@jbrowse/plugin-alignments 1.7.8 → 1.7.11

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

@@ -152,7 +152,7 @@ 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: "staticBlocks" | "dynamicBlocks";
+    readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -305,8 +305,8 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     }): void;
     setColorBy(colorBy?: {
         type: string;
-        tag?: string | undefined;
-    } | undefined): void;
+        tag?: string;
+    }): void;
     updateModificationColorMap(uniqueModifications: string[]): void;
 } & {
     readonly rendererConfig: any;

package/dist/PileupRenderer/PileupRenderer.d.ts

@@ -65,24 +65,56 @@ export default class PileupRenderer extends BoxRendererType {
     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: {
+    colorByPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, contrastForBase, charWidth, charHeight, canvasWidth, }: {
+        ctx: CanvasRenderingContext2D;
+        feat: LayoutFeature;
+        region: Region;
+        bpPerPx: number;
         colorForBase: Record<string, string>;
         contrastForBase: Record<string, string>;
         charWidth: number;
         charHeight: number;
+        canvasWidth: number;
+    }): void;
+    colorByPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth, }: {
+        ctx: CanvasRenderingContext2D;
+        feat: LayoutFeature;
+        region: Region;
+        bpPerPx: number;
+        canvasWidth: number;
+    }): void;
+    colorByModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, }: {
+        ctx: CanvasRenderingContext2D;
+        feat: LayoutFeature;
+        region: Region;
+        bpPerPx: number;
+        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
+        canvasWidth: number;
+    }): void;
+    colorByMethylation({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, }: {
+        ctx: CanvasRenderingContext2D;
+        feat: LayoutFeature;
+        region: Region;
+        bpPerPx: number;
+        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
+        canvasWidth: 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 & {
+    drawAlignmentRect({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, canvasWidth, }: {
+        ctx: CanvasRenderingContext2D;
+        feat: LayoutFeature;
+        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
         colorForBase: Record<string, string>;
         contrastForBase: Record<string, string>;
         charWidth: number;
         charHeight: number;
         defaultColor: boolean;
+        canvasWidth: number;
     }): void;
-    drawMismatches(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout, opts: {
+    drawMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, canvasWidth, drawSNPs, drawIndels, }: {
+        ctx: CanvasRenderingContext2D;
+        feat: LayoutFeature;
+        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
         colorForBase: {
             [key: string]: string;
         };
@@ -96,18 +128,42 @@ export default class PileupRenderer extends BoxRendererType {
         largeInsertionIndicatorScale: number;
         charWidth: number;
         charHeight: number;
+        canvasWidth: number;
+    }): void;
+    drawSoftClipping({ ctx, feat, renderArgs, config, theme, canvasWidth, }: {
+        ctx: CanvasRenderingContext2D;
+        feat: LayoutFeature;
+        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
+        config: AnyConfigurationModel;
+        theme: Theme;
+        canvasWidth: number;
+    }): void;
+    makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }: {
+        ctx: CanvasRenderingContext2D;
+        canvasWidth: number;
+        layoutRecords: (LayoutFeature | null)[];
+        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
     }): void;
-    drawSoftClipping(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout, config: AnyConfigurationModel, theme: Theme): void;
-    makeImageData(ctx: CanvasRenderingContext2D, layoutRecords: (LayoutFeature | null)[], props: RenderArgsDeserializedWithFeaturesAndLayout): void;
     layoutFeats(props: RenderArgsDeserializedWithFeaturesAndLayout): (LayoutRecord | null)[];
     fetchSequence(renderProps: RenderArgsDeserialized): Promise<any>;
     render(renderProps: RenderArgsDeserialized): Promise<{
+        features: Map<any, any>;
+        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
+        height: number;
+        width: number;
+        maxHeightReached: boolean;
+        canvasRecordedData: any;
+        reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        imageData?: undefined;
+        html?: string | undefined;
+    } | {
         features: Map<any, any>;
         layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
         height: number;
         width: number;
         maxHeightReached: boolean;
         reactElement: JSX.Element;
+        canvasRecordedData?: undefined;
         imageData?: undefined;
         html?: string | undefined;
     } | {
@@ -116,7 +172,8 @@ export default class PileupRenderer extends BoxRendererType {
         height: number;
         width: number;
         maxHeightReached: boolean;
-        imageData: import("@jbrowse/core/util/offscreenCanvas/types").AbstractImageBitmap;
+        imageData: any;
+        canvasRecordedData?: undefined;
         reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         html?: string | undefined;
     }>;