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/dist/LinearSNPCoverageDisplay/models/configSchema.d.ts CHANGED Viewed

@@ -1,2 +1,80 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function SNPCoverageConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default function SNPCoverageConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    autoscale: {
+        type: string;
+        defaultValue: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    minScore: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    maxScore: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    scaleType: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */ inverted: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    multiTicks: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        SNPCoverageRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, 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>>;

package/dist/LinearSNPCoverageDisplay/models/model.d.ts CHANGED Viewed

@@ -19,7 +19,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             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>;
+            assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
+             * #property
+             */
         }, {
             setRefName(newRefName: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
@@ -38,7 +40,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
             model: any;
-        }) => any;
+        }) => any; /**
+         * #action
+         */
         renderProps: any;
     } & {
         doReload(): void;
@@ -59,9 +63,34 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     }, 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;
+            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<"LinearWiggleDisplay">;
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
     selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
@@ -73,9 +102,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     rendererTypeNameState: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     scale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     autoscale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    displayCrossHatches: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>; /**
-     * #action
-     */
+    displayCrossHatches: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     constraints: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         max: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
         min: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
@@ -136,7 +163,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             rendererTypeName: string;
             error: unknown;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function | undefined;
+        onHorizontalScroll?: Function | undefined; /**
+         * #getter
+         */
         blockState?: Record<string, any> | undefined;
     }>;
     readonly DisplayBlurb: import("react").FC<{
@@ -144,12 +173,10 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             id: string;
             type: string;
             rpcDriverName: string | undefined; /**
-             * #getter
+             * #method
              */
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string; /**
-             * #getter
-             */
+            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]>;
@@ -178,8 +205,8 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     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";
@@ -198,26 +225,26 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     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;
 } & {
@@ -246,7 +273,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     } | undefined;
     statsFetchInProgress: AbortController | undefined;
 } & {
-    updateStats(stats: {
+    updateQuantitativeStats(stats: {
         scoreMin: number;
         scoreMax: number;
     }): void;

package/dist/LinearSNPCoverageDisplay/models/model.js CHANGED Viewed

@@ -176,7 +176,7 @@ function stateModelFactory(pluginManager, configSchema) {
                     const { colorBy } = self;
                     const view = (0, util_1.getContainingView)(self);
                     if (!view.initialized ||
-                        !self.estimatedStatsReady ||
+                        !self.featureDensityStatsReady ||
                         self.regionTooLarge) {
                         return;
                     }

package/dist/LinearSNPCoverageDisplay/models/model.js.map CHANGED Viewed

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1	+ 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package/dist/PileupRenderer/PileupLayoutSession.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
 import GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout';
 import MultiLayout from '@jbrowse/core/util/layouts/MultiLayout';

package/dist/PileupRenderer/PileupRenderer.js CHANGED Viewed

@@ -208,6 +208,9 @@ class PileupRenderer extends BoxRendererType_1.default {
         const start = feature.get('start');
         let soffset = 0; // sequence offset
         let roffset = 0; // reference offset
+        if (!seq) {
+            return;
+        }
         for (let i = 0; i < cigarOps.length; i += 2) {
             const len = +cigarOps[i];
             const op = cigarOps[i + 1];
@@ -288,6 +291,9 @@ class PileupRenderer extends BoxRendererType_1.default {
         const seq = feature.get('seq');
         const strand = feature.get('strand');
         const cigarOps = (0, MismatchParser_1.parseCigar)(cigar);
+        if (!seq) {
+            return;
+        }
         const modifications = (0, MismatchParser_1.getModificationPositions)(mm, seq, strand);
         // probIndex applies across multiple modifications e.g.
         let probIndex = 0;
@@ -327,6 +333,9 @@ class PileupRenderer extends BoxRendererType_1.default {
         const seq = feature.get('seq');
         const strand = feature.get('strand');
         const cigarOps = (0, MismatchParser_1.parseCigar)(cigar);
+        if (!seq) {
+            return;
+        }
         const methBins = new Array(region.end - region.start).fill(0);
         const modifications = (0, MismatchParser_1.getModificationPositions)(mm, seq, strand);
         for (let i = 0; i < modifications.length; i++) {

package/dist/PileupRenderer/PileupRenderer.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/PileupRenderer/configSchema.d.ts CHANGED Viewed

@@ -1,2 +1,88 @@
-declare const PileupRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const PileupRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     * default magenta here is used to detect the user has not customized this
+     */
+    color: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+    /**
+     * #slot
+     */
+    orientationType: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        defaultValue: string;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    displayMode: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    minSubfeatureWidth: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    maxHeight: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    maxClippingSize: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    height: {
+        type: string;
+        description: string;
+        defaultValue: number;
+        contextVariable: string[];
+    };
+    /**
+     * #slot
+     */
+    noSpacing: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    largeInsertionIndicatorScale: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    mismatchAlpha: {
+        type: string;
+        defaultValue: boolean;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default PileupRenderer;

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts CHANGED Viewed

@@ -8,7 +8,7 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
     }>;
     fetchSequence(region: Region): Promise<any>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+    getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     freeResources(): void;
 }

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js CHANGED Viewed

@@ -71,9 +71,9 @@ class SNPCoverageAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         }, opts.signal);
     }
-    async estimateRegionsStats(regions, opts) {
+    async getMultiRegionFeatureDensityStats(regions, opts) {
         const { subadapter } = await this.configure();
-        return subadapter.estimateRegionsStats(regions, opts);
+        return subadapter.getMultiRegionFeatureDensityStats(regions, opts);
     }
     async getRefNames(opts = {}) {
         const { subadapter } = await this.configure();

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/SNPCoverageAdapter/configSchema.d.ts CHANGED Viewed

@@ -1,2 +1,11 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     * normally refers to a BAM or CRAM adapter
+     */
+    subadapter: {
+        type: string;
+        defaultValue: null;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;