@jbrowse/plugin-variants 2.1.7 → 2.2.0

package/dist/VariantTrack/configSchema.js

@@ -0,0 +1,18 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+const pluggableElementTypes_1 = require("@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) => (0, configuration_1.ConfigurationSchema)('VariantTrack', {}, {
+    /**
+     * #baseConfiguration
+     */
+    baseConfiguration: (0, pluggableElementTypes_1.createBaseTrackConfig)(pluginManager),
+});
+exports.default = configSchema;
+//# sourceMappingURL=configSchema.js.map

package/dist/VariantTrack/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/VariantTrack/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,+EAA2E;AAG3E;;;;GAIG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,CAAC,aAA4B,EAAE,EAAE,CACpD,IAAA,mCAAmB,EACjB,cAAc,EACd,EAAE,EACF;IACE;;OAEG;IACH,iBAAiB,EAAE,IAAA,6CAAqB,EAAC,aAAa,CAAC;CACxD,CACF,CAAA;AAEH,kBAAe,YAAY,CAAA"}

package/dist/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/dist/VariantTrack/index.js

@@ -3,16 +3,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
 const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-exports.default = (pluginManager) => {
-    pluginManager.addTrackType(() => {
-        const configSchema = (0, configuration_1.ConfigurationSchema)('VariantTrack', {}, { baseConfiguration: (0, models_1.createBaseTrackConfig)(pluginManager) });
+const configSchema_1 = __importDefault(require("./configSchema"));
+exports.default = (pm) => {
+    pm.addTrackType(() => {
+        const configSchema = (0, configSchema_1.default)(pm);
         return new TrackType_1.default({
             name: 'VariantTrack',
             configSchema,
-            stateModel: (0, models_1.createBaseTrackModel)(pluginManager, 'VariantTrack', configSchema),
+            stateModel: (0, models_1.createBaseTrackModel)(pm, 'VariantTrack', configSchema),
         });
     });
 };

package/dist/VariantTrack/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VariantTrack/index.ts"],"names":[],"mappings":";;;;;AACA,+DAAiE;AACjE,8FAAqE;AACrE,uEAGmD;AAEnD,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE;QAC9B,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,cAAc,EACd,EAAE,EACF,EAAE,iBAAiB,EAAE,IAAA,8BAAqB,EAAC,aAAa,CAAC,EAAE,CAC5D,CAAA;QACD,OAAO,IAAI,mBAAS,CAAC;YACnB,IAAI,EAAE,cAAc;YACpB,YAAY;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAC9B,aAAa,EACb,cAAc,EACd,YAAY,CACb;SACF,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VariantTrack/index.ts"],"names":[],"mappings":";;;;;AACA,8FAAqE;AACrE,uEAAiF;AACjF,kEAA0C;AAE1C,kBAAe,CAAC,EAAiB,EAAE,EAAE;IACnC,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,IAAA,sBAAa,EAAC,EAAE,CAAC,CAAA;QACtC,OAAO,IAAI,mBAAS,CAAC;YACnB,IAAI,EAAE,cAAc;YACpB,YAAY;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAAC,EAAE,EAAE,cAAc,EAAE,YAAY,CAAC;SACnE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/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/dist/VcfAdapter/configSchema.js

@@ -1,10 +1,18 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-exports.default = (0, configuration_1.ConfigurationSchema)('VcfAdapter', {
+/**
+ * #config VcfAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const VcfAdapter = (0, configuration_1.ConfigurationSchema)('VcfAdapter', {
+    /**
+     * #slot
+     */
     vcfLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.vcf', locationType: 'UriLocation' },
     },
 }, { explicitlyTyped: true });
+exports.default = VcfAdapter;
 //# sourceMappingURL=configSchema.js.map

package/dist/VcfAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/VcfAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,YAAY,EACZ;IACE,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"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/VcfAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,UAAU,GAAG,IAAA,mCAAmB,EACpC,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,kBAAe,UAAU,CAAA"}

package/dist/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/dist/VcfTabixAdapter/configSchema.js

@@ -2,17 +2,30 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const mobx_state_tree_1 = require("mobx-state-tree");
 const configuration_1 = require("@jbrowse/core/configuration");
-exports.default = (0, configuration_1.ConfigurationSchema)('VcfTabixAdapter', {
+/**
+ * #config VcfTabixAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const VcfTabixAdapter = (0, configuration_1.ConfigurationSchema)('VcfTabixAdapter', {
+    /**
+     * #slot
+     */
     vcfGzLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.vcf.gz', locationType: 'UriLocation' },
     },
     index: (0, configuration_1.ConfigurationSchema)('VcfIndex', {
+        /**
+         * #slot index.indexType
+         */
         indexType: {
             model: mobx_state_tree_1.types.enumeration('IndexType', ['TBI', 'CSI']),
             type: 'stringEnum',
             defaultValue: 'TBI',
         },
+        /**
+         * #slot index.location
+         */
         location: {
             type: 'fileLocation',
             defaultValue: {
@@ -22,4 +35,5 @@ exports.default = (0, configuration_1.ConfigurationSchema)('VcfTabixAdapter', {
         },
     }),
 }, { explicitlyTyped: true });
+exports.default = VcfTabixAdapter;
 //# sourceMappingURL=configSchema.js.map

package/dist/VcfTabixAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,qDAAuC;AACvC,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,iBAAiB,EACjB;IACE,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IACD,KAAK,EAAE,IAAA,mCAAmB,EAAC,UAAU,EAAE;QACrC,SAAS,EAAE;YACT,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;YACrD,IAAI,EAAE,YAAY;YAClB,YAAY,EAAE,KAAK;SACpB;QACD,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"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,qDAAuC;AACvC,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,eAAe,GAAG,IAAA,mCAAmB,EACzC,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,IAAA,mCAAmB,EAAC,UAAU,EAAE;QACrC;;WAEG;QACH,SAAS,EAAE;YACT,KAAK,EAAE,uBAAK,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,kBAAe,eAAe,CAAA"}

package/dist/index.js

@@ -25,8 +25,8 @@ class VariantsPlugin extends Plugin_1.default {
         (0, VariantTrack_1.default)(pluginManager);
         (0, extensionPoints_1.default)(pluginManager);
         (0, LinearVariantDisplay_1.default)(pluginManager);
-        pluginManager.addRendererType(() => pluginManager.jbrequire(StructuralVariantChordRenderer_1.default));
-        pluginManager.addDisplayType(() => pluginManager.jbrequire(ChordVariantDisplay_1.default));
+        (0, StructuralVariantChordRenderer_1.default)(pluginManager);
+        (0, ChordVariantDisplay_1.default)(pluginManager);
     }
 }
 exports.default = VariantsPlugin;

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,8DAAsC;AACtC,wEAAgD;AAChD,wEAAgD;AAChD,kEAA0C;AAC1C,kEAAyC;AAEzC,gFAAuD;AACvD,kFAA0D;AAC1D,sGAAoF;AACpF,kFAA0D;AAE1D,MAAqB,cAAe,SAAQ,gBAAM;IAAlD;;QACE,SAAI,GAAG,gBAAgB,CAAA;IAkBzB,CAAC;IAhBC,OAAO,CAAC,aAA4B;QAClC,IAAA,oBAAW,EAAC,aAAa,CAAC,CAAA;QAC1B,IAAA,yBAAgB,EAAC,aAAa,CAAC,CAAA;QAC/B,IAAA,8BAAqB,EAAC,aAAa,CAAC,CAAA;QACpC,IAAA,sBAAa,EAAC,aAAa,CAAC,CAAA;QAC5B,IAAA,yBAAgB,EAAC,aAAa,CAAC,CAAA;QAC/B,IAAA,8BAAqB,EAAC,aAAa,CAAC,CAAA;QAEpC,aAAa,CAAC,eAAe,CAAC,GAAG,EAAE,CACjC,aAAa,CAAC,SAAS,CAAC,wCAAqC,CAAC,CAC/D,CAAA;QAED,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE,CAChC,aAAa,CAAC,SAAS,CAAC,6BAAmB,CAAC,CAC7C,CAAA;IACH,CAAC;CACF;AAnBD,iCAmBC;AAED,2DAAoE;AAA3D,yHAAA,OAAO,OAAc"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,8DAAsC;AACtC,wEAAgD;AAChD,wEAAgD;AAChD,kEAA0C;AAC1C,kEAAyC;AAEzC,gFAAwD;AACxD,kFAA0D;AAC1D,sGAA8E;AAC9E,kFAA0D;AAE1D,MAAqB,cAAe,SAAQ,gBAAM;IAAlD;;QACE,SAAI,GAAG,gBAAgB,CAAA;IAYzB,CAAC;IAVC,OAAO,CAAC,aAA4B;QAClC,IAAA,oBAAW,EAAC,aAAa,CAAC,CAAA;QAC1B,IAAA,yBAAgB,EAAC,aAAa,CAAC,CAAA;QAC/B,IAAA,8BAAqB,EAAC,aAAa,CAAC,CAAA;QACpC,IAAA,sBAAa,EAAC,aAAa,CAAC,CAAA;QAC5B,IAAA,yBAAgB,EAAC,aAAa,CAAC,CAAA;QAC/B,IAAA,8BAAqB,EAAC,aAAa,CAAC,CAAA;QACpC,IAAA,wCAA+B,EAAC,aAAa,CAAC,CAAA;QAC9C,IAAA,6BAAoB,EAAC,aAAa,CAAC,CAAA;IACrC,CAAC;CACF;AAbD,iCAaC;AAED,2DAAoE;AAA3D,yHAAA,OAAO,OAAc"}

package/esm/ChordVariantDisplay/index.d.ts

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

package/esm/ChordVariantDisplay/index.js

@@ -1,16 +1,19 @@
 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) => {
-    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,
+        });
     });
 };
 //# sourceMappingURL=index.js.map

package/esm/ChordVariantDisplay/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ChordVariantDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,yBAAyB,EAAE,MAAM,+BAA+B,CAAA;AACzE,OAAO,mBAAmB,MAAM,8BAA8B,CAAA;AAC9D,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,MAAM,EAAE,IAAI,EAAE,GAAG,aAAa,CAAA;IAE9B,MAAM,EAAE,UAAU,EAAE,YAAY,EAAE,GAAG,IAAI,CAAC,mBAAmB,CAAC,CAAA;IAE9D,OAAO,IAAI,WAAW,CAAC;QACrB,IAAI,EAAE,qBAAqB;QAC3B,YAAY;QACZ,UAAU;QACV,SAAS,EAAE,cAAc;QACzB,QAAQ,EAAE,cAAc;QACxB,cAAc,EAAE,yBAAyB;KAC1C,CAAC,CAAA;AACJ,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ChordVariantDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,yBAAyB,EAAE,MAAM,+BAA+B,CAAA;AACzE,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,aAAa,MAAM,uBAAuB,CAAA;AACjD,OAAO,WAAW,MAAM,4BAA4B,CAAA;AAEpD,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,aAAa,CAAC,aAAa,CAAC,CAAA;QACjD,MAAM,UAAU,GAAG,WAAW,CAAC,YAAY,CAAC,CAAA;QAC5C,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,YAAY;YACZ,UAAU;YACV,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,cAAc;YACxB,cAAc,EAAE,yBAAyB;SAC1C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/ChordVariantDisplay/models/ChordVariantDisplay.d.ts

@@ -1,5 +1,9 @@
 /// <reference types="react" />
 import PluginManager from '@jbrowse/core/PluginManager';
+/**
+ * #stateModel ChordVariantDisplay
+ * extends `BaseChordDisplay`
+ */
 declare const ChordVariantDisplayF: (pluginManager: PluginManager) => {
     stateModel: import("mobx-state-tree").IModelType<{
         id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -9,7 +13,13 @@ declare const ChordVariantDisplayF: (pluginManager: PluginManager) => {
         bezierRadiusRatio: import("mobx-state-tree").IType<number | undefined, number, number>;
         assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     } & {
+        /**
+         * #property
+         */
         type: import("mobx-state-tree").ISimpleType<"ChordVariantDisplay">;
+        /**
+         * #property
+         */
         configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
     }, {
         rendererTypeName: string;
@@ -17,7 +27,9 @@ declare const ChordVariantDisplayF: (pluginManager: PluginManager) => {
     } & {
         readonly RenderingComponent: import("react").FC<{
             model: {
-                id: string;
+                id: string; /**
+                 * #property
+                 */
                 type: string;
                 rpcDriverName: string | undefined;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -91,7 +103,13 @@ declare const ChordVariantDisplayF: (pluginManager: PluginManager) => {
     } & {
         afterAttach(): void;
     } & {
+        /**
+         * #getter
+         */
         readonly rendererTypeName: any;
+        /**
+         * #method
+         */
         renderProps(): Record<string, unknown>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
     configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/esm/ChordVariantDisplay/models/ChordVariantDisplay.js

@@ -1,21 +1,37 @@
-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';
+// locals
+import configSchemaF from './configSchema';
+/**
+ * #stateModel ChordVariantDisplay
+ * extends `BaseChordDisplay`
+ */
 const ChordVariantDisplayF = (pluginManager) => {
-    const configSchema = ConfigurationSchema('ChordVariantDisplay', {
-        renderer: types.optional(pluginManager.pluggableConfigSchemaType('renderer'), { type: 'StructuralVariantChordRenderer' }),
-    }, { baseConfiguration: baseChordDisplayConfig, explicitlyTyped: true });
+    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() {
             const view = getContainingView(self);
             return {

package/esm/ChordVariantDisplay/models/ChordVariantDisplay.js.map

@@ -1 +1 @@
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package/esm/ChordVariantDisplay/models/configSchema.d.ts

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

package/esm/ChordVariantDisplay/models/configSchema.js

@@ -0,0 +1,23 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+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) {
+    return ConfigurationSchema('ChordVariantDisplay', {
+        /**
+         * #slot
+         */
+        renderer: types.optional(pluginManager.pluggableConfigSchemaType('renderer'), { type: 'StructuralVariantChordRenderer' }),
+    }, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: baseChordDisplayConfig,
+        explicitlyTyped: true,
+    });
+}
+export default stateModelFactory;
+//# sourceMappingURL=configSchema.js.map

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

@@ -0,0 +1 @@
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package/esm/ChordVariantDisplay/models/stateModelFactory.d.ts

@@ -0,0 +1,112 @@
+/// <reference types="react" />
+import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+/**
+ * #stateModel ChordVariantDisplay
+ * extends `BaseChordDisplay`
+ */
+declare const stateModelFactory: (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>>;
+} & {
+    bezierRadiusRatio: import("mobx-state-tree").IType<number | undefined, number, number>;
+    assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+} & {
+    /**
+     * #property
+     */
+    type: import("mobx-state-tree").ISimpleType<"ChordVariantDisplay">;
+    /**
+     * #property
+     */
+    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+}, {
+    rendererTypeName: string;
+    error: unknown;
+} & {
+    readonly RenderingComponent: import("react").FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            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]>;
+            type: import("mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        onHorizontalScroll?: Function | undefined;
+        blockState?: Record<string, any> | undefined;
+    }>;
+    readonly DisplayBlurb: import("react").FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            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]>;
+            type: import("mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }> | null;
+    readonly adapterConfig: any;
+    readonly parentTrack: any;
+    renderProps(): any;
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+    regionCannotBeRendered(): undefined;
+} & {
+    setError(error?: unknown): void;
+    setRpcDriverName(rpcDriverName: string): void;
+    reload(): void;
+} & {
+    filled: boolean;
+    reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+    data: undefined;
+    message: string;
+    renderingComponent: import("@jbrowse/core/util").AnyReactComponentType | undefined;
+    refNameMap: Record<string, string> | undefined;
+} & {
+    onChordClick(feature: import("@jbrowse/core/util").Feature): void;
+} & {
+    readonly blockDefinitions: any;
+    renderProps(): any;
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+    isCompatibleWithRenderer(renderer: import("@jbrowse/core/pluggableElementTypes").RendererType): boolean;
+    readonly selectedFeatureId: string | undefined;
+} & {
+    renderStarted(): void;
+    renderSuccess({ message, data, reactElement, renderingComponent, }: {
+        message: string;
+        data: any;
+        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+        renderingComponent: import("@jbrowse/core/util").AnyReactComponentType;
+    }): void;
+    renderError(error: unknown): void;
+    setRefNameMap(refNameMap: Record<string, string>): void;
+} & {
+    afterAttach(): void;
+} & {
+    /**
+     * #getter
+     */
+    readonly rendererTypeName: any;
+    /**
+     * #method
+     */
+    renderProps(): Record<string, unknown>;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export default stateModelFactory;

package/esm/ChordVariantDisplay/models/stateModelFactory.js

@@ -0,0 +1,53 @@
+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';
+/**
+ * #stateModel ChordVariantDisplay
+ * extends `BaseChordDisplay`
+ */
+const stateModelFactory = (configSchema) => {
+    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() {
+            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;
+//# sourceMappingURL=stateModelFactory.js.map

package/esm/ChordVariantDisplay/models/stateModelFactory.js.map

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package/esm/LinearVariantDisplay/configSchema.d.ts

@@ -1,5 +1,5 @@
 import { Instance } from 'mobx-state-tree';
 import PluginManager from '@jbrowse/core/PluginManager';
-export declare function LinearVariantDisplayConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export declare type LinearVariantDisplayConfigModel = ReturnType<typeof LinearVariantDisplayConfigFactory>;
+export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare type LinearVariantDisplayConfigModel = ReturnType<typeof configSchemaF>;
 export declare type LinearVariantDisplayConfig = Instance<LinearVariantDisplayConfigModel>;

package/esm/LinearVariantDisplay/configSchema.js

@@ -1,7 +1,19 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view';
-export function LinearVariantDisplayConfigFactory(pluginManager) {
-    const configSchema = linearBasicDisplayConfigSchemaFactory(pluginManager);
-    return ConfigurationSchema('LinearVariantDisplay', {}, { baseConfiguration: configSchema, explicitlyTyped: true });
+/**
+ * #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) {
+    return ConfigurationSchema('LinearVariantDisplay', {}, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager),
+        explicitlyTyped: true,
+    });
 }
 //# sourceMappingURL=configSchema.js.map

package/esm/LinearVariantDisplay/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAGjE,OAAO,EAAE,qCAAqC,EAAE,MAAM,oCAAoC,CAAA;AAE1F;;;;;GAKG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,CAAC,OAAO,UAAU,aAAa,CAAC,aAA4B;IAChE,OAAO,mBAAmB,CACxB,sBAAsB,EACtB,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,qCAAqC,CAAC,aAAa,CAAC;QACvE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC"}

package/esm/LinearVariantDisplay/index.js

@@ -1,10 +1,10 @@
-import { LinearVariantDisplayConfigFactory } from './configSchema';
 import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
 import stateModelFactory from './model';
+import configSchemaF from './configSchema';
 export default (pluginManager) => {
     pluginManager.addDisplayType(() => {
-        const configSchema = LinearVariantDisplayConfigFactory(pluginManager);
+        const configSchema = configSchemaF(pluginManager);
         return new DisplayType({
             name: 'LinearVariantDisplay',
             configSchema,

package/esm/LinearVariantDisplay/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,0BAA0B,EAAE,MAAM,oCAAoC,CAAA;AAC/E,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,iBAAiB,MAAM,SAAS,CAAA;AACvC,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAE1C,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,aAAa,CAAC,aAAa,CAAC,CAAA;QACjD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,sBAAsB;YAC5B,YAAY;YACZ,UAAU,EAAE,iBAAiB,CAAC,YAAY,CAAC;YAC3C,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,0BAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

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>;