@jbrowse/plugin-variants 2.1.7 → 2.2.1

package/dist/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/dist/ChordVariantDisplay/index.js

@@ -4,18 +4,21 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const plugin_circular_view_1 = require("@jbrowse/plugin-circular-view");
-const ChordVariantDisplay_1 = __importDefault(require("./models/ChordVariantDisplay"));
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
+const configSchema_1 = __importDefault(require("./models/configSchema"));
+const stateModelFactory_1 = __importDefault(require("./models/stateModelFactory"));
 exports.default = (pluginManager) => {
-    const { load } = pluginManager;
-    const { stateModel, configSchema } = load(ChordVariantDisplay_1.default);
-    return new DisplayType_1.default({
-        name: 'ChordVariantDisplay',
-        configSchema,
-        stateModel,
-        trackType: 'VariantTrack',
-        viewType: 'CircularView',
-        ReactComponent: plugin_circular_view_1.BaseChordDisplayComponent,
+    pluginManager.addDisplayType(() => {
+        const configSchema = (0, configSchema_1.default)(pluginManager);
+        const stateModel = (0, stateModelFactory_1.default)(configSchema);
+        return new DisplayType_1.default({
+            name: 'ChordVariantDisplay',
+            configSchema,
+            stateModel,
+            trackType: 'VariantTrack',
+            viewType: 'CircularView',
+            ReactComponent: plugin_circular_view_1.BaseChordDisplayComponent,
+        });
     });
 };
 //# sourceMappingURL=index.js.map

package/dist/ChordVariantDisplay/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ChordVariantDisplay/index.ts"],"names":[],"mappings":";;;;;AACA,wEAAyE;AACzE,kGAAyE;AACzE,yEAAiD;AACjD,mFAAoD;AAEpD,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAa,EAAC,aAAa,CAAC,CAAA;QACjD,MAAM,UAAU,GAAG,IAAA,2BAAW,EAAC,YAAY,CAAC,CAAA;QAC5C,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,YAAY;YACZ,UAAU;YACV,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,cAAc;YACxB,cAAc,EAAE,gDAAyB;SAC1C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/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/dist/ChordVariantDisplay/models/ChordVariantDisplay.js

@@ -1,23 +1,42 @@
 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 const plugin_circular_view_1 = require("@jbrowse/plugin-circular-view");
 const configuration_1 = require("@jbrowse/core/configuration");
 const mobx_state_tree_1 = require("mobx-state-tree");
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
+// locals
+const configSchema_1 = __importDefault(require("./configSchema"));
+/**
+ * #stateModel ChordVariantDisplay
+ * extends `BaseChordDisplay`
+ */
 const ChordVariantDisplayF = (pluginManager) => {
-    const configSchema = (0, configuration_1.ConfigurationSchema)('ChordVariantDisplay', {
-        renderer: mobx_state_tree_1.types.optional(pluginManager.pluggableConfigSchemaType('renderer'), { type: 'StructuralVariantChordRenderer' }),
-    }, { baseConfiguration: plugin_circular_view_1.baseChordDisplayConfig, explicitlyTyped: true });
+    const configSchema = (0, configSchema_1.default)(pluginManager);
     const stateModel = mobx_state_tree_1.types
         .compose('ChordVariantDisplay', plugin_circular_view_1.BaseChordDisplayModel, mobx_state_tree_1.types.model({
+        /**
+         * #property
+         */
         type: mobx_state_tree_1.types.literal('ChordVariantDisplay'),
+        /**
+         * #property
+         */
         configuration: (0, configuration_1.ConfigurationReference)(configSchema),
     }))
         .views(self => ({
+        /**
+         * #getter
+         */
         get rendererTypeName() {
             return self.configuration.renderer.type;
         },
+        /**
+         * #method
+         */
         renderProps() {
             const view = (0, util_1.getContainingView)(self);
             return {

package/dist/ChordVariantDisplay/models/ChordVariantDisplay.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ChordVariantDisplay.js","sourceRoot":"","sources":["../../../src/ChordVariantDisplay/models/ChordVariantDisplay.ts"],"names":[],"mappings":";;;;;AAAA,wEAAqE;AACrE,+DAAoE;AACpE,qDAAuC;AACvC,6CAAsD;AACtD,sDAAgE;AAGhE,SAAS;AACT,kEAA0C;AAE1C;;;GAGG;AACH,MAAM,oBAAoB,GAAG,CAAC,aAA4B,EAAE,EAAE;IAC5D,MAAM,YAAY,GAAG,IAAA,sBAAa,EAAC,aAAa,CAAC,CAAA;IACjD,MAAM,UAAU,GAAG,uBAAK;SACrB,OAAO,CACN,qBAAqB,EACrB,4CAAqB,EACrB,uBAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,qBAAqB,CAAC;QAC1C;;WAEG;QACH,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,gBAAgB;YAClB,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,IAAI,CAAA;QACzC,CAAC;QAED;;WAEG;QACH,WAAW;YACT,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAC,CAAA;YACpC,OAAO;gBACL,GAAG,IAAA,6BAAoB,EAAC,IAAI,CAAC;gBAC7B,aAAa,EAAE,IAAI,CAAC,aAAa;gBACjC,YAAY,EAAE,IAAI;gBAClB,YAAY,EAAE,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,iBAAiB;gBACpD,MAAM,EAAE,IAAI,CAAC,QAAQ;gBAErB,aAAa;gBACb,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;gBACvC,MAAM,EAAE,IAAI,CAAC,aAAa,CAAC,QAAQ;gBACnC,YAAY,EAAE,IAAI,CAAC,YAAY;aAChC,CAAA;QACH,CAAC;KACF,CAAC,CAAC,CAAA;IAEL,OAAO,EAAE,UAAU,EAAE,YAAY,EAAE,CAAA;AACrC,CAAC,CAAA;AAED,0EAA0E;AAE1E,wDAAwD;AAExD,2BAA2B;AAC3B,EAAE;AACF,kBAAe,oBAAoB,CAAA"}

package/dist/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/dist/ChordVariantDisplay/models/configSchema.js

@@ -0,0 +1,25 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+const plugin_circular_view_1 = require("@jbrowse/plugin-circular-view");
+const mobx_state_tree_1 = require("mobx-state-tree");
+/**
+ * #config ChordVariantDisplay
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function stateModelFactory(pluginManager) {
+    return (0, configuration_1.ConfigurationSchema)('ChordVariantDisplay', {
+        /**
+         * #slot
+         */
+        renderer: mobx_state_tree_1.types.optional(pluginManager.pluggableConfigSchemaType('renderer'), { type: 'StructuralVariantChordRenderer' }),
+    }, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: plugin_circular_view_1.baseChordDisplayConfig,
+        explicitlyTyped: true,
+    });
+}
+exports.default = stateModelFactory;
+//# sourceMappingURL=configSchema.js.map

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

@@ -0,0 +1 @@
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package/dist/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/dist/ChordVariantDisplay/models/stateModelFactory.js

@@ -0,0 +1,55 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const plugin_circular_view_1 = require("@jbrowse/plugin-circular-view");
+const configuration_1 = require("@jbrowse/core/configuration");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+/**
+ * #stateModel ChordVariantDisplay
+ * extends `BaseChordDisplay`
+ */
+const stateModelFactory = (configSchema) => {
+    return mobx_state_tree_1.types
+        .compose('ChordVariantDisplay', plugin_circular_view_1.BaseChordDisplayModel, mobx_state_tree_1.types.model({
+        /**
+         * #property
+         */
+        type: mobx_state_tree_1.types.literal('ChordVariantDisplay'),
+        /**
+         * #property
+         */
+        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get rendererTypeName() {
+            return self.configuration.renderer.type;
+        },
+        /**
+         * #method
+         */
+        renderProps() {
+            const view = (0, util_1.getContainingView)(self);
+            return {
+                ...(0, tracks_1.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
+//
+exports.default = stateModelFactory;
+//# sourceMappingURL=stateModelFactory.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"stateModelFactory.js","sourceRoot":"","sources":["../../../src/ChordVariantDisplay/models/stateModelFactory.ts"],"names":[],"mappings":";;AAAA,wEAAqE;AACrE,+DAGoC;AACpC,qDAAuC;AACvC,6CAAsD;AACtD,sDAAgE;AAEhE;;;GAGG;AACH,MAAM,iBAAiB,GAAG,CAAC,YAAwC,EAAE,EAAE;IACrE,OAAO,uBAAK;SACT,OAAO,CACN,qBAAqB,EACrB,4CAAqB,EACrB,uBAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,qBAAqB,CAAC;QAC1C;;WAEG;QACH,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,gBAAgB;YAClB,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,IAAI,CAAA;QACzC,CAAC;QAED;;WAEG;QACH,WAAW;YACT,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAC,CAAA;YACpC,OAAO;gBACL,GAAG,IAAA,6BAAoB,EAAC,IAAI,CAAC;gBAC7B,aAAa,EAAE,IAAI,CAAC,aAAa;gBACjC,YAAY,EAAE,IAAI;gBAClB,YAAY,EAAE,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,iBAAiB;gBACpD,MAAM,EAAE,IAAI,CAAC,QAAQ;gBAErB,aAAa;gBACb,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;gBACvC,MAAM,EAAE,IAAI,CAAC,aAAa,CAAC,QAAQ;gBACnC,YAAY,EAAE,IAAI,CAAC,YAAY;aAChC,CAAA;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC,CAAA;AAED,0EAA0E;AAE1E,wDAAwD;AAExD,2BAA2B;AAC3B,EAAE;AACF,kBAAe,iBAAiB,CAAA"}

package/dist/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 declare type LinearVariantDisplayConfig = Instance<LinearVariantDisplayConfigModel>;
+export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export type LinearVariantDisplayConfigModel = ReturnType<typeof configSchemaF>;
+export type LinearVariantDisplayConfig = Instance<LinearVariantDisplayConfigModel>;

package/dist/LinearVariantDisplay/configSchema.js

@@ -1,11 +1,22 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.LinearVariantDisplayConfigFactory = void 0;
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-function LinearVariantDisplayConfigFactory(pluginManager) {
-    const configSchema = (0, plugin_linear_genome_view_1.linearBasicDisplayConfigSchemaFactory)(pluginManager);
-    return (0, configuration_1.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
+function configSchemaF(pluginManager) {
+    return (0, configuration_1.ConfigurationSchema)('LinearVariantDisplay', {}, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: (0, plugin_linear_genome_view_1.linearBasicDisplayConfigSchemaFactory)(pluginManager),
+        explicitlyTyped: true,
+    });
 }
-exports.LinearVariantDisplayConfigFactory = LinearVariantDisplayConfigFactory;
+exports.default = configSchemaF;
 //# sourceMappingURL=configSchema.js.map

package/dist/LinearVariantDisplay/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAGjE,kFAA0F;AAE1F;;;;;GAKG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAwB,aAAa,CAAC,aAA4B;IAChE,OAAO,IAAA,mCAAmB,EACxB,sBAAsB,EACtB,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,IAAA,iEAAqC,EAAC,aAAa,CAAC;QACvE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAZD,gCAYC"}

package/dist/LinearVariantDisplay/index.js

@@ -3,13 +3,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const configSchema_1 = require("./configSchema");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 const model_1 = __importDefault(require("./model"));
+const configSchema_1 = __importDefault(require("./configSchema"));
 exports.default = (pluginManager) => {
     pluginManager.addDisplayType(() => {
-        const configSchema = (0, configSchema_1.LinearVariantDisplayConfigFactory)(pluginManager);
+        const configSchema = (0, configSchema_1.default)(pluginManager);
         return new DisplayType_1.default({
             name: 'LinearVariantDisplay',
             configSchema,

package/dist/LinearVariantDisplay/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/index.ts"],"names":[],"mappings":";;;;;AACA,iDAAkE;AAClE,kFAA+E;AAC/E,kGAAyE;AACzE,oDAAuC;AAEvC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,gDAAiC,EAAC,aAAa,CAAC,CAAA;QACrE,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,sBAAsB;YAC5B,YAAY;YACZ,UAAU,EAAE,IAAA,eAAiB,EAAC,YAAY,CAAC;YAC3C,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,sDAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/index.ts"],"names":[],"mappings":";;;;;AACA,kFAA+E;AAC/E,kGAAyE;AACzE,oDAAuC;AACvC,kEAA0C;AAE1C,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAa,EAAC,aAAa,CAAC,CAAA;QACjD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,sBAAsB;YAC5B,YAAY;YACZ,UAAU,EAAE,IAAA,eAAiB,EAAC,YAAY,CAAC;YAC3C,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,sDAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/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/dist/LinearVariantDisplay/model.js

@@ -5,13 +5,27 @@ const tracks_1 = require("@jbrowse/core/util/tracks");
 const util_1 = require("@jbrowse/core/util");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const mobx_state_tree_1 = require("mobx-state-tree");
-function default_1(configSchema) {
+/**
+ * #stateModel LinearVariantDisplay
+ * extends `LinearBasicDisplay`
+ * very similar to basic display, but provides custom widget on feature click
+ */
+function stateModelFactory(configSchema) {
     return mobx_state_tree_1.types
         .compose('LinearVariantDisplay', (0, plugin_linear_genome_view_1.linearBasicDisplayModelFactory)(configSchema), mobx_state_tree_1.types.model({
+        /**
+         * #property
+         */
         type: mobx_state_tree_1.types.literal('LinearVariantDisplay'),
+        /**
+         * #property
+         */
         configuration: (0, configuration_1.ConfigurationReference)(configSchema),
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
         async selectFeature(feature) {
             const session = (0, util_1.getSession)(self);
             if ((0, util_1.isSessionModelWithWidgets)(session)) {
@@ -34,5 +48,5 @@ function default_1(configSchema) {
         },
     }));
 }
-exports.default = default_1;
+exports.default = stateModelFactory;
 //# sourceMappingURL=model.js.map

package/dist/LinearVariantDisplay/model.js.map

@@ -1 +1 @@
-{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/model.ts"],"names":[],"mappings":";;AAAA,+DAA6E;AAC7E,sDAA2D;AAC3D,6CAK2B;AAG3B,kFAAmF;AACnF,qDAAuC;AAGvC,mBAAyB,YAA6C;IACpE,OAAO,uBAAK;SACT,OAAO,CACN,sBAAsB,EACtB,IAAA,0DAA8B,EAAC,YAAY,CAAC,EAC5C,uBAAK,CAAC,KAAK,CAAC;QACV,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,KAAK,CAAC,aAAa,CAAC,OAAgB;YAClC,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;YAChC,IAAI,IAAA,gCAAyB,EAAC,OAAO,CAAC,EAAE;gBACtC,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;gBAC9B,MAAM,SAAS,GAAG,IAAA,wBAAe,EAAC,IAAI,CAAC,CAAA;gBACvC,MAAM,KAAK,GAAG,IAAA,yBAAkB,EAAC,IAAI,CAAC,CAAA;gBACtC,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAC,CAAA;gBACpC,MAAM,aAAa,GAAG,IAAA,uBAAO,EAAC,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;AAvCD,4BAuCC"}
+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/model.ts"],"names":[],"mappings":";;AAAA,+DAA6E;AAC7E,sDAA2D;AAC3D,6CAK2B;AAG3B,kFAAmF;AACnF,qDAAuC;AAGvC;;;;GAIG;AACH,SAAwB,iBAAiB,CACvC,YAA6C;IAE7C,OAAO,uBAAK;SACT,OAAO,CACN,sBAAsB,EACtB,IAAA,0DAA8B,EAAC,YAAY,CAAC,EAC5C,uBAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C;;WAEG;QACH,aAAa,EAAE,IAAA,sCAAsB,EAAC,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,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;YAChC,IAAI,IAAA,gCAAyB,EAAC,OAAO,CAAC,EAAE;gBACtC,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;gBAC9B,MAAM,SAAS,GAAG,IAAA,wBAAe,EAAC,IAAI,CAAC,CAAA;gBACvC,MAAM,KAAK,GAAG,IAAA,yBAAkB,EAAC,IAAI,CAAC,CAAA;gBACtC,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAC,CAAA;gBACpC,MAAM,aAAa,GAAG,IAAA,uBAAO,EAAC,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;AAlDD,oCAkDC"}

package/dist/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/dist/StructuralVariantChordRenderer/configSchema.d.ts

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

package/dist/StructuralVariantChordRenderer/configSchema.js

@@ -0,0 +1,38 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+/**
+ * #config StructuralVariantChordRenderer
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const configSchema = (0, configuration_1.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 });
+exports.default = configSchema;
+//# sourceMappingURL=configSchema.js.map

package/dist/StructuralVariantChordRenderer/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/StructuralVariantChordRenderer/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,gCAAgC,EAChC;IACE;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,4BAA4B;QACzC,YAAY,EAAE,sBAAsB;QACpC,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD;;OAEG;IACH,mBAAmB,EAAE;QACnB,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,iDAAiD;QAC9D,YAAY,EAAE,OAAO;QACrB,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD;;OAEG;IACH,gBAAgB,EAAE;QAChB,IAAI,EAAE,OAAO;QACb,WAAW,EACT,oEAAoE;QACtE,YAAY,EAAE,MAAM;QACpB,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,YAAY,CAAA"}

package/dist/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/dist/StructuralVariantChordRenderer/index.js

@@ -4,35 +4,15 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const CircularChordRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType"));
-const configuration_1 = require("@jbrowse/core/configuration");
+const configSchema_1 = __importDefault(require("./configSchema"));
 const ReactComponent_1 = __importDefault(require("./ReactComponent"));
 const ChordRendererConfigF = (pluginManager) => {
-    const configSchema = (0, configuration_1.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 CircularChordRendererType_1.default({
+    pluginManager.addRendererType(() => new CircularChordRendererType_1.default({
         name: 'StructuralVariantChordRenderer',
         ReactComponent: ReactComponent_1.default,
-        configSchema,
+        configSchema: configSchema_1.default,
         pluginManager,
-    });
+    }));
 };
 exports.default = ChordRendererConfigF;
 //# sourceMappingURL=index.js.map

package/dist/StructuralVariantChordRenderer/index.js.map

@@ -1 +1 @@
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