@jbrowse/plugin-alignments 2.1.7 → 2.2.1

package/dist/LinearAlignmentsDisplay/models/model.d.ts

@@ -1,10 +1,13 @@
 import React from 'react';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { MenuItem } from '@jbrowse/core/ui';
 import { Instance } from 'mobx-state-tree';
-import { AlignmentsConfigModel } from './configSchema';
-declare const stateModelFactory: (pluginManager: PluginManager, configSchema: AlignmentsConfigModel) => import("mobx-state-tree").IModelType<{
+/**
+ * #stateModel LinearAlignmentsDisplay
+ * extends `BaseDisplay`
+ */
+declare function stateModelFactory(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>>;
@@ -32,7 +35,9 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Al
             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>;
+            type: import("mobx-state-tree").ISimpleType<string>; /**
+             * #property
+             */
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
@@ -50,7 +55,9 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Al
             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]>;
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>; /**
+             * #action
+             */
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
@@ -73,33 +80,93 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Al
 } & {
     scrollTop: number;
 } & {
+    /**
+     * #action
+     */
     toggleCoverage(): void;
+    /**
+     * #action
+     */
     togglePileup(): void;
+    /**
+     * #action
+     */
     setScrollTop(scrollTop: number): void;
+    /**
+     * #action
+     */
     setSNPCoverageHeight(n: number): void;
 } & {
+    /**
+     * #getter
+     */
     readonly pileupDisplayConfig: any;
+    /**
+     * #method
+     */
     getFeatureByID(blockKey: string, id: string): any;
+    /**
+     * #method
+     */
     searchFeatureByID(id: string): any;
+    /**
+     * #getter
+     */
     readonly features: any;
+    /**
+     * #getter
+     */
     readonly DisplayBlurb: any;
+    /**
+     * #getter
+     */
     readonly sortedBy: any;
+    /**
+     * #getter
+     */
     readonly sortedByPosition: any;
+    /**
+     * #getter
+     */
     readonly sortedByRefName: any;
+    /**
+     * #getter
+     */
     readonly snpCoverageDisplayConfig: any;
+    /**
+     * #method
+     */
     trackMenuItems(): MenuItem[];
 } & {
-    setSNPCoverageDisplay(displayConfig: AnyConfigurationModel): void;
-    setUserFeatureScreenDensity(limit: number): void;
-    setPileupDisplay(displayConfig: AnyConfigurationModel): void;
+    /**
+     * #action
+     */
+    setSNPCoverageDisplay(configuration: AnyConfigurationModel): void;
+    /**
+     * #action
+     */
+    updateStatsLimit(stats: unknown): void;
+    /**
+     * #action
+     */
+    setPileupDisplay(configuration: AnyConfigurationModel): void;
+    /**
+     * #action
+     */
     setHeight(displayHeight: number): number;
+    /**
+     * #action
+     */
     resizeHeight(distance: number): number;
 } & {
     afterAttach(): void;
+    /**
+     * #action
+     */
     renderSvg(opts: {
         rasterizeLayers?: boolean;
     }): Promise<JSX.Element>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export default stateModelFactory;
-export declare type AlignmentsDisplayStateModel = ReturnType<typeof stateModelFactory>;
-export declare type AlignmentsDisplayModel = Instance<AlignmentsDisplayStateModel>;
+export type AlignmentsDisplayStateModel = ReturnType<typeof stateModelFactory>;
+export type AlignmentsDisplayModel = Instance<AlignmentsDisplayStateModel>;

package/dist/LinearAlignmentsDisplay/models/model.js

@@ -11,32 +11,77 @@ const mobx_state_tree_1 = require("mobx-state-tree");
 const util_1 = require("@jbrowse/core/util");
 const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
 const minDisplayHeight = 20;
-const stateModelFactory = (pluginManager, configSchema) => {
+/**
+ * #stateModel LinearAlignmentsDisplay
+ * extends `BaseDisplay`
+ */
+function stateModelFactory(pluginManager, configSchema) {
     return mobx_state_tree_1.types
         .compose('LinearAlignmentsDisplay', models_1.BaseDisplay, mobx_state_tree_1.types.model({
+        /**
+         * #property
+         * refers to LinearPileupDisplay sub-display model
+         */
         PileupDisplay: mobx_state_tree_1.types.maybe(pluginManager.getDisplayType('LinearPileupDisplay').stateModel),
+        /**
+         * #property
+         * refers to LinearSNPCoverageDisplay sub-display model
+         */
         SNPCoverageDisplay: mobx_state_tree_1.types.maybe(pluginManager.getDisplayType('LinearSNPCoverageDisplay').stateModel),
+        /**
+         * #property
+         */
         snpCovHeight: 45,
+        /**
+         * #property
+         */
         type: mobx_state_tree_1.types.literal('LinearAlignmentsDisplay'),
+        /**
+         * #property
+         */
         configuration: (0, configuration_1.ConfigurationReference)(configSchema),
+        /**
+         * #property
+         */
         height: 250,
+        /**
+         * #property
+         */
         showCoverage: true,
+        /**
+         * #property
+         */
         showPileup: true,
+        /**
+         * #property
+         */
         userFeatureScreenDensity: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
     }))
         .volatile(() => ({
         scrollTop: 0,
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
         toggleCoverage() {
             self.showCoverage = !self.showCoverage;
         },
+        /**
+         * #action
+         */
         togglePileup() {
             self.showPileup = !self.showPileup;
         },
+        /**
+         * #action
+         */
         setScrollTop(scrollTop) {
             self.scrollTop = scrollTop;
         },
+        /**
+         * #action
+         */
         setSNPCoverageHeight(n) {
             self.snpCovHeight = n;
         },
@@ -44,6 +89,9 @@ const stateModelFactory = (pluginManager, configSchema) => {
         .views(self => {
         const { trackMenuItems: superTrackMenuItems } = self;
         return {
+            /**
+             * #getter
+             */
             get pileupDisplayConfig() {
                 const conf = (0, configuration_1.getConf)(self, 'pileupDisplay');
                 const track = (0, util_1.getContainingTrack)(self);
@@ -54,28 +102,52 @@ const stateModelFactory = (pluginManager, configSchema) => {
                     displayId: `${self.configuration.displayId}_pileup_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
                 };
             },
+            /**
+             * #method
+             */
             getFeatureByID(blockKey, id) {
                 return self.PileupDisplay.getFeatureByID(blockKey, id);
             },
+            /**
+             * #method
+             */
             searchFeatureByID(id) {
                 return self.PileupDisplay.searchFeatureByID(id);
             },
+            /**
+             * #getter
+             */
             get features() {
                 return self.PileupDisplay.features;
             },
+            /**
+             * #getter
+             */
             get DisplayBlurb() {
                 var _a;
                 return (_a = self.PileupDisplay) === null || _a === void 0 ? void 0 : _a.DisplayBlurb;
             },
+            /**
+             * #getter
+             */
             get sortedBy() {
                 return self.PileupDisplay.sortedBy;
             },
+            /**
+             * #getter
+             */
             get sortedByPosition() {
                 return self.PileupDisplay.sortedByPosition;
             },
+            /**
+             * #getter
+             */
             get sortedByRefName() {
                 return self.PileupDisplay.sortedByRefName;
             },
+            /**
+             * #getter
+             */
             get snpCoverageDisplayConfig() {
                 const conf = (0, configuration_1.getConf)(self, 'snpCoverageDisplay');
                 const track = (0, util_1.getContainingTrack)(self);
@@ -86,6 +158,9 @@ const stateModelFactory = (pluginManager, configSchema) => {
                     displayId: `${self.configuration.displayId}_snpcoverage_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
                 };
             },
+            /**
+             * #method
+             */
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
@@ -104,23 +179,35 @@ const stateModelFactory = (pluginManager, configSchema) => {
         };
     })
         .actions(self => ({
-        setSNPCoverageDisplay(displayConfig) {
+        /**
+         * #action
+         */
+        setSNPCoverageDisplay(configuration) {
             self.SNPCoverageDisplay = {
                 type: 'LinearSNPCoverageDisplay',
-                configuration: displayConfig,
+                configuration,
                 height: self.snpCovHeight,
             };
         },
-        setUserFeatureScreenDensity(limit) {
-            self.PileupDisplay.setUserFeatureScreenDensity(limit);
-            self.SNPCoverageDisplay.setUserFeatureScreenDensity(limit);
+        /**
+         * #action
+         */
+        updateStatsLimit(stats) {
+            self.PileupDisplay.updateStatsLimit(stats);
+            self.SNPCoverageDisplay.updateStatsLimit(stats);
         },
-        setPileupDisplay(displayConfig) {
+        /**
+         * #action
+         */
+        setPileupDisplay(configuration) {
             self.PileupDisplay = {
                 type: 'LinearPileupDisplay',
-                configuration: displayConfig,
+                configuration,
             };
         },
+        /**
+         * #action
+         */
         setHeight(displayHeight) {
             if (displayHeight > minDisplayHeight) {
                 self.height = displayHeight;
@@ -130,6 +217,9 @@ const stateModelFactory = (pluginManager, configSchema) => {
             }
             return self.height;
         },
+        /**
+         * #action
+         */
         resizeHeight(distance) {
             const oldHeight = self.height;
             const newHeight = this.setHeight(self.height + distance);
@@ -170,6 +260,9 @@ const stateModelFactory = (pluginManager, configSchema) => {
                 self.setSNPCoverageHeight(self.SNPCoverageDisplay.height);
             }));
         },
+        /**
+         * #action
+         */
         async renderSvg(opts) {
             const pileupHeight = self.height - self.SNPCoverageDisplay.height;
             await (0, mobx_1.when)(() => self.PileupDisplay.ready);
@@ -181,6 +274,6 @@ const stateModelFactory = (pluginManager, configSchema) => {
                 }))));
         },
     }));
-};
+}
 exports.default = stateModelFactory;
 //# sourceMappingURL=model.js.map

package/dist/LinearAlignmentsDisplay/models/model.js.map

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package/dist/LinearPileupDisplay/configSchema.d.ts

@@ -1,6 +1,6 @@
 import { Instance } from 'mobx-state-tree';
 import PluginManager from '@jbrowse/core/PluginManager';
-declare function PileupConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export declare type LinearPileupDisplayConfigModel = ReturnType<typeof PileupConfigFactory>;
-export declare type LinearPileupDisplayConfig = Instance<LinearPileupDisplayConfigModel>;
-export default PileupConfigFactory;
+declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export type LinearPileupDisplayConfigModel = ReturnType<typeof configSchemaF>;
+export type LinearPileupDisplayConfig = Instance<LinearPileupDisplayConfigModel>;
+export default configSchemaF;

package/dist/LinearPileupDisplay/configSchema.js

@@ -3,24 +3,38 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const mobx_state_tree_1 = require("mobx-state-tree");
-function PileupConfigFactory(pluginManager) {
-    const PileupRendererConfigSchema = pluginManager.getRendererType('PileupRenderer').configSchema;
+/**
+ * #config LinearPileupDisplay
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function configSchemaF(pluginManager) {
     // modify config schema to take in a sub coverage display
     return (0, configuration_1.ConfigurationSchema)('LinearPileupDisplay', {
+        /**
+         * #slot
+         */
         defaultRendering: {
             type: 'stringEnum',
             model: mobx_state_tree_1.types.enumeration('Rendering', ['pileup']),
             defaultValue: 'pileup',
         },
+        /**
+         * #slot
+         */
         renderers: (0, configuration_1.ConfigurationSchema)('RenderersConfiguration', {
-            PileupRenderer: PileupRendererConfigSchema,
+            PileupRenderer: pluginManager.getRendererType('PileupRenderer').configSchema,
         }),
-        renderer: '',
+        /**
+         * #slot
+         */
         maxFeatureScreenDensity: {
             type: 'number',
             description: 'maximum features per pixel that is displayed in the view',
             defaultValue: 5,
         },
+        /**
+         * #slot
+         */
         colorScheme: {
             type: 'stringEnum',
             model: mobx_state_tree_1.types.enumeration('colorScheme', [
@@ -35,9 +49,12 @@ function PileupConfigFactory(pluginManager) {
             defaultValue: 'normal',
         },
     }, {
+        /**
+         * #baseConfiguration
+         */
         baseConfiguration: (0, plugin_linear_genome_view_1.linearBasicDisplayConfigSchemaFactory)(pluginManager),
         explicitlyTyped: true,
     });
 }
-exports.default = PileupConfigFactory;
+exports.default = configSchemaF;
 //# sourceMappingURL=configSchema.js.map

package/dist/LinearPileupDisplay/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,kFAA0F;AAC1F,qDAAiD;AAGjD;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,aAAa,CAAC,aAA4B;IACjD,yDAAyD;IACzD,OAAO,IAAA,mCAAmB,EACxB,qBAAqB,EACrB;QACE;;WAEG;QACH,gBAAgB,EAAE;YAChB,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,CAAC;YACjD,YAAY,EAAE,QAAQ;SACvB;QACD;;WAEG;QACH,SAAS,EAAE,IAAA,mCAAmB,EAAC,wBAAwB,EAAE;YACvD,cAAc,EACZ,aAAa,CAAC,eAAe,CAAC,gBAAgB,CAAC,CAAC,YAAY;SAC/D,CAAC;QACF;;WAEG;QACH,uBAAuB,EAAE;YACvB,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,0DAA0D;YACvE,YAAY,EAAE,CAAC;SAChB;QAED;;WAEG;QACH,WAAW,EAAE;YACX,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,aAAa,EAAE;gBACtC,QAAQ;gBACR,QAAQ;gBACR,YAAY;gBACZ,0BAA0B;gBAC1B,gBAAgB;gBAChB,KAAK;aACN,CAAC;YACF,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,QAAQ;SACvB;KACF,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,IAAA,iEAAqC,EAAC,aAAa,CAAC;QACvE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAID,kBAAe,aAAa,CAAA"}

package/dist/LinearPileupDisplay/index.d.ts

@@ -1,2 +1,5 @@
+import configSchemaFactory from './configSchema';
+import modelFactory from './model';
 import PluginManager from '@jbrowse/core/PluginManager';
 export default function register(pluginManager: PluginManager): void;
+export { modelFactory as linearPileupDisplayStateModelFactory, configSchemaFactory as linearPileupDisplayConfigSchemaFactory, };

package/dist/LinearPileupDisplay/index.js

@@ -3,8 +3,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.linearPileupDisplayConfigSchemaFactory = exports.linearPileupDisplayStateModelFactory = void 0;
 const configSchema_1 = __importDefault(require("./configSchema"));
+exports.linearPileupDisplayConfigSchemaFactory = configSchema_1.default;
 const model_1 = __importDefault(require("./model"));
+exports.linearPileupDisplayStateModelFactory = model_1.default;
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 function register(pluginManager) {

package/dist/LinearPileupDisplay/index.js.map

@@ -1 +1 @@
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