npm - @jbrowse/plugin-alignments - Versions diffs - 2.0.1 → 2.1.0 - Mend

@jbrowse/plugin-alignments 2.0.1 → 2.1.0

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 (43) hide show

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

@@ -2,6 +2,10 @@ import { BamFile } from '@gmod/bam';
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Region } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
+interface Header {
+    idToName: string[];
+    nameToId: Record<string, number>;
+}
 export default class BamAdapter extends BaseFeatureDataAdapter {
     private samHeader?;
     private setupP?;
@@ -15,7 +19,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     }>;
     getHeader(opts?: BaseOptions): Promise<any>;
     private setupPre;
-    private setup;
+    setup(opts?: BaseOptions): Promise<Header>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     private seqFetch;
     getFeatures(region: Region & {
@@ -38,3 +42,4 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     freeResources(): void;
     refIdToName(refId: number): string | undefined;
 }
+export {};

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

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/LinearPileupDisplay/model.d.ts CHANGED Viewed

@@ -149,7 +149,7 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
-    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -320,9 +320,9 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
         subMenu?: undefined;
     })[];
 }, import("mobx-state-tree")._NotCustomized, {
-    type: string;
     height: number;
     id: string;
+    type: string;
     rpcDriverName: string | undefined;
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;

package/dist/LinearPileupDisplay/model.js CHANGED Viewed

@@ -542,7 +542,6 @@ var stateModelFactory = function (configSchema) {
                                     case 3:
                                         feature = (_a.sent()).feature;
                                         if (feature) {
-                                            // @ts-ignore
                                             self.setContextMenuFeature(new util_1.SimpleFeature(feature));
                                         }
                                         _a.label = 4;

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

	@@ -1 +1 @@
1	- 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package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts CHANGED Viewed

@@ -1,7 +1,10 @@
 /// <reference types="react" />
+import { Feature } from '@jbrowse/core/util/simpleFeature';
 declare type Coord = [number, number];
 declare const SNPCoverageTooltip: (props: {
-    model: any;
+    model: {
+        featureUnderMouse: Feature;
+    };
     height: number;
     offsetMouseCoord: Coord;
     clientMouseCoord: Coord;

package/dist/LinearSNPCoverageDisplay/components/Tooltip.js CHANGED Viewed

@@ -41,7 +41,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-/* eslint-disable @typescript-eslint/no-explicit-any */
 var react_1 = __importDefault(require("react"));
 var mobx_react_1 = require("mobx-react");
 var plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");

package/dist/LinearSNPCoverageDisplay/components/Tooltip.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LinearSNPCoverageDisplay/models/model.d.ts CHANGED Viewed

@@ -61,6 +61,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     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>>;
+    minSize: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -152,7 +153,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
-    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -224,7 +225,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     };
     statsFetchInProgress: AbortController | undefined;
 } & {
-    updateStats({ scoreMin, scoreMax, }: {
+    updateStats(stats: {
         scoreMin: number;
         scoreMax: number;
     }): void;
@@ -234,7 +235,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     setLoading(aborter: AbortController): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     setResolution(res: number): void;
-    setFill(fill: boolean): void;
+    setFill(fill: number): void;
     toggleLogScale(): void;
     setScaleType(scale?: string | undefined): void;
     setSummaryScoreMode(val: string): void;
@@ -247,6 +248,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
 } & {
     readonly TooltipComponent: import("react").FC<{}>;
     readonly adapterTypeName: any;
+    readonly rendererTypeNameSimple: any;
     readonly rendererTypeName: string;
     readonly filters: undefined;
     readonly scaleType: any;
@@ -273,18 +275,36 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly autoscaleType: any;
     readonly displayCrossHatchesSetting: any;
 } & {
-    readonly ticks: any;
+    readonly ticks: {
+        range: number[];
+        values: number[];
+        format: (d: import("d3-scale").NumberValue) => string;
+        position: import("d3-scale").ScaleLinear<number, number, never> | import("d3-scale").ScaleQuantize<number, never>;
+    };
+    readonly adapterCapabilities: string[];
 } & {
     renderProps(): any;
-    readonly adapterCapabilities: string[];
     readonly hasResolution: boolean;
     readonly hasGlobalStats: boolean;
+    readonly fillSetting: 0 | 1 | 2;
 } & {
     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;
+        subMenu: {
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+        }[];
+        type?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
+    } | {
         type: string;
         label: string;
         checked: any;
         onClick: () => void;
+        subMenu?: undefined;
     })[];
 } & {
     reload(): Promise<void>;
@@ -324,7 +344,9 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     afterAttach(): void;
 } & {
     readonly TooltipComponent: (props: {
-        model: any;
+        model: {
+            featureUnderMouse: import("@jbrowse/core/util").Feature;
+        };
         height: number;
         offsetMouseCoord: [number, number];
         clientMouseCoord: [number, number];

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

@@ -80,6 +80,7 @@ var mobx_1 = require("mobx");
 var configuration_1 = require("@jbrowse/core/configuration");
 var plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
 var util_1 = require("@jbrowse/core/util");
+// locals
 var Tooltip_1 = __importDefault(require("../components/Tooltip"));
 var shared_1 = require("../../shared");
 // using a map because it preserves order

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

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

@@ -154,7 +154,6 @@ export default class PileupRenderer extends BoxRendererType {
         maxHeightReached: boolean;
         canvasRecordedData: any;
         reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
-        imageData?: undefined;
         html?: string | undefined;
     } | {
         features: Map<any, any>;
@@ -163,8 +162,6 @@ export default class PileupRenderer extends BoxRendererType {
         width: number;
         maxHeightReached: boolean;
         reactElement: JSX.Element;
-        canvasRecordedData?: undefined;
-        imageData?: undefined;
         html?: string | undefined;
     } | {
         features: Map<any, any>;
@@ -173,7 +170,6 @@ export default class PileupRenderer extends BoxRendererType {
         width: number;
         maxHeightReached: boolean;
         imageData: any;
-        canvasRecordedData?: undefined;
         reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         html?: string | undefined;
     }>;

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

	@@ -1 +1 @@
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package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js CHANGED Viewed

@@ -183,13 +183,14 @@ var SNPCoverageAdapter = /** @class */ (function (_super) {
                     case 3:
                         _a = _b.sent(), bins = _a.bins, skipmap = _a.skipmap;
                         bins.forEach(function (bin, index) {
+                            var start = region.start + index;
                             observer.next(new simpleFeature_1.default({
-                                id: "".concat(_this.id, "-").concat(region.start + index),
+                                id: "".concat(_this.id, "-").concat(start),
                                 data: {
                                     score: bin.total,
                                     snpinfo: bin,
-                                    start: region.start + index,
-                                    end: region.start + index + 1,
+                                    start: start,
+                                    end: start + 1,
                                     refName: region.refName,
                                 },
                             }));

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

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

@@ -1,4 +1,4 @@
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { Feature } from '@jbrowse/core/util';
 import { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
 import { ScaleOpts, WiggleBaseRenderer } from '@jbrowse/plugin-wiggle';
 export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {