@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

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

@@ -1,21 +0,0 @@
-import { RcsbDistributionConfig } from "../../../../../RcsbAnnotationConfig/RcsbDistributionConfig";
-import { MultipleTrackDistributionFactory } from "./MultipleTrackDistributionFactory";
-import { NumericalTrackDistributionFactory } from "./NumericalTrackDistributionFactory";
-export class TrackDistributionFactory {
-    constructor(distributionConfig) {
-        this.distributionConfig = distributionConfig !== null && distributionConfig !== void 0 ? distributionConfig : new RcsbDistributionConfig();
-        this.multipleTrackDistributionFactory = new MultipleTrackDistributionFactory(distributionConfig);
-        this.numericalTrackDistributionFactory = new 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;
-        }
-    }
-}

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

@@ -1 +0,0 @@
-export {};

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

@@ -1,19 +0,0 @@
-import { RcsbDistributionConfig } from "../../../../../RcsbAnnotationConfig/RcsbDistributionConfig";
-export class TrackBlockFactory {
-    constructor(distributionConfig) {
-        this.distributionConfig = distributionConfig !== null && distributionConfig !== void 0 ? distributionConfig : new 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] }));
-    }
-}

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

@@ -1,22 +0,0 @@
-import { Assertions } from "../../../../RcsbUtils/Helpers/Assertions";
-export var Helper;
-(function (Helper) {
-    var assertDefined = 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 || (Helper = {}));

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

@@ -1,87 +0,0 @@
-import { __awaiter } from "tslib";
-import { AnnotationCollector } from "../../../../RcsbCollectTools/AnnotationCollector/AnnotationCollector";
-import { SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { filter, interfaceAnnotations } from "../../../../RcsbFvWeb/RcsbFvModule/RcsbFvInterface";
-import * as rcm from "../../../../RcsbAnnotationConfig/RcsbResidueConfig.ac.json";
-import { AnnotationBlockManager } from "../../../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationBlockManager";
-import { AnnotationTrackManagerFactory } from "../../../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationTrackManager";
-import { RcsbAnnotationConfig } from "../../../../RcsbAnnotationConfig/RcsbAnnotationConfig";
-import { TrackBlockFactory } from "../ResidueChartFactories/TrackBlockFactoryImpl/TrackBlockFactory";
-import { TrackDistributionFactory } from "../ResidueChartFactories/ResidueDistributionFactoryImpl/TrackDistributionFactory";
-import { DistributionChartFactory } from "../ResidueChartFactories/DistributionChartFactoryImpl/DistributionChartFactory";
-import { AlignmentCollector } from "../../../../RcsbCollectTools/AlignmentCollector/AlignmentCollector";
-import { rcsbRequestCtxManager } from "../../../../RcsbRequest/RcsbRequestContextManager";
-import { Helper } from "./Helper";
-import { Assertions } from "../../../../RcsbUtils/Helpers/Assertions";
-export var ResidueChartTools;
-(function (ResidueChartTools) {
-    var assertDefined = Assertions.assertDefined;
-    function getResidueDistribution(residueChart) {
-        return __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 __awaiter(this, void 0, void 0, function* () {
-            const instanceIds = (yield 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.mergeCharts(charts);
-        });
-    }
-    function getInstanceCharts(instanceId) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b;
-            const alignmentRequestContext = {
-                queryId: instanceId,
-                from: SequenceReference.PdbInstance,
-                to: SequenceReference.PdbInstance
-            };
-            const alignmentResponse = yield alignmentCollector.collect(alignmentRequestContext);
-            const annotationsRequestContext = {
-                queryId: instanceId,
-                reference: SequenceReference.PdbInstance,
-                sources: [Source.PdbEntity, Source.PdbInstance, Source.Uniprot, Source.PdbInterface],
-                annotationGenerator: interfaceAnnotations,
-                annotationFilter: 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 __awaiter(this, void 0, void 0, function* () {
-            return processAnnotations({
-                annotations,
-                annotationBlockManager: new AnnotationBlockManager(new AnnotationTrackManagerFactory(), new RcsbAnnotationConfig(rcm)),
-                annotationRequestContext,
-                trackBlockFactory: new TrackBlockFactory(),
-                residueDistributionFactory: new TrackDistributionFactory(),
-                distributionChartFactory: new DistributionChartFactory(),
-                numberResidues
-            });
-        });
-    }
-    function processAnnotations(config) {
-        return __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();
-    const alignmentCollector = new AlignmentCollector();
-})(ResidueChartTools || (ResidueChartTools = {}));

package/lib/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/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/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/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/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/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
-            }
-        }
-    }
-}