@jbrowse/plugin-alignments 2.4.1 → 2.5.0

package/dist/LinearPileupDisplay/model.d.ts

@@ -3,6 +3,15 @@ import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { Feature } from '@jbrowse/core/util';
 import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
+export interface Filter {
+    flagInclude: number;
+    flagExclude: number;
+    readName?: string;
+    tagFilter?: {
+        tag: string;
+        value: string;
+    };
+}
 /**
  * #stateModel LinearPileupDisplay
  * extends `BaseLinearDisplay`
@@ -25,6 +34,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         }, {
             setRefName(newRefName: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        /**
+         * #stateModel LinearPileupDisplay
+         * extends `BaseLinearDisplay`
+         */
         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>;
@@ -34,15 +47,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         features: Map<string, Feature> | undefined;
         layout: any;
-        status: string; /**
-         * #property
-         */
+        status: string;
         error: unknown;
         message: string | undefined;
         maxHeightReached: boolean;
-        /**
-         * #property
-         */
         ReactComponent: ({ model, }: {
             model: any;
         }) => any;
@@ -52,13 +60,17 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void;
+        setMessage(messageText: string): void; /**
+         * #property
+         */
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
-            renderProps: any;
+            renderProps: any; /**
+             * #property
+             */
         } | undefined): void;
         setError(error: unknown): void;
         reload(): void;
@@ -66,9 +78,32 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }, 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>>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        maxFeatureScreenDensity: {
+            type: string;
+            description: string;
+            defaultValue: number;
+        };
+        fetchSizeLimit: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        height: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearPileupDisplay">;
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
     showSoftClipping: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
@@ -103,6 +138,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly RenderingComponent: import("react").FC<{
         model: {
             id: string;
+            /**
+             * #action
+             */
             type: string;
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -126,7 +164,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
-            error: unknown;
+            error: unknown; /**
+             * #action
+             */
         } & 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>;
@@ -154,8 +194,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: Feature | undefined;
-    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
+    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
 } & {
     readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
@@ -168,54 +208,49 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
-    getFeatureOverlapping(blockKey: string, x: number, y: number): any;
+    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;
     readonly currentBytesRequested: number;
     readonly currentFeatureScreenDensity: number;
     readonly maxFeatureScreenDensity: any;
-    readonly estimatedStatsReady: boolean;
+    readonly featureDensityStatsReady: boolean;
     readonly maxAllowableBytes: number;
 } & {
     setMessage(message: string): void;
+} & {
     afterAttach(): void;
-    estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
-        headers?: Record<string, string> | undefined;
-        signal?: AbortSignal | undefined;
-        filters?: string[] | undefined;
-    }): Promise<{}>;
-    setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
-    setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-    clearRegionStats(): void;
+    getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+    setFeatureDensityStatsP(arg: any): void;
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    clearFeatureDensityStats(): void;
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
-    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
     selectFeature(feature: Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature: string | undefined): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
     reload(): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
 } & {
     readonly regionTooLarge: boolean;
-    readonly regionTooLargeReason: string;
+    readonly regionTooLargeReason: string; /**
+     * #action
+     * uses copy-to-clipboard and generates notification
+     */
 } & {
     reload(): Promise<void>;
+} & {
     afterAttach(): void;
 } & {
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    contextMenuItems(): {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        onClick: () => void;
-    }[];
+    contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
@@ -294,30 +329,18 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     /**
      * #action
      */
-    setConfig(configuration: AnyConfigurationModel): void;
+    setConfig(conf: AnyConfigurationModel): void;
     /**
      * #action
      */
     setSortedBy(type: string, tag?: string): void;
-    setFilterBy(filter: {
-        flagInclude: number;
-        flagExclude: number;
-        readName?: string;
-        tagFilter?: {
-            tag: string;
-            value: string;
-        };
-    }): void;
+    setFilterBy(filter: Filter): void;
 } & {
     /**
      * #action
      */
     reload(): void;
 } & {
-    /**
-     * #getter
-     */
-    readonly maxHeight: any;
     /**
      * #getter
      */
@@ -326,6 +349,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
+} & {
+    /**
+     * #getter
+     */
+    readonly maxHeight: any;
     /**
      * #getter
      */
@@ -454,7 +482,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         layout: any;
         status: string;
         error: unknown;
-        message: string | undefined;
+        message: string | undefined; /**
+         * #getter
+         */
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
             model: any;
@@ -468,11 +498,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
-            features: Map<string, Feature>; /**
-             * #getter
-             */
+            features: Map<string, Feature>;
             layout: any;
-            maxHeightReached: boolean;
+            maxHeightReached: boolean; /**
+             * #method
+             */
             renderProps: any;
         } | undefined): void;
         setError(error: unknown): void;
@@ -481,9 +511,37 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }, 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>>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        maxFeatureScreenDensity: {
+            type: string;
+            description: string;
+            defaultValue: number;
+        };
+        fetchSizeLimit: {
+            type: string;
+            defaultValue: number; /**
+             * #getter
+             */
+            description: string;
+        };
+        height: {
+            type: string;
+            defaultValue: number; /**
+             * #method
+             */
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: string;
     id: string;
+    configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
     rpcDriverName: string | undefined;
     heightPreConfig: number | undefined;
     userBpPerPxLimit: number | undefined;

package/dist/LinearPileupDisplay/model.js

@@ -219,7 +219,7 @@ function stateModelFactory(configSchema) {
                     const view = (0, util_1.getContainingView)(self);
                     const { sortedBy, colorBy, parentTrack, adapterConfig, rendererType, } = self;
                     if (!view.initialized ||
-                        !self.estimatedStatsReady ||
+                        !self.featureDensityStatsReady ||
                         self.regionTooLarge) {
                         return;
                     }
@@ -291,9 +291,7 @@ 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-expect-error
                             if (self.featureIdUnderMouse === feature.uniqueId) {
-                                // @ts-expect-error
                                 self.setFeatureUnderMouse(new util_1.SimpleFeature(feature));
                             }
                         }
@@ -347,8 +345,8 @@ function stateModelFactory(configSchema) {
         /**
          * #action
          */
-        setConfig(configuration) {
-            self.configuration = configuration;
+        setConfig(conf) {
+            self.configuration = conf;
         },
         /**
          * #action
@@ -390,41 +388,41 @@ function stateModelFactory(configSchema) {
         };
     })
         .views(self => ({
-        /**
-         * #getter
-         */
-        get maxHeight() {
-            const conf = (0, configuration_1.getConf)(self, ['renderers', self.rendererTypeName]) || {};
-            return self.trackMaxHeight !== undefined
-                ? self.trackMaxHeight
-                : conf.maxHeight;
-        },
         /**
          * #getter
          */
         get rendererConfig() {
-            const configBlob = (0, configuration_1.getConf)(self, ['renderers', self.rendererTypeName]) || {};
+            const { featureHeight, noSpacing, trackMaxHeight, mismatchAlpha, rendererTypeName, } = self;
+            const configBlob = (0, configuration_1.getConf)(self, ['renderers', rendererTypeName]) || {};
             return self.rendererType.configSchema.create({
                 ...configBlob,
-                height: self.featureHeight,
-                noSpacing: self.noSpacing,
-                maxHeight: this.maxHeight,
-                mismatchAlpha: self.mismatchAlpha,
+                ...(featureHeight !== undefined ? { height: featureHeight } : {}),
+                ...(noSpacing !== undefined ? { noSpacing } : {}),
+                ...(mismatchAlpha !== undefined ? { mismatchAlpha } : {}),
+                ...(trackMaxHeight !== undefined
+                    ? { maxHeight: trackMaxHeight }
+                    : {}),
             }, (0, util_1.getEnv)(self));
         },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get maxHeight() {
+            return (0, configuration_1.readConfObject)(self.rendererConfig, 'maxHeight');
+        },
         /**
          * #getter
          */
         get featureHeightSetting() {
-            return (self.featureHeight || (0, configuration_1.readConfObject)(this.rendererConfig, 'height'));
+            return (0, configuration_1.readConfObject)(self.rendererConfig, 'height');
         },
         /**
          * #getter
          */
         get mismatchAlphaSetting() {
-            return self.mismatchAlpha !== undefined
-                ? self.mismatchAlpha
-                : (0, configuration_1.readConfObject)(this.rendererConfig, 'mismatchAlpha');
+            return (0, configuration_1.readConfObject)(self.rendererConfig, 'mismatchAlpha');
         },
         /**
          * #getter
@@ -521,7 +519,6 @@ function stateModelFactory(configSchema) {
                                     rendererType: 'PileupRenderer',
                                 }));
                                 if (feature) {
-                                    // @ts-expect-error
                                     self.selectFeature(new util_1.SimpleFeature(feature));
                                 }
                             }

package/dist/LinearPileupDisplay/model.js.map

@@ -1 +1 @@
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package/dist/LinearReadArcsDisplay/components/ReactComponent.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { LinearReadArcsDisplayModel } from '../model';
 declare const _default: ({ model, }: {
     model: LinearReadArcsDisplayModel;

package/dist/LinearReadArcsDisplay/configSchema.d.ts

@@ -2,5 +2,66 @@ import PluginManager from '@jbrowse/core/PluginManager';
 /**
  * #config LinearReadArcsDisplay
  */
-declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    lineWidth: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    jitter: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    colorScheme: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    renderer: import("mobx-state-tree").IAnyModelType;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    fetchSizeLimit: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    height: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    mouseover: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;
 export default configSchemaF;

package/dist/LinearReadArcsDisplay/drawFeats.js

@@ -49,8 +49,8 @@ async function drawFeats(self, ctx) {
         const f2 = s2 === -1;
         const p1 = f1 ? k1.start : k1.end;
         const p2 = hasPaired ? (f2 ? k2.start : k2.end) : f2 ? k2.end : k2.start;
-        const ra1 = assembly.getCanonicalRefName(k1.refName);
-        const ra2 = assembly.getCanonicalRefName(k2.refName);
+        const ra1 = assembly.getCanonicalRefName(k1.refName) || k1.refName;
+        const ra2 = assembly.getCanonicalRefName(k2.refName) || k2.refName;
         const r1 = view.bpToPx({ refName: ra1, coord: p1 });
         const r2 = view.bpToPx({ refName: ra2, coord: p2 });
         if (r1 && r2) {

package/dist/LinearReadArcsDisplay/drawFeats.js.map

@@ -1 +1 @@
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