@jbrowse/plugin-alignments 1.6.9 → 1.7.3

package/dist/PileupRenderer/PileupRenderer.d.ts

@@ -1,125 +1,125 @@
-/// <reference types="react" />
-import BoxRendererType, { RenderArgs, RenderArgsSerialized, RenderArgsDeserialized as BoxRenderArgsDeserialized, RenderResults, ResultsSerialized, ResultsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
-import { Theme } from '@material-ui/core';
-import { Region, Feature } from '@jbrowse/core/util';
-import { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { PileupLayoutSession, PileupLayoutSessionProps } from './PileupLayoutSession';
-export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
-    colorBy?: {
-        type: string;
-        tag?: string;
-    };
-    colorTagMap?: Record<string, string>;
-    modificationTagMap?: Record<string, string>;
-    sortedBy?: {
-        type: string;
-        pos: number;
-        refName: string;
-        assemblyName: string;
-        tag?: string;
-    };
-    showSoftClip: boolean;
-    highResolutionScaling: number;
-}
-export interface RenderArgsDeserializedWithFeaturesAndLayout extends RenderArgsDeserialized {
-    features: Map<string, Feature>;
-    layout: BaseLayout<Feature>;
-    regionSequence?: string;
-}
-interface LayoutRecord {
-    feature: Feature;
-    leftPx: number;
-    rightPx: number;
-    topPx: number;
-    heightPx: number;
-}
-interface LayoutFeature {
-    heightPx: number;
-    topPx: number;
-    feature: Feature;
-}
-export default class PileupRenderer extends BoxRendererType {
-    supportsSVG: boolean;
-    getCharWidthHeight(ctx: CanvasRenderingContext2D): {
-        charWidth: number;
-        charHeight: number;
-    };
-    layoutFeature({ feature, layout, bpPerPx, region, showSoftClip, heightPx, displayMode, }: {
-        feature: Feature;
-        layout: BaseLayout<Feature>;
-        bpPerPx: number;
-        region: Region;
-        showSoftClip?: boolean;
-        heightPx: number;
-        displayMode: string;
-    }): LayoutRecord | null;
-    getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized): {
-        start: number;
-        end: number;
-        refName: string;
-        assemblyName: string;
-        reversed?: boolean | undefined;
-    };
-    colorByOrientation(feature: Feature, config: AnyConfigurationModel): string;
-    getOrientation(feature: Feature, config: AnyConfigurationModel): string;
-    colorByInsertSize(feature: Feature, _config: AnyConfigurationModel): string;
-    colorByStranded(feature: Feature, _config: AnyConfigurationModel): "color_rev_strand" | "color_fwd_strand" | "color_rev_missing_mate" | "color_fwd_missing_mate" | "color_rev_strand_not_proper" | "color_fwd_strand_not_proper" | "color_fwd_diff_chr" | "color_rev_diff_chr";
-    colorByPerBaseLettering(ctx: CanvasRenderingContext2D, feat: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: {
-        colorForBase: Record<string, string>;
-        contrastForBase: Record<string, string>;
-        charWidth: number;
-        charHeight: number;
-    }): void;
-    colorByPerBaseQuality(ctx: CanvasRenderingContext2D, feat: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number): void;
-    colorByModifications(ctx: CanvasRenderingContext2D, layoutFeature: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: RenderArgsDeserializedWithFeaturesAndLayout): void;
-    colorByMethylation(ctx: CanvasRenderingContext2D, layoutFeature: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: RenderArgsDeserializedWithFeaturesAndLayout): void;
-    drawRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserialized): void;
-    drawAlignmentRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout & {
-        colorForBase: Record<string, string>;
-        contrastForBase: Record<string, string>;
-        charWidth: number;
-        charHeight: number;
-        defaultColor: boolean;
-    }): void;
-    drawMismatches(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout, opts: {
-        colorForBase: {
-            [key: string]: string;
-        };
-        contrastForBase: {
-            [key: string]: string;
-        };
-        mismatchAlpha?: boolean;
-        drawSNPs?: boolean;
-        drawIndels?: boolean;
-        minSubfeatureWidth: number;
-        largeInsertionIndicatorScale: number;
-        charWidth: number;
-        charHeight: number;
-    }): void;
-    drawSoftClipping(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout, config: AnyConfigurationModel, theme: Theme): void;
-    makeImageData(ctx: CanvasRenderingContext2D, layoutRecords: (LayoutFeature | null)[], props: RenderArgsDeserializedWithFeaturesAndLayout): Promise<void>;
-    layoutFeats(props: RenderArgsDeserializedWithFeaturesAndLayout): (LayoutRecord | null)[];
-    fetchSequence(renderProps: RenderArgsDeserialized): Promise<any>;
-    render(renderProps: RenderArgsDeserialized): Promise<{
-        features: Map<string, Feature>;
-        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
-        height: number;
-        width: number;
-        maxHeightReached: boolean;
-        reactElement: any;
-        imageData?: undefined;
-        html?: string | undefined;
-    } | {
-        features: Map<string, Feature>;
-        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
-        height: number;
-        width: number;
-        maxHeightReached: boolean;
-        imageData: any;
-        reactElement?: import("react").ReactElement<any, string | ((props: any) => import("react").ReactElement<any, any> | null) | (new (props: any) => import("react").Component<any, any, any>)> | undefined;
-        html?: string | undefined;
-    }>;
-    createSession(args: PileupLayoutSessionProps): PileupLayoutSession;
-}
-export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsSerialized, ResultsDeserialized, };
+/// <reference types="react" />
+import BoxRendererType, { RenderArgs, RenderArgsSerialized, RenderArgsDeserialized as BoxRenderArgsDeserialized, RenderResults, ResultsSerialized, ResultsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import { Theme } from '@material-ui/core';
+import { Region, Feature } from '@jbrowse/core/util';
+import { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { PileupLayoutSession, PileupLayoutSessionProps } from './PileupLayoutSession';
+export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
+    colorBy?: {
+        type: string;
+        tag?: string;
+    };
+    colorTagMap?: Record<string, string>;
+    modificationTagMap?: Record<string, string>;
+    sortedBy?: {
+        type: string;
+        pos: number;
+        refName: string;
+        assemblyName: string;
+        tag?: string;
+    };
+    showSoftClip: boolean;
+    highResolutionScaling: number;
+}
+export interface RenderArgsDeserializedWithFeaturesAndLayout extends RenderArgsDeserialized {
+    features: Map<string, Feature>;
+    layout: BaseLayout<Feature>;
+    regionSequence?: string;
+}
+interface LayoutRecord {
+    feature: Feature;
+    leftPx: number;
+    rightPx: number;
+    topPx: number;
+    heightPx: number;
+}
+interface LayoutFeature {
+    heightPx: number;
+    topPx: number;
+    feature: Feature;
+}
+export default class PileupRenderer extends BoxRendererType {
+    supportsSVG: boolean;
+    getCharWidthHeight(ctx: CanvasRenderingContext2D): {
+        charWidth: number;
+        charHeight: number;
+    };
+    layoutFeature({ feature, layout, bpPerPx, region, showSoftClip, heightPx, displayMode, }: {
+        feature: Feature;
+        layout: BaseLayout<Feature>;
+        bpPerPx: number;
+        region: Region;
+        showSoftClip?: boolean;
+        heightPx: number;
+        displayMode: string;
+    }): LayoutRecord | null;
+    getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized): {
+        start: number;
+        end: number;
+        refName: string;
+        assemblyName: string;
+        reversed?: boolean | undefined;
+    };
+    colorByOrientation(feature: Feature, config: AnyConfigurationModel): string;
+    getOrientation(feature: Feature, config: AnyConfigurationModel): string;
+    colorByInsertSize(feature: Feature, _config: AnyConfigurationModel): string;
+    colorByStranded(feature: Feature, _config: AnyConfigurationModel): "color_rev_strand" | "color_fwd_strand" | "color_rev_missing_mate" | "color_fwd_missing_mate" | "color_rev_strand_not_proper" | "color_fwd_strand_not_proper" | "color_fwd_diff_chr" | "color_rev_diff_chr";
+    colorByPerBaseLettering(ctx: CanvasRenderingContext2D, feat: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: {
+        colorForBase: Record<string, string>;
+        contrastForBase: Record<string, string>;
+        charWidth: number;
+        charHeight: number;
+    }): void;
+    colorByPerBaseQuality(ctx: CanvasRenderingContext2D, feat: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number): void;
+    colorByModifications(ctx: CanvasRenderingContext2D, layoutFeature: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: RenderArgsDeserializedWithFeaturesAndLayout): void;
+    colorByMethylation(ctx: CanvasRenderingContext2D, layoutFeature: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: RenderArgsDeserializedWithFeaturesAndLayout): void;
+    drawRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserialized): void;
+    drawAlignmentRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout & {
+        colorForBase: Record<string, string>;
+        contrastForBase: Record<string, string>;
+        charWidth: number;
+        charHeight: number;
+        defaultColor: boolean;
+    }): void;
+    drawMismatches(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout, opts: {
+        colorForBase: {
+            [key: string]: string;
+        };
+        contrastForBase: {
+            [key: string]: string;
+        };
+        mismatchAlpha?: boolean;
+        drawSNPs?: boolean;
+        drawIndels?: boolean;
+        minSubfeatureWidth: number;
+        largeInsertionIndicatorScale: number;
+        charWidth: number;
+        charHeight: number;
+    }): void;
+    drawSoftClipping(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout, config: AnyConfigurationModel, theme: Theme): void;
+    makeImageData(ctx: CanvasRenderingContext2D, layoutRecords: (LayoutFeature | null)[], props: RenderArgsDeserializedWithFeaturesAndLayout): Promise<void>;
+    layoutFeats(props: RenderArgsDeserializedWithFeaturesAndLayout): (LayoutRecord | null)[];
+    fetchSequence(renderProps: RenderArgsDeserialized): Promise<any>;
+    render(renderProps: RenderArgsDeserialized): Promise<{
+        features: Map<string, Feature>;
+        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
+        height: number;
+        width: number;
+        maxHeightReached: boolean;
+        reactElement: JSX.Element;
+        imageData?: undefined;
+        html?: string | undefined;
+    } | {
+        features: Map<string, Feature>;
+        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
+        height: number;
+        width: number;
+        maxHeightReached: boolean;
+        imageData: import("@jbrowse/core/util/offscreenCanvas/types").AbstractImageBitmap;
+        reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        html?: string | undefined;
+    }>;
+    createSession(args: PileupLayoutSessionProps): PileupLayoutSession;
+}
+export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsSerialized, ResultsDeserialized, };