@jbrowse/plugin-variants 2.1.7 → 2.2.1

package/esm/LinearVariantDisplay/model.d.ts

@@ -1,7 +1,12 @@
 /// <reference types="react" />
 import { Feature } from '@jbrowse/core/util/simpleFeature';
 import { LinearVariantDisplayConfigModel } from './configSchema';
-export default function (configSchema: LinearVariantDisplayConfigModel): import("mobx-state-tree").IModelType<{
+/**
+ * #stateModel LinearVariantDisplay
+ * extends `LinearBasicDisplay`
+ * very similar to basic display, but provides custom widget on feature click
+ */
+export default function stateModelFactory(configSchema: LinearVariantDisplayConfigModel): 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>>;
@@ -56,14 +61,24 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 } & {
-    type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
-    trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">; /**
+     * #property
+     */
+    trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>; /**
+     * #property
+     */
     trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     trackDisplayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
 } & {
+    /**
+     * #property
+     */
     type: import("mobx-state-tree").ISimpleType<"LinearVariantDisplay">;
+    /**
+     * #property
+     */
     configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
 }, {
     rendererTypeName: string;
@@ -216,5 +231,8 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
     };
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
 } & {
+    /**
+     * #action
+     */
     selectFeature(feature: Feature): Promise<void>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/LinearVariantDisplay/model.js

@@ -3,13 +3,27 @@ import { getRpcSessionId } from '@jbrowse/core/util/tracks';
 import { getContainingTrack, getSession, getContainingView, isSessionModelWithWidgets, } from '@jbrowse/core/util';
 import { linearBasicDisplayModelFactory } from '@jbrowse/plugin-linear-genome-view';
 import { types } from 'mobx-state-tree';
-export default function (configSchema) {
+/**
+ * #stateModel LinearVariantDisplay
+ * extends `LinearBasicDisplay`
+ * very similar to basic display, but provides custom widget on feature click
+ */
+export default function stateModelFactory(configSchema) {
     return types
         .compose('LinearVariantDisplay', linearBasicDisplayModelFactory(configSchema), types.model({
+        /**
+         * #property
+         */
         type: types.literal('LinearVariantDisplay'),
+        /**
+         * #property
+         */
         configuration: ConfigurationReference(configSchema),
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
         async selectFeature(feature) {
             const session = getSession(self);
             if (isSessionModelWithWidgets(session)) {

package/esm/LinearVariantDisplay/model.js.map

@@ -1 +1 @@
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+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,sBAAsB,EAAE,MAAM,6BAA6B,CAAA;AAC7E,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AAC3D,OAAO,EACL,kBAAkB,EAClB,UAAU,EACV,iBAAiB,EACjB,yBAAyB,GAC1B,MAAM,oBAAoB,CAAA;AAG3B,OAAO,EAAE,8BAA8B,EAAE,MAAM,oCAAoC,CAAA;AACnF,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAGvC;;;;GAIG;AACH,MAAM,CAAC,OAAO,UAAU,iBAAiB,CACvC,YAA6C;IAE7C,OAAO,KAAK;SACT,OAAO,CACN,sBAAsB,EACtB,8BAA8B,CAAC,YAAY,CAAC,EAC5C,KAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C;;WAEG;QACH,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,KAAK,CAAC,aAAa,CAAC,OAAgB;YAClC,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YAChC,IAAI,yBAAyB,CAAC,OAAO,CAAC,EAAE;gBACtC,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;gBAC9B,MAAM,SAAS,GAAG,eAAe,CAAC,IAAI,CAAC,CAAA;gBACvC,MAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,CAAC,CAAA;gBACtC,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAA;gBACpC,MAAM,aAAa,GAAG,OAAO,CAAC,KAAK,EAAE,SAAS,CAAC,CAAA;gBAC/C,MAAM,YAAY,GAAG,MAAM,UAAU,CAAC,IAAI,CACxC,SAAS,EACT,iBAAiB,EACjB;oBACE,aAAa;iBACd,CACF,CAAA;gBACD,OAAO,CAAC,UAAU,CAChB,OAAO,CAAC,SAAS,CAAC,sBAAsB,EAAE,gBAAgB,EAAE;oBAC1D,WAAW,EAAE,OAAO,CAAC,MAAM,EAAE;oBAC7B,IAAI;oBACJ,KAAK;oBACL,YAAY;iBACb,CAAC,CACH,CAAA;aACF;YAED,OAAO,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;QAC/B,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}

package/esm/StructuralVariantChordRenderer/ReactComponent.d.ts

@@ -11,7 +11,7 @@ interface ElidedRegion {
     elided: true;
     regions: Region[];
 }
-declare type AnyRegion = Region | ElidedRegion;
+type AnyRegion = Region | ElidedRegion;
 interface Block {
     flipped: boolean;
     bpPerRadian: number;

package/esm/StructuralVariantChordRenderer/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchema;

package/esm/StructuralVariantChordRenderer/configSchema.js

@@ -0,0 +1,36 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config StructuralVariantChordRenderer
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const configSchema = ConfigurationSchema('StructuralVariantChordRenderer', {
+    /**
+     * #slot
+     */
+    strokeColor: {
+        type: 'color',
+        description: 'the line color of each arc',
+        defaultValue: 'rgba(255,133,0,0.32)',
+        contextVariable: ['feature'],
+    },
+    /**
+     * #slot
+     */
+    strokeColorSelected: {
+        type: 'color',
+        description: 'the line color of an arc that has been selected',
+        defaultValue: 'black',
+        contextVariable: ['feature'],
+    },
+    /**
+     * #slot
+     */
+    strokeColorHover: {
+        type: 'color',
+        description: 'the line color of an arc that is being hovered over with the mouse',
+        defaultValue: '#555',
+        contextVariable: ['feature'],
+    },
+}, { explicitlyTyped: true });
+export default configSchema;
+//# sourceMappingURL=configSchema.js.map

package/esm/StructuralVariantChordRenderer/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/StructuralVariantChordRenderer/index.d.ts

@@ -1,4 +1,3 @@
-import ChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType';
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const ChordRendererConfigF: (pluginManager: PluginManager) => ChordRendererType;
+declare const ChordRendererConfigF: (pluginManager: PluginManager) => void;
 export default ChordRendererConfigF;

package/esm/StructuralVariantChordRenderer/index.js

@@ -1,33 +1,13 @@
 import ChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType';
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import configSchema from './configSchema';
 import ReactComponent from './ReactComponent';
 const ChordRendererConfigF = (pluginManager) => {
-    const configSchema = ConfigurationSchema('StructuralVariantChordRenderer', {
-        strokeColor: {
-            type: 'color',
-            description: 'the line color of each arc',
-            defaultValue: 'rgba(255,133,0,0.32)',
-            contextVariable: ['feature'],
-        },
-        strokeColorSelected: {
-            type: 'color',
-            description: 'the line color of an arc that has been selected',
-            defaultValue: 'black',
-            contextVariable: ['feature'],
-        },
-        strokeColorHover: {
-            type: 'color',
-            description: 'the line color of an arc that is being hovered over with the mouse',
-            defaultValue: '#555',
-            contextVariable: ['feature'],
-        },
-    }, { explicitlyTyped: true });
-    return new ChordRendererType({
+    pluginManager.addRendererType(() => new ChordRendererType({
         name: 'StructuralVariantChordRenderer',
         ReactComponent,
         configSchema,
         pluginManager,
-    });
+    }));
 };
 export default ChordRendererConfigF;
 //# sourceMappingURL=index.js.map

package/esm/StructuralVariantChordRenderer/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/StructuralVariantChordRenderer/index.ts"],"names":[],"mappings":"AAAA,OAAO,iBAAiB,MAAM,yEAAyE,CAAA;AAEvG,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAE7C,MAAM,oBAAoB,GAAG,CAAC,aAA4B,EAAE,EAAE;IAC5D,aAAa,CAAC,eAAe,CAC3B,GAAG,EAAE,CACH,IAAI,iBAAiB,CAAC;QACpB,IAAI,EAAE,gCAAgC;QACtC,cAAc;QACd,YAAY;QACZ,aAAa;KACd,CAAC,CACL,CAAA;AACH,CAAC,CAAA;AAED,eAAe,oBAAoB,CAAA"}

package/esm/VariantTrack/configSchema.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchema;

package/esm/VariantTrack/configSchema.js

@@ -0,0 +1,16 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
+/**
+ * #config VariantTrack
+ * Mostly similar to feature track, but has `ChordDisplayType` registered to it,
+ * and custom feature details in `LinearVariantDisplay`
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const configSchema = (pluginManager) => ConfigurationSchema('VariantTrack', {}, {
+    /**
+     * #baseConfiguration
+     */
+    baseConfiguration: createBaseTrackConfig(pluginManager),
+});
+export default configSchema;
+//# sourceMappingURL=configSchema.js.map

package/esm/VariantTrack/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/VariantTrack/index.d.ts

@@ -1,3 +1,3 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
+declare const _default: (pm: PluginManager) => void;
 export default _default;

package/esm/VariantTrack/index.js

@@ -1,13 +1,13 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
-import { createBaseTrackConfig, createBaseTrackModel, } from '@jbrowse/core/pluggableElementTypes/models';
-export default (pluginManager) => {
-    pluginManager.addTrackType(() => {
-        const configSchema = ConfigurationSchema('VariantTrack', {}, { baseConfiguration: createBaseTrackConfig(pluginManager) });
+import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
+import configSchemaF from './configSchema';
+export default (pm) => {
+    pm.addTrackType(() => {
+        const configSchema = configSchemaF(pm);
         return new TrackType({
             name: 'VariantTrack',
             configSchema,
-            stateModel: createBaseTrackModel(pluginManager, 'VariantTrack', configSchema),
+            stateModel: createBaseTrackModel(pm, 'VariantTrack', configSchema),
         });
     });
 };

package/esm/VariantTrack/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VariantTrack/index.ts"],"names":[],"mappings":"AACA,OAAO,SAAS,MAAM,+CAA+C,CAAA;AACrE,OAAO,EAAE,oBAAoB,EAAE,MAAM,4CAA4C,CAAA;AACjF,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAE1C,eAAe,CAAC,EAAiB,EAAE,EAAE;IACnC,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,aAAa,CAAC,EAAE,CAAC,CAAA;QACtC,OAAO,IAAI,SAAS,CAAC;YACnB,IAAI,EAAE,cAAc;YACpB,YAAY;YACZ,UAAU,EAAE,oBAAoB,CAAC,EAAE,EAAE,cAAc,EAAE,YAAY,CAAC;SACnE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/VcfAdapter/configSchema.d.ts

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

package/esm/VcfAdapter/configSchema.js

@@ -1,8 +1,16 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-export default ConfigurationSchema('VcfAdapter', {
+/**
+ * #config VcfAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const VcfAdapter = ConfigurationSchema('VcfAdapter', {
+    /**
+     * #slot
+     */
     vcfLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.vcf', locationType: 'UriLocation' },
     },
 }, { explicitlyTyped: true });
+export default VcfAdapter;
 //# sourceMappingURL=configSchema.js.map

package/esm/VcfAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/VcfAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,UAAU,GAAG,mBAAmB,CACpC,YAAY,EACZ;IACE;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,iBAAiB,EAAE,YAAY,EAAE,aAAa,EAAE;KACtE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,UAAU,CAAA"}

package/esm/VcfTabixAdapter/configSchema.d.ts

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

package/esm/VcfTabixAdapter/configSchema.js

@@ -1,16 +1,29 @@
 import { types } from 'mobx-state-tree';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-export default ConfigurationSchema('VcfTabixAdapter', {
+/**
+ * #config VcfTabixAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const VcfTabixAdapter = ConfigurationSchema('VcfTabixAdapter', {
+    /**
+     * #slot
+     */
     vcfGzLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.vcf.gz', locationType: 'UriLocation' },
     },
     index: ConfigurationSchema('VcfIndex', {
+        /**
+         * #slot index.indexType
+         */
         indexType: {
             model: types.enumeration('IndexType', ['TBI', 'CSI']),
             type: 'stringEnum',
             defaultValue: 'TBI',
         },
+        /**
+         * #slot index.location
+         */
         location: {
             type: 'fileLocation',
             defaultValue: {
@@ -20,4 +33,5 @@ export default ConfigurationSchema('VcfTabixAdapter', {
         },
     }),
 }, { explicitlyTyped: true });
+export default VcfTabixAdapter;
 //# sourceMappingURL=configSchema.js.map

package/esm/VcfTabixAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACvC,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,eAAe,GAAG,mBAAmB,CACzC,iBAAiB,EACjB;IACE;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IACD,KAAK,EAAE,mBAAmB,CAAC,UAAU,EAAE;QACrC;;WAEG;QACH,SAAS,EAAE;YACT,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;YACrD,IAAI,EAAE,YAAY;YAClB,YAAY,EAAE,KAAK;SACpB;QACD;;WAEG;QACH,QAAQ,EAAE;YACR,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,wBAAwB;gBAC7B,YAAY,EAAE,aAAa;aAC5B;SACF;KACF,CAAC;CACH,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,eAAe,CAAA"}

package/esm/index.js

@@ -3,9 +3,9 @@ import VcfTabixAdapterF from './VcfTabixAdapter';
 import ExtensionPointsF from './extensionPoints';
 import VariantTrackF from './VariantTrack';
 import Plugin from '@jbrowse/core/Plugin';
-import ChordVariantDisplay from './ChordVariantDisplay';
+import ChordVariantDisplayF from './ChordVariantDisplay';
 import LinearVariantDisplayF from './LinearVariantDisplay';
-import StructuralVariantChordRendererFactory from './StructuralVariantChordRenderer';
+import StructuralVariantChordRendererF from './StructuralVariantChordRenderer';
 import VariantFeatureWidgetF from './VariantFeatureWidget';
 export default class VariantsPlugin extends Plugin {
     constructor() {
@@ -19,8 +19,8 @@ export default class VariantsPlugin extends Plugin {
         VariantTrackF(pluginManager);
         ExtensionPointsF(pluginManager);
         LinearVariantDisplayF(pluginManager);
-        pluginManager.addRendererType(() => pluginManager.jbrequire(StructuralVariantChordRendererFactory));
-        pluginManager.addDisplayType(() => pluginManager.jbrequire(ChordVariantDisplay));
+        StructuralVariantChordRendererF(pluginManager);
+        ChordVariantDisplayF(pluginManager);
     }
 }
 export { default as VcfFeature } from './VcfTabixAdapter/VcfFeature';

package/esm/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,WAAW,MAAM,cAAc,CAAA;AACtC,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAC1C,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AACvD,OAAO,qBAAqB,MAAM,wBAAwB,CAAA;AAC1D,OAAO,qCAAqC,MAAM,kCAAkC,CAAA;AACpF,OAAO,qBAAqB,MAAM,wBAAwB,CAAA;AAE1D,MAAM,CAAC,OAAO,OAAO,cAAe,SAAQ,MAAM;IAAlD;;QACE,SAAI,GAAG,gBAAgB,CAAA;IAkBzB,CAAC;IAhBC,OAAO,CAAC,aAA4B;QAClC,WAAW,CAAC,aAAa,CAAC,CAAA;QAC1B,gBAAgB,CAAC,aAAa,CAAC,CAAA;QAC/B,qBAAqB,CAAC,aAAa,CAAC,CAAA;QACpC,aAAa,CAAC,aAAa,CAAC,CAAA;QAC5B,gBAAgB,CAAC,aAAa,CAAC,CAAA;QAC/B,qBAAqB,CAAC,aAAa,CAAC,CAAA;QAEpC,aAAa,CAAC,eAAe,CAAC,GAAG,EAAE,CACjC,aAAa,CAAC,SAAS,CAAC,qCAAqC,CAAC,CAC/D,CAAA;QAED,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE,CAChC,aAAa,CAAC,SAAS,CAAC,mBAAmB,CAAC,CAC7C,CAAA;IACH,CAAC;CACF;AAED,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,8BAA8B,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,WAAW,MAAM,cAAc,CAAA;AACtC,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAC1C,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,qBAAqB,MAAM,wBAAwB,CAAA;AAC1D,OAAO,+BAA+B,MAAM,kCAAkC,CAAA;AAC9E,OAAO,qBAAqB,MAAM,wBAAwB,CAAA;AAE1D,MAAM,CAAC,OAAO,OAAO,cAAe,SAAQ,MAAM;IAAlD;;QACE,SAAI,GAAG,gBAAgB,CAAA;IAYzB,CAAC;IAVC,OAAO,CAAC,aAA4B;QAClC,WAAW,CAAC,aAAa,CAAC,CAAA;QAC1B,gBAAgB,CAAC,aAAa,CAAC,CAAA;QAC/B,qBAAqB,CAAC,aAAa,CAAC,CAAA;QACpC,aAAa,CAAC,aAAa,CAAC,CAAA;QAC5B,gBAAgB,CAAC,aAAa,CAAC,CAAA;QAC/B,qBAAqB,CAAC,aAAa,CAAC,CAAA;QACpC,+BAA+B,CAAC,aAAa,CAAC,CAAA;QAC9C,oBAAoB,CAAC,aAAa,CAAC,CAAA;IACrC,CAAC;CACF;AAED,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,8BAA8B,CAAA"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "2.1.7",
+  "version": "2.2.1",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -65,5 +65,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "a1344081f61e22e0f597517efa7386023eef9f33"
+  "gitHead": "896d175c5d9345049faea8e1155f243c912aac42"
 }

package/src/ChordVariantDisplay/index.ts

@@ -1,19 +1,20 @@
 import PluginManager from '@jbrowse/core/PluginManager'
 import { BaseChordDisplayComponent } from '@jbrowse/plugin-circular-view'
-import ChordVariantDisplay from './models/ChordVariantDisplay'
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
+import configSchemaF from './models/configSchema'
+import stateModelF from './models/stateModelFactory'
 
 export default (pluginManager: PluginManager) => {
-  const { load } = pluginManager
-
-  const { stateModel, configSchema } = load(ChordVariantDisplay)
-
-  return new DisplayType({
-    name: 'ChordVariantDisplay',
-    configSchema,
-    stateModel,
-    trackType: 'VariantTrack',
-    viewType: 'CircularView',
-    ReactComponent: BaseChordDisplayComponent,
+  pluginManager.addDisplayType(() => {
+    const configSchema = configSchemaF(pluginManager)
+    const stateModel = stateModelF(configSchema)
+    return new DisplayType({
+      name: 'ChordVariantDisplay',
+      configSchema,
+      stateModel,
+      trackType: 'VariantTrack',
+      viewType: 'CircularView',
+      ReactComponent: BaseChordDisplayComponent,
+    })
   })
 }

package/src/ChordVariantDisplay/models/ChordVariantDisplay.ts

@@ -1,42 +1,45 @@
-import {
-  baseChordDisplayConfig,
-  BaseChordDisplayModel,
-} from '@jbrowse/plugin-circular-view'
-import {
-  ConfigurationSchema,
-  ConfigurationReference,
-} from '@jbrowse/core/configuration'
+import { BaseChordDisplayModel } from '@jbrowse/plugin-circular-view'
+import { ConfigurationReference } from '@jbrowse/core/configuration'
 import { types } from 'mobx-state-tree'
 import { getContainingView } from '@jbrowse/core/util'
 import { getParentRenderProps } from '@jbrowse/core/util/tracks'
 import PluginManager from '@jbrowse/core/PluginManager'
 
-const ChordVariantDisplayF = (pluginManager: PluginManager) => {
-  const configSchema = ConfigurationSchema(
-    'ChordVariantDisplay',
-    {
-      renderer: types.optional(
-        pluginManager.pluggableConfigSchemaType('renderer'),
-        { type: 'StructuralVariantChordRenderer' },
-      ),
-    },
-    { baseConfiguration: baseChordDisplayConfig, explicitlyTyped: true },
-  )
+// locals
+import configSchemaF from './configSchema'
 
+/**
+ * #stateModel ChordVariantDisplay
+ * extends `BaseChordDisplay`
+ */
+const ChordVariantDisplayF = (pluginManager: PluginManager) => {
+  const configSchema = configSchemaF(pluginManager)
   const stateModel = types
     .compose(
       'ChordVariantDisplay',
       BaseChordDisplayModel,
       types.model({
+        /**
+         * #property
+         */
         type: types.literal('ChordVariantDisplay'),
+        /**
+         * #property
+         */
         configuration: ConfigurationReference(configSchema),
       }),
     )
     .views(self => ({
+      /**
+       * #getter
+       */
       get rendererTypeName() {
         return self.configuration.renderer.type
       },
 
+      /**
+       * #method
+       */
       renderProps(): Record<string, unknown> {
         const view = getContainingView(self)
         return {

package/src/ChordVariantDisplay/models/configSchema.ts

@@ -0,0 +1,33 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import PluginManager from '@jbrowse/core/PluginManager'
+import { baseChordDisplayConfig } from '@jbrowse/plugin-circular-view'
+import { types } from 'mobx-state-tree'
+
+/**
+ * #config ChordVariantDisplay
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+function stateModelFactory(pluginManager: PluginManager) {
+  return ConfigurationSchema(
+    'ChordVariantDisplay',
+    {
+      /**
+       * #slot
+       */
+      renderer: types.optional(
+        pluginManager.pluggableConfigSchemaType('renderer'),
+        { type: 'StructuralVariantChordRenderer' },
+      ),
+    },
+    {
+      /**
+       * #baseConfiguration
+       */
+      baseConfiguration: baseChordDisplayConfig,
+      explicitlyTyped: true,
+    },
+  )
+}
+
+export default stateModelFactory

package/src/ChordVariantDisplay/models/stateModelFactory.ts

@@ -0,0 +1,65 @@
+import { BaseChordDisplayModel } from '@jbrowse/plugin-circular-view'
+import {
+  AnyConfigurationSchemaType,
+  ConfigurationReference,
+} from '@jbrowse/core/configuration'
+import { types } from 'mobx-state-tree'
+import { getContainingView } from '@jbrowse/core/util'
+import { getParentRenderProps } from '@jbrowse/core/util/tracks'
+
+/**
+ * #stateModel ChordVariantDisplay
+ * extends `BaseChordDisplay`
+ */
+const stateModelFactory = (configSchema: AnyConfigurationSchemaType) => {
+  return types
+    .compose(
+      'ChordVariantDisplay',
+      BaseChordDisplayModel,
+      types.model({
+        /**
+         * #property
+         */
+        type: types.literal('ChordVariantDisplay'),
+        /**
+         * #property
+         */
+        configuration: ConfigurationReference(configSchema),
+      }),
+    )
+    .views(self => ({
+      /**
+       * #getter
+       */
+      get rendererTypeName() {
+        return self.configuration.renderer.type
+      },
+
+      /**
+       * #method
+       */
+      renderProps(): Record<string, unknown> {
+        const view = getContainingView(self)
+        return {
+          ...getParentRenderProps(self),
+          rpcDriverName: self.rpcDriverName,
+          displayModel: self,
+          bezierRadius: view.radiusPx * self.bezierRadiusRatio,
+          radius: view.radiusPx,
+
+          // @ts-ignore
+          blockDefinitions: this.blockDefinitions,
+          config: self.configuration.renderer,
+          onChordClick: self.onChordClick,
+        }
+      },
+    }))
+}
+
+// http://localhost:3000/test_data/hs37d5.HG002-SequelII-CCS.sv.vcf.gz.tbi
+
+// render request is for 1.5x the current viewing window
+
+// tracks all have a height
+//
+export default stateModelFactory

package/src/LinearVariantDisplay/configSchema.test.js

@@ -6,7 +6,7 @@ import {
   configSchema as svgFeatureRendererConfigSchema,
   ReactComponent as SvgFeatureRendererReactComponent,
 } from '@jbrowse/plugin-svg/src/SvgFeatureRenderer'
-import { LinearVariantDisplayConfigFactory as configSchemaFactory } from './configSchema'
+import configSchemaFactory from './configSchema'
 
 // mock warnings to avoid unnecessary outputs
 beforeEach(() => {

package/src/LinearVariantDisplay/configSchema.ts

@@ -3,20 +3,28 @@ import { Instance } from 'mobx-state-tree'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view'
 
-export function LinearVariantDisplayConfigFactory(
-  pluginManager: PluginManager,
-) {
-  const configSchema = linearBasicDisplayConfigSchemaFactory(pluginManager)
+/**
+ * #config LinearVariantDisplay
+ * mostly empty, this display type is very much
+ * like a `FeatureTrack` with a `LinearBasicDisplay` except it has a custom
+ * feature details widget
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
 
+export default function configSchemaF(pluginManager: PluginManager) {
   return ConfigurationSchema(
     'LinearVariantDisplay',
     {},
-    { baseConfiguration: configSchema, explicitlyTyped: true },
+    {
+      /**
+       * #baseConfiguration
+       */
+      baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager),
+      explicitlyTyped: true,
+    },
   )
 }
 
-export type LinearVariantDisplayConfigModel = ReturnType<
-  typeof LinearVariantDisplayConfigFactory
->
+export type LinearVariantDisplayConfigModel = ReturnType<typeof configSchemaF>
 export type LinearVariantDisplayConfig =
   Instance<LinearVariantDisplayConfigModel>