@jbrowse/plugin-alignments 2.1.7 → 2.2.1

package/esm/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/esm/LinearAlignmentsDisplay/models/model.js

@@ -6,32 +6,77 @@ import { addDisposer, getSnapshot, types } from 'mobx-state-tree';
 import { getContainingTrack } from '@jbrowse/core/util';
 import deepEqual from 'fast-deep-equal';
 const minDisplayHeight = 20;
-const stateModelFactory = (pluginManager, configSchema) => {
+/**
+ * #stateModel LinearAlignmentsDisplay
+ * extends `BaseDisplay`
+ */
+function stateModelFactory(pluginManager, configSchema) {
     return types
         .compose('LinearAlignmentsDisplay', BaseDisplay, types.model({
+        /**
+         * #property
+         * refers to LinearPileupDisplay sub-display model
+         */
         PileupDisplay: types.maybe(pluginManager.getDisplayType('LinearPileupDisplay').stateModel),
+        /**
+         * #property
+         * refers to LinearSNPCoverageDisplay sub-display model
+         */
         SNPCoverageDisplay: types.maybe(pluginManager.getDisplayType('LinearSNPCoverageDisplay').stateModel),
+        /**
+         * #property
+         */
         snpCovHeight: 45,
+        /**
+         * #property
+         */
         type: types.literal('LinearAlignmentsDisplay'),
+        /**
+         * #property
+         */
         configuration: ConfigurationReference(configSchema),
+        /**
+         * #property
+         */
         height: 250,
+        /**
+         * #property
+         */
         showCoverage: true,
+        /**
+         * #property
+         */
         showPileup: true,
+        /**
+         * #property
+         */
         userFeatureScreenDensity: types.maybe(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;
         },
@@ -39,6 +84,9 @@ const stateModelFactory = (pluginManager, configSchema) => {
         .views(self => {
         const { trackMenuItems: superTrackMenuItems } = self;
         return {
+            /**
+             * #getter
+             */
             get pileupDisplayConfig() {
                 const conf = getConf(self, 'pileupDisplay');
                 const track = getContainingTrack(self);
@@ -49,28 +97,52 @@ const stateModelFactory = (pluginManager, configSchema) => {
                     displayId: `${self.configuration.displayId}_pileup_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
                 };
             },
+            /**
+             * #method
+             */
             getFeatureByID(blockKey, id) {
                 return self.PileupDisplay.getFeatureByID(blockKey, id);
             },
+            /**
+             * #method
+             */
             searchFeatureByID(id) {
                 return self.PileupDisplay.searchFeatureByID(id);
             },
+            /**
+             * #getter
+             */
             get features() {
                 return self.PileupDisplay.features;
             },
+            /**
+             * #getter
+             */
             get DisplayBlurb() {
                 var _a;
                 return (_a = self.PileupDisplay) === null || _a === void 0 ? void 0 : _a.DisplayBlurb;
             },
+            /**
+             * #getter
+             */
             get sortedBy() {
                 return self.PileupDisplay.sortedBy;
             },
+            /**
+             * #getter
+             */
             get sortedByPosition() {
                 return self.PileupDisplay.sortedByPosition;
             },
+            /**
+             * #getter
+             */
             get sortedByRefName() {
                 return self.PileupDisplay.sortedByRefName;
             },
+            /**
+             * #getter
+             */
             get snpCoverageDisplayConfig() {
                 const conf = getConf(self, 'snpCoverageDisplay');
                 const track = getContainingTrack(self);
@@ -81,6 +153,9 @@ const stateModelFactory = (pluginManager, configSchema) => {
                     displayId: `${self.configuration.displayId}_snpcoverage_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
                 };
             },
+            /**
+             * #method
+             */
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
@@ -99,23 +174,35 @@ 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;
@@ -125,6 +212,9 @@ const stateModelFactory = (pluginManager, configSchema) => {
             }
             return self.height;
         },
+        /**
+         * #action
+         */
         resizeHeight(distance) {
             const oldHeight = self.height;
             const newHeight = this.setHeight(self.height + distance);
@@ -165,6 +255,9 @@ const stateModelFactory = (pluginManager, configSchema) => {
                 self.setSNPCoverageHeight(self.SNPCoverageDisplay.height);
             }));
         },
+        /**
+         * #action
+         */
         async renderSvg(opts) {
             const pileupHeight = self.height - self.SNPCoverageDisplay.height;
             await when(() => self.PileupDisplay.ready);
@@ -176,6 +269,6 @@ const stateModelFactory = (pluginManager, configSchema) => {
                 }))));
         },
     }));
-};
+}
 export default stateModelFactory;
 //# sourceMappingURL=model.js.map

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

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package/esm/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/esm/LinearPileupDisplay/configSchema.js

@@ -1,24 +1,38 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view';
 import { types } from '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 ConfigurationSchema('LinearPileupDisplay', {
+        /**
+         * #slot
+         */
         defaultRendering: {
             type: 'stringEnum',
             model: types.enumeration('Rendering', ['pileup']),
             defaultValue: 'pileup',
         },
+        /**
+         * #slot
+         */
         renderers: 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: types.enumeration('colorScheme', [
@@ -33,9 +47,12 @@ function PileupConfigFactory(pluginManager) {
             defaultValue: 'normal',
         },
     }, {
+        /**
+         * #baseConfiguration
+         */
         baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager),
         explicitlyTyped: true,
     });
 }
-export default PileupConfigFactory;
+export default configSchemaF;
 //# sourceMappingURL=configSchema.js.map

package/esm/LinearPileupDisplay/configSchema.js.map

@@ -1 +1 @@
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package/esm/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/esm/LinearPileupDisplay/index.js

@@ -15,4 +15,5 @@ export default function register(pluginManager) {
         });
     });
 }
+export { modelFactory as linearPileupDisplayStateModelFactory, configSchemaFactory as linearPileupDisplayConfigSchemaFactory, };
 //# sourceMappingURL=index.js.map

package/esm/LinearPileupDisplay/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/index.ts"],"names":[],"mappings":"AAAA,OAAO,mBAAmB,MAAM,gBAAgB,CAAA;AAChD,OAAO,YAAY,MAAM,SAAS,CAAA;AAClC,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,EAAE,0BAA0B,EAAE,MAAM,oCAAoC,CAAA;AAE/E,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,YAAY;YACZ,UAAU,EAAE,YAAY,CAAC,YAAY,CAAC;YACtC,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,0BAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAED,OAAO,EACL,YAAY,IAAI,oCAAoC,EACpD,mBAAmB,IAAI,sCAAsC,GAC9D,CAAA"}

package/esm/LinearPileupDisplay/model.d.ts

@@ -4,7 +4,11 @@ import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { Feature } from '@jbrowse/core/util';
 import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
 import { LinearPileupDisplayConfigModel } from './configSchema';
-declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel) => import("mobx-state-tree").IModelType<{
+/**
+ * #stateModel LinearPileupDisplay
+ * extends `BaseLinearDisplay`
+ */
+declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel): 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>>;
@@ -26,10 +30,14 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        renderInProgress: AbortController | undefined; /**
+         * #property
+         */
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
-        features: Map<string, Feature> | undefined;
+        features: Map<string, Feature> | undefined; /**
+         * #property
+         */
         layout: any;
         status: string;
         error: unknown;
@@ -40,7 +48,9 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
         }) => any;
         renderProps: any;
     } & {
-        doReload(): void;
+        doReload(): void; /**
+         * #property
+         */
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
@@ -216,27 +226,78 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
     colorTagMap: import("mobx").ObservableMap<string, string>;
     modificationTagMap: import("mobx").ObservableMap<string, string>;
     featureUnderMouseVolatile: Feature | undefined;
+    currSortBpPerPx: number;
     ready: boolean;
 } & {
+    /**
+     * #action
+     */
     setReady(flag: boolean): void;
+    /**
+     * #action
+     */
+    setCurrSortBpPerPx(n: number): void;
+    /**
+     * #action
+     */
     setMaxHeight(n: number): void;
+    /**
+     * #action
+     */
     setFeatureHeight(n: number): void;
+    /**
+     * #action
+     */
     setNoSpacing(flag: boolean): void;
+    /**
+     * #action
+     */
     setColorScheme(colorScheme: {
         type: string;
         tag?: string;
     }): void;
+    /**
+     * #action
+     */
     updateModificationColorMap(uniqueModifications: string[]): void;
+    /**
+     * #action
+     */
     updateColorTagMap(uniqueTag: string[]): void;
+    /**
+     * #action
+     */
     setFeatureUnderMouse(feat?: Feature): void;
 } & {
     afterAttach(): void;
+    /**
+     * #action
+     */
     selectFeature(feature: Feature): void;
+    /**
+     * #action
+     */
     clearSelected(): void;
+    /**
+     * #action
+     * uses copy-to-clipboard and generates notification
+     */
     copyFeatureToClipboard(feature: Feature): void;
+    /**
+     * #action
+     */
     toggleSoftClipping(): void;
+    /**
+     * #action
+     */
     toggleMismatchAlpha(): void;
+    /**
+     * #action
+     */
     setConfig(configuration: AnyConfigurationModel): void;
+    /**
+     * #action
+     */
     setSortedBy(type: string, tag?: string): void;
     setFilterBy(filter: {
         flagInclude: number;
@@ -248,26 +309,59 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
         };
     }): void;
 } & {
+    /**
+     * #action
+     */
     reload(): void;
 } & {
+    /**
+     * #getter
+     */
     readonly maxHeight: any;
+    /**
+     * #getter
+     */
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+    /**
+     * #getter
+     */
     readonly featureHeightSetting: any;
+    /**
+     * #getter
+     */
     readonly mismatchAlphaSetting: any;
+    /**
+     * #getter
+     */
     readonly featureUnderMouse: Feature | undefined;
 } & {
+    /**
+     * #getter
+     */
     readonly rendererTypeName: string;
+    /**
+     * #method
+     */
     contextMenuItems(): {
         label: string;
         icon: typeof ContentCopyIcon;
         onClick: () => void;
     }[];
+    /**
+     * #getter
+     */
     readonly DisplayBlurb: (props: import("./components/LinearPileupDisplayBlurb").LinearPileupDisplayBlurbProps) => JSX.Element | null;
+    /**
+     * #method
+     */
     renderProps(): any;
+    /**
+     * #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;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
@@ -331,6 +425,6 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;
-export declare type LinearPileupDisplayStateModel = ReturnType<typeof stateModelFactory>;
-export declare type LinearPileupDisplayModel = Instance<LinearPileupDisplayStateModel>;
+export type LinearPileupDisplayStateModel = ReturnType<typeof stateModelFactory>;
+export type LinearPileupDisplayModel = Instance<LinearPileupDisplayStateModel>;
 export default stateModelFactory;