npm - @jbrowse/plugin-alignments - Versions diffs - 2.4.2 → 2.5.0 - Mend

@jbrowse/plugin-alignments 2.4.2 → 2.5.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (147) hide show

package/esm/LinearPileupDisplay/model.js CHANGED Viewed

@@ -191,7 +191,7 @@ function stateModelFactory(configSchema) {
                     const view = getContainingView(self);
                     const { sortedBy, colorBy, parentTrack, adapterConfig, rendererType, } = self;
                     if (!view.initialized ||
-                        !self.estimatedStatsReady ||
+                        !self.featureDensityStatsReady ||
                         self.regionTooLarge) {
                         return;
                     }
@@ -263,9 +263,7 @@ 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 SimpleFeature(feature));
                             }
                         }
@@ -319,8 +317,8 @@ function stateModelFactory(configSchema) {
         /**
          * #action
          */
-        setConfig(configuration) {
-            self.configuration = configuration;
+        setConfig(conf) {
+            self.configuration = conf;
         },
         /**
          * #action
@@ -362,41 +360,41 @@ function stateModelFactory(configSchema) {
         };
     })
         .views(self => ({
-        /**
-         * #getter
-         */
-        get maxHeight() {
-            const conf = getConf(self, ['renderers', self.rendererTypeName]) || {};
-            return self.trackMaxHeight !== undefined
-                ? self.trackMaxHeight
-                : conf.maxHeight;
-        },
         /**
          * #getter
          */
         get rendererConfig() {
-            const configBlob = getConf(self, ['renderers', self.rendererTypeName]) || {};
+            const { featureHeight, noSpacing, trackMaxHeight, mismatchAlpha, rendererTypeName, } = self;
+            const configBlob = 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 }
+                    : {}),
             }, getEnv(self));
         },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get maxHeight() {
+            return readConfObject(self.rendererConfig, 'maxHeight');
+        },
         /**
          * #getter
          */
         get featureHeightSetting() {
-            return (self.featureHeight || readConfObject(this.rendererConfig, 'height'));
+            return readConfObject(self.rendererConfig, 'height');
         },
         /**
          * #getter
          */
         get mismatchAlphaSetting() {
-            return self.mismatchAlpha !== undefined
-                ? self.mismatchAlpha
-                : readConfObject(this.rendererConfig, 'mismatchAlpha');
+            return readConfObject(self.rendererConfig, 'mismatchAlpha');
         },
         /**
          * #getter
@@ -493,7 +491,6 @@ function stateModelFactory(configSchema) {
                                     rendererType: 'PileupRenderer',
                                 }));
                                 if (feature) {
-                                    // @ts-expect-error
                                     self.selectFeature(new SimpleFeature(feature));
                                 }
                             }

package/esm/LinearPileupDisplay/model.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/LinearReadArcsDisplay/components/ReactComponent.d.ts CHANGED Viewed

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

package/esm/LinearReadArcsDisplay/configSchema.d.ts CHANGED Viewed

@@ -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/esm/LinearReadArcsDisplay/drawFeats.js CHANGED Viewed

@@ -45,8 +45,8 @@ export default 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/esm/LinearReadArcsDisplay/drawFeats.js.map CHANGED Viewed

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

@@ -23,9 +23,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     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>;
@@ -36,7 +33,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         }, {
             setRefName(newRefName: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
+        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>; /**
+         * #property
+         */
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
@@ -47,7 +46,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         layout: any;
         status: string;
         error: unknown;
-        message: string | undefined;
+        message: string | undefined; /**
+         * #action
+         * internal, a reference to a HTMLCanvas because we use a autorun to draw the canvas
+         */
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
             model: any;
@@ -55,14 +57,18 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         renderProps: any;
     } & {
         doReload(): void;
-        afterAttach(): void;
+        afterAttach(): void; /**
+         * #action
+         */
         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;
+            layout: any; /**
+             * #action
+             */
             maxHeightReached: boolean;
             renderProps: any;
         } | undefined): void;
@@ -72,9 +78,36 @@ 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; /**
+             * #action
+             * jitter val, helpful to jitter the x direction so you see better evidence when e.g. 100
+             * long reads map to same x position
+             */
+        };
+        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<"LinearReadArcsDisplay">;
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
     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]>;
@@ -99,7 +132,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     readonly RenderingComponent: React.FC<{
         model: {
-            id: string;
+            id: string; /**
+             * #getter
+             */
             type: string;
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -127,9 +162,7 @@ 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>>; /**
-             * #method
-             */
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
@@ -153,8 +186,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-    estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionsStats: 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";
@@ -173,26 +206,26 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     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(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
-    setRegionsStatsP(arg: any): void;
-    setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-    clearRegionsStats(): 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 | undefined): 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: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature: string | undefined): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
     reload(): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
 } & {
@@ -401,9 +434,33 @@ 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">>;
 }>> & 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/esm/LinearReadCloudDisplay/components/ReactComponent.d.ts CHANGED Viewed

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

package/esm/LinearReadCloudDisplay/configSchema.d.ts CHANGED Viewed

@@ -2,5 +2,54 @@ import PluginManager from '@jbrowse/core/PluginManager';
 /**
  * #config LinearReadCloudDisplay
  */
-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
+     */
+    featureHeight: {
+        type: 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;
+    };
+    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/esm/LinearReadCloudDisplay/drawFeats.d.ts CHANGED Viewed

@@ -1,3 +1,4 @@
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { ChainData } from '../shared/fetchChains';
 export default function drawFeats(self: {
     setLastDrawnOffsetPx: (n: number) => void;
@@ -7,4 +8,5 @@ export default function drawFeats(self: {
     };
     height: number;
     chainData?: ChainData;
+    configuration: AnyConfigurationModel;
 }, ctx: CanvasRenderingContext2D): Promise<void>;

package/esm/LinearReadCloudDisplay/drawFeats.js CHANGED Viewed

@@ -43,8 +43,8 @@ export default async function drawFeats(self, ctx) {
         if (chain[0].flags & 1 && chain.length > 1) {
             const v0 = chain[0];
             const v1 = chain[1];
-            const ra1 = asm.getCanonicalRefName(v0.refName);
-            const ra2 = asm.getCanonicalRefName(v1.refName);
+            const ra1 = asm.getCanonicalRefName(v0.refName) || v0.refName;
+            const ra2 = asm.getCanonicalRefName(v1.refName) || v1.refName;
             const r1s = view.bpToPx({ refName: ra1, coord: v0.start });
             const r1e = view.bpToPx({ refName: ra1, coord: v0.end });
             const r2s = view.bpToPx({ refName: ra2, coord: v1.start });
@@ -76,8 +76,8 @@ export default async function drawFeats(self, ctx) {
             for (let i = 1; i < chain.length; i++) {
                 const v0 = chain[i - 1];
                 const v1 = chain[i];
-                const ra1 = asm.getCanonicalRefName(v0.refName);
-                const ra2 = asm.getCanonicalRefName(v1.refName);
+                const ra1 = asm.getCanonicalRefName(v0.refName) || v0.refName;
+                const ra2 = asm.getCanonicalRefName(v1.refName) || v1.refName;
                 const r1s = view.bpToPx({ refName: ra1, coord: v0.start });
                 const r1e = view.bpToPx({ refName: ra1, coord: v0.end });
                 const r2s = view.bpToPx({ refName: ra2, coord: v1.start });

package/esm/LinearReadCloudDisplay/drawFeats.js.map CHANGED Viewed

	@@ -1 +1 @@
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