@jbrowse/plugin-alignments 2.3.4 → 2.4.1

package/esm/LinearPileupDisplay/model.d.ts

@@ -12,7 +12,7 @@ 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>>;
 } & {
-    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
         region: import("mobx-state-tree").IModelType<{
@@ -29,17 +29,20 @@ 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>;
     }, {
-        renderInProgress: AbortController | undefined; /**
-         * #property
-         */
+        renderInProgress: AbortController | undefined;
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         features: Map<string, Feature> | undefined;
         layout: any;
-        status: string;
+        status: string; /**
+         * #property
+         */
         error: unknown;
         message: string | undefined;
         maxHeightReached: boolean;
+        /**
+         * #property
+         */
         ReactComponent: ({ model, }: {
             model: any;
         }) => any;
@@ -154,6 +157,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
+    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -216,6 +220,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
         overrideHeight: number;
+        theme: import("@mui/material").ThemeOptions;
     }): Promise<JSX.Element>;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
@@ -418,13 +423,69 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         disabled?: undefined;
         subMenu?: undefined;
     })[];
-}, import("mobx-state-tree")._NotCustomized, {
+}, {
+    type: string;
+} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    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>>;
+} & {
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+        key: import("mobx-state-tree").ISimpleType<string>;
+        region: import("mobx-state-tree").IModelType<{
+            refName: import("mobx-state-tree").ISimpleType<string>;
+            start: import("mobx-state-tree").ISimpleType<number>;
+            end: import("mobx-state-tree").ISimpleType<number>;
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        }, {
+            setRefName(newRefName: string): void;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
+        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    }, {
+        renderInProgress: AbortController | undefined;
+        filled: boolean;
+        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        features: Map<string, Feature> | undefined;
+        layout: any;
+        status: string;
+        error: unknown;
+        message: string | undefined;
+        maxHeightReached: boolean;
+        ReactComponent: ({ model, }: {
+            model: any;
+        }) => any;
+        renderProps: any;
+    } & {
+        doReload(): void;
+        afterAttach(): void;
+        setStatus(message: string): void;
+        setLoading(abortController: AbortController): void;
+        setMessage(messageText: string): void;
+        setRendered(props: {
+            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            features: Map<string, Feature>; /**
+             * #getter
+             */
+            layout: any;
+            maxHeightReached: boolean;
+            renderProps: any;
+        } | undefined): void;
+        setError(error: unknown): void;
+        reload(): void;
+        beforeDestroy(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: string;
-    height: number; /**
-     * #action
-     */
     id: string;
     rpcDriverName: string | undefined;
+    heightPreConfig: number | undefined;
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;

package/esm/LinearPileupDisplay/model.js

@@ -208,7 +208,7 @@ function stateModelFactory(configSchema) {
                     if (sortedBy) {
                         const { pos, refName, assemblyName } = sortedBy;
                         // render just the sorted region first
-                        // @ts-ignore
+                        // @ts-expect-error
                         await self.rendererType.renderInClient(rpcManager, {
                             assemblyName,
                             regions: [
@@ -263,9 +263,9 @@ function stateModelFactory(configSchema) {
                             // feature.id that was returned e.g. that the user hasn't
                             // moused over to a new position during the async operation
                             // above
-                            // @ts-ignore
+                            // @ts-expect-error
                             if (self.featureIdUnderMouse === feature.uniqueId) {
-                                // @ts-ignore
+                                // @ts-expect-error
                                 self.setFeatureUnderMouse(new SimpleFeature(feature));
                             }
                         }
@@ -493,7 +493,7 @@ function stateModelFactory(configSchema) {
                                     rendererType: 'PileupRenderer',
                                 }));
                                 if (feature) {
-                                    // @ts-ignore
+                                    // @ts-expect-error
                                     self.selectFeature(new SimpleFeature(feature));
                                 }
                             }

package/esm/LinearPileupDisplay/model.js.map

@@ -1 +1 @@
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package/esm/LinearReadArcsDisplay/components/ReactComponent.js

@@ -5,17 +5,20 @@ import { observer } from 'mobx-react';
 import { getContainingView } from '@jbrowse/core/util';
 import { LoadingEllipses } from '@jbrowse/core/ui';
 import { BlockMsg, } from '@jbrowse/plugin-linear-genome-view';
-const useStyles = makeStyles()(theme => ({
-    loading: {
-        paddingLeft: '0.6em',
-        backgroundColor: theme.palette.action.disabledBackground,
-        backgroundImage: 'repeating-linear-gradient(45deg, transparent, transparent 5px, rgba(255,255,255,.5) 5px, rgba(255,255,255,.5) 10px)',
-        height: '100%',
-        width: '100%',
-        pointerEvents: 'none',
-        textAlign: 'center',
-    },
-}));
+const useStyles = makeStyles()(theme => {
+    const bg = theme.palette.action.disabledBackground;
+    return {
+        loading: {
+            paddingLeft: '0.6em',
+            backgroundColor: theme.palette.background.default,
+            backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${bg} 5px, ${bg} 10px)`,
+            height: '100%',
+            width: '100%',
+            pointerEvents: 'none',
+            textAlign: 'center',
+        },
+    };
+});
 const Arcs = observer(function ({ model, }) {
     const view = getContainingView(model);
     return (React.createElement("canvas", { "data-testid": `Arc-display-${model.drawn}`, ref: ref => {

package/esm/LinearReadArcsDisplay/components/ReactComponent.js.map

@@ -1 +1 @@
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package/esm/LinearReadArcsDisplay/model.d.ts

@@ -2,7 +2,6 @@ import React from 'react';
 import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { ChainData } from '../shared/fetchChains';
-import { ExportSvgOptions } from '@jbrowse/plugin-linear-genome-view/src/LinearGenomeView';
 interface Filter {
     flagInclude: number;
     flagExclude: number;
@@ -21,9 +20,12 @@ 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>>;
 } & {
-    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
+        /**
+         * #property
+         */
         region: import("mobx-state-tree").IModelType<{
             refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
@@ -52,28 +54,21 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         }) => any;
         renderProps: any;
     } & {
-        doReload(): void; /**
-         * #action
-         */
+        doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
-            features: Map<string, import("@jbrowse/core/util").Feature>; /**
-             * #action
-             */
+            features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;
         } | undefined): void;
         setError(error: unknown): void;
         reload(): void;
-        beforeDestroy(): void; /**
-         * #action
-         * used during tests to detect when we can complete a snapshot test
-         */
+        beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
@@ -81,9 +76,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     type: import("mobx-state-tree").ISimpleType<"LinearReadArcsDisplay">;
     configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
     filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
-        flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>; /**
-         * #property
-         */
+        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>>;
         tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
@@ -134,7 +127,9 @@ 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>>; /**
+             * #method
+             */
         }, {
             rendererTypeName: string;
             error: unknown;
@@ -161,6 +156,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
+    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -221,8 +217,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }[];
     renderProps(): any;
 } & {
-    renderSvg(opts: ExportSvgOptions & {
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
         overrideHeight: number;
+        theme: import("@mui/material").ThemeOptions;
     }): Promise<JSX.Element>;
 } & {
     loading: boolean;
@@ -309,10 +306,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     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">> & {
-            muiName: string; /**
-             * #action
-             * used during tests to detect when we can complete a snapshot test
-             */
+            muiName: string;
         };
         onClick: () => void;
         subMenu?: undefined;
@@ -340,10 +334,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     } | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string; /**
-             * #action
-             * used during tests to detect when we can complete a snapshot test
-             */
+            muiName: string;
         };
         subMenu: {
             label: string;
@@ -357,14 +348,72 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     /**
      * #method
      */
-    renderSvg(opts: ExportSvgOptions): Promise<JSX.Element | undefined>;
+    renderSvg(opts: {
+        rasterizeLayers?: boolean;
+    }): Promise<JSX.Element | undefined>;
 } & {
     afterAttach(): void;
-}, import("mobx-state-tree")._NotCustomized, {
+}, {
+    type: string;
+} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    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>>;
+} & {
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+        key: import("mobx-state-tree").ISimpleType<string>;
+        region: import("mobx-state-tree").IModelType<{
+            refName: import("mobx-state-tree").ISimpleType<string>;
+            start: import("mobx-state-tree").ISimpleType<number>;
+            end: import("mobx-state-tree").ISimpleType<number>;
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        }, {
+            setRefName(newRefName: string): void;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
+        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    }, {
+        renderInProgress: AbortController | undefined;
+        filled: boolean;
+        reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
+        layout: any;
+        status: string;
+        error: unknown;
+        message: string | undefined;
+        maxHeightReached: boolean;
+        ReactComponent: ({ model, }: {
+            model: any;
+        }) => any;
+        renderProps: any;
+    } & {
+        doReload(): void;
+        afterAttach(): void;
+        setStatus(message: string): void;
+        setLoading(abortController: AbortController): void;
+        setMessage(messageText: string): void;
+        setRendered(props: {
+            reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
+            features: Map<string, import("@jbrowse/core/util").Feature>;
+            layout: any;
+            maxHeightReached: boolean;
+            renderProps: any;
+        } | undefined): void;
+        setError(error: unknown): void;
+        reload(): void;
+        beforeDestroy(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: string;
-    height: number;
     id: string;
     rpcDriverName: string | undefined;
+    heightPreConfig: number | undefined;
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;

package/esm/LinearReadArcsDisplay/model.js

@@ -13,6 +13,11 @@ import drawFeats from './drawFeats';
 import { fetchChains } from '../shared/fetchChains';
 // async
 const FilterByTagDlg = lazy(() => import('../shared/FilterByTag'));
+// stabilize clipid under test for snapshot
+function getId(id) {
+    const isJest = typeof jest === 'undefined';
+    return `arc-clip-${isJest ? id : 'jest'}`;
+}
 /**
  * #stateModel LinearReadArcsDisplay
  * extends `BaseLinearDisplay`
@@ -303,11 +308,18 @@ function stateModelFactory(configSchema) {
                 const C2S = await import('canvas2svg');
                 const ctx = new C2S.default(width, height);
                 await drawFeats(self, ctx);
-                str = (
-                // eslint-disable-next-line react/no-danger
-                React.createElement("g", { dangerouslySetInnerHTML: { __html: ctx.getSvg().innerHTML } }));
+                const clipid = getId(self.id);
+                str = (React.createElement(React.Fragment, null,
+                    React.createElement("defs", null,
+                        React.createElement("clipPath", { id: clipid },
+                            React.createElement("rect", { x: 0, y: 0, width: width, height: height }))),
+                    React.createElement("g", { 
+                        /* eslint-disable-next-line react/no-danger */
+                        dangerouslySetInnerHTML: {
+                            __html: ctx.getSvg().innerHTML,
+                        }, clipPath: `url(#${clipid})` })));
             }
-            return React.createElement("g", null, str);
+            return React.createElement(React.Fragment, null, str);
         },
     }))
         .actions(self => ({

package/esm/LinearReadArcsDisplay/model.js.map

@@ -1 +1 @@
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