@jbrowse/plugin-sequence 2.10.3 → 2.11.1

package/dist/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/dist/BgzipFastaAdapter/BgzipFastaAdapter.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const indexedfasta_1 = require("@gmod/indexedfasta");
 const io_1 = require("@jbrowse/core/util/io");
 const IndexedFastaAdapter_1 = __importDefault(require("../IndexedFastaAdapter/IndexedFastaAdapter"));
-class default_1 extends IndexedFastaAdapter_1.default {
+class BgzipFastaAdapter extends IndexedFastaAdapter_1.default {
     async setupPre() {
         const fastaLocation = this.getConf('fastaLocation');
         const faiLocation = this.getConf('faiLocation');
@@ -19,4 +19,4 @@ class default_1 extends IndexedFastaAdapter_1.default {
         return { fasta: new indexedfasta_1.BgzipIndexedFasta(fastaOpts) };
     }
 }
-exports.default = default_1;
+exports.default = BgzipFastaAdapter;

package/dist/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/dist/BgzipFastaAdapter/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 BgzipFastaAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'BgzipFastaAdapter',
         displayName: 'Bgzip-indexed FASTA adapter',
@@ -38,4 +38,5 @@ exports.default = (pluginManager) => {
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BgzipFastaAdapter'))).then(r => r.default),
     }));
-};
+}
+exports.default = BgzipFastaAdapterF;

package/dist/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/dist/ChromSizesAdapter/ChromSizesAdapter.js

@@ -2,7 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const io_1 = require("@jbrowse/core/util/io");
-class default_1 extends BaseAdapter_1.BaseAdapter {
+class ChromSizesAdapter extends BaseAdapter_1.BaseAdapter {
     async setupPre() {
         const pm = this.pluginManager;
         const file = (0, io_1.openLocation)(this.getConf('chromSizesLocation'), pm);
@@ -38,4 +38,4 @@ class default_1 extends BaseAdapter_1.BaseAdapter {
     }
     freeResources( /* { region } */) { }
 }
-exports.default = default_1;
+exports.default = ChromSizesAdapter;

package/dist/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/dist/ChromSizesAdapter/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 ChromSizesAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'ChromSizesAdapter',
         displayName: 'Chrom sizes adapter',
@@ -38,4 +38,5 @@ exports.default = (pluginManager) => {
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./ChromSizesAdapter'))).then(r => r.default),
     }));
-};
+}
+exports.default = ChromSizesAdapterF;

package/dist/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/dist/DivSequenceRenderer/components/DivSequenceRendering.js

@@ -7,42 +7,54 @@ const react_1 = __importDefault(require("react"));
 const ui_1 = require("@jbrowse/core/ui");
 const mobx_react_1 = require("mobx-react");
 const util_1 = require("@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 ? (0, util_1.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_1.default.createElement(react_1.default.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_1.default.createElement(react_1.default.Fragment, { key: `${index}-${letter}` },
-            react_1.default.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: util_1.defaultStarts.includes(codon)
-                    ? theme === null || theme === void 0 ? void 0 : theme.palette.startCodon
-                    : util_1.defaultStops.includes(codon)
-                        ? theme === null || theme === void 0 ? void 0 : theme.palette.stopCodon
-                        : map[Math.abs(frame)] }),
-            render ? (react_1.default.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_1.default.createElement(react_1.default.Fragment, null,
+        react_1.default.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 = util_1.defaultStarts.includes(codon)
+                ? theme === null || theme === void 0 ? void 0 : theme.palette.startCodon
+                : util_1.defaultStops.includes(codon)
+                    ? theme === null || theme === void 0 ? void 0 : theme.palette.stopCodon
+                    : undefined;
+            if (!(renderLetter || codonFill)) {
+                return null;
+            }
+            return (react_1.default.createElement(react_1.default.Fragment, { key: `${index}-${letter}` },
+                react_1.default.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_1.default.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;
@@ -60,7 +72,7 @@ function DNA(props) {
             render ? (react_1.default.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 = (0, ui_1.createJBrowseTheme)(configTheme);
     const codonTable = (0, util_1.generateCodonTable)(util_1.defaultCodonTable);
@@ -75,23 +87,26 @@ 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_1.default.createElement(react_1.default.Fragment, null,
-        showTranslation && (region.reversed ? showReverse : showForward)
-            ? [2, 1, 0].map(index => (react_1.default.createElement(Translation, { key: `translation-${index}`, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: rowHeight, reverse: region.reversed })))
-            : null,
-        showForward ? (react_1.default.createElement(DNA, { height: rowHeight, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? (0, util_1.complement)(seq) : seq, bpPerPx: bpPerPx, theme: theme })) : null,
-        showReverse ? (react_1.default.createElement(DNA, { height: rowHeight, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? seq : (0, util_1.complement)(seq), bpPerPx: bpPerPx, theme: theme })) : null,
-        showTranslation && (region.reversed ? showForward : showReverse)
-            ? [0, -1, -2].map(index => (react_1.default.createElement(Translation, { key: `rev-translation-${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_1.default.createElement(Translation, { key: `translation-${index}`, colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), theme: theme, height: rowHeight, reverse: region.reversed }))),
+        showForward && showDNA ? (react_1.default.createElement(DNA, { height: rowHeight, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? (0, util_1.complement)(seq) : seq, bpPerPx: bpPerPx, theme: theme })) : null,
+        showReverse && showDNA ? (react_1.default.createElement(DNA, { height: rowHeight, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? seq : (0, util_1.complement)(seq), bpPerPx: bpPerPx, theme: theme })) : null,
+        bottomFrames.map(index => (react_1.default.createElement(Translation, { key: `rev-translation-${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_1.default.createElement(react_1.default.Fragment, null, children)) : (react_1.default.createElement("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: {
+    return exportSVG ? (children) : (react_1.default.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 = (0, mobx_react_1.observer)(function (props) {

package/dist/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/dist/DivSequenceRenderer/index.js

@@ -20,11 +20,12 @@ class DivSequenceRenderer extends FeatureRendererType_1.default {
         };
     }
 }
-exports.default = (pluginManager) => {
+function DivSequenceRendererF(pluginManager) {
     pluginManager.addRendererType(() => new DivSequenceRenderer({
         name: 'DivSequenceRenderer',
         ReactComponent: DivSequenceRendering_1.default,
         configSchema: configSchema_1.default,
         pluginManager,
     }));
-};
+}
+exports.default = DivSequenceRendererF;

package/dist/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/dist/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -10,7 +10,7 @@ const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const util_1 = require("@jbrowse/core/util");
 const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
 const QuickLRU_1 = __importDefault(require("@jbrowse/core/util/QuickLRU"));
-class default_1 extends BaseAdapter_1.BaseSequenceAdapter {
+class IndexedFastaAdapter extends BaseAdapter_1.BaseSequenceAdapter {
     constructor() {
         super(...arguments);
         this.seqCache = new abortable_promise_cache_1.default({
@@ -97,4 +97,4 @@ class default_1 extends BaseAdapter_1.BaseSequenceAdapter {
      */
     freeResources( /* { region } */) { }
 }
-exports.default = default_1;
+exports.default = IndexedFastaAdapter;

package/dist/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/dist/IndexedFastaAdapter/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 IndexedFastaAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'IndexedFastaAdapter',
         displayName: 'Indexed FASTA adapter',
@@ -38,4 +38,5 @@ exports.default = (pluginManager) => {
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./IndexedFastaAdapter'))).then(r => r.default),
     }));
-};
+}
+exports.default = IndexedFastaAdapterF;

package/dist/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/dist/LinearReferenceSequenceDisplay/index.js

@@ -4,7 +4,7 @@ const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const configSchema_1 = require("./configSchema");
 const model_1 = require("./model");
-exports.default = (pluginManager) => {
+function LinearReferenceSequenceDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const stateModel = (0, model_1.modelFactory)(configSchema_1.configSchema);
         return new pluggableElementTypes_1.DisplayType({
@@ -17,4 +17,5 @@ exports.default = (pluginManager) => {
             ReactComponent: plugin_linear_genome_view_1.BaseLinearDisplayComponent,
         });
     });
-};
+}
+exports.default = LinearReferenceSequenceDisplayF;

package/dist/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/dist/LinearReferenceSequenceDisplay/model.js

@@ -4,6 +4,7 @@ exports.modelFactory = void 0;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const configuration_1 = require("@jbrowse/core/configuration");
+const tracks_1 = require("@jbrowse/core/util/tracks");
 const util_1 = require("@jbrowse/core/util");
 const mobx_1 = require("mobx");
 /**
@@ -64,6 +65,7 @@ function modelFactory(configSchema) {
                 const { showForward, rpcDriverName, showReverse, showTranslation, rowHeight, sequenceHeight, } = self;
                 return {
                     ...superRenderProps(),
+                    ...(0, tracks_1.getParentRenderProps)(self),
                     config: self.configuration.renderer,
                     rpcDriverName,
                     showForward,
@@ -81,7 +83,7 @@ function modelFactory(configSchema) {
          */
         regionCannotBeRendered( /* region */) {
             const view = (0, util_1.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
@@ -112,7 +114,7 @@ function modelFactory(configSchema) {
         afterAttach() {
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
                 const view = (0, util_1.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/dist/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/dist/ReferenceSequenceTrack/index.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const configSchema_1 = require("./configSchema");
-exports.default = (pluginManager) => {
+function ReferenceSequenceTrackF(pluginManager) {
     pluginManager.addTrackType(() => {
         const configSchema = (0, configSchema_1.createReferenceSeqTrackConfig)(pluginManager);
         return new TrackType_1.default({
@@ -16,4 +16,5 @@ exports.default = (pluginManager) => {
             stateModel: (0, models_1.createBaseTrackModel)(pluginManager, 'ReferenceSequenceTrack', configSchema),
         });
     });
-};
+}
+exports.default = ReferenceSequenceTrackF;

package/dist/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/dist/SequenceSearchAdapter/SequenceSearchAdapter.js

@@ -5,7 +5,7 @@ const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const util_1 = require("@jbrowse/core/util");
 const operators_1 = require("rxjs/operators");
 const rxjs_2 = require("rxjs");
-class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
+class SequenceSearchAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async configure() {
         var _a;
         const adapter = await ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, this.getConf('sequenceAdapter')));
@@ -22,10 +22,9 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
         return (0, rxjs_1.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;
@@ -46,13 +45,14 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
                 if (searchForward) {
                     const matches = residues.matchAll(re);
                     for (const match of matches) {
-                        const s = queryStart + (match.index || 0);
-                        if ((0, util_1.doesIntersect2)(s, s + search.length, query.start, query.end)) {
+                        const s = queryStart + match.index;
+                        const e = queryStart + match.index + match[0].length;
+                        if ((0, util_1.doesIntersect2)(s, e, query.start, query.end)) {
                             observer.next(new util_1.SimpleFeature({
-                                uniqueId: `${this.id}-match-${s}-p`,
+                                uniqueId: `${this.id}-${s}-${match[0]}-pos`,
                                 refName: query.refName,
                                 start: s,
-                                end: s + match[0].length,
+                                end: e,
                                 name: match[0],
                                 strand: 1,
                             }));
@@ -62,14 +62,15 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
                 if (searchReverse) {
                     const matches = (0, util_1.revcom)(residues).matchAll(re);
                     for (const match of matches) {
-                        const s = queryEnd - (match.index || 0);
-                        if ((0, util_1.doesIntersect2)(s, s + search.length, query.start, query.end)) {
+                        const e = queryEnd - match.index;
+                        const s = queryEnd - match.index - match[0].length;
+                        if ((0, util_1.doesIntersect2)(s, e, query.start, query.end)) {
                             observer.next(new util_1.SimpleFeature({
-                                uniqueId: `${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,
                             }));
                         }
@@ -81,4 +82,4 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     freeResources() { }
 }
-exports.default = default_1;
+exports.default = SequenceSearchAdapter;

package/dist/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/dist/SequenceSearchAdapter/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 SequenceSearchAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'SequenceSearchAdapter',
         displayName: 'Sequence search adapter',
@@ -38,4 +38,5 @@ exports.default = (pluginManager) => {
         configSchema: configSchema_1.default,
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./SequenceSearchAdapter'))).then(r => r.default),
     }));
-};
+}
+exports.default = SequenceSearchAdapterF;

package/dist/TwoBitAdapter/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 TwoBitAdapterF(pluginManager: PluginManager): void;