@jbrowse/plugin-sequence 2.10.3 → 2.11.1

package/dist/TwoBitAdapter/index.js

@@ -28,7 +28,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pluginManager) => {
+function TwoBitAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'TwoBitAdapter',
         displayName: 'TwoBit adapter',
@@ -38,4 +38,5 @@ exports.default = (pluginManager) => {
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./TwoBitAdapter'))).then(r => r.default),
     }));
-};
+}
+exports.default = TwoBitAdapterF;

package/dist/createExtensionPoints.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function ExtensionPointsF(pluginManager: PluginManager): void;

package/dist/createExtensionPoints.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const tracks_1 = require("@jbrowse/core/util/tracks");
-exports.default = (pluginManager) => {
+function ExtensionPointsF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
             const regexGuess = /\.2bit$/i;
@@ -82,4 +82,5 @@ exports.default = (pluginManager) => {
             return trackTypeGuesser(adapterName);
         };
     });
-};
+}
+exports.default = ExtensionPointsF;

package/esm/BgzipFastaAdapter/BgzipFastaAdapter.d.ts

@@ -1,6 +1,6 @@
 import { BgzipIndexedFasta } from '@gmod/indexedfasta';
 import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter';
-export default class extends IndexedFasta {
+export default class BgzipFastaAdapter extends IndexedFasta {
     setupPre(): Promise<{
         fasta: BgzipIndexedFasta;
     }>;

package/esm/BgzipFastaAdapter/BgzipFastaAdapter.js

@@ -1,7 +1,7 @@
 import { BgzipIndexedFasta } from '@gmod/indexedfasta';
 import { openLocation } from '@jbrowse/core/util/io';
 import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter';
-export default class extends IndexedFasta {
+export default class BgzipFastaAdapter extends IndexedFasta {
     async setupPre() {
         const fastaLocation = this.getConf('fastaLocation');
         const faiLocation = this.getConf('faiLocation');

package/esm/BgzipFastaAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function BgzipFastaAdapterF(pluginManager: PluginManager): void;

package/esm/BgzipFastaAdapter/index.js

@@ -1,6 +1,6 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function BgzipFastaAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'BgzipFastaAdapter',
         displayName: 'Bgzip-indexed FASTA adapter',
@@ -10,4 +10,4 @@ export default (pluginManager) => {
         },
         getAdapterClass: () => import('./BgzipFastaAdapter').then(r => r.default),
     }));
-};
+}

package/esm/ChromSizesAdapter/ChromSizesAdapter.d.ts

@@ -1,5 +1,5 @@
 import { RegionsAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-export default class extends BaseAdapter implements RegionsAdapter {
+export default class ChromSizesAdapter extends BaseAdapter implements RegionsAdapter {
     protected setupP?: Promise<Record<string, number>>;
     setupPre(): Promise<{
         [k: string]: number;

package/esm/ChromSizesAdapter/ChromSizesAdapter.js

@@ -1,6 +1,6 @@
 import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { openLocation } from '@jbrowse/core/util/io';
-export default class extends BaseAdapter {
+export default class ChromSizesAdapter extends BaseAdapter {
     async setupPre() {
         const pm = this.pluginManager;
         const file = openLocation(this.getConf('chromSizesLocation'), pm);

package/esm/ChromSizesAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function ChromSizesAdapterF(pluginManager: PluginManager): void;

package/esm/ChromSizesAdapter/index.js

@@ -1,6 +1,6 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function ChromSizesAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'ChromSizesAdapter',
         displayName: 'Chrom sizes adapter',
@@ -10,4 +10,4 @@ export default (pluginManager) => {
         },
         getAdapterClass: () => import('./ChromSizesAdapter').then(r => r.default),
     }));
-};
+}

package/esm/DivSequenceRenderer/components/DivSequenceRendering.d.ts

@@ -8,6 +8,7 @@ declare const DivSequenceRendering: (props: {
     };
     features: Map<string, Feature>;
     regions: Region[];
+    colorByCDS: boolean;
     bpPerPx: number;
     rowHeight: number;
     sequenceHeight: number;

package/esm/DivSequenceRenderer/components/DivSequenceRendering.js

@@ -2,42 +2,54 @@ import React from 'react';
 import { createJBrowseTheme } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
 import { bpSpanPx, revcom, complement, defaultStarts, defaultStops, defaultCodonTable, generateCodonTable, } from '@jbrowse/core/util';
-function Translation(props) {
-    const { codonTable, seq, frame, bpPerPx, region, height, y, reverse = false, theme, } = props;
-    const scale = bpPerPx;
-    // the tilt variable normalizes the frame to where we are starting from,
-    // which increases consistency across blocks
-    const tilt = 3 - (region.start % 3);
-    // the effectiveFrame incorporates tilt and the frame to say what the
-    // effective frame that is plotted. The +3 is for when frame is -2 and this
-    // can otherwise result in effectiveFrame -1
-    const effectiveFrame = (frame + tilt + 3) % 3;
-    const seqSliced = seq.slice(effectiveFrame);
+function Translation({ codonTable, seq, frame, bpPerPx, colorByCDS, region, seqStart, height, y, reverse = false, theme, }) {
+    var _a, _b;
+    const normalizedFrame = Math.abs(frame) - 1;
+    const seqFrame = seqStart % 3;
+    const frameShift = (normalizedFrame - seqFrame + 3) % 3;
+    const frameShiftAdjustedSeqLength = seq.length - frameShift;
+    const multipleOfThreeLength = frameShiftAdjustedSeqLength - (frameShiftAdjustedSeqLength % 3);
+    const seqSliced = seq.slice(frameShift, frameShift + multipleOfThreeLength);
     const translated = [];
     for (let i = 0; i < seqSliced.length; i += 3) {
         const codon = seqSliced.slice(i, i + 3);
         const normalizedCodon = reverse ? revcom(codon) : codon;
         const aminoAcid = codonTable[normalizedCodon] || '';
-        translated.push({ letter: aminoAcid, codon: normalizedCodon.toUpperCase() });
+        translated.push({
+            letter: aminoAcid,
+            codon: normalizedCodon.toUpperCase(),
+        });
     }
-    const w = (1 / scale) * 3;
-    const drop = region.start === 0 ? 0 : w;
-    const render = 1 / bpPerPx >= 12;
     const width = (region.end - region.start) / bpPerPx;
-    const map = ['#d8d8d8', '#adadad', '#8f8f8f'].reverse();
-    return (React.createElement(React.Fragment, null, translated.map((element, index) => {
-        const x = region.reversed
-            ? width - (w * (index + 1) + effectiveFrame / scale - drop)
-            : w * index + effectiveFrame / scale - drop;
-        const { letter, codon } = element;
-        return (React.createElement(React.Fragment, { key: `${index}-${letter}` },
-            React.createElement("rect", { x: x, y: y, width: render ? w : w + 0.7 /* small fudge factor when zoomed out*/, height: height, stroke: render ? '#555' : 'none', fill: defaultStarts.includes(codon)
-                    ? theme === null || theme === void 0 ? void 0 : theme.palette.startCodon
-                    : defaultStops.includes(codon)
-                        ? theme === null || theme === void 0 ? void 0 : theme.palette.stopCodon
-                        : map[Math.abs(frame)] }),
-            render ? (React.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fontSize: height - 2 }, letter)) : null));
-    })));
+    const codonWidth = (1 / bpPerPx) * 3;
+    const renderLetter = 1 / bpPerPx >= 12;
+    const frameOffset = frameShift / bpPerPx;
+    const startOffset = (region.start - seqStart) / bpPerPx;
+    const offset = frameOffset - startOffset;
+    const defaultFill = colorByCDS
+        ? (_a = theme === null || theme === void 0 ? void 0 : theme.palette.framesCDS.at(frame)) === null || _a === void 0 ? void 0 : _a.main
+        : (_b = theme === null || theme === void 0 ? void 0 : theme.palette.frames.at(frame)) === null || _b === void 0 ? void 0 : _b.main;
+    return (React.createElement(React.Fragment, null,
+        React.createElement("rect", { x: 0, y: y, width: width, height: height, fill: defaultFill }),
+        translated.map((element, index) => {
+            const x = region.reversed
+                ? width - (index + 1) * codonWidth - offset
+                : codonWidth * index + offset;
+            const { letter, codon } = element;
+            const codonFill = defaultStarts.includes(codon)
+                ? theme === null || theme === void 0 ? void 0 : theme.palette.startCodon
+                : defaultStops.includes(codon)
+                    ? theme === null || theme === void 0 ? void 0 : theme.palette.stopCodon
+                    : undefined;
+            if (!(renderLetter || codonFill)) {
+                return null;
+            }
+            return (React.createElement(React.Fragment, { key: `${index}-${letter}` },
+                React.createElement("rect", { x: x, y: y, width: renderLetter
+                        ? codonWidth
+                        : codonWidth + 0.7 /* small fudge factor when zoomed out*/, height: height, stroke: renderLetter ? '#555' : 'none', fill: codonFill || 'none' }),
+                renderLetter ? (React.createElement("text", { x: x + codonWidth / 2, fontSize: height - 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle" }, letter)) : null));
+        })));
 }
 function DNA(props) {
     const { bpPerPx, region, feature, theme, height, seq, y } = props;
@@ -55,7 +67,7 @@ function DNA(props) {
             render ? (React.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fontSize: height - 2, fill: color ? theme.palette.getContrastText(color.main) : 'black' }, letter)) : null));
     })));
 }
-function SequenceSVG({ regions, theme: configTheme, features = new Map(), showReverse = true, showForward = true, showTranslation = true, bpPerPx, rowHeight, }) {
+function SequenceSVG({ regions, theme: configTheme, colorByCDS, features = new Map(), showReverse = true, showForward = true, showTranslation = true, bpPerPx, rowHeight, }) {
     const [region] = regions;
     const theme = createJBrowseTheme(configTheme);
     const codonTable = generateCodonTable(defaultCodonTable);
@@ -70,23 +82,26 @@ function SequenceSVG({ regions, theme: configTheme, features = new Map(), showRe
     // incrementer for the y-position of the current sequence being rendered
     // (applies to both translation rows and dna rows)
     let currY = -rowHeight;
+    const showDNA = bpPerPx <= 1;
+    const forwardFrames = showTranslation && showForward ? [3, 2, 1] : [];
+    const reverseFrames = showTranslation && showReverse ? [-1, -2, -3] : [];
+    // if region.reversed, the forward translation is on bottom, reverse on top
+    const [topFrames, bottomFrames] = region.reversed
+        ? [reverseFrames.toReversed(), forwardFrames.toReversed()]
+        : [forwardFrames, reverseFrames];
     return (React.createElement(React.Fragment, null,
-        showTranslation && (region.reversed ? showReverse : showForward)
-            ? [2, 1, 0].map(index => (React.createElement(Translation, { key: `translation-${index}`, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: rowHeight, reverse: region.reversed })))
-            : null,
-        showForward ? (React.createElement(DNA, { height: rowHeight, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? complement(seq) : seq, bpPerPx: bpPerPx, theme: theme })) : null,
-        showReverse ? (React.createElement(DNA, { height: rowHeight, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? seq : complement(seq), bpPerPx: bpPerPx, theme: theme })) : null,
-        showTranslation && (region.reversed ? showForward : showReverse)
-            ? [0, -1, -2].map(index => (React.createElement(Translation, { key: `rev-translation-${index}`, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: rowHeight, reverse: !region.reversed })))
-            : null));
+        topFrames.map(index => (React.createElement(Translation, { key: `translation-${index}`, colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), theme: theme, height: rowHeight, reverse: region.reversed }))),
+        showForward && showDNA ? (React.createElement(DNA, { height: rowHeight, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? complement(seq) : seq, bpPerPx: bpPerPx, theme: theme })) : null,
+        showReverse && showDNA ? (React.createElement(DNA, { height: rowHeight, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? seq : complement(seq), bpPerPx: bpPerPx, theme: theme })) : null,
+        bottomFrames.map(index => (React.createElement(Translation, { key: `rev-translation-${index}`, colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), theme: theme, height: rowHeight, reverse: !region.reversed })))));
 }
 function Wrapper({ exportSVG, width, totalHeight, children, }) {
-    return exportSVG ? (React.createElement(React.Fragment, null, children)) : (React.createElement("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: {
+    return exportSVG ? (children) : (React.createElement("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: {
+            // use block because svg by default is inline, which adds a margin
+            display: 'block',
             width,
             height: totalHeight,
             userSelect: 'none',
-            // use block because svg by default is inline, which adds a margin
-            display: 'block',
         } }, children));
 }
 const DivSequenceRendering = observer(function (props) {

package/esm/DivSequenceRenderer/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function DivSequenceRendererF(pluginManager: PluginManager): void;

package/esm/DivSequenceRenderer/index.js

@@ -15,11 +15,11 @@ class DivSequenceRenderer extends FeatureRendererType {
         };
     }
 }
-export default (pluginManager) => {
+export default function DivSequenceRendererF(pluginManager) {
     pluginManager.addRendererType(() => new DivSequenceRenderer({
         name: 'DivSequenceRenderer',
         ReactComponent,
         configSchema,
         pluginManager,
     }));
-};
+}

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.d.ts

@@ -2,7 +2,7 @@ import { IndexedFasta } from '@gmod/indexedfasta';
 import { BaseSequenceAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util';
-export default class extends BaseSequenceAdapter {
+export default class IndexedFastaAdapter extends BaseSequenceAdapter {
     protected setupP?: Promise<{
         fasta: IndexedFasta;
     }>;

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -5,7 +5,7 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { SimpleFeature } from '@jbrowse/core/util';
 import AbortablePromiseCache from 'abortable-promise-cache';
 import QuickLRU from '@jbrowse/core/util/QuickLRU';
-export default class extends BaseSequenceAdapter {
+export default class IndexedFastaAdapter extends BaseSequenceAdapter {
     constructor() {
         super(...arguments);
         this.seqCache = new AbortablePromiseCache({

package/esm/IndexedFastaAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function IndexedFastaAdapterF(pluginManager: PluginManager): void;

package/esm/IndexedFastaAdapter/index.js

@@ -1,6 +1,6 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function IndexedFastaAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'IndexedFastaAdapter',
         displayName: 'Indexed FASTA adapter',
@@ -10,4 +10,4 @@ export default (pluginManager) => {
         },
         getAdapterClass: () => import('./IndexedFastaAdapter').then(r => r.default),
     }));
-};
+}

package/esm/LinearReferenceSequenceDisplay/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function LinearReferenceSequenceDisplayF(pluginManager: PluginManager): void;

package/esm/LinearReferenceSequenceDisplay/index.js

@@ -2,7 +2,7 @@ import { DisplayType } from '@jbrowse/core/pluggableElementTypes';
 import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
 import { configSchema } from './configSchema';
 import { modelFactory } from './model';
-export default (pluginManager) => {
+export default function LinearReferenceSequenceDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const stateModel = modelFactory(configSchema);
         return new DisplayType({
@@ -15,4 +15,4 @@ export default (pluginManager) => {
             ReactComponent: BaseLinearDisplayComponent,
         });
     });
-};
+}

package/esm/LinearReferenceSequenceDisplay/model.d.ts

@@ -70,24 +70,31 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         maxFeatureScreenDensity: {
             type: string;
-            description: string;
+            description: string; /**
+             * #property
+             */
             defaultValue: number;
         };
         fetchSizeLimit: {
-            type: string;
+            type: string; /**
+             * #property
+             */
             defaultValue: number;
             description: string;
         };
         height: {
             type: string;
-            defaultValue: number;
-            description: string; /**
+            defaultValue: number; /**
              * #property
              */
+            description: string;
         };
         mouseover: {
             type: string;
             description: string;
+            /**
+             * #getter
+             */
             defaultValue: string;
             contextVariable: string[];
         };
@@ -107,13 +114,15 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
         model: {
             id: string;
             type: string;
-            rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string; /**
+            rpcDriverName: string | undefined; /**
              * #property
              */
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
             error: unknown;
-            message: string | undefined;
+            message: string | undefined; /**
+             * #property
+             */
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
@@ -161,13 +170,15 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
 } & {
     scrollTop: number;
 } & {
-    readonly height: number;
-} & {
-    setScrollTop(scrollTop: number): void; /**
+    readonly height: number; /**
      * #property
      */
+} & {
+    setScrollTop(scrollTop: number): void;
     setHeight(displayHeight: number): number;
-    resizeHeight(distance: number): number;
+    resizeHeight(distance: number): number; /**
+     * #getter
+     */
 } & {
     featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
     featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
@@ -175,13 +186,13 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
 } & {
     readonly currentBytesRequested: number;
     readonly currentFeatureScreenDensity: number;
-    readonly maxFeatureScreenDensity: any;
+    readonly maxFeatureScreenDensity: any; /**
+     * #method
+     */
     readonly featureDensityStatsReady: boolean;
     readonly maxAllowableBytes: number;
 } & {
-    afterAttach(): void; /**
-     * #getter
-     */
+    afterAttach(): void;
 } & {
     setCurrStatsBpPerPx(n: number): void;
     setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
@@ -344,24 +355,31 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         maxFeatureScreenDensity: {
             type: string;
-            description: string;
+            description: string; /**
+             * #property
+             */
             defaultValue: number;
         };
         fetchSizeLimit: {
-            type: string;
+            type: string; /**
+             * #property
+             */
             defaultValue: number;
             description: string;
         };
         height: {
             type: string;
-            defaultValue: number;
-            description: string; /**
+            defaultValue: number; /**
              * #property
              */
+            description: string;
         };
         mouseover: {
             type: string;
             description: string;
+            /**
+             * #getter
+             */
             defaultValue: string;
             contextVariable: string[];
         };

package/esm/LinearReferenceSequenceDisplay/model.js

@@ -1,6 +1,7 @@
 import { addDisposer, types } from 'mobx-state-tree';
 import { BaseLinearDisplay, } from '@jbrowse/plugin-linear-genome-view';
 import { ConfigurationReference, } from '@jbrowse/core/configuration';
+import { getParentRenderProps } from '@jbrowse/core/util/tracks';
 import { getContainingView } from '@jbrowse/core/util';
 import { autorun } from 'mobx';
 /**
@@ -61,6 +62,7 @@ export function modelFactory(configSchema) {
                 const { showForward, rpcDriverName, showReverse, showTranslation, rowHeight, sequenceHeight, } = self;
                 return {
                     ...superRenderProps(),
+                    ...getParentRenderProps(self),
                     config: self.configuration.renderer,
                     rpcDriverName,
                     showForward,
@@ -78,7 +80,7 @@ export function modelFactory(configSchema) {
          */
         regionCannotBeRendered( /* region */) {
             const view = getContainingView(self);
-            return (view === null || view === void 0 ? void 0 : view.bpPerPx) >= 1 ? 'Zoom in to see sequence' : undefined;
+            return (view === null || view === void 0 ? void 0 : view.bpPerPx) > 3 ? 'Zoom in to see sequence' : undefined;
         },
         /**
          * #getter
@@ -109,7 +111,7 @@ export function modelFactory(configSchema) {
         afterAttach() {
             addDisposer(self, autorun(() => {
                 const view = getContainingView(self);
-                if ((view === null || view === void 0 ? void 0 : view.bpPerPx) >= 1) {
+                if ((view === null || view === void 0 ? void 0 : view.bpPerPx) > 3) {
                     self.setHeight(50);
                 }
                 else {

package/esm/ReferenceSequenceTrack/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function ReferenceSequenceTrackF(pluginManager: PluginManager): void;

package/esm/ReferenceSequenceTrack/index.js

@@ -1,7 +1,7 @@
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
 import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
 import { createReferenceSeqTrackConfig } from './configSchema';
-export default (pluginManager) => {
+export default function ReferenceSequenceTrackF(pluginManager) {
     pluginManager.addTrackType(() => {
         const configSchema = createReferenceSeqTrackConfig(pluginManager);
         return new TrackType({
@@ -11,4 +11,4 @@ export default (pluginManager) => {
             stateModel: createBaseTrackModel(pluginManager, 'ReferenceSequenceTrack', configSchema),
         });
     });
-};
+}

package/esm/SequenceSearchAdapter/SequenceSearchAdapter.d.ts

@@ -1,6 +1,6 @@
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Feature, Region } from '@jbrowse/core/util';
-export default class extends BaseFeatureDataAdapter {
+export default class SequenceSearchAdapter extends BaseFeatureDataAdapter {
     configure(): Promise<BaseFeatureDataAdapter>;
     getRefNames(): Promise<string[]>;
     getFeatures(query: Region, opts: BaseOptions): import("rxjs").Observable<Feature>;

package/esm/SequenceSearchAdapter/SequenceSearchAdapter.js

@@ -3,7 +3,7 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { SimpleFeature, revcom, doesIntersect2, } from '@jbrowse/core/util';
 import { toArray } from 'rxjs/operators';
 import { firstValueFrom } from 'rxjs';
-export default class extends BaseFeatureDataAdapter {
+export default class SequenceSearchAdapter extends BaseFeatureDataAdapter {
     async configure() {
         var _a;
         const adapter = await ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, this.getConf('sequenceAdapter')));
@@ -20,10 +20,9 @@ export default class extends BaseFeatureDataAdapter {
         return ObservableCreate(async (observer) => {
             var _a;
             const sequenceAdapter = await this.configure();
-            const hw = 1000;
-            let { start: queryStart, end: queryEnd } = query;
-            queryStart = Math.max(0, queryStart - hw);
-            queryEnd += hw;
+            const hw = 10000;
+            const queryEnd = query.end + hw;
+            const queryStart = Math.max(0, query.start - hw);
             if (queryEnd < 0 || queryStart > queryEnd) {
                 observer.complete();
                 return;
@@ -44,13 +43,14 @@ export default class extends BaseFeatureDataAdapter {
                 if (searchForward) {
                     const matches = residues.matchAll(re);
                     for (const match of matches) {
-                        const s = queryStart + (match.index || 0);
-                        if (doesIntersect2(s, s + search.length, query.start, query.end)) {
+                        const s = queryStart + match.index;
+                        const e = queryStart + match.index + match[0].length;
+                        if (doesIntersect2(s, e, query.start, query.end)) {
                             observer.next(new SimpleFeature({
-                                uniqueId: `${this.id}-match-${s}-p`,
+                                uniqueId: `${this.id}-${s}-${match[0]}-pos`,
                                 refName: query.refName,
                                 start: s,
-                                end: s + match[0].length,
+                                end: e,
                                 name: match[0],
                                 strand: 1,
                             }));
@@ -60,14 +60,15 @@ export default class extends BaseFeatureDataAdapter {
                 if (searchReverse) {
                     const matches = revcom(residues).matchAll(re);
                     for (const match of matches) {
-                        const s = queryEnd - (match.index || 0);
-                        if (doesIntersect2(s, s + search.length, query.start, query.end)) {
+                        const e = queryEnd - match.index;
+                        const s = queryEnd - match.index - match[0].length;
+                        if (doesIntersect2(s, e, query.start, query.end)) {
                             observer.next(new SimpleFeature({
-                                uniqueId: `${this.id}-match-${s}-n`,
+                                uniqueId: `${this.id}-${s}-${match[0]}-neg`,
                                 refName: query.refName,
-                                start: s - match[0].length,
+                                start: s,
+                                end: e,
                                 name: match[0],
-                                end: s,
                                 strand: -1,
                             }));
                         }

package/esm/SequenceSearchAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function SequenceSearchAdapterF(pluginManager: PluginManager): void;

package/esm/SequenceSearchAdapter/index.js

@@ -1,6 +1,6 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function SequenceSearchAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'SequenceSearchAdapter',
         displayName: 'Sequence search adapter',
@@ -10,4 +10,4 @@ export default (pluginManager) => {
         configSchema,
         getAdapterClass: () => import('./SequenceSearchAdapter').then(r => r.default),
     }));
-};
+}