@jbrowse/plugin-gccontent 2.10.3 → 2.11.1

package/dist/GCContentAdapter/GCContentAdapter.d.ts

@@ -1,6 +1,6 @@
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Feature, Region } from '@jbrowse/core/util';
-export default class extends BaseFeatureDataAdapter {
+export default class GCContentAdapter extends BaseFeatureDataAdapter {
     private gcMode;
     static capabilities: string[];
     configure(): Promise<BaseFeatureDataAdapter>;

package/dist/GCContentAdapter/GCContentAdapter.js

@@ -5,7 +5,7 @@ const rxjs_1 = require("rxjs");
 const rxjs_2 = require("@jbrowse/core/util/rxjs");
 const util_1 = require("@jbrowse/core/util");
 const operators_1 = require("rxjs/operators");
-class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
+class GCContentAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor() {
         super(...arguments);
         this.gcMode = 'content';
@@ -70,6 +70,7 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
                 }
                 observer.next(new util_1.SimpleFeature({
                     uniqueId: `${this.id}_${pos + i}`,
+                    refName: query.refName,
                     start: pos + i,
                     end: pos + i + windowDelta,
                     score,
@@ -85,5 +86,5 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
      */
     freeResources( /* { region } */) { }
 }
-default_1.capabilities = ['hasLocalStats'];
-exports.default = default_1;
+GCContentAdapter.capabilities = ['hasLocalStats'];
+exports.default = GCContentAdapter;

package/dist/GCContentAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function GCContentAdapterF(pluginManager: PluginManager): void;

package/dist/GCContentAdapter/index.js

@@ -28,7 +28,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pluginManager) => {
+function GCContentAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'GCContentAdapter',
         displayName: 'GC content adapter',
@@ -38,4 +38,5 @@ exports.default = (pluginManager) => {
         configSchema: (0, configSchema_1.default)(pluginManager),
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./GCContentAdapter'))).then(r => r.default),
     }));
-};
+}
+exports.default = GCContentAdapterF;

package/dist/GCContentTrack/configSchema.d.ts

@@ -0,0 +1,82 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    name: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    assemblyNames: {
+        description: string;
+        type: string; /**
+         * #baseConfiguration
+         */
+        defaultValue: string[];
+    };
+    description: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    category: {
+        description: string;
+        type: string;
+        defaultValue: never[];
+    };
+    metadata: {
+        type: string;
+        description: string;
+        defaultValue: {};
+    };
+    adapter: import("mobx-state-tree").IAnyModelType;
+    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        indexingAttributes: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        indexingFeatureTypesToExclude: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        feature: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        subfeatures: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        depth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        maxDepth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        config: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        hideUris: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
+export default configSchema;

package/dist/GCContentTrack/configSchema.js

@@ -0,0 +1,16 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
+/**
+ * #config GCContentTrack
+ * used for having a gc content track outside of the "reference sequence display"
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const configSchema = (pluginManager) => (0, configuration_1.ConfigurationSchema)('GCContentTrack', {}, {
+    /**
+     * #baseConfiguration
+     */
+    baseConfiguration: (0, pluggableElementTypes_1.createBaseTrackConfig)(pluginManager),
+});
+exports.default = configSchema;

package/dist/GCContentTrack/index.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function GCContentTrackF(pm: PluginManager): void;

package/dist/GCContentTrack/index.js

@@ -0,0 +1,20 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
+const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
+const configSchema_1 = __importDefault(require("./configSchema"));
+function GCContentTrackF(pm) {
+    pm.addTrackType(() => {
+        const configSchema = (0, configSchema_1.default)(pm);
+        return new TrackType_1.default({
+            name: 'GCContentTrack',
+            displayName: 'GCContent track',
+            configSchema,
+            stateModel: (0, models_1.createBaseTrackModel)(pm, 'GCContentTrack', configSchema),
+        });
+    });
+}
+exports.default = GCContentTrackF;

package/dist/LinearGCContentDisplay/{config.d.ts → config1.d.ts}

@@ -4,7 +4,7 @@ import PluginManager from '@jbrowse/core/PluginManager';
  * #category display
  * extends LinearWiggleDisplay
  */
-export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+export default function LinearGCContentDisplay(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     windowSize: {
         type: string;
         defaultValue: number;

package/dist/LinearGCContentDisplay/{config.js → config1.js}

@@ -6,7 +6,7 @@ const configuration_1 = require("@jbrowse/core/configuration");
  * #category display
  * extends LinearWiggleDisplay
  */
-function WiggleConfigFactory(pluginManager) {
+function LinearGCContentDisplay(pluginManager) {
     return (0, configuration_1.ConfigurationSchema)('LinearGCContentDisplay', {
         windowSize: {
             type: 'number',
@@ -25,4 +25,4 @@ function WiggleConfigFactory(pluginManager) {
         explicitlyTyped: true,
     });
 }
-exports.default = WiggleConfigFactory;
+exports.default = LinearGCContentDisplay;

package/dist/LinearGCContentDisplay/config2.d.ts

@@ -0,0 +1,16 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+/**
+ * #config LinearGCContentTrackDisplay
+ * #category display
+ * extends LinearWiggleDisplay, used specifically for GCContentTrack
+ */
+export default function LinearGCContentTrackDisplayF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    windowSize: {
+        type: string;
+        defaultValue: number;
+    };
+    windowDelta: {
+        type: string;
+        defaultValue: number;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration").AnyConfigurationSchemaType, undefined>>;

package/dist/LinearGCContentDisplay/config2.js

@@ -0,0 +1,28 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+/**
+ * #config LinearGCContentTrackDisplay
+ * #category display
+ * extends LinearWiggleDisplay, used specifically for GCContentTrack
+ */
+function LinearGCContentTrackDisplayF(pluginManager) {
+    return (0, configuration_1.ConfigurationSchema)('LinearGCContentTrackDisplay', {
+        windowSize: {
+            type: 'number',
+            defaultValue: 100,
+        },
+        windowDelta: {
+            type: 'number',
+            defaultValue: 100,
+        },
+    }, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: pluginManager.getDisplayType('LinearWiggleDisplay')
+            .configSchema,
+        explicitlyTyped: true,
+    });
+}
+exports.default = LinearGCContentTrackDisplayF;

package/dist/LinearGCContentDisplay/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function LinearGCContentDisplayF(pluginManager: PluginManager): void;

package/dist/LinearGCContentDisplay/index.js

@@ -5,12 +5,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
-const config_1 = __importDefault(require("./config"));
-const stateModel_1 = __importDefault(require("./stateModel"));
-exports.default = (pluginManager) => {
+const config1_1 = __importDefault(require("./config1"));
+const config2_1 = __importDefault(require("./config2"));
+const stateModel1_1 = __importDefault(require("./stateModel1"));
+const stateModel2_1 = __importDefault(require("./stateModel2"));
+function LinearGCContentDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
-        const configSchema = (0, config_1.default)(pluginManager);
-        const stateModel = (0, stateModel_1.default)(pluginManager, configSchema);
+        const configSchema = (0, config1_1.default)(pluginManager);
+        const stateModel = (0, stateModel1_1.default)(pluginManager, configSchema);
         return new pluggableElementTypes_1.DisplayType({
             name: 'LinearGCContentDisplay',
             configSchema,
@@ -21,4 +23,18 @@ exports.default = (pluginManager) => {
             ReactComponent: plugin_wiggle_1.LinearWiggleDisplayReactComponent,
         });
     });
-};
+    pluginManager.addDisplayType(() => {
+        const configSchema = (0, config2_1.default)(pluginManager);
+        const stateModel = (0, stateModel2_1.default)(pluginManager, configSchema);
+        return new pluggableElementTypes_1.DisplayType({
+            name: 'LinearGCContentTrackDisplay',
+            configSchema,
+            stateModel,
+            displayName: 'GC content display',
+            trackType: 'GCContentTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: plugin_wiggle_1.LinearWiggleDisplayReactComponent,
+        });
+    });
+}
+exports.default = LinearGCContentDisplayF;

package/{esm/LinearGCContentDisplay/stateModel.d.ts → dist/LinearGCContentDisplay/shared.d.ts}

@@ -2,11 +2,12 @@
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
 /**
- * #stateModel LinearGCContentDisplay
+ * #stateModel SharedGCContentModel
  * #category display
- * base model `BaseWiggleDisplayModel`
+ * extends
+ * - [LinearWiggleDisplay](../linearwiggledisplay)
  */
-export default function stateModelFactory(pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
+export default function SharedModelF(pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -76,7 +77,9 @@ export default function stateModelFactory(pluginManager: PluginManager, configSc
             defaultValue: number;
         };
         fetchSizeLimit: {
-            type: string;
+            type: string; /**
+             * #property
+             */
             defaultValue: number;
             description: string;
         };
@@ -109,18 +112,10 @@ export default function stateModelFactory(pluginManager: PluginManager, configSc
         max: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
         min: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-    configuration: AnyConfigurationSchemaType; /**
-     * #method
-     * retrieves the sequence adapter from parent track, and puts it as a
-     * subadapter on a GCContentAdapter
-     */
+    configuration: AnyConfigurationSchemaType;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
 } & {
-    /**
-     * #property
-     */
-    type: import("mobx-state-tree").ISimpleType<"LinearGCContentDisplay">;
     /**
      * #property
      */
@@ -138,13 +133,13 @@ export default function stateModelFactory(pluginManager: PluginManager, configSc
         model: {
             id: string;
             type: string;
-            rpcDriverName: string | undefined;
+            rpcDriverName: string | undefined; /**
+             * #property
+             */
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined; /**
-             * #property
-             */
+            message: string | undefined;
         } & 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>;

package/dist/LinearGCContentDisplay/{stateModel.js → shared.js}

@@ -30,17 +30,14 @@ const mobx_state_tree_1 = require("mobx-state-tree");
 const react_1 = require("react");
 const EditGCContentParamsDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/EditGCContentParams'))));
 /**
- * #stateModel LinearGCContentDisplay
+ * #stateModel SharedGCContentModel
  * #category display
- * base model `BaseWiggleDisplayModel`
+ * extends
+ * - [LinearWiggleDisplay](../linearwiggledisplay)
  */
-function stateModelFactory(pluginManager, configSchema) {
+function SharedModelF(pluginManager, configSchema) {
     return mobx_state_tree_1.types
-        .compose('LinearGCContentDisplay', (0, plugin_wiggle_1.linearWiggleDisplayModelFactory)(pluginManager, configSchema), mobx_state_tree_1.types.model({
-        /**
-         * #property
-         */
-        type: mobx_state_tree_1.types.literal('LinearGCContentDisplay'),
+        .compose('SharedGCContentModel', (0, plugin_wiggle_1.linearWiggleDisplayModelFactory)(pluginManager, configSchema), mobx_state_tree_1.types.model({
         /**
          * #property
          */
@@ -103,4 +100,4 @@ function stateModelFactory(pluginManager, configSchema) {
         };
     });
 }
-exports.default = stateModelFactory;
+exports.default = SharedModelF;