@jbrowse/plugin-sequence 1.7.11 → 2.0.0

package/dist/referenceSeqTrackConfig.js

@@ -1,93 +1,78 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.createReferenceSeqTrackConfig = createReferenceSeqTrackConfig;
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
-
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
-
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.createReferenceSeqTrackConfig = void 0;
+/* eslint-disable @typescript-eslint/no-explicit-any */
+var mobx_state_tree_1 = require("mobx-state-tree");
+var configuration_1 = require("@jbrowse/core/configuration");
 /*
 Note: this is primarily a copy of createBaseTrackConfig, except with a subset
 of the config slots, to avoid including fields that don't make sense for the
 ReferenceSequenceTrack
 */
 function createReferenceSeqTrackConfig(pluginManager) {
-  return (0, _configuration.ConfigurationSchema)('ReferenceSequenceTrack', {
-    adapter: pluginManager.pluggableConfigSchemaType('adapter'),
-    displays: _mobxStateTree.types.array(pluginManager.pluggableConfigSchemaType('display')),
-    name: {
-      type: 'string',
-      description: 'optional track name',
-      defaultValue: ''
-    },
-    metadata: {
-      type: 'frozen',
-      description: 'anything to add about this track',
-      defaultValue: {}
-    }
-  }, {
-    preProcessSnapshot: function preProcessSnapshot(s) {
-      var snap = JSON.parse(JSON.stringify(s));
-      var displayTypes = new Set();
-      var _snap$displays = snap.displays,
-          displays = _snap$displays === void 0 ? [] : _snap$displays;
-
-      if (snap.trackId !== 'placeholderId') {
-        // Gets the displays on the track snapshot and the possible displays
-        // from the track type and adds any missing possible displays to the
-        // snapshot
-        displays.forEach(function (d) {
-          return d && displayTypes.add(d.type);
-        });
-        var trackType = pluginManager.getTrackType(snap.type);
-        trackType.displayTypes.forEach(function (displayType) {
-          if (!displayTypes.has(displayType.name)) {
-            displays.push({
-              displayId: "".concat(snap.trackId, "-").concat(displayType.name),
-              type: displayType.name
-            });
-          }
-        });
-      }
-
-      return _objectSpread(_objectSpread({}, snap), {}, {
-        displays: displays
-      });
-    },
-    explicitIdentifier: 'trackId',
-    explicitlyTyped: true,
-    actions: function actions(self) {
-      return {
-        addDisplayConf: function addDisplayConf(displayConf) {
-          var type = displayConf.type;
-
-          if (!type) {
-            throw new Error("unknown display type ".concat(type));
-          }
-
-          var display = self.displays.find(function (d) {
-            return d && d.displayId === displayConf.displayId;
-          });
-
-          if (display) {
-            return display;
-          }
-
-          var length = self.displays.push(displayConf);
-          return self.displays[length - 1];
-        }
-      };
-    }
-  });
-}
+    return (0, configuration_1.ConfigurationSchema)('ReferenceSequenceTrack', {
+        adapter: pluginManager.pluggableConfigSchemaType('adapter'),
+        displays: mobx_state_tree_1.types.array(pluginManager.pluggableConfigSchemaType('display')),
+        name: {
+            type: 'string',
+            description: 'optional track name',
+            defaultValue: '',
+        },
+        metadata: {
+            type: 'frozen',
+            description: 'anything to add about this track',
+            defaultValue: {},
+        },
+    }, {
+        preProcessSnapshot: function (s) {
+            var snap = JSON.parse(JSON.stringify(s));
+            var displayTypes = new Set();
+            var _a = snap.displays, displays = _a === void 0 ? [] : _a;
+            if (snap.trackId !== 'placeholderId') {
+                // Gets the displays on the track snapshot and the possible displays
+                // from the track type and adds any missing possible displays to the
+                // snapshot
+                displays.forEach(function (d) { return d && displayTypes.add(d.type); });
+                var trackType = pluginManager.getTrackType(snap.type);
+                trackType.displayTypes.forEach(function (displayType) {
+                    if (!displayTypes.has(displayType.name)) {
+                        displays.push({
+                            displayId: "".concat(snap.trackId, "-").concat(displayType.name),
+                            type: displayType.name,
+                        });
+                    }
+                });
+            }
+            return __assign(__assign({}, snap), { displays: displays });
+        },
+        explicitIdentifier: 'trackId',
+        explicitlyTyped: true,
+        actions: function (self) { return ({
+            addDisplayConf: function (displayConf) {
+                var type = displayConf.type;
+                if (!type) {
+                    throw new Error("unknown display type ".concat(type));
+                }
+                var display = self.displays.find(function (d) { return d && d.displayId === displayConf.displayId; });
+                if (display) {
+                    return display;
+                }
+                var length = self.displays.push(displayConf);
+                return self.displays[length - 1];
+            },
+        }); },
+    });
+}
+exports.createReferenceSeqTrackConfig = createReferenceSeqTrackConfig;
+//# sourceMappingURL=referenceSeqTrackConfig.js.map

package/dist/referenceSeqTrackConfig.js.map

@@ -0,0 +1 @@
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package/esm/BgzipFastaAdapter/BgzipFastaAdapter.d.ts

@@ -0,0 +1,7 @@
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+export default class extends IndexedFasta {
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+}

package/esm/BgzipFastaAdapter/BgzipFastaAdapter.js

@@ -0,0 +1,28 @@
+import { BgzipIndexedFasta } from '@gmod/indexedfasta';
+import { openLocation } from '@jbrowse/core/util/io';
+import { readConfObject } from '@jbrowse/core/configuration';
+import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter';
+export default class extends IndexedFasta {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        const fastaLocation = readConfObject(config, 'fastaLocation');
+        const faiLocation = readConfObject(config, 'faiLocation');
+        const gziLocation = readConfObject(config, 'gziLocation');
+        if (!fastaLocation) {
+            throw new Error('must provide fastaLocation');
+        }
+        if (!faiLocation) {
+            throw new Error('must provide faiLocation');
+        }
+        if (!gziLocation) {
+            throw new Error('must provide gziLocation');
+        }
+        const fastaOpts = {
+            fasta: openLocation(fastaLocation, this.pluginManager),
+            fai: openLocation(faiLocation, this.pluginManager),
+            gzi: openLocation(gziLocation, this.pluginManager),
+        };
+        this.fasta = new BgzipIndexedFasta(fastaOpts);
+    }
+}
+//# sourceMappingURL=BgzipFastaAdapter.js.map

package/esm/BgzipFastaAdapter/BgzipFastaAdapter.js.map

@@ -0,0 +1 @@
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package/esm/BgzipFastaAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/BgzipFastaAdapter/configSchema.js

@@ -0,0 +1,30 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('BgzipFastaAdapter', {
+    fastaLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/seq.fa.gz', locationType: 'UriLocation' },
+    },
+    faiLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/seq.fa.gz.fai',
+            locationType: 'UriLocation',
+        },
+    },
+    metadataLocation: {
+        description: 'Optional metadata file',
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/fa.metadata.yaml',
+            locationType: 'UriLocation',
+        },
+    },
+    gziLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/seq.fa.gz.gzi',
+            locationType: 'UriLocation',
+        },
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/BgzipFastaAdapter/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/BgzipFastaAdapter/index.d.ts

@@ -0,0 +1 @@
+export { default as configSchema } from './configSchema';

package/esm/BgzipFastaAdapter/index.js

@@ -0,0 +1,2 @@
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/BgzipFastaAdapter/index.js.map

@@ -0,0 +1 @@
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package/esm/ChromSizesAdapter/ChromSizesAdapter.d.ts

@@ -0,0 +1,19 @@
+import { RegionsAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Instance } from 'mobx-state-tree';
+import MyConfigSchema from './configSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+export default class extends BaseAdapter implements RegionsAdapter {
+    protected refSeqs: Promise<Record<string, number>>;
+    protected source: string;
+    constructor(config: Instance<typeof MyConfigSchema>, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    private init;
+    getRegions(): Promise<{
+        refName: string;
+        start: number;
+        end: number;
+    }[]>;
+    getFeatures(): void;
+    getHeader(): {};
+    freeResources(): void;
+}

package/esm/ChromSizesAdapter/ChromSizesAdapter.js

@@ -0,0 +1,45 @@
+import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { readConfObject } from '@jbrowse/core/configuration';
+export default class extends BaseAdapter {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        const chromSizesLocation = readConfObject(config, 'chromSizesLocation');
+        if (!chromSizesLocation) {
+            throw new Error('must provide chromSizesLocation');
+        }
+        const file = openLocation(chromSizesLocation, this.pluginManager);
+        this.source = file.toString();
+        this.refSeqs = this.init(file);
+    }
+    async init(file) {
+        const data = await file.readFile('utf8');
+        const refSeqs = {};
+        if (!data.length) {
+            throw new Error(`Could not read file ${file.toString()}`);
+        }
+        data.split('\n').forEach((line) => {
+            if (line.length) {
+                const [name, length] = line.split('\t');
+                refSeqs[name] = +length;
+            }
+        });
+        return refSeqs;
+    }
+    async getRegions() {
+        const refSeqs = await this.refSeqs;
+        return Object.keys(refSeqs).map(refName => ({
+            refName,
+            start: 0,
+            end: refSeqs[refName],
+        }));
+    }
+    getFeatures() {
+        throw new Error('sequence not available');
+    }
+    getHeader() {
+        return {};
+    }
+    freeResources( /* { region } */) { }
+}
+//# sourceMappingURL=ChromSizesAdapter.js.map

package/esm/ChromSizesAdapter/ChromSizesAdapter.js.map

@@ -0,0 +1 @@
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package/esm/ChromSizesAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/ChromSizesAdapter/configSchema.js

@@ -0,0 +1,11 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('ChromSizesAdapter', {
+    chromSizesLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/species.chrom.sizes',
+            locationType: 'UriLocation',
+        },
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/ChromSizesAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/ChromSizesAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,mBAAmB,EACnB;IACE,kBAAkB,EAAE;QAClB,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,8BAA8B;YACnC,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/esm/ChromSizesAdapter/index.d.ts

@@ -0,0 +1 @@
+export { default as configSchema } from './configSchema';

package/esm/ChromSizesAdapter/index.js

@@ -0,0 +1,2 @@
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/ChromSizesAdapter/index.js.map

@@ -0,0 +1 @@
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package/esm/DivSequenceRenderer/components/DivSequenceRendering.d.ts

@@ -0,0 +1,21 @@
+/// <reference types="react" />
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { Region } from '@jbrowse/core/util/types';
+interface MyProps {
+    exportSVG?: {
+        rasterizeLayers: boolean;
+    };
+    features: Map<string, Feature>;
+    regions: Region[];
+    bpPerPx: number;
+    config: AnyConfigurationModel;
+    highResolutionScaling: number;
+    theme: any;
+    showForward: boolean;
+    showReverse: boolean;
+    showTranslation: boolean;
+}
+declare function Sequence(props: MyProps): JSX.Element;
+declare const _default: typeof Sequence;
+export default _default;

package/esm/DivSequenceRenderer/components/DivSequenceRendering.js

@@ -0,0 +1,97 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import React from 'react';
+import { contrastingTextColor } from '@jbrowse/core/util/color';
+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);
+    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() });
+    }
+    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.palette.startCodon
+                    : defaultStops.includes(codon)
+                        ? theme.palette.stopCodon
+                        : map[Math.abs(frame)] }),
+            render ? (React.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle" }, letter)) : null));
+    })));
+}
+function DNA(props) {
+    const { bpPerPx, region, feature, theme, height, seq, y } = props;
+    const render = 1 / bpPerPx >= 12;
+    const [leftPx, rightPx] = bpSpanPx(feature.get('start'), feature.get('end'), region, bpPerPx);
+    const reverse = region.reversed;
+    const len = feature.get('end') - feature.get('start');
+    const w = Math.max((rightPx - leftPx) / len, 0.8);
+    return (React.createElement(React.Fragment, null, seq.split('').map((letter, index) => {
+        const color = theme.palette.bases[letter.toUpperCase()];
+        const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
+        return (React.createElement(React.Fragment, { key: index },
+            React.createElement("rect", { x: x, y: y, width: w, height: height, fill: color ? color.main : '#aaa', stroke: render ? '#555' : 'none' }),
+            render ? (React.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fill: color ? contrastingTextColor(color.main) : 'black' }, letter)) : null));
+    })));
+}
+const SequenceSVG = ({ regions, theme: configTheme, features = new Map(), showReverse, showForward, showTranslation, bpPerPx, }) => {
+    const [region] = regions;
+    const theme = createJBrowseTheme(configTheme);
+    const codonTable = generateCodonTable(defaultCodonTable);
+    const height = 20;
+    const [feature] = [...features.values()];
+    if (!feature) {
+        return null;
+    }
+    const seq = feature.get('seq');
+    if (!seq) {
+        return null;
+    }
+    // incrementer for the y-position of the current sequence being rendered
+    // (applies to both translation rows and dna rows)
+    let currY = -20;
+    return (React.createElement(React.Fragment, null,
+        showTranslation && (region.reversed ? showReverse : showForward)
+            ? [2, 1, 0].map(index => (React.createElement(Translation, { key: `translation-${index}`, seq: seq, y: (currY += 20), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: height, reverse: region.reversed })))
+            : null,
+        showForward ? (React.createElement(DNA, { height: height, y: (currY += 20), feature: feature, region: region, seq: region.reversed ? complement(seq) : seq, bpPerPx: bpPerPx, theme: theme })) : null,
+        showReverse ? (React.createElement(DNA, { height: height, y: (currY += 20), feature: feature, region: region, seq: region.reversed ? seq : complement(seq), bpPerPx: bpPerPx, theme: theme })) : null,
+        showTranslation && (region.reversed ? showForward : showReverse)
+            ? [0, -1, -2].map(index => (React.createElement(Translation, { key: `rev-translation-${index}`, seq: seq, y: (currY += 20), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: height, reverse: !region.reversed })))
+            : null));
+};
+const 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: { width, height: totalHeight } }, children));
+};
+function Sequence(props) {
+    const { regions, bpPerPx } = props;
+    const [region] = regions;
+    const width = (region.end - region.start) / bpPerPx;
+    const totalHeight = 200;
+    return (React.createElement(Wrapper, { ...props, totalHeight: totalHeight, width: width },
+        React.createElement(SequenceSVG, { ...props })));
+}
+export default observer(Sequence);
+//# sourceMappingURL=DivSequenceRendering.js.map

package/esm/DivSequenceRenderer/components/DivSequenceRendering.js.map

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package/esm/DivSequenceRenderer/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/DivSequenceRenderer/configSchema.js

@@ -0,0 +1,9 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('DivSequenceRenderer', {
+    height: {
+        type: 'number',
+        description: 'height in pixels of each line of sequence',
+        defaultValue: 16,
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/DivSequenceRenderer/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/DivSequenceRenderer/index.d.ts

@@ -0,0 +1,2 @@
+export { default as ReactComponent } from './components/DivSequenceRendering';
+export { default as configSchema } from './configSchema';

package/esm/DivSequenceRenderer/index.js

@@ -0,0 +1,3 @@
+export { default as ReactComponent } from './components/DivSequenceRendering';
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/DivSequenceRenderer/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/DivSequenceRenderer/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,cAAc,EAAE,MAAM,mCAAmC,CAAA;AAC7E,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}

package/esm/GCContentAdapter/GCContentAdapter.d.ts

@@ -0,0 +1,23 @@
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+export default class extends BaseFeatureDataAdapter {
+    private windowSize;
+    private windowDelta;
+    private gcMode;
+    static capabilities: string[];
+    configure(): Promise<BaseFeatureDataAdapter>;
+    getRefNames(): Promise<string[]>;
+    /**
+     * Fetch features for a certain region
+     * @param param -
+     * @returns Observable of Feature objects in the region
+     */
+    getFeatures(query: Region, opts: BaseOptions): import("rxjs").Observable<Feature>;
+    /**
+     * called to provide a hint that data tied to a certain region
+     * will not be needed for the forseeable future and can be purged
+     * from caches, etc
+     */
+    freeResources(): void;
+}