@jbrowse/plugin-alignments 2.6.3 → 2.7.0

package/dist/LinearPileupDisplay/components/SortByTag.js

@@ -27,7 +27,7 @@ const react_1 = __importStar(require("react"));
 const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
-function SortByTagDlg(props) {
+const SortByTagDialog = (0, mobx_react_1.observer)(function (props) {
     const { model, handleClose } = props;
     const [tag, setTag] = (0, react_1.useState)('');
     const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
@@ -45,5 +45,5 @@ function SortByTagDlg(props) {
                         handleClose();
                     } }, "Submit"),
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
-}
-exports.default = (0, mobx_react_1.observer)(SortByTagDlg);
+});
+exports.default = SortByTagDialog;

package/dist/LinearPileupDisplay/model.d.ts

@@ -1,15 +1,6 @@
 /// <reference types="react" />
 import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-export interface Filter {
-    flagInclude: number;
-    flagExclude: number;
-    readName?: string;
-    tagFilter?: {
-        tag: string;
-        value: string;
-    };
-}
 /**
  * #stateModel LinearPileupDisplay
  * #category display
@@ -41,11 +32,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        /**
-         * #stateModel LinearPileupDisplay
-         * #category display
-         * extends `BaseLinearDisplay`
-         */
         renderInProgress: AbortController | undefined;
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
@@ -55,10 +41,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         error: unknown;
         message: string | undefined;
         maxHeightReached: boolean;
+        /**
+         * #property
+         */
         ReactComponent: ({ model, }: {
             model: any;
         }) => any;
-        renderProps: any;
+        renderProps: any; /**
+         * #property
+         */
     } & {
         doReload(): void;
         afterAttach(): void;
@@ -87,14 +78,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             defaultValue: number;
             description: string;
         };
+        /**
+         * #stateModel LinearPileupDisplay
+         * #category display
+         * extends `BaseLinearDisplay`
+         */
         height: {
             type: string;
             defaultValue: number;
-            description: string; /**
-             * #stateModel LinearPileupDisplay
-             * #category display
-             * extends `BaseLinearDisplay`
-             */
+            description: string;
         };
         mouseover: {
             type: string;
@@ -123,6 +115,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             value: import("mobx-state-tree").ISimpleType<string>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearPileupDisplay">;
     configuration: AnyConfigurationSchemaType;
@@ -168,12 +161,17 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
+            /**
+             * #action
+             */
             error: unknown;
             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>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
+             * #action
+             */
         }, {
             rendererTypeName: string;
             error: unknown;
@@ -200,7 +198,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     setScrollTop(scrollTop: number): void;
     setHeight(displayHeight: number): number;
-    resizeHeight(distance: number): number;
+    resizeHeight(distance: number): number; /**
+     * #property
+     */
 } & {
     featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
     featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
@@ -215,7 +215,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     afterAttach(): void;
 } & {
     setCurrStatsBpPerPx(n: number): void;
-    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void; /**
+     * #action
+     */
     getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
     setFeatureDensityStatsP(arg: any): void;
     setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
@@ -239,20 +241,20 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
-    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined; /**
-     * #getter
-     */
+    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    searchFeatureByID(id: string): [number, number, number, number] | undefined; /**
+     * #getter
+     */
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
-    clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature?: string | undefined): void; /**
+    clearFeatureSelection(): void; /**
      * #method
      */
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
 } & {
     reload(): Promise<void>;
@@ -282,24 +284,32 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     updateColorTagMap(uniqueTag: string[]): void;
     setFeatureUnderMouse(feat?: import("@jbrowse/core/util").Feature | undefined): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
-    copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void;
+    copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void; /**
+     * #method
+     */
     setConfig(conf: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
+        setSubschema(slotName: string, data: unknown): any; /**
+         * #property
+         */
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>): void;
-    setFilterBy(filter: import("./SharedLinearPileupDisplayMixin").Filter): void;
+    setFilterBy(filter: import("../shared").IFilter): void;
+    setJexlFilters(filters: string[]): void;
 } & {
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
+        setSubschema(slotName: string, data: unknown): any; /**
+         * #property
+         */
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
     readonly maxHeight: any;
     readonly featureHeightSetting: any;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
     renderReady(): boolean;
+    readonly filters: import("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain").default;
 } & {
     readonly rendererTypeName: string;
     contextMenuItems(): ({
@@ -313,7 +323,16 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         icon: typeof import("@jbrowse/core/ui/Icons").ContentCopy;
         onClick: () => void;
     })[];
-    readonly DisplayBlurb: (props: import("./components/LinearPileupDisplayBlurb").LinearPileupDisplayBlurbProps) => import("react").JSX.Element | null;
+    readonly DisplayBlurb: ({ model, }: {
+        model: {
+            sortedBy?: {
+                pos: number;
+                refName: number;
+                type: string;
+                tag?: string | undefined;
+            } | undefined;
+        };
+    }) => import("react").JSX.Element | null;
     renderPropsPre(): any;
     colorSchemeSubMenuItems(): {
         label: string;
@@ -380,7 +399,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
+        setSubschema(slotName: string, data: unknown): any; /**
+         * #property
+         */
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
     /**

package/dist/LinearPileupDisplay/model.js

@@ -324,9 +324,10 @@ function stateModelFactory(configSchema) {
                 if (!self.autorunReady) {
                     return;
                 }
-                const { sortedBy, adapterConfig, rendererType } = self;
+                const { sortedBy, adapterConfig, rendererType, sortReady } = self;
                 const { bpPerPx } = view;
-                if (sortedBy) {
+                if (sortedBy &&
+                    (!sortReady || self.currSortBpPerPx === view.bpPerPx)) {
                     const { pos, refName, assemblyName } = sortedBy;
                     // render just the sorted region first
                     // @ts-expect-error

package/dist/LinearReadArcsDisplay/components/ReactComponent.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
 import { LinearReadArcsDisplayModel } from '../model';
-declare const _default: ({ model, }: {
+declare const LinearReadArcsReactComponent: ({ model, }: {
     model: LinearReadArcsDisplayModel;
 }) => React.JSX.Element;
-export default _default;
+export default LinearReadArcsReactComponent;

package/dist/LinearReadArcsDisplay/components/ReactComponent.js

@@ -42,7 +42,8 @@ const Arcs = (0, mobx_react_1.observer)(function ({ model, }) {
     // note: the position absolute below avoids scrollbar from appearing on track
     return (react_1.default.createElement("canvas", { "data-testid": "arc-canvas", ref: cb, style: { width, height, position: 'absolute' }, width: width * 2, height: height * 2 }));
 });
-exports.default = (0, mobx_react_1.observer)(function ({ model, }) {
+const LinearReadArcsReactComponent = (0, mobx_react_1.observer)(function ({ model, }) {
     return (react_1.default.createElement(BaseDisplayComponent_1.default, { model: model },
         react_1.default.createElement(Arcs, { model: model })));
 });
+exports.default = LinearReadArcsReactComponent;

package/dist/LinearReadArcsDisplay/model.d.ts

@@ -1,16 +1,8 @@
 import React from 'react';
 import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import { IFilter } from '../shared';
 import { ChainData } from '../shared/fetchChains';
-interface Filter {
-    flagInclude: number;
-    flagExclude: number;
-    readName?: string;
-    tagFilter?: {
-        tag: string;
-        value: string;
-    };
-}
 /**
  * #stateModel LinearReadArcsDisplay
  * extends `BaseDisplay`, it is not a block based track, hence not
@@ -31,7 +23,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
         flagExclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-        readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
+         * #property
+         */
         tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
             tag: import("mobx-state-tree").ISimpleType<string>;
             value: import("mobx-state-tree").ISimpleType<string>;
@@ -74,9 +68,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }>;
     readonly DisplayBlurb: React.FC<{
         model: {
-            id: string; /**
-             * #property
-             */
+            id: string;
             type: string;
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -84,6 +76,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             error: unknown;
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+            /**
+             * #action
+             */
             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>>;
@@ -189,7 +184,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     /**
      * #action
      */
-    setFilterBy(filter: Filter): void;
+    setFilterBy(filter: IFilter): void;
     /**
      * #action
      * thin, bold, extrabold, etc

package/dist/LinearReadCloudDisplay/components/ReactComponent.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
 import { LinearReadCloudDisplayModel } from '../model';
-declare const _default: ({ model, }: {
+declare const LinearReadCloudReactComponent: ({ model, }: {
     model: LinearReadCloudDisplayModel;
 }) => React.JSX.Element;
-export default _default;
+export default LinearReadCloudReactComponent;

package/dist/LinearReadCloudDisplay/components/ReactComponent.js

@@ -40,7 +40,8 @@ const Cloud = (0, mobx_react_1.observer)(function ({ model, }) {
     // note: the position absolute below avoids scrollbar from appearing on track
     return (react_1.default.createElement("canvas", { "data-testid": "cloud-canvas", ref: cb, style: { width, height, position: 'absolute' }, width: width * 2, height: height * 2 }));
 });
-exports.default = (0, mobx_react_1.observer)(function ({ model, }) {
+const LinearReadCloudReactComponent = (0, mobx_react_1.observer)(function ({ model, }) {
     return (react_1.default.createElement(BaseDisplayComponent_1.default, { model: model },
         react_1.default.createElement(Cloud, { model: model })));
 });
+exports.default = LinearReadCloudReactComponent;

package/dist/LinearReadCloudDisplay/drawPairChains.js

@@ -60,8 +60,7 @@ function drawPairChains({ ctx, self, chainData, view, asm, }) {
     const maxD = Math.log((0, util_1.max)(coords.map(c => c.distance)));
     const minD = Math.max(Math.log((0, util_1.min)(coords.map(c => c.distance))) - 1, 0);
     const scaler = (self.height - 20) / (maxD - minD);
-    for (let i = 0; i < coords.length; i++) {
-        const { r1e, r1s, r2e, r2s, distance, v0, v1 } = coords[i];
+    for (const { r1e, r1s, r2e, r2s, distance, v0, v1 } of coords) {
         const w1 = Math.max(r1e - r1s, 2);
         const w2 = Math.max(r2e - r2s, 2);
         const [fill, stroke] = getPairedColor({ type, v0, v1, stats }) || [];

package/dist/LinearReadCloudDisplay/model.d.ts

@@ -1,16 +1,8 @@
 import React from 'react';
 import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import { IFilter } from '../shared';
 import { ChainData } from '../shared/fetchChains';
-interface Filter {
-    flagInclude: number;
-    flagExclude: number;
-    readName?: string;
-    tagFilter?: {
-        tag: string;
-        value: string;
-    };
-}
 /**
  * #stateModel LinearReadCloudDisplay
  * extends `BaseDisplay`, it is not a block based track, hence not BaseLinearDisplay
@@ -61,7 +53,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
-            rendererTypeName: string;
+            rendererTypeName: string; /**
+             * #property
+             */
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -78,12 +72,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             error: unknown;
             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>; /**
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>; /**
              * #action
              * internal, a reference to a HTMLCanvas because we use a autorun to draw
              * the canvas
              */
+            type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
@@ -111,7 +105,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     setScrollTop(scrollTop: number): void;
     setHeight(displayHeight: number): number;
-    resizeHeight(distance: number): number;
+    resizeHeight(distance: number): number; /**
+     * #property
+     */
 } & {
     featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
     featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
@@ -128,7 +124,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     setCurrStatsBpPerPx(n: number): void;
     setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
     getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
-    setFeatureDensityStatsP(arg: any): void;
+    setFeatureDensityStatsP(arg: any): void; /**
+     * #method
+     */
     setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
     clearFeatureDensityStats(): void;
 } & {
@@ -180,7 +178,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     /**
      * #action
      */
-    setFilterBy(filter: Filter): void;
+    setFilterBy(filter: IFilter): void;
 } & {
     readonly drawn: boolean;
 } & {

package/dist/LinearSNPCoverageDisplay/components/Tooltip.js

@@ -9,7 +9,7 @@ const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
 const en = (n) => n.toLocaleString('en-US');
 const toP = (s = 0) => +(+s).toFixed(1);
 const pct = (n, total) => `${toP((n / (total || 1)) * 100)}%`;
-const TooltipContents = react_1.default.forwardRef(function ({ feature }, reactRef) {
+const TooltipContents = react_1.default.forwardRef(function TooltipContents2({ feature }, reactRef) {
     const start = feature.get('start');
     const end = feature.get('end');
     const name = feature.get('refName');