@jbrowse/plugin-alignments 2.4.0 → 2.4.2

package/dist/LinearReadCloudDisplay/model.d.ts

@@ -160,10 +160,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+    estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
+    estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
-    readonly height: any;
+    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -174,7 +174,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
-    getFeatureOverlapping(blockKey: string, x: number, y: number): any;
+    getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
     readonly currentBytesRequested: number;
@@ -184,19 +184,16 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly maxAllowableBytes: number;
 } & {
     setMessage(message: string): void;
+} & {
     afterAttach(): void;
-    estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
-        headers?: Record<string, string> | undefined;
-        signal?: AbortSignal | undefined;
-        filters?: string[] | undefined;
-    }): Promise<{}>;
-    setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
-    setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-    clearRegionStats(): void;
-    setHeight(displayHeight: number): any;
+    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;
+    setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
-    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
+    updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
@@ -210,18 +207,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly regionTooLargeReason: string;
 } & {
     reload(): Promise<void>;
+} & {
     afterAttach(): void;
 } & {
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    contextMenuItems(): {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        onClick: () => void;
-    }[];
+    contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {

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

@@ -73,7 +73,9 @@ 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>>;
+    displayCrossHatches: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>; /**
+     * #action
+     */
     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>>;
@@ -141,9 +143,13 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         model: {
             id: string;
             type: string;
-            rpcDriverName: string | undefined;
+            rpcDriverName: string | undefined; /**
+             * #getter
+             */
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string;
+            rendererTypeName: string; /**
+             * #getter
+             */
             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]>;
@@ -172,10 +178,10 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+    estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
+    estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
-    readonly height: any;
+    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -186,7 +192,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
-    getFeatureOverlapping(blockKey: string, x: number, y: number): any;
+    getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
     readonly currentBytesRequested: number;
@@ -196,19 +202,16 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     readonly maxAllowableBytes: number;
 } & {
     setMessage(message: string): void;
+} & {
     afterAttach(): void;
-    estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
-        headers?: Record<string, string> | undefined;
-        signal?: AbortSignal | undefined;
-        filters?: string[] | undefined;
-    }): Promise<{}>;
-    setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
-    setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-    clearRegionStats(): void;
-    setHeight(displayHeight: number): any;
+    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;
+    setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
-    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
+    updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
@@ -222,18 +225,13 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     readonly regionTooLargeReason: string;
 } & {
     reload(): Promise<void>;
+} & {
     afterAttach(): void;
 } & {
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    contextMenuItems(): {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        onClick: () => void;
-    }[];
+    contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {

package/dist/MismatchParser/index.js

@@ -284,21 +284,20 @@ function getModificationPositions(mm, fseq, fstrand) {
 }
 exports.getModificationPositions = getModificationPositions;
 function getModificationTypes(mm) {
-    const mods = mm.split(';');
-    return mods
+    return mm
+        .split(';')
         .filter(mod => !!mod)
-        .map(mod => {
+        .flatMap(mod => {
         const [basemod] = mod.split(',');
         const matches = basemod.match(modificationRegex);
         if (!matches) {
             throw new Error(`bad format for MM tag: ${mm}`);
         }
-        const [, , , typestr] = matches;
+        const typestr = matches[3];
         // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so
         // split, and they can also be chemical codes (ChEBI) e.g. C+16061
         return typestr.split(/(\d+|.)/).filter(f => !!f);
-    })
-        .flat();
+    });
 }
 exports.getModificationTypes = getModificationTypes;
 function getOrientedCigar(flip, cigar) {
@@ -313,8 +312,7 @@ function getOrientedCigar(flip, cigar) {
             else if (op === 'I') {
                 op = 'D';
             }
-            ret.push(len);
-            ret.push(op);
+            ret.push(len, op);
         }
         return ret;
     }

package/dist/MismatchParser/index.js.map

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package/dist/PileupRPC/rpcMethods.d.ts

@@ -1,4 +1,3 @@
-import PileupGetReducedFeatures from './methods/GetReducedFeatures';
-import PileupGetGlobalValueForTag from './methods/GetGlobalValueForTag';
-import PileupGetVisibleModifications from './methods/GetVisibleModifications';
-export { PileupGetReducedFeatures, PileupGetVisibleModifications, PileupGetGlobalValueForTag, };
+export { default as PileupGetReducedFeatures } from './methods/GetReducedFeatures';
+export { default as PileupGetVisibleModifications } from './methods/GetVisibleModifications';
+export { default as PileupGetGlobalValueForTag } from './methods/GetGlobalValueForTag';

package/dist/PileupRPC/rpcMethods.js

@@ -4,10 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PileupGetGlobalValueForTag = exports.PileupGetVisibleModifications = exports.PileupGetReducedFeatures = void 0;
-const GetReducedFeatures_1 = __importDefault(require("./methods/GetReducedFeatures"));
-exports.PileupGetReducedFeatures = GetReducedFeatures_1.default;
-const GetGlobalValueForTag_1 = __importDefault(require("./methods/GetGlobalValueForTag"));
-exports.PileupGetGlobalValueForTag = GetGlobalValueForTag_1.default;
-const GetVisibleModifications_1 = __importDefault(require("./methods/GetVisibleModifications"));
-exports.PileupGetVisibleModifications = GetVisibleModifications_1.default;
+var GetReducedFeatures_1 = require("./methods/GetReducedFeatures");
+Object.defineProperty(exports, "PileupGetReducedFeatures", { enumerable: true, get: function () { return __importDefault(GetReducedFeatures_1).default; } });
+var GetVisibleModifications_1 = require("./methods/GetVisibleModifications");
+Object.defineProperty(exports, "PileupGetVisibleModifications", { enumerable: true, get: function () { return __importDefault(GetVisibleModifications_1).default; } });
+var GetGlobalValueForTag_1 = require("./methods/GetGlobalValueForTag");
+Object.defineProperty(exports, "PileupGetGlobalValueForTag", { enumerable: true, get: function () { return __importDefault(GetGlobalValueForTag_1).default; } });
 //# sourceMappingURL=rpcMethods.js.map

package/dist/PileupRPC/rpcMethods.js.map

@@ -1 +1 @@
-{"version":3,"file":"rpcMethods.js","sourceRoot":"","sources":["../../src/PileupRPC/rpcMethods.ts"],"names":[],"mappings":";;;;;;AAAA,sFAAmE;AAKjE,mCALK,4BAAwB,CAKL;AAJ1B,0FAAuE;AAMrE,qCANK,8BAA0B,CAML;AAL5B,gGAA6E;AAI3E,wCAJK,iCAA6B,CAIL"}
+{"version":3,"file":"rpcMethods.js","sourceRoot":"","sources":["../../src/PileupRPC/rpcMethods.ts"],"names":[],"mappings":";;;;;;AAAA,mEAAkF;AAAzE,+IAAA,OAAO,OAA4B;AAC5C,6EAA4F;AAAnF,yJAAA,OAAO,OAAiC;AACjD,uEAAsF;AAA7E,mJAAA,OAAO,OAA8B"}

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 BoxRendererType, { RenderArgsDeserialized as BoxRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
 import { Region, Feature } from '@jbrowse/core/util';
 import { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
@@ -100,7 +100,7 @@ export default class PileupRenderer extends BoxRendererType {
         canvasWidth: number;
     }): void;
     drawRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserialized): void;
-    drawAlignmentRect({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, canvasWidth, }: {
+    drawAlignmentRect({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, theme, canvasWidth, }: {
         ctx: CanvasRenderingContext2D;
         feat: LayoutFeature;
         renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
@@ -110,6 +110,7 @@ export default class PileupRenderer extends BoxRendererType {
         charHeight: number;
         defaultColor: boolean;
         canvasWidth: number;
+        theme: Theme;
     }): void;
     drawMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, canvasWidth, drawSNPsMuted, drawIndels, }: {
         ctx: CanvasRenderingContext2D;
@@ -129,6 +130,7 @@ export default class PileupRenderer extends BoxRendererType {
         charWidth: number;
         charHeight: number;
         canvasWidth: number;
+        theme: Theme;
     }): void;
     drawSoftClipping({ ctx, feat, renderArgs, config, theme, canvasWidth, }: {
         ctx: CanvasRenderingContext2D;
@@ -175,4 +177,4 @@ export default class PileupRenderer extends BoxRendererType {
     }>;
     createSession(args: PileupLayoutSessionProps): PileupLayoutSession;
 }
-export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsSerialized, ResultsDeserialized, };
+export { type RenderArgs, type RenderResults, type RenderArgsSerialized, type ResultsSerialized, type ResultsDeserialized, } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';

package/dist/PileupRenderer/PileupRenderer.js

@@ -116,14 +116,16 @@ class PileupRenderer extends BoxRendererType_1.default {
                 }
             }
         }
-        const [leftPx, rightPx] = (0, util_1.bpSpanPx)(feature.get('start') - expansionBefore, feature.get('end') + expansionAfter, region, bpPerPx);
+        const s = feature.get('start') - expansionBefore;
+        const e = feature.get('end') + expansionAfter;
+        const [leftPx, rightPx] = (0, util_1.bpSpanPx)(s, e, region, bpPerPx);
         if (displayMode === 'compact') {
             heightPx /= 3;
         }
         if (feature.get('refName') !== region.refName) {
             throw new Error(`feature ${feature.id()} is not on the current region's reference sequence ${region.refName}`);
         }
-        const topPx = layout.addRect(feature.id(), feature.get('start') - expansionBefore, feature.get('end') + expansionAfter, heightPx, feature);
+        const topPx = layout.addRect(feature.id(), s, e, heightPx, feature);
         if (topPx === null) {
             return null;
         }
@@ -289,10 +291,9 @@ class PileupRenderer extends BoxRendererType_1.default {
         const modifications = (0, MismatchParser_1.getModificationPositions)(mm, seq, strand);
         // probIndex applies across multiple modifications e.g.
         let probIndex = 0;
-        for (let i = 0; i < modifications.length; i++) {
-            const { type, positions } = modifications[i];
+        for (const { type, positions } of modifications) {
             const col = modificationTagMap[type] || 'black';
-            // @ts-ignore
+            // @ts-expect-error
             const base = Color(col);
             for (const readPos of (0, MismatchParser_1.getNextRefPos)(cigarOps, positions)) {
                 const r = start + readPos;
@@ -399,7 +400,7 @@ class PileupRenderer extends BoxRendererType_1.default {
             ctx.fillRect(leftPx, topPx, rightPx - leftPx, heightPx);
         }
     }
-    drawAlignmentRect({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, canvasWidth, }) {
+    drawAlignmentRect({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, theme, canvasWidth, }) {
         const { config, bpPerPx, regions, colorBy, colorTagMap = {} } = renderArgs;
         const { tag = '', type: colorType = '' } = colorBy || {};
         const { feature } = feat;
@@ -454,30 +455,23 @@ class PileupRenderer extends BoxRendererType_1.default {
                 }
                 break;
             }
-            case 'insertSizeAndPairOrientation':
+            case 'insertSizeAndPairOrientation': {
                 break;
+            }
             case 'modifications':
-            case 'methylation':
+            case 'methylation': {
                 // this coloring is similar to igv.js, and is helpful to color negative
                 // strand reads differently because their c-g will be flipped (e.g. g-c
                 // read right to left)
-                if (feature.get('flags') & 16) {
-                    ctx.fillStyle = '#c8dcc8';
-                }
-                else {
-                    ctx.fillStyle = '#c8c8c8';
-                }
+                ctx.fillStyle = feature.get('flags') & 16 ? '#c8dcc8' : '#c8c8c8';
                 break;
-            case 'normal':
-            default:
-                if (defaultColor) {
-                    // avoid a readConfObject call here
-                    ctx.fillStyle = '#c8c8c8';
-                }
-                else {
-                    ctx.fillStyle = (0, configuration_1.readConfObject)(config, 'color', { feature });
-                }
+            }
+            default: {
+                ctx.fillStyle = defaultColor
+                    ? 'lightgrey'
+                    : (0, configuration_1.readConfObject)(config, 'color', { feature });
                 break;
+            }
         }
         this.drawRect(ctx, feat, renderArgs);
         // second pass for color types that render per-base things that go over the
@@ -556,30 +550,30 @@ class PileupRenderer extends BoxRendererType_1.default {
             if (mismatch.type === 'mismatch') {
                 if (!drawSNPsMuted) {
                     const baseColor = colorForBase[mismatch.base] || '#888';
-                    fillRect(ctx, leftPx, topPx, widthPx, heightPx, canvasWidth, !mismatchAlpha
-                        ? baseColor
-                        : mismatch.qual !== undefined
-                            ? // @ts-ignore
+                    fillRect(ctx, Math.round(leftPx), topPx, widthPx, heightPx, canvasWidth, mismatchAlpha
+                        ? mismatch.qual === undefined
+                            ? baseColor
+                            : // @ts-expect-error
                                 Color(baseColor)
                                     .alpha(Math.min(1, mismatch.qual / 50))
                                     .hsl()
                                     .string()
-                            : baseColor);
+                        : baseColor);
                 }
                 if (widthPx >= charWidth && heightPx >= heightLim) {
                     // normal SNP coloring
                     const contrastColor = drawSNPsMuted
                         ? 'black'
                         : contrastForBase[mismatch.base] || 'black';
-                    ctx.fillStyle = !mismatchAlpha
-                        ? contrastColor
-                        : mismatch.qual !== undefined
-                            ? // @ts-ignore
+                    ctx.fillStyle = mismatchAlpha
+                        ? mismatch.qual === undefined
+                            ? contrastColor
+                            : // @ts-expect-error
                                 Color(contrastColor)
                                     .alpha(Math.min(1, mismatch.qual / 50))
                                     .hsl()
                                     .string()
-                            : contrastColor;
+                        : contrastColor;
                     ctx.fillText(mbase, leftPx + (widthPx - charWidth) / 2 + 1, topPx + heightPx);
                 }
             }
@@ -736,6 +730,7 @@ class PileupRenderer extends BoxRendererType_1.default {
                 charWidth,
                 charHeight,
                 canvasWidth,
+                theme,
             });
             this.drawMismatches({
                 ctx,
@@ -751,6 +746,7 @@ class PileupRenderer extends BoxRendererType_1.default {
                 colorForBase,
                 contrastForBase,
                 canvasWidth,
+                theme,
             });
             if (showSoftClip) {
                 this.drawSoftClipping({