@jbrowse/plugin-circular-view 2.1.6 → 2.2.0

package/dist/BaseChordDisplay/models/BaseChordDisplayModel.d.ts

@@ -69,30 +69,56 @@ export declare const BaseChordDisplayModel: import("mobx-state-tree").IModelType
     renderingComponent: AnyReactComponentType | undefined;
     refNameMap: Record<string, string> | undefined;
 } & {
+    /**
+     * #action
+     */
     onChordClick(feature: Feature): void;
 } & {
+    /**
+     * #getter
+     */
     readonly blockDefinitions: any;
+    /**
+     * #method
+     */
     renderProps(): any;
     /**
+     * #getter
      * the pluggable element type object for this diplay's
      * renderer
      */
     readonly rendererType: RendererType;
+    /**
+     * #method
+     */
     isCompatibleWithRenderer(renderer: RendererType): boolean;
     /**
+     * #getter
      * returns a string feature ID if the globally-selected object
      * is probably a feature
      */
     readonly selectedFeatureId: string | undefined;
 } & {
+    /**
+     * #action
+     */
     renderStarted(): void;
+    /**
+     * #action
+     */
     renderSuccess({ message, data, reactElement, renderingComponent, }: {
         message: string;
         data: any;
         reactElement: React.ReactElement;
         renderingComponent: AnyReactComponentType;
     }): void;
+    /**
+     * #action
+     */
     renderError(error: unknown): void;
+    /**
+     * #action
+     */
     setRefNameMap(refNameMap: Record<string, string>): void;
 } & {
     afterAttach(): void;

package/dist/BaseChordDisplay/models/BaseChordDisplayModel.js

@@ -11,175 +11,215 @@ const util_1 = require("@jbrowse/core/util");
 const simpleFeature_1 = require("@jbrowse/core/util/simpleFeature");
 const tracks_1 = require("@jbrowse/core/util/tracks");
 const mobx_state_tree_1 = require("mobx-state-tree");
+// locals
 const renderReaction_1 = require("./renderReaction");
-exports.BaseChordDisplayModel = mobx_state_tree_1.types
-    .compose('BaseChordDisplay', models_1.BaseDisplay, mobx_state_tree_1.types.model({
-    bezierRadiusRatio: 0.1,
-    assemblyName: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-}))
-    .volatile(() => {
-    return {
-        // NOTE: all this volatile stuff has to be filled in at once
-        // so that it stays consistent
-        filled: false,
-        reactElement: undefined,
-        data: undefined,
-        message: '',
-        renderingComponent: undefined,
-        refNameMap: undefined,
-    };
-})
-    .actions(self => {
-    const { pluginManager } = (0, util_1.getEnv)(self);
-    const track = self;
-    return {
-        onChordClick(feature) {
-            (0, configuration_1.getConf)(self, 'onChordClick', { feature, track, pluginManager });
-        },
-    };
-})
-    .views(self => ({
-    get blockDefinitions() {
-        const origSlices = (0, util_1.getContainingView)(self)
-            .staticSlices;
-        if (!self.refNameMap) {
-            return origSlices;
-        }
-        const slices = JSON.parse(JSON.stringify(origSlices));
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        slices.forEach((slice) => {
-            const regions = slice.region.elided
-                ? slice.region.regions
-                : [slice.region];
-            regions.forEach((region) => {
-                var _a;
-                const renamed = (_a = self.refNameMap) === null || _a === void 0 ? void 0 : _a[region.refName];
-                if (renamed && region.refName !== renamed) {
-                    region.refName = renamed;
-                }
-            });
-        });
-        return slices;
-    },
-    renderProps() {
-        const view = (0, util_1.getContainingView)(self);
+/**
+ * #stateModel BaseChordDisplay
+ * extends `BaseDisplay`
+ */
+function stateModelFactory() {
+    return mobx_state_tree_1.types
+        .compose('BaseChordDisplay', models_1.BaseDisplay, mobx_state_tree_1.types.model({
+        /**
+         * #property
+         */
+        bezierRadiusRatio: 0.1,
+        /**
+         * #property
+         */
+        assemblyName: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+    }))
+        .volatile(() => {
         return {
-            ...(0, tracks_1.getParentRenderProps)(self),
-            rpcDriverName: self.rpcDriverName,
-            displayModel: self,
-            bezierRadius: view.radiusPx * self.bezierRadiusRatio,
-            radius: view.radiusPx,
-            blockDefinitions: this.blockDefinitions,
-            onChordClick: self.onChordClick,
+            // NOTE: all this volatile stuff has to be filled in at once
+            // so that it stays consistent
+            filled: false,
+            reactElement: undefined,
+            data: undefined,
+            message: '',
+            renderingComponent: undefined,
+            refNameMap: undefined,
         };
-    },
-    /**
-     * the pluggable element type object for this diplay's
-     * renderer
-     */
-    get rendererType() {
-        const display = self;
+    })
+        .actions(self => {
         const { pluginManager } = (0, util_1.getEnv)(self);
-        const ThisRendererType = pluginManager.getRendererType(self.rendererTypeName);
-        if (!ThisRendererType) {
-            throw new Error(`renderer "${display.rendererTypeName}" not found`);
-        }
-        if (!ThisRendererType.ReactComponent) {
-            throw new Error(`renderer ${display.rendererTypeName} has no ReactComponent, it may not be completely implemented yet`);
-        }
-        return ThisRendererType;
-    },
-    isCompatibleWithRenderer(renderer) {
-        return !!(renderer instanceof CircularChordRendererType_1.default);
-    },
-    /**
-     * returns a string feature ID if the globally-selected object
-     * is probably a feature
-     */
-    get selectedFeatureId() {
-        if (!(0, mobx_state_tree_1.isAlive)(self)) {
-            return undefined;
-        }
-        const session = (0, util_1.getSession)(self);
-        if (!session) {
+        const track = self;
+        return {
+            /**
+             * #action
+             */
+            onChordClick(feature) {
+                (0, configuration_1.getConf)(self, 'onChordClick', { feature, track, pluginManager });
+            },
+        };
+    })
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get blockDefinitions() {
+            const origSlices = (0, util_1.getContainingView)(self)
+                .staticSlices;
+            if (!self.refNameMap) {
+                return origSlices;
+            }
+            const slices = JSON.parse(JSON.stringify(origSlices));
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            slices.forEach((slice) => {
+                const regions = slice.region.elided
+                    ? slice.region.regions
+                    : [slice.region];
+                regions.forEach((region) => {
+                    var _a;
+                    const renamed = (_a = self.refNameMap) === null || _a === void 0 ? void 0 : _a[region.refName];
+                    if (renamed && region.refName !== renamed) {
+                        region.refName = renamed;
+                    }
+                });
+            });
+            return slices;
+        },
+        /**
+         * #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,
+                blockDefinitions: this.blockDefinitions,
+                onChordClick: self.onChordClick,
+            };
+        },
+        /**
+         * #getter
+         * the pluggable element type object for this diplay's
+         * renderer
+         */
+        get rendererType() {
+            const display = self;
+            const { pluginManager } = (0, util_1.getEnv)(self);
+            const ThisRendererType = pluginManager.getRendererType(self.rendererTypeName);
+            if (!ThisRendererType) {
+                throw new Error(`renderer "${display.rendererTypeName}" not found`);
+            }
+            if (!ThisRendererType.ReactComponent) {
+                throw new Error(`renderer ${display.rendererTypeName} has no ReactComponent, it may not be completely implemented yet`);
+            }
+            return ThisRendererType;
+        },
+        /**
+         * #method
+         */
+        isCompatibleWithRenderer(renderer) {
+            return !!(renderer instanceof CircularChordRendererType_1.default);
+        },
+        /**
+         * #getter
+         * returns a string feature ID if the globally-selected object
+         * is probably a feature
+         */
+        get selectedFeatureId() {
+            if (!(0, mobx_state_tree_1.isAlive)(self)) {
+                return undefined;
+            }
+            const session = (0, util_1.getSession)(self);
+            if (!session) {
+                return undefined;
+            }
+            const { selection } = session;
+            // does it quack like a feature?
+            if ((0, simpleFeature_1.isFeature)(selection)) {
+                return selection.id();
+            }
             return undefined;
-        }
-        const { selection } = session;
-        // does it quack like a feature?
-        if ((0, simpleFeature_1.isFeature)(selection)) {
-            return selection.id();
-        }
-        return undefined;
-    },
-}))
-    .actions(self => ({
-    renderStarted() {
-        self.filled = false;
-        self.message = '';
-        self.reactElement = undefined;
-        self.data = undefined;
-        self.error = undefined;
-        self.renderingComponent = undefined;
-    },
-    renderSuccess({ message, data, reactElement, renderingComponent, }) {
-        if (message) {
+        },
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        renderStarted() {
             self.filled = false;
-            self.message = message;
+            self.message = '';
             self.reactElement = undefined;
             self.data = undefined;
             self.error = undefined;
             self.renderingComponent = undefined;
-        }
-        else {
-            self.filled = true;
+        },
+        /**
+         * #action
+         */
+        renderSuccess({ message, data, reactElement, renderingComponent, }) {
+            if (message) {
+                self.filled = false;
+                self.message = message;
+                self.reactElement = undefined;
+                self.data = undefined;
+                self.error = undefined;
+                self.renderingComponent = undefined;
+            }
+            else {
+                self.filled = true;
+                self.message = '';
+                self.reactElement = reactElement;
+                self.data = data;
+                self.error = undefined;
+                self.renderingComponent = renderingComponent;
+            }
+        },
+        /**
+         * #action
+         */
+        renderError(error) {
+            console.error(error);
+            // the rendering failed for some reason
+            self.filled = false;
             self.message = '';
-            self.reactElement = reactElement;
-            self.data = data;
-            self.error = undefined;
-            self.renderingComponent = renderingComponent;
-        }
-    },
-    renderError(error) {
-        console.error(error);
-        // the rendering failed for some reason
-        self.filled = false;
-        self.message = '';
-        self.reactElement = undefined;
-        self.data = undefined;
-        self.error = error;
-        self.renderingComponent = undefined;
-    },
-    setRefNameMap(refNameMap) {
-        self.refNameMap = refNameMap;
-    },
-}))
-    .actions(self => ({
-    afterAttach() {
-        (0, util_1.makeAbortableReaction)(self, renderReaction_1.renderReactionData, 
-        // @ts-ignore
-        renderReaction_1.renderReactionEffect, {
-            name: `${self.type} ${self.id} rendering`,
-            // delay: self.renderDelay || 300,
-            fireImmediately: true,
-        }, self.renderStarted, self.renderSuccess, self.renderError);
-        (0, util_1.makeAbortableReaction)(self, () => ({
-            assemblyNames: (0, tracks_1.getTrackAssemblyNames)(self.parentTrack),
+            self.reactElement = undefined;
+            self.data = undefined;
+            self.error = error;
+            self.renderingComponent = undefined;
+        },
+        /**
+         * #action
+         */
+        setRefNameMap(refNameMap) {
+            self.refNameMap = refNameMap;
+        },
+    }))
+        .actions(self => ({
+        afterAttach() {
+            (0, util_1.makeAbortableReaction)(self, renderReaction_1.renderReactionData, 
+            // @ts-ignore
+            renderReaction_1.renderReactionEffect, {
+                name: `${self.type} ${self.id} rendering`,
+                // delay: self.renderDelay || 300,
+                fireImmediately: true,
+            }, self.renderStarted, self.renderSuccess, self.renderError);
+            (0, util_1.makeAbortableReaction)(self, () => ({
+                assemblyNames: (0, tracks_1.getTrackAssemblyNames)(self.parentTrack),
+                // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                adapter: (0, configuration_1.getConf)((0, mobx_state_tree_1.getParent)(self, 2), 'adapter'),
+                assemblyManager: (0, util_1.getSession)(self).assemblyManager,
+            }), 
             // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            adapter: (0, configuration_1.getConf)((0, mobx_state_tree_1.getParent)(self, 2), 'adapter'),
-            assemblyManager: (0, util_1.getSession)(self).assemblyManager,
-        }), 
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        async ({ assemblyNames, adapter, assemblyManager }, signal) => {
-            return assemblyManager.getRefNameMapForAdapter(adapter, assemblyNames[0], { signal, sessionId: (0, tracks_1.getRpcSessionId)(self) });
-        }, {
-            name: `${self.type} ${self.id} getting refNames`,
-            fireImmediately: true,
-        }, () => { }, refNameMap => {
-            self.setRefNameMap(refNameMap);
-        }, error => {
-            console.error(error);
-            self.setError(error);
-        });
-    },
-}));
+            async ({ assemblyNames, adapter, assemblyManager }, signal) => {
+                return assemblyManager.getRefNameMapForAdapter(adapter, assemblyNames[0], { signal, sessionId: (0, tracks_1.getRpcSessionId)(self) });
+            }, {
+                name: `${self.type} ${self.id} getting refNames`,
+                fireImmediately: true,
+            }, () => { }, refNameMap => {
+                self.setRefNameMap(refNameMap);
+            }, error => {
+                console.error(error);
+                self.setError(error);
+            });
+        },
+    }));
+}
+exports.BaseChordDisplayModel = stateModelFactory();
 //# sourceMappingURL=BaseChordDisplayModel.js.map

package/dist/BaseChordDisplay/models/BaseChordDisplayModel.js.map

@@ -1 +1 @@
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package/dist/BaseChordDisplay/models/baseChordDisplayConfig.js

@@ -2,13 +2,25 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.baseChordDisplayConfig = void 0;
 const configuration_1 = require("@jbrowse/core/configuration");
+/**
+ * #config BaseChordDisplay
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 const baseChordDisplayConfig = (0, configuration_1.ConfigurationSchema)('BaseChordDisplay', {
+    /**
+     * #slot
+     */
     onChordClick: {
         type: 'boolean',
         description: 'callback that should be run when a chord in the track is clicked',
         defaultValue: false,
         contextVariable: ['feature', 'track', 'pluginManager'],
     },
-}, { explicitIdentifier: 'displayId' });
+}, {
+    /**
+     * #identifier
+     */
+    explicitIdentifier: 'displayId',
+});
 exports.baseChordDisplayConfig = baseChordDisplayConfig;
 //# sourceMappingURL=baseChordDisplayConfig.js.map

package/dist/BaseChordDisplay/models/baseChordDisplayConfig.js.map

@@ -1 +1 @@
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package/dist/CircularView/components/ImportForm.js

@@ -59,7 +59,7 @@ const ImportForm = (0, mobx_react_1.observer)(({ model }) => {
                         setSelectedAsm(val);
                     }, session: session, selected: selectedAsm })),
             react_1.default.createElement(material_1.Grid, { item: true },
-                react_1.default.createElement(material_1.Button, { disabled: !(regions === null || regions === void 0 ? void 0 : regions.length), onClick: () => model.setDisplayedRegions(regions), variant: "contained", color: "primary" }, regions.length ? 'Open' : 'Loading…')))));
+                react_1.default.createElement(material_1.Button, { disabled: !(regions === null || regions === void 0 ? void 0 : regions.length), onClick: () => model.setDisplayedRegions(regions), variant: "contained", color: "primary" }, regions.length ? 'Open' : 'Loading…')))));
 });
 exports.default = ImportForm;
 //# sourceMappingURL=ImportForm.js.map

package/dist/CircularView/components/ImportForm.js.map

@@ -1 +1 @@
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