@jbrowse/plugin-linear-comparative-view 2.9.0 → 2.10.1

package/dist/LGVSyntenyDisplay/configSchemaF.d.ts

@@ -1,6 +1,8 @@
 import PluginManager from '@jbrowse/core/PluginManager';
 /**
  * #config LGVSyntenyDisplay
+ * extends config
+ * - [LinearPileupDisplay](../linearpileupdisplay)
  */
 declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     defaultRendering: {

package/dist/LGVSyntenyDisplay/configSchemaF.js

@@ -4,6 +4,8 @@ const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
 /**
  * #config LGVSyntenyDisplay
+ * extends config
+ * - [LinearPileupDisplay](../linearpileupdisplay)
  */
 function configSchemaF(pluginManager) {
     return (0, configuration_1.ConfigurationSchema)('LGVSyntenyDisplay', {}, {

package/dist/LGVSyntenyDisplay/model.d.ts

@@ -2,8 +2,11 @@
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 /**
  * #stateModel LGVSyntenyDisplay
- * extends `LinearPileupDisplay`, displays location of "synteny" feature in a
- * plain LGV, allowing linking out to external synteny views
+ * displays location of "synteny" feature in a plain LGV, allowing linking out
+ * to external synteny views
+ *
+ * extends
+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
  */
 declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -69,15 +72,15 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         };
         fetchSizeLimit: {
             type: string;
-            defaultValue: number; /**
-             * #property
-             */
+            defaultValue: number;
             description: string;
         };
         height: {
             type: string;
             defaultValue: number;
-            description: string;
+            description: string; /**
+             * #method
+             */
         };
         mouseover: {
             type: string;
@@ -146,7 +149,9 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         model: {
             id: string;
             type: string;
-            rpcDriverName: string | undefined;
+            rpcDriverName: string | undefined; /**
+             * #method
+             */
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
@@ -319,8 +324,14 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
 } & {
     afterAttach(): void;
 } & {
+    /**
+     * #method
+     */
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
 } & {
+    /**
+     * #method
+     */
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
         label: string;
         subMenu: {

package/dist/LGVSyntenyDisplay/model.js

@@ -31,8 +31,11 @@ const mobx_state_tree_1 = require("mobx-state-tree");
 const LaunchSyntenyViewDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/LaunchSyntenyViewDialog'))));
 /**
  * #stateModel LGVSyntenyDisplay
- * extends `LinearPileupDisplay`, displays location of "synteny" feature in a
- * plain LGV, allowing linking out to external synteny views
+ * displays location of "synteny" feature in a plain LGV, allowing linking out
+ * to external synteny views
+ *
+ * extends
+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
  */
 function stateModelFactory(schema) {
     return mobx_state_tree_1.types
@@ -49,6 +52,9 @@ function stateModelFactory(schema) {
         .views(self => {
         const superContextMenuItems = self.contextMenuItems;
         return {
+            /**
+             * #method
+             */
             contextMenuItems() {
                 const feature = self.contextMenuFeature;
                 return [
@@ -77,6 +83,9 @@ function stateModelFactory(schema) {
         .views(self => {
         const { trackMenuItems: superTrackMenuItems, colorSchemeSubMenuItems: superColorSchemeSubMenuItems, } = self;
         return {
+            /**
+             * #method
+             */
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
@@ -90,7 +99,8 @@ function stateModelFactory(schema) {
     })
         .actions(self => ({
         afterCreate() {
-            // use color by stand to help indicate inversions better on first load, otherwise use selected orientation
+            // use color by stand to help indicate inversions better on first load,
+            // otherwise use selected orientation
             if (self.colorBy) {
                 self.setColorScheme({ ...self.colorBy });
             }

package/dist/LinearComparativeDisplay/stateModelFactory.d.ts

@@ -4,6 +4,8 @@ import { Instance } from 'mobx-state-tree';
 import { Feature } from '@jbrowse/core/util';
 /**
  * #stateModel LinearComparativeDisplay
+ * extends
+ * - [BaseDisplay](../basedisplay)
  */
 declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -21,7 +23,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly RenderingComponent: import("react").FC<{
         model: {
             id: string;
-            type: string;
+            type: string; /**
+             * #property
+             */
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
@@ -30,12 +34,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         } & 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>>; /**
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string; /**
              * #action
              * controlled by a reaction
              */
-        }, {
-            rendererTypeName: string;
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -48,10 +52,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             type: string;
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string; /**
-             * #action
-             * controlled by a reaction
-             */
+            rendererTypeName: string;
             error: unknown;
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -67,7 +68,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
-    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType; /**
+     * #action
+     * controlled by a reaction
+     */
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -105,7 +109,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             readonly RenderingComponent: import("react").FC<{
                 model: {
                     id: string;
-                    type: string;
+                    type: string; /**
+                     * #property
+                     */
                     rpcDriverName: string | undefined;
                 } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                     rendererTypeName: string;
@@ -114,12 +120,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                 } & 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>>; /**
+                    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string; /**
                      * #action
                      * controlled by a reaction
                      */
-                }, {
-                    rendererTypeName: string;
                     error: unknown;
                     message: string | undefined;
                 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -132,10 +138,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     type: string;
                     rpcDriverName: string | undefined;
                 } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                    rendererTypeName: string; /**
-                     * #action
-                     * controlled by a reaction
-                     */
+                    rendererTypeName: string;
                     error: unknown;
                     message: string | undefined;
                 } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -151,7 +154,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             readonly adapterConfig: any;
             readonly parentTrack: any;
             renderProps(): any;
-            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType; /**
+             * #action
+             * controlled by a reaction
+             */
             readonly DisplayMessageComponent: import("react").FC<any> | undefined;
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
             readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -181,7 +187,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             readonly RenderingComponent: import("react").FC<{
                 model: {
                     id: string;
-                    type: string;
+                    type: string; /**
+                     * #property
+                     */
                     rpcDriverName: string | undefined;
                 } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                     rendererTypeName: string;
@@ -190,12 +198,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                 } & 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>>; /**
+                    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string; /**
                      * #action
                      * controlled by a reaction
                      */
-                }, {
-                    rendererTypeName: string;
                     error: unknown;
                     message: string | undefined;
                 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -208,10 +216,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     type: string;
                     rpcDriverName: string | undefined;
                 } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                    rendererTypeName: string; /**
-                     * #action
-                     * controlled by a reaction
-                     */
+                    rendererTypeName: string;
                     error: unknown;
                     message: string | undefined;
                 } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -227,7 +232,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             readonly adapterConfig: any;
             readonly parentTrack: any;
             renderProps(): any;
-            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType; /**
+             * #action
+             * controlled by a reaction
+             */
             readonly DisplayMessageComponent: import("react").FC<any> | undefined;
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
             readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];

package/dist/LinearComparativeDisplay/stateModelFactory.js

@@ -7,6 +7,8 @@ const tracks_1 = require("@jbrowse/core/util/tracks");
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 /**
  * #stateModel LinearComparativeDisplay
+ * extends
+ * - [BaseDisplay](../basedisplay)
  */
 function stateModelFactory(configSchema) {
     return mobx_state_tree_1.types

package/dist/LinearComparativeView/model.d.ts

@@ -5,6 +5,8 @@ import PluginManager from '@jbrowse/core/PluginManager';
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 /**
  * #stateModel LinearComparativeView
+ * extends
+ * - [BaseViewModel](../baseviewmodel)
  */
 declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -34,9 +36,6 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
             end: import("mobx-state-tree").ISimpleType<number>;
             reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
-            /**
-             * #property
-             */
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         }, {
             setRefName(newRefName: string): void;
@@ -64,7 +63,9 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         draggingTrackId: string | undefined;
         volatileError: unknown;
         afterDisplayedRegionsSetCallbacks: Function[];
-        scaleFactor: number;
+        scaleFactor: number; /**
+         * #action
+         */
         trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
         coarseTotalBp: number;
@@ -192,7 +193,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
             } & {
                 getConf(arg: string): any;
             } & {
-                readonly initialized: boolean; /**
+                readonly initialized: boolean;
+                /**
                  * #property
                  */
                 readonly name: string;
@@ -226,11 +228,17 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
-                getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                getAdapterMapEntry(adapterConf: {
+                    [x: string]: unknown;
+                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                     [x: string]: string | undefined;
                 }>;
-                getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                getReverseRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                     [x: string]: string | undefined;
                 }>;
             } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -250,7 +258,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
             } & {
                 getConf(arg: string): any;
             } & {
-                readonly initialized: boolean; /**
+                readonly initialized: boolean;
+                /**
                  * #property
                  */
                 readonly name: string;
@@ -284,11 +293,17 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
-                getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                getAdapterMapEntry(adapterConf: {
+                    [x: string]: unknown;
+                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                     [x: string]: string | undefined;
                 }>;
-                getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                getReverseRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                     [x: string]: string | undefined;
                 }>;
             }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;

package/dist/LinearComparativeView/model.js

@@ -40,6 +40,8 @@ const FolderOpen_1 = __importDefault(require("@mui/icons-material/FolderOpen"));
 const ReturnToImportFormDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@jbrowse/core/ui/ReturnToImportFormDialog'))));
 /**
  * #stateModel LinearComparativeView
+ * extends
+ * - [BaseViewModel](../baseviewmodel)
  */
 function stateModelFactory(pluginManager) {
     return mobx_state_tree_1.types

package/dist/LinearReadVsRef/index.js

@@ -1,13 +1,37 @@
 "use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = require("react");
 const util_1 = require("@jbrowse/core/util");
 // icons
 const Add_1 = __importDefault(require("@mui/icons-material/Add"));
 // locals
-const LinearReadVsRef_1 = __importDefault(require("./LinearReadVsRef"));
+const ReadVsRefDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./LinearReadVsRef'))));
 function isDisplay(elt) {
     return elt.name === 'LinearPileupDisplay';
 }
@@ -32,7 +56,7 @@ function default_1(pm) {
                                         icon: Add_1.default,
                                         onClick: () => {
                                             (0, util_1.getSession)(self).queueDialog(handleClose => [
-                                                LinearReadVsRef_1.default,
+                                                ReadVsRefDialog,
                                                 {
                                                     track,
                                                     feature,