@jbrowse/plugin-alignments 3.2.0 → 3.4.0

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -1,4 +1,4 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 import { lazy } from 'react';
 import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails';
 import { Paper } from '@mui/material';
@@ -10,12 +10,16 @@ import { tags } from './tagInfo';
 import { getTag } from './util';
 const SupplementaryAlignments = lazy(() => import('./SupplementaryAlignments'));
 const LinkedPairedAlignments = lazy(() => import('./LinkedPairedAlignments'));
+const FeatDefined = observer(function (props) {
+    const { model, feat } = props;
+    const flags = feat.flags;
+    const SA = getTag('SA', feat);
+    return (_jsxs(Paper, { "data-testid": "alignment-side-drawer", children: [_jsx(FeatureDetails, { ...props, descriptions: { tags }, feature: feat, formatter: (value, key) => key === 'next_segment_position' ? (_jsx(PairLink, { model: model, locString: value })) : (_jsx(Formatter, { value: value })) }), SA !== undefined ? (_jsx(SupplementaryAlignments, { model: model, tag: SA, feature: feat })) : null, flags != null ? (_jsxs(_Fragment, { children: [flags & 1 ? (_jsx(LinkedPairedAlignments, { model: model, feature: feat })) : null, _jsx(Flags, { flags: flags, ...props })] })) : null] }));
+});
 const AlignmentsFeatureDetails = observer(function (props) {
     const { model } = props;
     const { featureData } = model;
     const feat = structuredClone(featureData);
-    const SA = getTag('SA', feat);
-    const { flags } = feat;
-    return (_jsxs(Paper, { "data-testid": "alignment-side-drawer", children: [_jsx(FeatureDetails, { ...props, descriptions: { tags }, feature: feat, formatter: (value, key) => key === 'next_segment_position' ? (_jsx(PairLink, { model: model, locString: value })) : (_jsx(Formatter, { value: value })) }), SA !== undefined ? (_jsx(SupplementaryAlignments, { model: model, tag: SA, feature: feat })) : null, flags & 1 ? (_jsx(LinkedPairedAlignments, { model: model, feature: feat })) : null, flags !== undefined ? _jsx(Flags, { feature: feat, ...props }) : null] }));
+    return feat ? (_jsx(FeatDefined, { feat: feat, ...props })) : (_jsx("div", { children: "No feature loaded, may not be available after page refresh because it was too large for localStorage" }));
 });
 export default AlignmentsFeatureDetails;

package/esm/AlignmentsFeatureDetail/Flags.d.ts

@@ -1,5 +1,3 @@
 export default function AlignmentFlags(props: {
-    feature: {
-        flags: number;
-    };
+    flags: number;
 }): import("react/jsx-runtime").JSX.Element;

package/esm/AlignmentsFeatureDetail/Flags.js

@@ -26,8 +26,7 @@ const flagNames = [
 ];
 export default function AlignmentFlags(props) {
     const { classes } = useStyles();
-    const { feature } = props;
-    const { flags } = feature;
+    const { flags } = props;
     return (_jsxs(BaseCard, { ...props, title: "Flags", children: [_jsx(SimpleField, { name: "Flag", value: flags }), _jsx(FormGroup, { children: flagNames.map((name, idx) => {
                     const val = flags & (1 << idx);
                     const key = `${name}_${val}`;

package/esm/AlignmentsFeatureDetail/LinkedPairedAlignments.d.ts

@@ -3,4 +3,4 @@ import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function SuppAlignments(props: {
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
-}): import("react/jsx-runtime").JSX.Element;
+}): import("react/jsx-runtime").JSX.Element | null;

package/esm/AlignmentsFeatureDetail/LinkedPairedAlignments.js

@@ -12,5 +12,5 @@ export default function SuppAlignments(props) {
     }
     catch (e) {
     }
-    return (_jsx(BaseCard, { ...props, title: "Paired alignments", children: hasBreakendSplitView ? (_jsx(LaunchPairedEndBreakpointSplitViewPanel, { model: model, feature: feature })) : null }));
+    return hasBreakendSplitView ? (_jsx(BaseCard, { ...props, title: "Paired alignments", children: _jsx(LaunchPairedEndBreakpointSplitViewPanel, { model: model, feature: feature }) })) : null;
 }

package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -3,9 +3,9 @@ import type { Instance } from 'mobx-state-tree';
 export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
-    featureData: import("mobx-state-tree").IType<any, any, any>;
+    featureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
     formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -35,14 +35,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    descriptions: import("mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
 }, {
     error: unknown;
 } & {
-    setFeatureData(featureData: Record<string, unknown>): void;
+    setFeatureData(featureData: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
     clearFeatureData(): void;
-    setFormattedData(feat: Record<string, unknown>): void;
+    setFormattedData(feat: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
     setExtra(type?: string, trackId?: string, maxDepth?: number): void;
     setError(e: unknown): void;
 } & {
@@ -52,9 +53,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
 } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
-    featureData: import("mobx-state-tree").IType<any, any, any>;
+    featureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
     formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -84,6 +85,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    descriptions: import("mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: "BaseFeatureWidget";
     id: string;
@@ -94,6 +96,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     maxDepth: number | undefined;
     sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
     formattedFields: any;
+    descriptions: Record<string, unknown> | undefined;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type AlignmentFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/esm/AlignmentsFeatureDetail/stateModelFactory.js

@@ -1,8 +1,7 @@
 import { stateModelFactory as baseModelFactory } from '@jbrowse/core/BaseFeatureWidget';
 import { types } from 'mobx-state-tree';
 export function stateModelFactory(pluginManager) {
-    const baseModel = baseModelFactory(pluginManager);
-    return types.compose(baseModel, types.model('AlignmentsFeatureWidget', {
+    return types.compose(baseModelFactory(pluginManager), types.model('AlignmentsFeatureWidget', {
         type: types.literal('AlignmentsFeatureWidget'),
     }));
 }

package/esm/BamAdapter/BamAdapter.d.ts

@@ -39,7 +39,6 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         bytes: number;
         fetchSizeLimit: any;
     }>;
-    freeResources(): void;
     refIdToName(refId: number): string | undefined;
 }
 export {};

package/esm/BamAdapter/BamAdapter.js

@@ -168,7 +168,6 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         }
         return super.getMultiRegionFeatureDensityStats(regions, opts);
     }
-    freeResources() { }
     refIdToName(refId) {
         var _a;
         return (_a = this.samHeader) === null || _a === void 0 ? void 0 : _a.idToName[refId];

package/esm/CramAdapter/CramAdapter.d.ts

@@ -43,7 +43,6 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     }, opts?: BaseOptions & {
         filterBy: FilterBy;
     }): import("rxjs").Observable<Feature>;
-    freeResources(): void;
     cramRecordToFeature(record: CramRecord): CramSlightlyLazyFeature;
     getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<{
         bytes: number;

package/esm/CramAdapter/CramAdapter.js

@@ -197,7 +197,6 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
             });
         }, stopToken);
     }
-    freeResources() { }
     cramRecordToFeature(record) {
         return new CramSlightlyLazyFeature(record, this);
     }

package/esm/CramAdapter/CramTestAdapters.d.ts

@@ -24,6 +24,5 @@ export declare class SequenceAdapter extends BaseFeatureDataAdapter {
         start: number;
         end: number;
     }): Observable<SimpleFeature>;
-    freeResources(): void;
 }
 export {};

package/esm/CramAdapter/CramTestAdapters.js

@@ -73,5 +73,4 @@ export class SequenceAdapter extends BaseFeatureDataAdapter {
             return { unsubscribe: () => { } };
         });
     }
-    freeResources() { }
 }

package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -201,7 +201,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void;
+    selectFeature(feature: Feature): Promise<void>;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;

package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -186,7 +186,9 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
                             icon: MenuOpenIcon,
                             onClick: () => {
                                 self.clearFeatureSelection();
-                                self.selectFeature(feat);
+                                self.selectFeature(feat).catch((e) => {
+                                    getSession(self).notifyError(`${e}`, e);
+                                });
                             },
                         },
                         {
@@ -232,13 +234,13 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
                                     rendererType: 'PileupRenderer',
                                 }));
                                 if (isAlive(self) && feature) {
-                                    self.selectFeature(new SimpleFeature(feature));
+                                    await self.selectFeature(new SimpleFeature(feature));
                                 }
                             }
                         }
                         catch (e) {
                             console.error(e);
-                            session.notify(`${e}`);
+                            session.notifyError(`${e}`, e);
                         }
                     },
                     onClick() {
@@ -267,7 +269,7 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
                         }
                         catch (e) {
                             console.error(e);
-                            session.notify(`${e}`);
+                            session.notifyError(`${e}`, e);
                         }
                     },
                 };

package/esm/LinearPileupDisplay/model.d.ts

@@ -205,7 +205,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;

package/esm/PileupRenderer/PileupRenderer.d.ts

@@ -20,7 +20,7 @@ export default class PileupRenderer extends BoxRendererType {
         width: number;
         maxHeightReached: boolean;
         containsNoTransferables: boolean;
-        canvasRecordedData: any;
+        canvasRecordedData: Record<string, unknown>;
         reactElement?: React.ReactElement;
         html?: string;
     } | {
@@ -30,7 +30,8 @@ export default class PileupRenderer extends BoxRendererType {
         width: number;
         maxHeightReached: boolean;
         containsNoTransferables: boolean;
-        reactElement: import("react/jsx-runtime").JSX.Element;
+        imageData: any;
+        reactElement?: React.ReactElement;
         html?: string;
     } | {
         features: Map<any, any>;
@@ -39,8 +40,7 @@ export default class PileupRenderer extends BoxRendererType {
         width: number;
         maxHeightReached: boolean;
         containsNoTransferables: boolean;
-        imageData: any;
-        reactElement?: React.ReactElement;
+        reactElement: React.ReactElement;
         html?: string;
     }>;
     createLayoutSession(args: PileupLayoutSessionProps): PileupLayoutSession;

package/esm/PileupRenderer/makeImageData.js

@@ -1,6 +1,6 @@
 import { readConfObject } from '@jbrowse/core/configuration';
 import { createJBrowseTheme } from '@jbrowse/core/ui';
-import { checkStopToken } from '@jbrowse/core/util/stopToken';
+import { forEachWithStopTokenCheck } from '@jbrowse/core/util';
 import { renderAlignment } from './renderAlignment';
 import { renderMismatches } from './renderMismatches';
 import { renderSoftClipping } from './renderSoftClipping';
@@ -19,12 +19,7 @@ export function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, })
     const { charWidth, charHeight } = getCharWidthHeight();
     const drawSNPsMuted = shouldDrawSNPsMuted(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type);
     const drawIndels = shouldDrawIndels();
-    let start = performance.now();
-    for (const feat of layoutRecords) {
-        if (performance.now() - start > 400) {
-            checkStopToken(stopToken);
-            start = performance.now();
-        }
+    forEachWithStopTokenCheck(layoutRecords, stopToken, feat => {
         renderAlignment({
             ctx,
             feat,
@@ -63,6 +58,6 @@ export function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, })
                 canvasWidth,
             });
         }
-    }
+    });
     return undefined;
 }

package/esm/PileupRenderer/renderModifications.js

@@ -3,7 +3,7 @@ import { fillRect } from './util';
 import { getMaxProbModAtEachPosition } from '../shared/getMaximumModificationAtEachPosition';
 import { alphaColor } from '../shared/util';
 export function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, cigarOps, }) {
-    var _a, _b;
+    var _a, _b, _c;
     const { feature, topPx, heightPx } = feat;
     const { colorBy, visibleModifications = {} } = renderArgs;
     const seq = feature.get('seq');
@@ -13,33 +13,29 @@ export function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, ca
     const start = feature.get('start');
     const isolatedModification = (_a = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _a === void 0 ? void 0 : _a.isolatedModification;
     const twoColor = (_b = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _b === void 0 ? void 0 : _b.twoColor;
-    const probs = getMaxProbModAtEachPosition(feature, cigarOps);
-    if (probs) {
-        let pos = 0;
-        for (const { allProbs, prob, type } of probs) {
-            const r = start + pos;
-            const [leftPx, rightPx] = bpSpanPx(r, r + 1, region, bpPerPx);
-            const mod = visibleModifications[type];
-            if (!mod) {
-                console.warn(`${type} not known yet`);
-                return;
-            }
-            if (isolatedModification && mod.type !== isolatedModification) {
-                return;
-            }
-            const col = mod.color || 'black';
-            const s = 1 - sum(allProbs);
-            if (twoColor && s > max(allProbs)) {
-                const c = alphaColor('blue', s);
-                const w = rightPx - leftPx + 0.5;
-                fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
-            }
-            else {
-                const c = alphaColor(col, prob);
-                const w = rightPx - leftPx + 0.5;
-                fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
-            }
-            pos++;
+    (_c = getMaxProbModAtEachPosition(feature, cigarOps)) === null || _c === void 0 ? void 0 : _c.forEach(({ allProbs, prob, type }, pos) => {
+        const r = start + pos;
+        const [leftPx, rightPx] = bpSpanPx(r, r + 1, region, bpPerPx);
+        const mod = visibleModifications[type];
+        if (!mod) {
+            console.warn(`${type} not known yet`);
+            return;
         }
-    }
+        if (isolatedModification && mod.type !== isolatedModification) {
+            return;
+        }
+        const col = mod.color || 'black';
+        const s = 1 - sum(allProbs);
+        if (twoColor && s > max(allProbs)) {
+            const c = alphaColor('blue', s);
+            const w = rightPx - leftPx + 0.5;
+            fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
+        }
+        else {
+            const c = alphaColor(col, prob);
+            const w = rightPx - leftPx + 0.5;
+            fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
+        }
+        pos++;
+    });
 }

package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts

@@ -11,5 +11,4 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
-    freeResources(): void;
 }

package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js

@@ -80,5 +80,4 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
         const { subadapter } = await this.configure();
         return subadapter.getRefNames(opts);
     }
-    freeResources() { }
 }

package/esm/SNPCoverageAdapter/processModifications.js

@@ -2,50 +2,46 @@ import { max, sum } from '@jbrowse/core/util';
 import { incWithProbabilities } from './util';
 import { getMaxProbModAtEachPosition } from '../shared/getMaximumModificationAtEachPosition';
 export function processModifications({ feature, colorBy, region, bins, regionSequence, }) {
-    var _a, _b;
+    var _a, _b, _c;
     const fstart = feature.get('start');
     const fstrand = feature.get('strand');
     const fend = feature.get('end');
     const twoColor = (_a = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _a === void 0 ? void 0 : _a.twoColor;
     const isolatedModification = (_b = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _b === void 0 ? void 0 : _b.isolatedModification;
-    const probs = getMaxProbModAtEachPosition(feature);
-    if (probs) {
-        let pos = 0;
-        for (const { type, prob, allProbs } of probs) {
-            if (isolatedModification && type !== isolatedModification) {
-                return;
+    (_c = getMaxProbModAtEachPosition(feature)) === null || _c === void 0 ? void 0 : _c.forEach(({ allProbs, prob, type }, pos) => {
+        if (isolatedModification && type !== isolatedModification) {
+            return;
+        }
+        const epos = pos + fstart - region.start;
+        if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
+            if (bins[epos] === undefined) {
+                bins[epos] = {
+                    depth: 0,
+                    readsCounted: 0,
+                    snps: {},
+                    ref: {
+                        probabilities: [],
+                        entryDepth: 0,
+                        '-1': 0,
+                        0: 0,
+                        1: 0,
+                    },
+                    mods: {},
+                    nonmods: {},
+                    delskips: {},
+                    noncov: {},
+                };
+            }
+            const s = 1 - sum(allProbs);
+            const bin = bins[epos];
+            bin.refbase = regionSequence[epos];
+            if (twoColor && s > max(allProbs)) {
+                incWithProbabilities(bin, fstrand, 'nonmods', `nonmod_${type}`, s);
             }
-            const epos = pos + fstart - region.start;
-            if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
-                if (bins[epos] === undefined) {
-                    bins[epos] = {
-                        depth: 0,
-                        readsCounted: 0,
-                        snps: {},
-                        ref: {
-                            probabilities: [],
-                            entryDepth: 0,
-                            '-1': 0,
-                            0: 0,
-                            1: 0,
-                        },
-                        mods: {},
-                        nonmods: {},
-                        delskips: {},
-                        noncov: {},
-                    };
-                }
-                const s = 1 - sum(allProbs);
-                const bin = bins[epos];
-                bin.refbase = regionSequence[epos];
-                if (twoColor && s > max(allProbs)) {
-                    incWithProbabilities(bin, fstrand, 'nonmods', `nonmod_${type}`, s);
-                }
-                else {
-                    incWithProbabilities(bin, fstrand, 'mods', `mod_${type}`, prob);
-                }
+            else {
+                incWithProbabilities(bin, fstrand, 'mods', `mod_${type}`, prob);
             }
-            pos++;
         }
-    }
+        pos++;
+    });
 }

package/esm/SNPCoverageRenderer/makeImage.js

@@ -1,7 +1,6 @@
 import { readConfObject } from '@jbrowse/core/configuration';
 import { createJBrowseTheme } from '@jbrowse/core/ui';
-import { bpSpanPx, featureSpanPx } from '@jbrowse/core/util';
-import { checkStopToken } from '@jbrowse/core/util/stopToken';
+import { bpSpanPx, featureSpanPx, forEachWithStopTokenCheck, } from '@jbrowse/core/util';
 import { YSCALEBAR_LABEL_OFFSET, getOrigin, getScale, } from '@jbrowse/plugin-wiggle';
 import { alphaColor } from '../shared/util';
 const INTERBASE_INDICATOR_WIDTH = 7;
@@ -15,7 +14,7 @@ const complementBase = {
 };
 const fudgeFactor = 0.6;
 export async function makeImage(ctx, props) {
-    var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k;
+    var _a;
     const { features, regions, bpPerPx, colorBy, displayCrossHatches, visibleModifications = {}, scaleOpts, height: unadjustedHeight, theme: configTheme, config: cfg, ticks, stopToken, } = props;
     const theme = createJBrowseTheme(configTheme);
     const region = regions[0];
@@ -53,35 +52,25 @@ export async function makeImage(ctx, props) {
         cpg_meth: 'red',
         cpg_unmeth: 'blue',
     };
-    const feats = [...features.values()];
     ctx.fillStyle = colorMap.total;
-    let start = performance.now();
-    for (const feature of feats) {
+    forEachWithStopTokenCheck(features.values(), stopToken, feature => {
         if (feature.get('type') === 'skip') {
-            continue;
+            return;
         }
         const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
         const w = rightPx - leftPx + fudgeFactor;
         const score = feature.get('score');
         ctx.fillRect(leftPx, toY(score), w, toHeight(score));
-        if (performance.now() - start > 400) {
-            checkStopToken(stopToken);
-            start = performance.now();
-        }
-    }
+    });
     let prevTotal = 0;
     const extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx : 0;
     const drawingModifications = colorBy.type === 'modifications';
     const drawingMethylation = colorBy.type === 'methylation';
     const isolatedModification = (_a = colorBy.modifications) === null || _a === void 0 ? void 0 : _a.isolatedModification;
-    start = performance.now();
-    for (const feature of feats) {
-        const now = performance.now();
-        if (now - start > 400) {
-            checkStopToken(stopToken);
-        }
+    forEachWithStopTokenCheck(features.values(), stopToken, feature => {
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j;
         if (feature.get('type') === 'skip') {
-            continue;
+            return;
         }
         const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
         const snpinfo = feature.get('snpinfo');
@@ -89,7 +78,7 @@ export async function makeImage(ctx, props) {
         const score0 = feature.get('score');
         if (drawingModifications) {
             let curr = 0;
-            const refbase = (_b = snpinfo.refbase) === null || _b === void 0 ? void 0 : _b.toUpperCase();
+            const refbase = (_a = snpinfo.refbase) === null || _a === void 0 ? void 0 : _a.toUpperCase();
             const { nonmods, mods, snps, ref } = snpinfo;
             for (const m of Object.keys(nonmods).sort().reverse()) {
                 const mod = visibleModifications[m.replace('nonmod_', '')] ||
@@ -104,14 +93,14 @@ export async function makeImage(ctx, props) {
                 const cmp = complementBase[mod.base];
                 const detectable = mod.base === 'N'
                     ? score0
-                    : (((_c = snps[mod.base]) === null || _c === void 0 ? void 0 : _c.entryDepth) || 0) +
-                        (((_d = snps[cmp]) === null || _d === void 0 ? void 0 : _d.entryDepth) || 0) +
+                    : (((_b = snps[mod.base]) === null || _b === void 0 ? void 0 : _b.entryDepth) || 0) +
+                        (((_c = snps[cmp]) === null || _c === void 0 ? void 0 : _c.entryDepth) || 0) +
                         (refbase === mod.base ? ref['1'] : 0) +
                         (refbase === cmp ? ref['-1'] : 0);
                 const modifiable = mod.base === 'N'
                     ? score0
-                    : (((_e = snps[mod.base]) === null || _e === void 0 ? void 0 : _e.entryDepth) || 0) +
-                        (((_f = snps[cmp]) === null || _f === void 0 ? void 0 : _f.entryDepth) || 0) +
+                    : (((_d = snps[mod.base]) === null || _d === void 0 ? void 0 : _d.entryDepth) || 0) +
+                        (((_e = snps[cmp]) === null || _e === void 0 ? void 0 : _e.entryDepth) || 0) +
                         (refbase === mod.base ? ref.entryDepth : 0) +
                         (refbase === cmp ? ref.entryDepth : 0);
                 const { entryDepth, avgProbability = 0 } = snpinfo.nonmods[m];
@@ -136,14 +125,14 @@ export async function makeImage(ctx, props) {
                 const cmp = complementBase[mod.base];
                 const detectable = mod.base === 'N'
                     ? score0
-                    : (((_g = snps[mod.base]) === null || _g === void 0 ? void 0 : _g.entryDepth) || 0) +
-                        (((_h = snps[cmp]) === null || _h === void 0 ? void 0 : _h.entryDepth) || 0) +
+                    : (((_f = snps[mod.base]) === null || _f === void 0 ? void 0 : _f.entryDepth) || 0) +
+                        (((_g = snps[cmp]) === null || _g === void 0 ? void 0 : _g.entryDepth) || 0) +
                         (refbase === mod.base ? ref['1'] : 0) +
                         (refbase === cmp ? ref['-1'] : 0);
                 const modifiable = mod.base === 'N'
                     ? score0
-                    : (((_j = snps[mod.base]) === null || _j === void 0 ? void 0 : _j.entryDepth) || 0) +
-                        (((_k = snps[cmp]) === null || _k === void 0 ? void 0 : _k.entryDepth) || 0) +
+                    : (((_h = snps[mod.base]) === null || _h === void 0 ? void 0 : _h.entryDepth) || 0) +
+                        (((_j = snps[cmp]) === null || _j === void 0 ? void 0 : _j.entryDepth) || 0) +
                         (refbase === mod.base ? ref.entryDepth : 0) +
                         (refbase === cmp ? ref.entryDepth : 0);
                 const { entryDepth, avgProbability = 0 } = mods[m];
@@ -225,17 +214,17 @@ export async function makeImage(ctx, props) {
             }
         }
         prevTotal = score0;
-    }
+    });
     if (showArcs) {
-        for (const f of feats) {
-            if (f.get('type') !== 'skip') {
-                continue;
+        forEachWithStopTokenCheck(features.values(), stopToken, feature => {
+            if (feature.get('type') !== 'skip') {
+                return;
             }
-            const s = f.get('start');
-            const e = f.get('end');
+            const s = feature.get('start');
+            const e = feature.get('end');
             const [left, right] = bpSpanPx(s, e, region, bpPerPx);
             ctx.beginPath();
-            const effectiveStrand = f.get('effectiveStrand');
+            const effectiveStrand = feature.get('effectiveStrand');
             const pos = 'rgba(255,200,200,0.7)';
             const neg = 'rgba(200,200,255,0.7)';
             const neutral = 'rgba(200,200,200,0.7)';
@@ -248,11 +237,11 @@ export async function makeImage(ctx, props) {
             else {
                 ctx.strokeStyle = neutral;
             }
-            ctx.lineWidth = Math.log(f.get('score') + 1);
+            ctx.lineWidth = Math.log(feature.get('score') + 1);
             ctx.moveTo(left, height - offset * 2);
             ctx.bezierCurveTo(left, 0, right, 0, right, height - offset * 2);
             ctx.stroke();
-        }
+        });
     }
     if (displayCrossHatches) {
         ctx.lineWidth = 1;