@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/RcsbResidueChartComponent.js

@@ -1,36 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.RcsbResidueChartComponent = void 0;
-const tslib_1 = require("tslib");
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = tslib_1.__importDefault(require("react"));
-const GroupChartLayout_1 = require("../RcsbGroupChart/GroupChartLayout");
-const ResidueChartTools_1 = require("./ResidueChartTools/ResidueChartTools");
-const classes = tslib_1.__importStar(require("../../../scss/bootstrap-group-display.module.scss"));
-const FacetTools_1 = require("../../../RcsbSeacrh/FacetTools");
-class RcsbResidueChartComponent extends react_1.default.Component {
-    render() {
-        var _a, _b;
-        if ((_b = (_a = this.state) === null || _a === void 0 ? void 0 : _a.layout) === null || _b === void 0 ? void 0 : _b.flat().filter((e) => { var _a, _b; return ((_b = (_a = this.state) === null || _a === void 0 ? void 0 : _a.chartMap) === null || _b === void 0 ? void 0 : _b.get(e)); })) {
-            return ((0, jsx_runtime_1.jsx)("div", { className: classes.bootstrapGroupComponentScope, children: (0, jsx_runtime_1.jsx)(GroupChartLayout_1.GroupChartLayout, { layout: this.state.layout, chartMap: this.state.chartMap }) }));
-        }
-        return (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, {});
-    }
-    componentDidMount() {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            yield this.updateState();
-        });
-    }
-    updateState() {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            const charts = (yield (yield ResidueChartTools_1.ResidueChartTools.getResidueDistribution(this.props)))
-                .filter(chart => (!this.props.facetLayoutGrid || this.props.facetLayoutGrid.includes(chart.attribute)))
-                .map(ch => { var _a; return FacetTools_1.FacetTools.addChartDisplayConfig(ch, (_a = this.props.chartDisplayConfig) !== null && _a !== void 0 ? _a : {}); });
-            this.setState({
-                layout: charts.map(c => c.attribute),
-                chartMap: charts.reduce((prev, curr) => (prev.set(curr.attribute, [curr])), new Map())
-            });
-        });
-    }
-}
-exports.RcsbResidueChartComponent = RcsbResidueChartComponent;

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/DistributionChartFactoryImpl/DistributionChartFactory.d.ts

@@ -1,8 +0,0 @@
-import { DistributionChartFactoryInterface, ResidueDistributionInterface } from "../ResidueDistributionFactoryInterface";
-import { RcsbChartInterface } from "../../../../../RcsbSeacrh/FacetTools";
-import { RcsbDistributionConfig } from "../../../../../RcsbAnnotationConfig/RcsbDistributionConfig";
-export declare class DistributionChartFactory implements DistributionChartFactoryInterface {
-    private readonly distributionConfig;
-    constructor(distributionConfig?: RcsbDistributionConfig);
-    getChart(residueDistribution: ResidueDistributionInterface): RcsbChartInterface;
-}

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/DistributionChartFactoryImpl/DistributionChartFactory.js

@@ -1,38 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.DistributionChartFactory = void 0;
-const RcsbDistributionConfig_1 = require("../../../../../RcsbAnnotationConfig/RcsbDistributionConfig");
-const Operator_1 = require("../../../../../RcsbUtils/Helpers/Operator");
-const ChartConfigInterface_1 = require("@rcsb/rcsb-charts/lib/RcsbChartComponent/ChartConfigInterface");
-class DistributionChartFactory {
-    constructor(distributionConfig) {
-        this.distributionConfig = distributionConfig !== null && distributionConfig !== void 0 ? distributionConfig : new RcsbDistributionConfig_1.RcsbDistributionConfig();
-    }
-    getChart(residueDistribution) {
-        var _a, _b;
-        const sort = (_a = this.distributionConfig.getBlockConfig(residueDistribution.attribute)) === null || _a === void 0 ? void 0 : _a.sort;
-        const axisLabel = (_b = this.distributionConfig.getBlockConfig(residueDistribution.attribute)) === null || _b === void 0 ? void 0 : _b.axisLabel;
-        return {
-            chartType: ChartConfigInterface_1.ChartType.barplot,
-            attribute: residueDistribution.attribute,
-            attributeName: residueDistribution.attribute,
-            contentType: "number",
-            data: residueDistribution.buckets.map(b => ({
-                label: b.label,
-                population: b.residueSet.size,
-                objectConfig: {
-                    color: b.color,
-                    objectId: b.id
-                }
-            })),
-            title: residueDistribution.title,
-            chartConfig: {
-                sort: sort ? (a, b) => (sort.findIndex(x => x === a.x) - sort.findIndex(x => x === b.x)) : undefined,
-                tooltipText: (d) => (`${Operator_1.Operator.digitGrouping(d.y)} residues`),
-                axisLabel,
-                domainEmptyBins: true
-            }
-        };
-    }
-}
-exports.DistributionChartFactory = DistributionChartFactory;

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryImpl/MultipleTrackDistributionFactory.d.ts

@@ -1,8 +0,0 @@
-import { ResidueDistributionFactoryInterface, ResidueDistributionInterface } from "../ResidueDistributionFactoryInterface";
-import { TrackManagerInterface } from "../../../../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/TrackManagerInterface";
-import { RcsbDistributionConfig } from "../../../../../RcsbAnnotationConfig/RcsbDistributionConfig";
-export declare class MultipleTrackDistributionFactory implements ResidueDistributionFactoryInterface<[string, number]> {
-    private readonly distributionConfig;
-    constructor(distributionConfig?: RcsbDistributionConfig);
-    getDistribution(tracks: TrackManagerInterface[], blockType: string, numberResidues: number): ResidueDistributionInterface;
-}

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryImpl/MultipleTrackDistributionFactory.js

@@ -1,36 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.MultipleTrackDistributionFactory = void 0;
-const RcsbDistributionConfig_1 = require("../../../../../RcsbAnnotationConfig/RcsbDistributionConfig");
-const lodash_1 = require("lodash");
-const Assertions_1 = require("../../../../../RcsbUtils/Helpers/Assertions");
-var assertDefined = Assertions_1.Assertions.assertDefined;
-class MultipleTrackDistributionFactory {
-    constructor(distributionConfig) {
-        this.distributionConfig = distributionConfig !== null && distributionConfig !== void 0 ? distributionConfig : new RcsbDistributionConfig_1.RcsbDistributionConfig();
-    }
-    getDistribution(tracks, blockType, numberResidues) {
-        const undefResidues = new Set((0, lodash_1.range)(1, numberResidues + 1));
-        const blockConfig = this.distributionConfig.getBlockConfig(blockType);
-        assertDefined(blockConfig);
-        const undefTrack = blockConfig.undefTrack;
-        return {
-            attribute: blockConfig.type,
-            title: blockConfig.title,
-            buckets: tracks.map(track => {
-                const trackConfig = this.distributionConfig.getTrackConfig(track.getId());
-                assertDefined(trackConfig), assertDefined(trackConfig.label), assertDefined(trackConfig === null || trackConfig === void 0 ? void 0 : trackConfig.color);
-                return {
-                    label: trackConfig.label,
-                    color: trackConfig.color,
-                    id: trackConfig.type,
-                    residueSet: new Set(track.values().reduce((prev, curr) => { var _a; return (prev.concat((0, lodash_1.range)(curr.begin, ((_a = curr.end) !== null && _a !== void 0 ? _a : curr.begin) + 1))); }, []).map(n => {
-                        undefResidues.delete(n);
-                        return n;
-                    }))
-                };
-            }).concat(undefTrack && undefResidues.size > 0 ? [Object.assign(Object.assign({}, undefTrack), { residueSet: undefResidues })] : [])
-        };
-    }
-}
-exports.MultipleTrackDistributionFactory = MultipleTrackDistributionFactory;

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryImpl/NumericalTrackDistributionFactory.d.ts

@@ -1,8 +0,0 @@
-import { ResidueDistributionFactoryInterface, ResidueDistributionInterface } from "../ResidueDistributionFactoryInterface";
-import { TrackManagerInterface } from "../../../../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/TrackManagerInterface";
-import { RcsbDistributionConfig } from "../../../../../RcsbAnnotationConfig/RcsbDistributionConfig";
-export declare class NumericalTrackDistributionFactory implements ResidueDistributionFactoryInterface<[string, number]> {
-    private readonly distributionConfig;
-    constructor(distributionConfig?: RcsbDistributionConfig);
-    getDistribution(tracks: [TrackManagerInterface], blockType: string, numberResidues: number): ResidueDistributionInterface;
-}

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryImpl/NumericalTrackDistributionFactory.js

@@ -1,41 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.NumericalTrackDistributionFactory = void 0;
-const RcsbDistributionConfig_1 = require("../../../../../RcsbAnnotationConfig/RcsbDistributionConfig");
-const lodash_1 = require("lodash");
-const Assertions_1 = require("../../../../../RcsbUtils/Helpers/Assertions");
-var assertDefined = Assertions_1.Assertions.assertDefined;
-class NumericalTrackDistributionFactory {
-    constructor(distributionConfig) {
-        this.distributionConfig = distributionConfig !== null && distributionConfig !== void 0 ? distributionConfig : new RcsbDistributionConfig_1.RcsbDistributionConfig();
-    }
-    getDistribution(tracks, blockType, numberResidues) {
-        var _a;
-        const track = tracks[0];
-        const numericalCategories = (_a = this.distributionConfig.getTrackConfig(track.getId())) === null || _a === void 0 ? void 0 : _a.numericalCategories;
-        assertDefined(numericalCategories);
-        const bucketMap = new Map();
-        const undefResidues = new Set((0, lodash_1.range)(1, numberResidues + 1));
-        numericalCategories.categories.forEach(category => {
-            const label = category.label;
-            bucketMap.set(label, Object.assign(Object.assign({}, category), { residueSet: new Set() }));
-        });
-        track.forEach(ann => {
-            var _a;
-            let index = numericalCategories.thresholds.findIndex((x) => { var _a; return x >= ((_a = ann.value) !== null && _a !== void 0 ? _a : Number.MAX_SAFE_INTEGER); });
-            if (index < 0)
-                index = numericalCategories.thresholds.length;
-            const label = numericalCategories.categories[index].label;
-            (_a = bucketMap.get(label)) === null || _a === void 0 ? void 0 : _a.residueSet.add(ann.begin);
-            undefResidues.delete(ann.begin);
-        });
-        const bc = this.distributionConfig.getBlockConfig(blockType);
-        assertDefined(bc);
-        return {
-            attribute: bc.type,
-            title: bc.title,
-            buckets: Array.from(bucketMap.values()).concat(bc.undefTrack && undefResidues.size > 0 ? [Object.assign(Object.assign({}, bc.undefTrack), { residueSet: undefResidues })] : [])
-        };
-    }
-}
-exports.NumericalTrackDistributionFactory = NumericalTrackDistributionFactory;

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryImpl/TrackDistributionFactory.d.ts

@@ -1,10 +0,0 @@
-import { ResidueDistributionFactoryInterface, ResidueDistributionInterface } from "../ResidueDistributionFactoryInterface";
-import { RcsbDistributionConfig } from "../../../../../RcsbAnnotationConfig/RcsbDistributionConfig";
-import { TrackManagerInterface } from "../../../../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/TrackManagerInterface";
-export declare class TrackDistributionFactory implements ResidueDistributionFactoryInterface<[string, number]> {
-    private readonly distributionConfig;
-    private readonly multipleTrackDistributionFactory;
-    private readonly numericalTrackDistributionFactory;
-    constructor(distributionConfig?: RcsbDistributionConfig);
-    getDistribution(tracks: TrackManagerInterface[], blockType: string, numberResidues: number): ResidueDistributionInterface | undefined;
-}

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryImpl/TrackDistributionFactory.js

@@ -1,25 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.TrackDistributionFactory = void 0;
-const RcsbDistributionConfig_1 = require("../../../../../RcsbAnnotationConfig/RcsbDistributionConfig");
-const MultipleTrackDistributionFactory_1 = require("./MultipleTrackDistributionFactory");
-const NumericalTrackDistributionFactory_1 = require("./NumericalTrackDistributionFactory");
-class TrackDistributionFactory {
-    constructor(distributionConfig) {
-        this.distributionConfig = distributionConfig !== null && distributionConfig !== void 0 ? distributionConfig : new RcsbDistributionConfig_1.RcsbDistributionConfig();
-        this.multipleTrackDistributionFactory = new MultipleTrackDistributionFactory_1.MultipleTrackDistributionFactory(distributionConfig);
-        this.numericalTrackDistributionFactory = new NumericalTrackDistributionFactory_1.NumericalTrackDistributionFactory(distributionConfig);
-    }
-    getDistribution(tracks, blockType, numberResidues) {
-        var _a;
-        switch ((_a = this.distributionConfig.getBlockConfig(blockType)) === null || _a === void 0 ? void 0 : _a.contentType) {
-            case "binary":
-                return this.multipleTrackDistributionFactory.getDistribution(tracks, blockType, numberResidues);
-            case "numerical":
-                return this.numericalTrackDistributionFactory.getDistribution([tracks[0]], blockType, numberResidues);
-            default:
-                return undefined;
-        }
-    }
-}
-exports.TrackDistributionFactory = TrackDistributionFactory;

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryInterface.d.ts

@@ -1,24 +0,0 @@
-import { TrackManagerInterface } from "../../../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/TrackManagerInterface";
-import { RcsbChartInterface } from "../../../../RcsbSeacrh/FacetTools";
-export interface ResidueDistributionInterface {
-    attribute: string;
-    title: string;
-    buckets: ResidueBucket[];
-}
-export interface ResidueBucket {
-    label: string;
-    id: string;
-    color: string;
-    residueSet: Set<number>;
-}
-export interface TrackBlockFactoryInterface<S = {}> {
-    getTrackBlocks(tracks: TrackManagerInterface[]): ({
-        tracks: TrackManagerInterface[];
-    } & S)[];
-}
-export interface ResidueDistributionFactoryInterface<T extends any[] = []> {
-    getDistribution(tracks: TrackManagerInterface[], ...args: T): ResidueDistributionInterface | undefined;
-}
-export interface DistributionChartFactoryInterface {
-    getChart(residueDistribution: ResidueDistributionInterface): RcsbChartInterface;
-}

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryInterface.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/TrackBlockFactoryImpl/TrackBlockFactory.d.ts

@@ -1,14 +0,0 @@
-import { TrackBlockFactoryInterface } from "../ResidueDistributionFactoryInterface";
-import { TrackManagerInterface } from "../../../../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/TrackManagerInterface";
-import { RcsbDistributionConfig } from "../../../../../RcsbAnnotationConfig/RcsbDistributionConfig";
-export declare class TrackBlockFactory implements TrackBlockFactoryInterface<{
-    blockType: string;
-}> {
-    private readonly distributionConfig;
-    constructor(distributionConfig?: RcsbDistributionConfig);
-    getTrackBlocks(tracks: TrackManagerInterface[]): ({
-        tracks: TrackManagerInterface[];
-    } & {
-        blockType: string;
-    })[];
-}

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/TrackBlockFactoryImpl/TrackBlockFactory.js

@@ -1,23 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.TrackBlockFactory = void 0;
-const RcsbDistributionConfig_1 = require("../../../../../RcsbAnnotationConfig/RcsbDistributionConfig");
-class TrackBlockFactory {
-    constructor(distributionConfig) {
-        this.distributionConfig = distributionConfig !== null && distributionConfig !== void 0 ? distributionConfig : new RcsbDistributionConfig_1.RcsbDistributionConfig();
-    }
-    getTrackBlocks(tracks) {
-        const trackMap = new Map();
-        tracks.forEach(t => {
-            var _a;
-            const blockType = this.distributionConfig.getBlockType(t.getId());
-            if (!blockType)
-                return;
-            if (!trackMap.has(blockType))
-                trackMap.set(blockType, []);
-            (_a = trackMap.get(blockType)) === null || _a === void 0 ? void 0 : _a.push(t);
-        });
-        return Array.from(trackMap.entries()).map(e => ({ blockType: e[0], tracks: e[1] }));
-    }
-}
-exports.TrackBlockFactory = TrackBlockFactory;

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartTools/Helper.d.ts

@@ -1,4 +0,0 @@
-import { RcsbChartInterface } from "../../../../RcsbSeacrh/FacetTools";
-export declare namespace Helper {
-    function mergeCharts(charts: RcsbChartInterface[]): RcsbChartInterface[];
-}

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartTools/Helper.js

@@ -1,25 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.Helper = void 0;
-const Assertions_1 = require("../../../../RcsbUtils/Helpers/Assertions");
-var Helper;
-(function (Helper) {
-    var assertDefined = Assertions_1.Assertions.assertDefined;
-    function mergeCharts(charts) {
-        const attributes = Array.from(new Set(charts.map(ch => ch.attribute)));
-        return attributes.map(attr => (mergeChartData(charts.filter(ch => ch.attribute == attr))));
-    }
-    Helper.mergeCharts = mergeCharts;
-    function mergeChartData(charts) {
-        return Object.assign(Object.assign({}, charts[0]), { data: mergeData(charts.map(ch => ch.data).flat()) });
-    }
-    function mergeData(data) {
-        const labels = Array.from(new Set(data.map(d => d.label)));
-        return labels.map(label => {
-            var _a, _b;
-            const d = data.find(d => d.label === label);
-            assertDefined(d);
-            return Object.assign(Object.assign({}, d), { population: (_b = (_a = data.filter(d => d.label === label)) === null || _a === void 0 ? void 0 : _a.reduce((prev, curr) => (prev + curr.population), 0)) !== null && _b !== void 0 ? _b : 0 });
-        });
-    }
-})(Helper || (exports.Helper = Helper = {}));

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartTools/ResidueChartTools.d.ts

@@ -1,8 +0,0 @@
-import { RcsbChartInterface } from "../../../../RcsbSeacrh/FacetTools";
-export interface ResidueChartInterface {
-    granularity: "entry" | "assembly" | "instance" | "entity";
-    rcsbId: string;
-}
-export declare namespace ResidueChartTools {
-    function getResidueDistribution(residueChart: ResidueChartInterface): Promise<Promise<RcsbChartInterface[]>>;
-}

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartTools/ResidueChartTools.js

@@ -1,90 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.ResidueChartTools = void 0;
-const tslib_1 = require("tslib");
-const AnnotationCollector_1 = require("../../../../RcsbCollectTools/AnnotationCollector/AnnotationCollector");
-const GqlTypes_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes");
-const RcsbFvInterface_1 = require("../../../../RcsbFvWeb/RcsbFvModule/RcsbFvInterface");
-const rcm = tslib_1.__importStar(require("../../../../RcsbAnnotationConfig/RcsbResidueConfig.ac.json"));
-const AnnotationBlockManager_1 = require("../../../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationBlockManager");
-const AnnotationTrackManager_1 = require("../../../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationTrackManager");
-const RcsbAnnotationConfig_1 = require("../../../../RcsbAnnotationConfig/RcsbAnnotationConfig");
-const TrackBlockFactory_1 = require("../ResidueChartFactories/TrackBlockFactoryImpl/TrackBlockFactory");
-const TrackDistributionFactory_1 = require("../ResidueChartFactories/ResidueDistributionFactoryImpl/TrackDistributionFactory");
-const DistributionChartFactory_1 = require("../ResidueChartFactories/DistributionChartFactoryImpl/DistributionChartFactory");
-const AlignmentCollector_1 = require("../../../../RcsbCollectTools/AlignmentCollector/AlignmentCollector");
-const RcsbRequestContextManager_1 = require("../../../../RcsbRequest/RcsbRequestContextManager");
-const Helper_1 = require("./Helper");
-const Assertions_1 = require("../../../../RcsbUtils/Helpers/Assertions");
-var ResidueChartTools;
-(function (ResidueChartTools) {
-    var assertDefined = Assertions_1.Assertions.assertDefined;
-    function getResidueDistribution(residueChart) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            switch (residueChart.granularity) {
-                case "entry":
-                    return yield getEntryCharts(residueChart.rcsbId);
-                case "assembly":
-                    return [];
-                case "instance":
-                    return yield getInstanceCharts(residueChart.rcsbId);
-                case "entity":
-                    return [];
-            }
-        });
-    }
-    ResidueChartTools.getResidueDistribution = getResidueDistribution;
-    function getEntryCharts(entryId) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            const instanceIds = (yield RcsbRequestContextManager_1.rcsbRequestCtxManager.getEntryProperties(entryId)).map(e => Array.from(e.entityToInstance.values()).flat()).flat();
-            let charts = [];
-            for (const id of instanceIds) {
-                charts = charts.concat(yield getInstanceCharts(id));
-            }
-            return Helper_1.Helper.mergeCharts(charts);
-        });
-    }
-    function getInstanceCharts(instanceId) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            var _a, _b;
-            const alignmentRequestContext = {
-                queryId: instanceId,
-                from: GqlTypes_1.SequenceReference.PdbInstance,
-                to: GqlTypes_1.SequenceReference.PdbInstance
-            };
-            const alignmentResponse = yield alignmentCollector.collect(alignmentRequestContext);
-            const annotationsRequestContext = {
-                queryId: instanceId,
-                reference: GqlTypes_1.SequenceReference.PdbInstance,
-                sources: [GqlTypes_1.Source.PdbEntity, GqlTypes_1.Source.PdbInstance, GqlTypes_1.Source.Uniprot, GqlTypes_1.Source.PdbInterface],
-                annotationGenerator: RcsbFvInterface_1.interfaceAnnotations,
-                annotationFilter: RcsbFvInterface_1.filter
-            };
-            return yield getCharts(annotationsRequestContext, yield annotationCollector.collect(annotationsRequestContext), (_b = (_a = alignmentResponse.query_sequence) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : -1);
-        });
-    }
-    function getCharts(annotationRequestContext, annotations, numberResidues) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            return processAnnotations({
-                annotations,
-                annotationBlockManager: new AnnotationBlockManager_1.AnnotationBlockManager(new AnnotationTrackManager_1.AnnotationTrackManagerFactory(), new RcsbAnnotationConfig_1.RcsbAnnotationConfig(rcm)),
-                annotationRequestContext,
-                trackBlockFactory: new TrackBlockFactory_1.TrackBlockFactory(),
-                residueDistributionFactory: new TrackDistributionFactory_1.TrackDistributionFactory(),
-                distributionChartFactory: new DistributionChartFactory_1.DistributionChartFactory(),
-                numberResidues
-            });
-        });
-    }
-    function processAnnotations(config) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            yield config.annotationBlockManager.setData(config.annotationRequestContext, config.annotations);
-            return config.trackBlockFactory.getTrackBlocks(config.annotationBlockManager.getTracks()).map(block => (config.residueDistributionFactory.getDistribution(block.tracks, block.blockType, config.numberResidues))).map(distribution => {
-                assertDefined(distribution);
-                return config.distributionChartFactory.getChart(distribution);
-            });
-        });
-    }
-    const annotationCollector = new AnnotationCollector_1.AnnotationCollector();
-    const alignmentCollector = new AlignmentCollector_1.AlignmentCollector();
-})(ResidueChartTools || (exports.ResidueChartTools = ResidueChartTools = {}));

package/lib/commonjs/RcsbQueries/Borrego/.graphqlconfig

@@ -1,15 +0,0 @@
-{
-  "name": "Untitled GraphQL Schema",
-  "schemaPath": "schema.graphql",
-  "extensions": {
-    "endpoints": {
-      "Default GraphQL Endpoint": {
-        "url": "https://1d-coordinates.rcsb.org/graphql",
-        "headers": {
-          "user-agent": "JS GraphQL"
-        },
-        "introspect": false
-      }
-    }
-  }
-}

package/lib/commonjs/RcsbQueries/Borrego/QueryAlignments.graphql

@@ -1,29 +0,0 @@
-query QueryAlignment($queryId: String!, $from: SequenceReference, $to:SequenceReference, $range:[Int]){
-    alignment(
-        queryId:$queryId
-        from:$from
-        to:$to
-        range:$range
-    ){
-        query_sequence
-        target_alignment {
-            target_id
-            orientation
-            target_sequence
-            coverage {
-                query_coverage
-                query_length
-                target_coverage
-                target_length
-            }
-            aligned_regions {
-                query_begin
-                query_end
-                target_begin
-                target_end
-                exon_shift
-            }
-        }
-
-    }
-}

package/lib/commonjs/RcsbQueries/Borrego/QueryAnnotations.graphql

@@ -1,40 +0,0 @@
-query QueryAnnotations($queryId: String!, $reference: SequenceReference, $sources:[Source], $range:[Int], $filters: [FilterInput]){
-    annotations(
-        queryId:$queryId
-        reference:$reference
-        sources:$sources
-        range:$range
-        filters:$filters
-    ){
-        source
-        target_id
-        target_identifiers{
-            target_id
-            entry_id
-            assembly_id
-            entity_id
-            asym_id
-            interface_id
-            interface_partner_index
-        }
-        features {
-            type
-            provenance_source
-            description
-            feature_id
-            name
-            value
-            feature_positions {
-                beg_seq_id
-                end_seq_id
-                beg_ori_id
-                end_ori_id
-                range_id
-                open_begin
-                open_end
-                value
-                values
-            }
-        }
-    }
-}

package/lib/commonjs/RcsbQueries/Borrego/QueryGroupAlignments.graphql

@@ -1,43 +0,0 @@
-query QueryGroupAlignment($group: GroupReference!, $groupId: String!, $filter: [String], $first: Int!, $after: String){
-    group_alignment(
-        group: $group
-        groupId: $groupId
-        filter: $filter
-    ){
-        alignment_length
-        alignment_logo{
-            symbol
-            value
-        }
-        query_sequence
-        target_alignment_subset(first: $first, after: $after) {
-            pageInfo{
-                startCursor
-                endCursor
-                hasNextPage
-                hasPreviousPage
-            }
-            edges{
-                node{
-                    target_id
-                    orientation
-                    target_sequence
-                    coverage {
-                        query_coverage
-                        query_length
-                        target_coverage
-                        target_length
-                    }
-                    aligned_regions {
-                        query_begin
-                        query_end
-                        target_begin
-                        target_end
-                        exon_shift
-                    }
-                }
-                cursor
-            }
-        }
-    }
-}

package/lib/commonjs/RcsbQueries/Borrego/QueryGroupAlignmentsNoLogo.graphql

@@ -1,39 +0,0 @@
-query QueryGroupAlignmentNoLogo($group: GroupReference!, $groupId: String!, $filter: [String], $first: Int!, $after: String){
-    group_alignment(
-        group: $group
-        groupId: $groupId
-        filter: $filter
-    ){
-        alignment_length
-        query_sequence
-        target_alignment_subset(first: $first, after: $after) {
-            pageInfo{
-                startCursor
-                endCursor
-                hasNextPage
-                hasPreviousPage
-            }
-            edges{
-                node{
-                    target_id
-                    orientation
-                    target_sequence
-                    coverage {
-                        query_coverage
-                        query_length
-                        target_coverage
-                        target_length
-                    }
-                    aligned_regions {
-                        query_begin
-                        query_end
-                        target_begin
-                        target_end
-                        exon_shift
-                    }
-                }
-                cursor
-            }
-        }
-    }
-}

package/lib/commonjs/RcsbQueries/Borrego/QueryGroupAnnotations.graphql

@@ -1,31 +0,0 @@
-query QueryGroupAnnotations($group: GroupReference!, $groupId: String!, $sources:[Source], $filters: [FilterInput], $histogram:Boolean){
-    group_annotations(
-        group:$group
-        groupId:$groupId
-        sources:$sources
-        filters:$filters
-        histogram:$histogram
-    ){
-        source
-        target_id
-        features {
-            type
-            provenance_source
-            description
-            feature_id
-            name
-            value
-            feature_positions {
-                beg_seq_id
-                end_seq_id
-                beg_ori_id
-                end_ori_id
-                range_id
-                open_begin
-                open_end
-                value
-                values
-            }
-        }
-    }
-}