #stateModel LinearAlignmentsDisplay
+ * extends `BaseDisplay`
+ */
+declare function stateModelFactory(pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -32,7 +35,9 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Al
             error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            type: import("mobx-state-tree").ISimpleType<string>;
+            type: import("mobx-state-tree").ISimpleType<string>; /**
+             * #property
+             */
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
@@ -50,7 +55,9 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Al
             rendererTypeName: string;
             error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>; /**
+             * #action
+             */
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
@@ -73,29 +80,89 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Al
 } & {
     scrollTop: number;
 } & {
+    /**
+     * #action
+     */
     toggleCoverage(): void;
+    /**
+     * #action
+     */
     togglePileup(): void;
+    /**
+     * #action
+     */
     setScrollTop(scrollTop: number): void;
+    /**
+     * #action
+     */
     setSNPCoverageHeight(n: number): void;
 } & {
+    /**
+     * #getter
+     */
     readonly pileupDisplayConfig: any;
+    /**
+     * #method
+     */
     getFeatureByID(blockKey: string, id: string): any;
+    /**
+     * #method
+     */
     searchFeatureByID(id: string): any;
+    /**
+     * #getter
+     */
     readonly features: any;
+    /**
+     * #getter
+     */
     readonly DisplayBlurb: any;
+    /**
+     * #getter
+     */
     readonly sortedBy: any;
+    /**
+     * #getter
+     */
     readonly sortedByPosition: any;
+    /**
+     * #getter
+     */
     readonly sortedByRefName: any;
+    /**
+     * #getter
+     */
     readonly snpCoverageDisplayConfig: any;
+    /**
+     * #method
+     */
     trackMenuItems(): MenuItem[];
 } & {
+    /**
+     * #action
+     */
     setSNPCoverageDisplay(displayConfig: AnyConfigurationModel): void;
+    /**
+     * #action
+     */
     setUserFeatureScreenDensity(limit: number): void;
+    /**
+     * #action
+     */
     setPileupDisplay(displayConfig: AnyConfigurationModel): void;
+    /**
+     * #action
+     */
     setHeight(displayHeight: number): number;
+    /**
+     * #action
+     */
     resizeHeight(distance: number): number;
 } & {
     afterAttach(): void;
+    /**
+     * #action
+     */
     renderSvg(opts: {
         rasterizeLayers?: boolean;
     }): Promise<JSX.Element>;

package/esm/LinearAlignmentsDisplay/models/model.js

@@ -6,32 +6,77 @@ import { addDisposer, getSnapshot, types } from 'mobx-state-tree';
 import { getContainingTrack } from '@jbrowse/core/util';
 import deepEqual from 'fast-deep-equal';
 const minDisplayHeight = 20;
-const stateModelFactory = (pluginManager, configSchema) => {
+/**
+ * #stateModel LinearAlignmentsDisplay
+ * extends `BaseDisplay`
+ */
+function stateModelFactory(pluginManager, configSchema) {
     return types
         .compose('LinearAlignmentsDisplay', BaseDisplay, types.model({
+        /**
+         * #property
+         * refers to LinearPileupDisplay sub-display model
+         */
         PileupDisplay: types.maybe(pluginManager.getDisplayType('LinearPileupDisplay').stateModel),
+        /**
+         * #property
+         * refers to LinearSNPCoverageDisplay sub-display model
+         */
         SNPCoverageDisplay: types.maybe(pluginManager.getDisplayType('LinearSNPCoverageDisplay').stateModel),
+        /**
+         * #property
+         */
         snpCovHeight: 45,
+        /**
+         * #property
+         */
         type: types.literal('LinearAlignmentsDisplay'),
+        /**
+         * #property
+         */
         configuration: ConfigurationReference(configSchema),
+        /**
+         * #property
+         */
         height: 250,
+        /**
+         * #property
+         */
         showCoverage: true,
+        /**
+         * #property
+         */
         showPileup: true,
+        /**
+         * #property
+         */
         userFeatureScreenDensity: types.maybe(types.number),
     }))
         .volatile(() => ({
         scrollTop: 0,
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
         toggleCoverage() {
             self.showCoverage = !self.showCoverage;
         },
+        /**
+         * #action
+         */
         togglePileup() {
             self.showPileup = !self.showPileup;
         },
+        /**
+         * #action
+         */
         setScrollTop(scrollTop) {
             self.scrollTop = scrollTop;
         },
+        /**
+         * #action
+         */
         setSNPCoverageHeight(n) {
             self.snpCovHeight = n;
         },
@@ -39,6 +84,9 @@ const stateModelFactory = (pluginManager, configSchema) => {
         .views(self => {
         const { trackMenuItems: superTrackMenuItems } = self;
         return {
+            /**
+             * #getter
+             */
             get pileupDisplayConfig() {
                 const conf = getConf(self, 'pileupDisplay');
                 const track = getContainingTrack(self);
@@ -49,28 +97,52 @@ const stateModelFactory = (pluginManager, configSchema) => {
                     displayId: `${self.configuration.displayId}_pileup_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
                 };
             },
+            /**
+             * #method
+             */
             getFeatureByID(blockKey, id) {
                 return self.PileupDisplay.getFeatureByID(blockKey, id);
             },
+            /**
+             * #method
+             */
             searchFeatureByID(id) {
                 return self.PileupDisplay.searchFeatureByID(id);
             },
+            /**
+             * #getter
+             */
             get features() {
                 return self.PileupDisplay.features;
             },
+            /**
+             * #getter
+             */
             get DisplayBlurb() {
                 var _a;
                 return (_a = self.PileupDisplay) === null || _a === void 0 ? void 0 : _a.DisplayBlurb;
             },
+            /**
+             * #getter
+             */
             get sortedBy() {
                 return self.PileupDisplay.sortedBy;
             },
+            /**
+             * #getter
+             */
             get sortedByPosition() {
                 return self.PileupDisplay.sortedByPosition;
             },
+            /**
+             * #getter
+             */
             get sortedByRefName() {
                 return self.PileupDisplay.sortedByRefName;
             },
+            /**
+             * #getter
+             */
             get snpCoverageDisplayConfig() {
                 const conf = getConf(self, 'snpCoverageDisplay');
                 const track = getContainingTrack(self);
@@ -81,6 +153,9 @@ const stateModelFactory = (pluginManager, configSchema) => {
                     displayId: `${self.configuration.displayId}_snpcoverage_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
                 };
             },
+            /**
+             * #method
+             */
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
@@ -99,6 +174,9 @@ const stateModelFactory = (pluginManager, configSchema) => {
         };
     })
         .actions(self => ({
+        /**
+         * #action
+         */
         setSNPCoverageDisplay(displayConfig) {
             self.SNPCoverageDisplay = {
                 type: 'LinearSNPCoverageDisplay',
@@ -106,16 +184,25 @@ const stateModelFactory = (pluginManager, configSchema) => {
                 height: self.snpCovHeight,
             };
         },
+        /**
+         * #action
+         */
         setUserFeatureScreenDensity(limit) {
             self.PileupDisplay.setUserFeatureScreenDensity(limit);
             self.SNPCoverageDisplay.setUserFeatureScreenDensity(limit);
         },
+        /**
+         * #action
+         */
         setPileupDisplay(displayConfig) {
             self.PileupDisplay = {
                 type: 'LinearPileupDisplay',
                 configuration: displayConfig,
             };
         },
+        /**
+         * #action
+         */
         setHeight(displayHeight) {
             if (displayHeight > minDisplayHeight) {
                 self.height = displayHeight;
@@ -125,6 +212,9 @@ const stateModelFactory = (pluginManager, configSchema) => {
             }
             return self.height;
         },
+        /**
+         * #action
+         */
         resizeHeight(distance) {
             const oldHeight = self.height;
             const newHeight = this.setHeight(self.height + distance);
@@ -165,6 +255,9 @@ const stateModelFactory = (pluginManager, configSchema) => {
                 self.setSNPCoverageHeight(self.SNPCoverageDisplay.height);
             }));
         },
+        /**
+         * #action
+         */
         async renderSvg(opts) {
             const pileupHeight = self.height - self.SNPCoverageDisplay.height;
             await when(() => self.PileupDisplay.ready);
@@ -176,6 +269,6 @@ const stateModelFactory = (pluginManager, configSchema) => {
                 }))));
         },
     }));
-};
+}
 export default stateModelFactory;
 //# sourceMappingURL=model.js.map

package/esm/LinearAlignmentsDisplay/models/model.js.map

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package/esm/LinearPileupDisplay/configSchema.js

@@ -1,24 +1,38 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view';
 import { types } from 'mobx-state-tree';
+/**
+ * #config LinearPileupDisplay
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 function PileupConfigFactory(pluginManager) {
-    const PileupRendererConfigSchema = pluginManager.getRendererType('PileupRenderer').configSchema;
     // modify config schema to take in a sub coverage display
     return ConfigurationSchema('LinearPileupDisplay', {
+        /**
+         * #slot
+         */
         defaultRendering: {
             type: 'stringEnum',
             model: types.enumeration('Rendering', ['pileup']),
             defaultValue: 'pileup',
         },
+        /**
+         * #slot
+         */
         renderers: ConfigurationSchema('RenderersConfiguration', {
-            PileupRenderer: PileupRendererConfigSchema,
+            PileupRenderer: pluginManager.getRendererType('PileupRenderer').configSchema,
         }),
-        renderer: '',
+        /**
+         * #slot
+         */
         maxFeatureScreenDensity: {
             type: 'number',
             description: 'maximum features per pixel that is displayed in the view',
             defaultValue: 5,
         },
+        /**
+         * #slot
+         */
         colorScheme: {
             type: 'stringEnum',
             model: types.enumeration('colorScheme', [
@@ -33,6 +47,9 @@ function PileupConfigFactory(pluginManager) {
             defaultValue: 'normal',
         },
     }, {
+        /**
+         * #baseConfiguration
+         */
         baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager),
         explicitlyTyped: true,
     });

package/esm/LinearPileupDisplay/configSchema.js.map

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