@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/dist/PileupRenderer/PileupRenderer.d.ts

@@ -1,6 +1,6 @@
 /// <reference types="react" />
+import { Theme } from '@mui/material/styles';
 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';
@@ -57,32 +57,64 @@ export default class PileupRenderer extends BoxRendererType {
     getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized): {
         start: number;
         end: number;
+        reversed?: boolean | undefined;
         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: {
+    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, drawSNPsMuted, drawIndels, }: {
+        ctx: CanvasRenderingContext2D;
+        feat: LayoutFeature;
+        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
         colorForBase: {
             [key: string]: string;
         };
@@ -90,15 +122,28 @@ export default class PileupRenderer extends BoxRendererType {
             [key: string]: string;
         };
         mismatchAlpha?: boolean;
-        drawSNPs?: boolean;
         drawIndels?: boolean;
+        drawSNPsMuted?: boolean;
         minSubfeatureWidth: number;
         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<{