@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationTrackManager.js

@@ -1,245 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.AnnotationTrackManagerFactory = void 0;
-const GqlTypes_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes");
-const TrackUtils_1 = require("../../RcsbFvTrackFactory/TrackFactoryImpl/Helper/TrackUtils");
-const Assertions_1 = require("../../../../RcsbUtils/Helpers/Assertions");
-var assertElementListDefined = Assertions_1.Assertions.assertElementListDefined;
-var assertDefined = Assertions_1.Assertions.assertDefined;
-const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter");
-class AnnotationTrackManagerFactory {
-    getTrackManager(trackId, annotationConfig, entityInstanceTranslator) {
-        return new AnnotationTrackManager(trackId, annotationConfig, entityInstanceTranslator);
-    }
-}
-exports.AnnotationTrackManagerFactory = AnnotationTrackManagerFactory;
-class AnnotationTrackManager {
-    constructor(type, annotationConfig, entityInstanceTranslator) {
-        this.valueRange = { max: Number.MIN_SAFE_INTEGER, min: Number.MAX_SAFE_INTEGER };
-        this.trackElementMap = new Map();
-        this.entityInstanceTranslator = entityInstanceTranslator;
-        this.type = type;
-        this.annotationConfig = annotationConfig;
-    }
-    getId() {
-        return this.type;
-    }
-    getConfig() {
-        return this.annotationConfig;
-    }
-    getRange() {
-        return this.valueRange;
-    }
-    addFeature(ann, annotationProcessing) {
-        assertElementListDefined(ann.feature.feature_positions);
-        computeFeatureGaps(ann.feature.feature_positions).forEach(p => {
-            if (p.beg_seq_id != null) {
-                this.annotationRangeKeys(p).forEach(rangeKey => {
-                    this.addRange(ann.reference, ann.queryId, ann.source, ann.targetId, ann.feature, p, rangeKey, annotationProcessing);
-                });
-            }
-        });
-    }
-    size() {
-        return this.trackElementMap.size;
-    }
-    forEach(f) {
-        this.trackElementMap.forEach((ann, loc) => {
-            f(ann, loc);
-        });
-    }
-    addAll(trackElementsMap, color) {
-        trackElementsMap.forEach((ann, loc) => {
-            ann.color = color !== null && color !== void 0 ? color : ann.color;
-            this.trackElementMap.set(loc, ann);
-        });
-    }
-    getTrackProvenance() {
-        return new Set(Array.from(this.trackElementMap.values()).map(e => e.provenanceName).filter((x) => x != null));
-    }
-    values() {
-        return Array.from(this.trackElementMap.values());
-    }
-    buildRcsbFvTrackDataElement(p, d, targetId, source, provenance) {
-        var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l;
-        let title = (_b = (_a = this.annotationConfig) === null || _a === void 0 ? void 0 : _a.title) !== null && _b !== void 0 ? _b : this.type;
-        let value = undefined;
-        if (this.isNumericalDisplay(this.type)) {
-            if ((_c = this.annotationConfig) === null || _c === void 0 ? void 0 : _c.transformToNumerical) {
-                value = 1;
-            }
-            else {
-                value = Array.isArray(p.values) && p.values[0] ? p.values[0] : 0;
-            }
-        }
-        if (Array.isArray(p.values) && p.values.length > 0) {
-            assertElementListDefined(p.values);
-            if (Math.max(...p.values) > this.valueRange.max)
-                this.valueRange.max = Math.max(...p.values);
-            if (Math.min(...p.values) < this.valueRange.min)
-                this.valueRange.min = Math.min(...p.values);
-        }
-        else if (typeof value === "number") {
-            if (value > this.valueRange.max)
-                this.valueRange.max = value;
-            if (value < this.valueRange.min)
-                this.valueRange.min = value;
-        }
-        const sourceId = source == GqlTypes_1.Source.PdbInstance && this.entityInstanceTranslator != null ?
-            TagDelimiter_1.TagDelimiter.parseInstance(targetId).entryId + TagDelimiter_1.TagDelimiter.instance + this.entityInstanceTranslator.translateAsymToAuth(TagDelimiter_1.TagDelimiter.parseInstance(targetId).instanceId) : targetId;
-        assertDefined(p.beg_seq_id);
-        return {
-            begin: p.beg_seq_id,
-            end: (_d = p.end_seq_id) !== null && _d !== void 0 ? _d : p.beg_seq_id,
-            oriBegin: (_e = p.beg_ori_id) !== null && _e !== void 0 ? _e : undefined,
-            oriEnd: (_g = ((_f = p.end_ori_id) !== null && _f !== void 0 ? _f : p.beg_ori_id)) !== null && _g !== void 0 ? _g : undefined,
-            description: new Array(),
-            featureId: (_h = d.feature_id) !== null && _h !== void 0 ? _h : undefined,
-            type: this.type,
-            title: title,
-            name: (_j = d.name) !== null && _j !== void 0 ? _j : undefined,
-            value: value,
-            gaps: p.gaps,
-            sourceId: sourceId,
-            source: TrackUtils_1.TrackUtils.transformSourceFromTarget(targetId, source),
-            provenanceName: provenance,
-            provenanceColor: TrackUtils_1.TrackUtils.getProvenanceColorFromProvenance(provenance),
-            openBegin: (_k = p.open_begin) !== null && _k !== void 0 ? _k : undefined,
-            openEnd: (_l = p.open_end) !== null && _l !== void 0 ? _l : undefined
-        };
-    }
-    addRange(reference, queryId, source, targetId, d, p, rangeKey, annotationProcessing) {
-        var _a, _b, _c, _d;
-        const key = rangeKey.join(":");
-        if (!this.trackElementMap.has(key)) {
-            const a = this.buildRcsbFvTrackDataElement(p, d, targetId, source, (_a = d.provenance_source) !== null && _a !== void 0 ? _a : undefined);
-            if ((_b = this.annotationConfig) === null || _b === void 0 ? void 0 : _b.transformToNumerical)
-                this.transformToNumerical(targetId, rangeKey, key, a, d, p, annotationProcessing === null || annotationProcessing === void 0 ? void 0 : annotationProcessing.getAnnotationValue);
-            if (typeof (annotationProcessing === null || annotationProcessing === void 0 ? void 0 : annotationProcessing.addTrackElementCallback) === "function")
-                annotationProcessing === null || annotationProcessing === void 0 ? void 0 : annotationProcessing.addTrackElementCallback({ type: this.type, targetId: targetId, positionKey: key, d: d, p: p });
-            const translateContext = {
-                from: reference,
-                to: source,
-                queryId: queryId,
-                targetId: targetId
-            };
-            this.addAuthorResIds(a, translateContext);
-            this.trackElementMap.set(key, a);
-            if (Array.isArray(p.values)) {
-                assertElementListDefined(p.values);
-                this.expandValues(a, p.values, translateContext);
-            }
-        }
-        else if (this.isNumericalDisplay(this.type) && ((_c = this.annotationConfig) === null || _c === void 0 ? void 0 : _c.transformToNumerical) && typeof ((_d = this.trackElementMap.get(key)) === null || _d === void 0 ? void 0 : _d.value) === "number") {
-            const o = this.trackElementMap.get(key);
-            assertDefined(o === null || o === void 0 ? void 0 : o.value);
-            if (typeof o.value !== "number")
-                return;
-            o.value += typeof (annotationProcessing === null || annotationProcessing === void 0 ? void 0 : annotationProcessing.getAnnotationValue) === "function" ? annotationProcessing.getAnnotationValue({ type: this.type, targetId: targetId, positionKey: key, d: d, p: p }) : 1;
-            if (o.value > this.valueRange.max)
-                this.valueRange.max = o.value;
-            if (o.value < this.valueRange.min)
-                this.valueRange.min = o.value;
-        }
-        if (typeof d.description === "string") {
-            const o = this.trackElementMap.get(key);
-            if (o) {
-                if (!o.description)
-                    o.description = [];
-                o.description.push(d.description);
-            }
-        }
-    }
-    transformToNumerical(targetId, rangeKey, key, a, d, p, getAnnotationValue) {
-        if (typeof getAnnotationValue === "function")
-            a.value = getAnnotationValue({ type: this.type, targetId: targetId, positionKey: key, d: d, p: p });
-        a.begin = rangeKey[0];
-        a.end = rangeKey[0];
-    }
-    expandValues(e, values, translateContext) {
-        values.forEach((v, i) => {
-            if (i > 0) {
-                const key = (e.begin + i).toString();
-                const a = Object.assign(Object.assign({}, e), { begin: (e.begin + i), end: undefined, oriBegin: e.oriBegin ? (e.oriBegin + i) : undefined, oriEnd: undefined, value: v });
-                this.addAuthorResIds(a, translateContext);
-                this.trackElementMap.set(key, a);
-            }
-        });
-    }
-    addAuthorResIds(e, annotationContext) {
-        let o = e;
-        if (this.entityInstanceTranslator != null && annotationContext.from) {
-            this.entityInstanceTranslator.addAuthorResIds(o, annotationContext);
-        }
-        return o;
-    }
-    isNumericalDisplay(type) {
-        return (this.annotationConfig != null && (this.annotationConfig.display === "area" /* RcsbFvDisplayTypes.AREA */ || this.annotationConfig.display === "block-area" /* RcsbFvDisplayTypes.BLOCK_AREA */ || this.annotationConfig.display === "multi-area" /* RcsbFvDisplayTypes.MULTI_AREA */ || this.annotationConfig.display === "line" /* RcsbFvDisplayTypes.LINE */));
-    }
-    annotationRangeKeys(p) {
-        var _a, _b, _c;
-        const rangeKeys = new Array();
-        if (((_a = this.annotationConfig) === null || _a === void 0 ? void 0 : _a.transformToNumerical) && p.beg_seq_id && p.end_seq_id != null) {
-            for (let i = p.beg_seq_id; i <= p.end_seq_id; i++) {
-                rangeKeys.push([i]);
-            }
-        }
-        else if (((_b = this.annotationConfig) === null || _b === void 0 ? void 0 : _b.transformToNumerical) && p.beg_seq_id) {
-            rangeKeys.push([p.beg_seq_id]);
-        }
-        else if (p.beg_seq_id) {
-            const key = p.end_seq_id != null ? [p.beg_seq_id, p.end_seq_id] : [p.beg_seq_id, p.beg_seq_id];
-            if ((_c = this.annotationConfig) === null || _c === void 0 ? void 0 : _c.displayCooccurrence)
-                key.push(Math.ceil(Math.random() * 1000000000000));
-            rangeKeys.push(key);
-        }
-        return rangeKeys;
-    }
-}
-function computeFeatureGaps(featurePositions) {
-    const rangeIdMap = new Map();
-    const out = new Array();
-    featurePositions.forEach(fp => {
-        var _a;
-        if (fp.range_id != null) {
-            if (!rangeIdMap.has(fp.range_id))
-                rangeIdMap.set(fp.range_id, new Array());
-            (_a = rangeIdMap.get(fp.range_id)) === null || _a === void 0 ? void 0 : _a.push(fp);
-        }
-        else {
-            out.push(fp);
-        }
-    });
-    rangeIdMap.forEach((fpList, rangeId) => {
-        var _a, _b, _c;
-        if (fpList.length == 1) {
-            out.push(fpList[0]);
-        }
-        else {
-            const sorted = fpList.sort((a, b) => {
-                if (a.beg_seq_id && b.beg_seq_id)
-                    return a.beg_seq_id - b.beg_seq_id;
-                return Number.MAX_SAFE_INTEGER;
-            });
-            const gapedFeaturePosition = Object.assign(Object.assign({}, sorted[0]), { end_seq_id: sorted[sorted.length - 1].end_seq_id, end_ori_id: sorted[sorted.length - 1].end_ori_id, open_end: sorted[sorted.length - 1].open_end, gaps: new Array() });
-            for (let n = 0; n < sorted.length - 1; n++) {
-                const prevEnd = sorted[n].end_seq_id;
-                const nextBeg = sorted[n + 1].beg_seq_id;
-                if (prevEnd && nextBeg)
-                    (_a = gapedFeaturePosition === null || gapedFeaturePosition === void 0 ? void 0 : gapedFeaturePosition.gaps) === null || _a === void 0 ? void 0 : _a.push({
-                        begin: prevEnd,
-                        end: nextBeg,
-                        isConnected: (sorted[n].beg_ori_id == null ||
-                            sorted[n].end_ori_id == null ||
-                            sorted[n + 1].beg_ori_id == null ||
-                            sorted[n + 1].end_ori_id == null ||
-                            ((_b = sorted[n].end_ori_id) !== null && _b !== void 0 ? _b : Number.MIN_SAFE_INTEGER) + 1 == sorted[n + 1].beg_ori_id ||
-                            sorted[n].end_ori_id == ((_c = sorted[n + 1].beg_ori_id) !== null && _c !== void 0 ? _c : Number.MIN_SAFE_INTEGER) + 1 ||
-                            sorted[n].end_ori_id == sorted[n + 1].beg_ori_id)
-                    });
-            }
-            out.push(gapedFeaturePosition);
-        }
-    });
-    return out;
-}

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/BlockManagerInterface.d.ts

@@ -1,5 +0,0 @@
-import { TrackManagerInterface } from "./TrackManagerInterface";
-export interface BlockManagerInterface<T extends any[]> {
-    setData(...args: T): Promise<void>;
-    getTracks(): TrackManagerInterface[];
-}

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/BlockManagerInterface.js

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

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/TrackManagerInterface.d.ts

@@ -1,28 +0,0 @@
-import { RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
-import { RcsbAnnotationConfigInterface } from "../../../../RcsbAnnotationConfig/AnnotationConfigInterface";
-import { Feature, SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { AnnotationProcessingInterface } from "../../../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
-import { RcsbFvTrackDataAnnotationInterface } from "../../RcsbFvTrackFactory/RcsbFvTrackDataAnnotationInterface";
-export interface TrackManagerFactoryInterface<T extends any[]> {
-    getTrackManager(...args: T): TrackManagerInterface;
-}
-export interface TrackManagerInterface {
-    getId(): string;
-    getConfig(): RcsbAnnotationConfigInterface | undefined;
-    getRange(): {
-        min: number;
-        max: number;
-    };
-    addFeature(ann: {
-        reference: SequenceReference | undefined;
-        queryId: string;
-        source: Source;
-        targetId: string;
-        feature: Feature;
-    }, annotationProcessing?: AnnotationProcessingInterface): void;
-    size(): number;
-    forEach(f: (ann: RcsbFvTrackDataAnnotationInterface, loc: string) => void): void;
-    addAll(trackElementsMap: TrackManagerInterface, color?: string): void;
-    getTrackProvenance(): Set<string>;
-    values(): Array<RcsbFvTrackDataElementInterface>;
-}

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/TrackManagerInterface.js

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

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/RcsbFvTrackDataAnnotationInterface.d.ts

@@ -1,35 +0,0 @@
-import { RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
-export interface RcsbFvTrackDataAnnotationInterface extends RcsbFvTrackDataElementInterface {
-    /**Name of the start position. This information might be displayed in the annotation tooltip*/
-    beginName?: string;
-    /**Name of the end position. This information might be displayed in the annotation tooltip*/
-    endName?: string;
-    /**Annotation original reference start position. This information might be displayed in the annotation tooltip*/
-    oriBegin?: number;
-    /**Annotation original reference end position. This information might be displayed in the annotation tooltip*/
-    oriEnd?: number;
-    /**Name of the original reference start position. This information might be displayed in the annotation tooltip*/
-    oriBeginName?: string;
-    /**Name of the original reference end position. This information might be displayed in the annotation tooltip*/
-    oriEndName?: string;
-    /**Name of the original reference. This information might be displayed in the annotation tooltip*/
-    indexName?: string;
-    /**Annotation name. This information might be displayed in the annotation tooltip*/
-    name?: string;
-    /**Id of the annotation element (protein or gene) source*/
-    sourceId?: string;
-    /**Source reference database name*/
-    source?: string;
-    /**Name of the resource that dispatched the data*/
-    provenanceName?: string;
-    /**color associated to the resource that dispatched the data*/
-    provenanceColor?: string;
-    /**Description associated to the annotation. This information might be displayed in the annotation tooltip*/
-    description?: Array<string>;
-    /**Annotation Id*/
-    featureId?: string;
-    /**Annotation type. This information might be displayed in the annotation tooltip*/
-    type?: string;
-    /**Track title. This information might be displayed in the annotation tooltip*/
-    title?: string;
-}

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/RcsbFvTrackDataAnnotationInterface.js

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

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory.d.ts

@@ -1,19 +0,0 @@
-import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
-import { AlignedRegion, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { PolymerEntityInstanceTranslate, AlignmentContextInterface } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { TrackFactoryInterface } from "../TrackFactoryInterface";
-import { AlignmentCollectConfig } from "../../../../RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface";
-import { TrackTitleFactoryInterface } from "../TrackTitleFactoryInterface";
-export type AlignmentRequestContextType = AlignmentCollectConfig & {
-    querySequence?: string;
-};
-export declare class AlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
-    private readonly sequenceTrackFactory;
-    private readonly trackTitleFactory;
-    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate, trackTitleFactory?: TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignment]>);
-    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignedRegionToTrackElementList?: (region: AlignedRegion, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>): Promise<RcsbFvRowConfigInterface>;
-    private getAlignmentTrackConfiguration;
-    alignedRegionToTrackElementList(region: AlignedRegion, alignmentContext: AlignmentContextInterface): Array<RcsbFvTrackDataElementInterface>;
-    addAuthorResIds(e: RcsbFvTrackDataElementInterface, alignmentContext: AlignmentContextInterface): RcsbFvTrackDataElementInterface;
-}

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory.js

@@ -1,132 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.AlignmentTrackFactory = void 0;
-const tslib_1 = require("tslib");
-const FeatureTools_1 = require("../../../../RcsbCollectTools/FeatureTools/FeatureTools");
-const SequenceTrackFactory_1 = require("./SequenceTrackFactory");
-const AlignmentTrackTitleFactory_1 = require("../TrackTitleFactoryImpl/AlignmentTrackTitleFactory");
-const TrackUtils_1 = require("./Helper/TrackUtils");
-const Assertions_1 = require("../../../../RcsbUtils/Helpers/Assertions");
-var assertDefined = Assertions_1.Assertions.assertDefined;
-class AlignmentTrackFactory {
-    constructor(entityInstanceTranslator, trackTitleFactory) {
-        this.sequenceTrackFactory = new SequenceTrackFactory_1.SequenceTrackFactory(entityInstanceTranslator);
-        this.trackTitleFactory = trackTitleFactory !== null && trackTitleFactory !== void 0 ? trackTitleFactory : new AlignmentTrackTitleFactory_1.AlignmentTrackTitleFactory(entityInstanceTranslator);
-    }
-    getTrack(alignmentRequestContext, targetAlignment, alignedRegionToTrackElementList) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            const { alignedBlocks, mismatchData, sequenceData } = this.getAlignmentTrackConfiguration(alignmentRequestContext, targetAlignment, alignedRegionToTrackElementList !== null && alignedRegionToTrackElementList !== void 0 ? alignedRegionToTrackElementList : this.alignedRegionToTrackElementList.bind(this));
-            const sequenceDisplay = {
-                displayType: "sequence" /* RcsbFvDisplayTypes.SEQUENCE */,
-                displayColor: "#000000",
-                displayData: sequenceData
-            };
-            const mismatchDisplay = {
-                displayType: "pin" /* RcsbFvDisplayTypes.PIN */,
-                displayColor: "#FF9999",
-                displayData: mismatchData
-            };
-            const alignmentDisplay = {
-                displayType: "block" /* RcsbFvDisplayTypes.BLOCK */,
-                displayColor: "#9999FF",
-                displayData: alignedBlocks
-            };
-            return {
-                trackId: "targetSequenceTrack_" + targetAlignment.target_id,
-                displayType: "composite" /* RcsbFvDisplayTypes.COMPOSITE */,
-                overlap: true,
-                trackColor: "#F9F9F9",
-                rowPrefix: yield this.trackTitleFactory.getTrackTitlePrefix(alignmentRequestContext, targetAlignment),
-                rowTitle: yield this.trackTitleFactory.getTrackTitle(alignmentRequestContext, targetAlignment),
-                fitTitleWidth: alignmentRequestContext.fitTitleWidth,
-                titleFlagColor: yield this.trackTitleFactory.getTrackTitleFlagColor(alignmentRequestContext, targetAlignment),
-                displayConfig: [alignmentDisplay, mismatchDisplay, sequenceDisplay]
-            };
-        });
-    }
-    getAlignmentTrackConfiguration(alignmentQueryContext, targetAlignment, alignedRegionToTrackElementList) {
-        var _a, _b, _c;
-        assertDefined(alignmentQueryContext.queryId), assertDefined(targetAlignment.target_id);
-        const alignedBlocks = [];
-        const mismatchData = [];
-        const targetSequence = targetAlignment.target_sequence;
-        const sequenceData = [];
-        const alignmentContext = {
-            queryId: alignmentQueryContext.queryId,
-            targetId: targetAlignment.target_id,
-            from: alignmentQueryContext.from,
-            to: alignmentQueryContext.to,
-            targetSequenceLength: (_a = targetAlignment.target_sequence) === null || _a === void 0 ? void 0 : _a.length,
-            querySequenceLength: (_b = alignmentQueryContext.querySequence) === null || _b === void 0 ? void 0 : _b.length
-        };
-        (_c = targetAlignment.aligned_regions) === null || _c === void 0 ? void 0 : _c.forEach(region => {
-            var _a, _b;
-            assertDefined(region);
-            const regionSequence = targetSequence && region.target_begin && region.target_end ? targetSequence.substring(region.target_begin - 1, region.target_end) : "";
-            this.sequenceTrackFactory.buildSequenceData(Object.assign(Object.assign({}, alignmentContext), { sequence: regionSequence, begin: region.query_begin, oriBegin: region === null || region === void 0 ? void 0 : region.target_begin }), "to").forEach(sd => {
-                sequenceData.push(sd);
-            });
-            alignedRegionToTrackElementList(region, Object.assign(Object.assign({}, alignmentContext), { targetSequenceLength: (_a = alignmentContext.targetSequenceLength) !== null && _a !== void 0 ? _a : (_b = targetAlignment.target_sequence) === null || _b === void 0 ? void 0 : _b.length })).forEach(r => {
-                alignedBlocks.push(r);
-            });
-            if (alignmentQueryContext.querySequence)
-                findMismatch(regionSequence, alignmentQueryContext.querySequence.substring(region.query_begin - 1, region.query_end)).forEach(m => {
-                    var _a;
-                    assertDefined(alignmentContext.to), assertDefined(alignmentQueryContext.to);
-                    mismatchData.push(this.sequenceTrackFactory.addAuthorResIds({
-                        begin: (m + region.query_begin),
-                        oriBegin: (m + region.target_begin),
-                        sourceId: (_a = targetAlignment.target_id) !== null && _a !== void 0 ? _a : undefined,
-                        source: TrackUtils_1.TrackUtils.transformSourceFromTarget(alignmentContext.targetId, alignmentContext.to),
-                        provenanceName: TrackUtils_1.TrackUtils.getProvenanceConfigFormTarget(alignmentContext.targetId, alignmentQueryContext.to).name,
-                        provenanceColor: TrackUtils_1.TrackUtils.getProvenanceConfigFormTarget(alignmentContext.targetId, alignmentQueryContext.to).color,
-                        type: "MISMATCH",
-                        title: "MISMATCH"
-                    }, alignmentContext));
-                });
-        });
-        FeatureTools_1.FeatureTools.mergeBlocks(alignedBlocks);
-        return { alignedBlocks, mismatchData, sequenceData };
-    }
-    alignedRegionToTrackElementList(region, alignmentContext) {
-        let openBegin = false;
-        if (region.target_begin != 1)
-            openBegin = true;
-        let openEnd = false;
-        if (alignmentContext.targetSequenceLength && region.target_end != alignmentContext.targetSequenceLength)
-            openEnd = true;
-        assertDefined(alignmentContext.to);
-        return [this.sequenceTrackFactory.addAuthorResIds({
-                begin: region.query_begin,
-                end: region.query_end,
-                oriBegin: region.target_begin,
-                oriEnd: region.target_end,
-                sourceId: alignmentContext.targetId,
-                source: TrackUtils_1.TrackUtils.transformSourceFromTarget(alignmentContext.targetId, alignmentContext.to),
-                provenanceName: TrackUtils_1.TrackUtils.getProvenanceConfigFormTarget(alignmentContext.targetId, alignmentContext.to).name,
-                provenanceColor: TrackUtils_1.TrackUtils.getProvenanceConfigFormTarget(alignmentContext.targetId, alignmentContext.to).color,
-                openBegin: openBegin,
-                openEnd: openEnd,
-                type: "ALIGNED_BLOCK",
-                title: "ALIGNED REGION"
-            }, alignmentContext)];
-    }
-    addAuthorResIds(e, alignmentContext) {
-        return this.sequenceTrackFactory.addAuthorResIds(e, alignmentContext);
-    }
-}
-exports.AlignmentTrackFactory = AlignmentTrackFactory;
-function findMismatch(seqA, seqB) {
-    const out = [];
-    if (seqA.length === seqB.length) {
-        for (let i = 0; i < seqA.length; i++) {
-            if (seqA.charAt(i) !== seqB.charAt(i)) {
-                out.push(i);
-            }
-        }
-    }
-    else {
-        console.error("Find alignment missmatch failed. Sequence regions of different length");
-    }
-    return out;
-}

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AnnotationsTrackFactory.d.ts

@@ -1,9 +0,0 @@
-import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { TrackFactoryInterface } from "../TrackFactoryInterface";
-import { TrackManagerInterface } from "../../RcsbFvBlockFactory/BlockManager/TrackManagerInterface";
-import { TrackTitleFactoryInterface } from "../TrackTitleFactoryInterface";
-export declare class AnnotationsTrackFactory implements TrackFactoryInterface<[TrackManagerInterface]> {
-    private readonly trackTitleFactory;
-    constructor(trackTitleFactory?: TrackTitleFactoryInterface<[TrackManagerInterface]>);
-    getTrack(annotations: TrackManagerInterface): Promise<RcsbFvRowConfigInterface>;
-}

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AnnotationsTrackFactory.js

@@ -1,149 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.AnnotationsTrackFactory = void 0;
-const tslib_1 = require("tslib");
-const RcsbAnnotationConfig_1 = require("../../../../RcsbAnnotationConfig/RcsbAnnotationConfig");
-const AnnotationsTrackTitleFactory_1 = require("../TrackTitleFactoryImpl/AnnotationsTrackTitleFactory");
-const Assertions_1 = require("../../../../RcsbUtils/Helpers/Assertions");
-var assertDefined = Assertions_1.Assertions.assertDefined;
-class AnnotationsTrackFactory {
-    constructor(trackTitleFactory) {
-        this.trackTitleFactory = trackTitleFactory !== null && trackTitleFactory !== void 0 ? trackTitleFactory : new AnnotationsTrackTitleFactory_1.AnnotationsTrackTitleFactory();
-    }
-    getTrack(annotations) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            let out;
-            const type = annotations.getId();
-            const rcsbAnnotationConfig = annotations.getConfig();
-            let displayType;
-            const annConfig = rcsbAnnotationConfig;
-            if (annConfig != null) {
-                displayType = annConfig === null || annConfig === void 0 ? void 0 : annConfig.display;
-            }
-            switch (displayType) {
-                case "composite" /* RcsbFvDisplayTypes.COMPOSITE */:
-                case "bond" /* RcsbFvDisplayTypes.BOND */:
-                case "pin" /* RcsbFvDisplayTypes.PIN */:
-                    assertDefined(rcsbAnnotationConfig);
-                    out = buildRcsbFvRowConfigComposite(annotations, type, rcsbAnnotationConfig);
-                    break;
-                case "area" /* RcsbFvDisplayTypes.AREA */:
-                case "line" /* RcsbFvDisplayTypes.LINE */:
-                    assertDefined(rcsbAnnotationConfig);
-                    out = buildRcsbFvRowConfigArea(annotations, type, rcsbAnnotationConfig);
-                    break;
-                case "block-area" /* RcsbFvDisplayTypes.BLOCK_AREA */:
-                    assertDefined(rcsbAnnotationConfig);
-                    out = buildRcsbFvRowConfigBlockArea(annotations, type, rcsbAnnotationConfig);
-                    break;
-                default:
-                    out = buildRcsbFvRowConfigTrack(annotations, type, rcsbAnnotationConfig);
-                    break;
-            }
-            if (annConfig != null && typeof annConfig.height === "number") {
-                out.trackHeight = annConfig.height;
-            }
-            return Object.assign(Object.assign({}, out), { titleFlagColor: yield this.trackTitleFactory.getTrackTitleFlagColor(annotations), rowTitle: yield this.trackTitleFactory.getTrackTitle(annotations), rowPrefix: yield this.trackTitleFactory.getTrackTitlePrefix(annotations) });
-        });
-    }
-}
-exports.AnnotationsTrackFactory = AnnotationsTrackFactory;
-function buildRcsbFvRowConfigArea(annotationTrack, type, rcsbAnnotationConfig) {
-    var _a;
-    const data = annotationTrack.values();
-    const annConfig = rcsbAnnotationConfig;
-    const displayType = annConfig === null || annConfig === void 0 ? void 0 : annConfig.display;
-    const displayColor = annConfig === null || annConfig === void 0 ? void 0 : annConfig.color;
-    let min = annotationTrack.getRange().min;
-    let max = annotationTrack.getRange().max;
-    if (min >= 0)
-        min = 0;
-    else if (Math.abs(min) > Math.abs(max))
-        max = -min;
-    else
-        min = -max;
-    const domain = (_a = annConfig === null || annConfig === void 0 ? void 0 : annConfig.domain) !== null && _a !== void 0 ? _a : [min, max];
-    return Object.assign(Object.assign({}, rcsbAnnotationConfig), { trackId: "annotationTrack_" + type, displayType: displayType, overlap: true, trackColor: "#F9F9F9", displayColor: displayColor, displayDomain: domain, interpolationType: "step" /* InterpolationTypes.STEP */, trackData: data });
-}
-function buildRcsbFvRowConfigBlockArea(annotationTrack, type, rcsbAnnotationConfig) {
-    var _a;
-    const data = annotationTrack.values();
-    const annConfig = rcsbAnnotationConfig;
-    const displayType = annConfig.display;
-    const displayColor = (_a = annConfig.color) !== null && _a !== void 0 ? _a : RcsbAnnotationConfig_1.RcsbAnnotationConfig.randomRgba();
-    return Object.assign(Object.assign({}, rcsbAnnotationConfig), { trackId: "annotationTrack_" + type, displayType: displayType, overlap: true, trackColor: "#F9F9F9", displayColor: displayColor, displayDomain: [0, 1], interpolationType: "step" /* InterpolationTypes.STEP */, trackData: data });
-}
-function buildRcsbFvRowConfigComposite(annotationTrack, type, rcsbAnnotationConfig) {
-    var _a;
-    const data = annotationTrack.values();
-    let out = undefined;
-    const annConfig = rcsbAnnotationConfig;
-    let altDisplayType = "block" /* RcsbFvDisplayTypes.BLOCK */;
-    if (annConfig.display === "bond" /* RcsbFvDisplayTypes.BOND */.toString()) {
-        altDisplayType = "bond" /* RcsbFvDisplayTypes.BOND */;
-        data.forEach(d => {
-            d.isEmpty = true;
-        });
-    }
-    const displayColor = (_a = annConfig.color) !== null && _a !== void 0 ? _a : RcsbAnnotationConfig_1.RcsbAnnotationConfig.randomRgba();
-    const pin = new Array();
-    const nonPin = new Array();
-    data.forEach(d => {
-        if (d.end !== null && d.end !== d.begin) {
-            nonPin.push(d);
-        }
-        else {
-            pin.push(d);
-        }
-    });
-    if (pin.length > 0 && nonPin.length > 0) {
-        const displayConfig = new Array();
-        displayConfig.push({
-            displayData: nonPin,
-            displayType: altDisplayType,
-            displayColor: displayColor
-        });
-        displayConfig.push({
-            displayData: pin,
-            displayType: "pin" /* RcsbFvDisplayTypes.PIN */,
-            displayColor: displayColor
-        });
-        out = {
-            displayType: "composite" /* RcsbFvDisplayTypes.COMPOSITE */,
-            trackColor: "#F9F9F9",
-            trackId: "annotationTrack_" + type,
-            displayConfig: displayConfig
-        };
-    }
-    else if (pin.length > 0) {
-        altDisplayType = "pin" /* RcsbFvDisplayTypes.PIN */;
-    }
-    if (out == undefined) {
-        out = {
-            trackId: "annotationTrack_" + type,
-            displayType: altDisplayType,
-            trackColor: "#F9F9F9",
-            displayColor: displayColor,
-            trackData: data
-        };
-    }
-    return out;
-}
-function buildRcsbFvRowConfigTrack(annotationTrack, type, rcsbAnnotationConfig) {
-    const data = annotationTrack.values();
-    let displayType = "block" /* RcsbFvDisplayTypes.BLOCK */;
-    if (data.length > 0 && data[0].end == null) {
-        displayType = "pin" /* RcsbFvDisplayTypes.PIN */;
-    }
-    let displayColor = RcsbAnnotationConfig_1.RcsbAnnotationConfig.randomRgba();
-    const annConfig = rcsbAnnotationConfig;
-    if (annConfig != null) {
-        displayType = annConfig.display;
-        if (annConfig.color)
-            displayColor = annConfig.color;
-    }
-    else {
-        console.warn("Annotation config type " + type + " not found. Using random config");
-    }
-    return Object.assign(Object.assign({}, rcsbAnnotationConfig), { trackId: "annotationTrack_" + type, displayType: displayType, trackColor: "#F9F9F9", displayColor: displayColor, trackData: data });
-}

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/Helper/TrackUtils.d.ts

@@ -1,9 +0,0 @@
-import { SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-export declare namespace TrackUtils {
-    function getProvenanceConfigFormTarget(targetId: string, targetSource: SequenceReference | Source): {
-        name: string;
-        color: string;
-    };
-    function transformSourceFromTarget(targetId: string, source: SequenceReference | Source): string;
-    function getProvenanceColorFromProvenance(provenance?: string): string;
-}