@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

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

@@ -1,145 +0,0 @@
-import { __awaiter } from "tslib";
-import { RcsbAnnotationConfig } from "../../../../RcsbAnnotationConfig/RcsbAnnotationConfig";
-import { AnnotationsTrackTitleFactory } from "../TrackTitleFactoryImpl/AnnotationsTrackTitleFactory";
-import { Assertions } from "../../../../RcsbUtils/Helpers/Assertions";
-var assertDefined = Assertions.assertDefined;
-export class AnnotationsTrackFactory {
-    constructor(trackTitleFactory) {
-        this.trackTitleFactory = trackTitleFactory !== null && trackTitleFactory !== void 0 ? trackTitleFactory : new AnnotationsTrackTitleFactory();
-    }
-    getTrack(annotations) {
-        return __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) });
-        });
-    }
-}
-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.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.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.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/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;
-}

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/Helper/TrackUtils.js

@@ -1,36 +0,0 @@
-import { RcsbAnnotationConstants } from "../../../../../RcsbAnnotationConfig/RcsbAnnotationConstants";
-import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
-export var TrackUtils;
-(function (TrackUtils) {
-    function getProvenanceConfigFormTarget(targetId, targetSource) {
-        if (TagDelimiter.isRcsbId(targetId))
-            return {
-                name: RcsbAnnotationConstants.provenanceName.pdb,
-                color: RcsbAnnotationConstants.provenanceColorCode.rcsbPdb,
-            };
-        else if (TagDelimiter.isModel(targetId))
-            return {
-                name: RcsbAnnotationConstants.provenanceName.csm,
-                color: RcsbAnnotationConstants.provenanceColorCode.csm,
-            };
-        else
-            return {
-                name: targetSource,
-                color: RcsbAnnotationConstants.provenanceColorCode.external,
-            };
-    }
-    TrackUtils.getProvenanceConfigFormTarget = getProvenanceConfigFormTarget;
-    function transformSourceFromTarget(targetId, source) {
-        if (TagDelimiter.isModel(targetId) && source.includes("PDB_"))
-            return source.replace("PDB_", "CSM ");
-        else
-            return source;
-    }
-    TrackUtils.transformSourceFromTarget = transformSourceFromTarget;
-    function getProvenanceColorFromProvenance(provenance) {
-        if (provenance === RcsbAnnotationConstants.provenanceName.pdb || provenance === RcsbAnnotationConstants.provenanceName.promotif)
-            return RcsbAnnotationConstants.provenanceColorCode.rcsbPdb;
-        return RcsbAnnotationConstants.provenanceColorCode.external;
-    }
-    TrackUtils.getProvenanceColorFromProvenance = getProvenanceColorFromProvenance;
-})(TrackUtils || (TrackUtils = {}));

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/MsaAlignmentTrackFactory.d.ts

@@ -1,12 +0,0 @@
-import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { TrackFactoryInterface } from "../TrackFactoryInterface";
-import { AlignmentRequestContextType } from "./AlignmentTrackFactory";
-import { AnnotationFeatures, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-export declare class MsaAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
-    private observedAlignmentTrackFactory;
-    private positionalScoreAlignmentTrackFactory;
-    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    getTrack(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<RcsbFvRowConfigInterface>;
-    prepareFeatures(unObservedRegions: Array<AnnotationFeatures>, positionalScores: Array<AnnotationFeatures>): Promise<void>;
-}

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/MsaAlignmentTrackFactory.js

@@ -1,24 +0,0 @@
-import { __awaiter } from "tslib";
-import { PositionalScoreAlignmentTrackFactory } from "./PositionalScoreAlignmentTrackFactory";
-import { PlainObservedAlignmentTrackFactory } from "./PlainObservedAlignmentTrackFactory";
-import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
-export class MsaAlignmentTrackFactory {
-    constructor(entityInstanceTranslator) {
-        this.observedAlignmentTrackFactory = new PlainObservedAlignmentTrackFactory(entityInstanceTranslator);
-        this.positionalScoreAlignmentTrackFactory = new PositionalScoreAlignmentTrackFactory(entityInstanceTranslator);
-    }
-    getTrack(alignmentQueryContext, targetAlignment) {
-        return __awaiter(this, void 0, void 0, function* () {
-            if (targetAlignment.target_id && TagDelimiter.isEntityOrInstanceId(targetAlignment.target_id))
-                return this.observedAlignmentTrackFactory.getTrack(alignmentQueryContext, targetAlignment);
-            else
-                return this.positionalScoreAlignmentTrackFactory.getTrack(alignmentQueryContext, targetAlignment);
-        });
-    }
-    prepareFeatures(unObservedRegions, positionalScores) {
-        return __awaiter(this, void 0, void 0, function* () {
-            yield this.observedAlignmentTrackFactory.prepareFeatures(unObservedRegions);
-            yield this.positionalScoreAlignmentTrackFactory.prepareFeatures(positionalScores);
-        });
-    }
-}

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainAlignmentTrackFactory.d.ts

@@ -1,23 +0,0 @@
-import { RcsbFvColorGradient, RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
-import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-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 { RcsbFvTrackDataAnnotationInterface } from "../RcsbFvTrackDataAnnotationInterface";
-export type AlignmentRequestContextType = AlignmentCollectConfig & {
-    querySequence?: string;
-};
-export declare class PlainAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
-    private readonly sequenceTrackFactory;
-    private readonly trackTitleFactory;
-    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignedRegionToTrackElementList?: (region: AlignedRegion, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>, alignmentColor?: RcsbFvColorGradient): Promise<RcsbFvRowConfigInterface>;
-    getAlignmentTrackConfiguration(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignedRegionToTrackElementList: (region: AlignedRegion, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>): {
-        alignedBlocks: Array<RcsbFvTrackDataElementInterface>;
-        mismatchData: Array<RcsbFvTrackDataElementInterface>;
-        sequenceData: Array<RcsbFvTrackDataElementInterface>;
-    };
-    alignedRegionToTrackElementList(region: AlignedRegion, alignmentContext: AlignmentContextInterface): Array<RcsbFvTrackDataElementInterface>;
-    addAuthorResIds(e: RcsbFvTrackDataAnnotationInterface, alignmentContext: AlignmentContextInterface): RcsbFvTrackDataElementInterface;
-}

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainAlignmentTrackFactory.js

@@ -1,128 +0,0 @@
-import { __awaiter } from "tslib";
-import { SequenceTrackFactory } from "./SequenceTrackFactory";
-import { range } from "lodash";
-import { AlignmentTrackTitleFactory } from "../TrackTitleFactoryImpl/AlignmentTrackTitleFactory";
-import { TrackUtils } from "./Helper/TrackUtils";
-import { Assertions } from "../../../../RcsbUtils/Helpers/Assertions";
-var assertDefined = Assertions.assertDefined;
-export class PlainAlignmentTrackFactory {
-    constructor(entityInstanceTranslator) {
-        this.sequenceTrackFactory = new SequenceTrackFactory(entityInstanceTranslator);
-        this.trackTitleFactory = new AlignmentTrackTitleFactory(entityInstanceTranslator);
-    }
-    getTrack(alignmentRequestContext, targetAlignment, alignedRegionToTrackElementList, alignmentColor) {
-        return __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-area" /* RcsbFvDisplayTypes.BLOCK_AREA */,
-                displayColor: alignmentColor !== null && alignmentColor !== void 0 ? alignmentColor : {
-                    colors: ["#dcdcdc", "#c7c7ff"],
-                    thresholds: [50]
-                },
-                displayData: alignedBlocks
-            };
-            return {
-                trackId: "targetSequenceTrack_" + targetAlignment.target_id,
-                displayType: "composite" /* RcsbFvDisplayTypes.COMPOSITE */,
-                overlap: true,
-                trackColor: "#F9F9F9",
-                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, _d;
-        const alignedBlocks = [];
-        const mismatchData = [];
-        const targetSequence = targetAlignment.target_sequence;
-        const sequenceData = [];
-        const queryId = (_a = alignmentQueryContext.queryId) !== null && _a !== void 0 ? _a : alignmentQueryContext.groupId;
-        assertDefined(queryId), assertDefined(targetAlignment.target_id);
-        const alignmentContext = {
-            queryId,
-            targetId: targetAlignment.target_id,
-            from: alignmentQueryContext.from,
-            to: alignmentQueryContext.to,
-            targetSequenceLength: (_b = targetAlignment.target_sequence) === null || _b === void 0 ? void 0 : _b.length,
-            querySequenceLength: (_c = alignmentQueryContext.querySequence) === null || _c === void 0 ? void 0 : _c.length
-        };
-        (_d = targetAlignment.aligned_regions) === null || _d === void 0 ? void 0 : _d.forEach(region => {
-            if (!(region === null || region === void 0 ? void 0 : region.target_begin) || !(region === null || region === void 0 ? void 0 : region.target_end))
-                return;
-            const regionSequence = targetSequence === null || targetSequence === void 0 ? void 0 : targetSequence.substring(region.target_begin - 1, region.target_end);
-            if (regionSequence)
-                this.sequenceTrackFactory.buildSequenceData(Object.assign(Object.assign({}, alignmentContext), { sequence: regionSequence, begin: region.query_begin, oriBegin: region.target_begin }), "to").forEach(sd => {
-                    sequenceData.push(sd);
-                });
-            alignedRegionToTrackElementList(region, alignmentContext).forEach(r => {
-                alignedBlocks.push(r);
-            });
-            if (regionSequence && alignmentQueryContext.querySequence)
-                findMismatch(regionSequence, alignmentQueryContext.querySequence.substring(region.query_begin - 1, region.query_end)).forEach(m => {
-                    if (alignmentQueryContext.querySequence && targetAlignment.target_id && alignmentContext.to)
-                        mismatchData.push(this.sequenceTrackFactory.addAuthorResIds({
-                            begin: (m + region.query_begin),
-                            oriBegin: (m + region.target_begin),
-                            sourceId: targetAlignment.target_id,
-                            source: TrackUtils.transformSourceFromTarget(alignmentContext.targetId, alignmentContext.to),
-                            provenanceName: TrackUtils.getProvenanceConfigFormTarget(alignmentContext.targetId, alignmentContext.to).name,
-                            provenanceColor: TrackUtils.getProvenanceConfigFormTarget(alignmentContext.targetId, alignmentContext.to).color,
-                            type: "MISMATCH",
-                            title: "MISMATCH"
-                        }, alignmentContext));
-                });
-        });
-        return { alignedBlocks, mismatchData, sequenceData };
-    }
-    alignedRegionToTrackElementList(region, alignmentContext) {
-        let openBegin = false;
-        if (region.target_begin != 1)
-            openBegin = true;
-        let openEnd = false;
-        if (region.target_end != alignmentContext.targetSequenceLength && alignmentContext.querySequenceLength)
-            openEnd = true;
-        return range(region.query_begin, region.query_end + 1).map((p, n) => {
-            assertDefined(alignmentContext.to);
-            return this.addAuthorResIds({
-                begin: p,
-                oriBegin: region.target_begin + n,
-                sourceId: alignmentContext.targetId,
-                source: TrackUtils.transformSourceFromTarget(alignmentContext.targetId, alignmentContext.to),
-                provenanceName: TrackUtils.getProvenanceConfigFormTarget(alignmentContext.targetId, alignmentContext.to).name,
-                provenanceColor: TrackUtils.getProvenanceConfigFormTarget(alignmentContext.targetId, alignmentContext.to).color,
-                openBegin: openBegin,
-                openEnd: openEnd,
-                type: "ALIGNED_BLOCK",
-                title: "ALIGNED REGION",
-                value: 100
-            }, alignmentContext);
-        });
-    }
-    addAuthorResIds(e, alignmentContext) {
-        return this.sequenceTrackFactory.addAuthorResIds(e, alignmentContext);
-    }
-}
-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);
-            }
-        }
-    }
-    return out;
-}

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainObservedAlignmentTrackFactory.d.ts

@@ -1,17 +0,0 @@
-import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { AnnotationFeatures, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { TrackFactoryInterface } from "../TrackFactoryInterface";
-import { AlignmentRequestContextType } from "./AlignmentTrackFactory";
-export declare class PlainObservedAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
-    private alignmentTrackFactory;
-    private unObservedResidues;
-    private readonly instanceEntityMap;
-    private readonly entityInstanceNumberMap;
-    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<RcsbFvRowConfigInterface>;
-    prepareFeatures(unObservedRegions: Array<AnnotationFeatures>): Promise<void>;
-    private collectFeatureEntryProperties;
-    private prepareFeaturesAlignmentMap;
-    private alignedRegionToTrackElementList;
-}

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainObservedAlignmentTrackFactory.js

@@ -1,110 +0,0 @@
-import { __awaiter } from "tslib";
-import { Operator } from "../../../../RcsbUtils/Helpers/Operator";
-import { range } from "lodash";
-import { PlainAlignmentTrackFactory } from "./PlainAlignmentTrackFactory";
-import { TrackUtils } from "./Helper/TrackUtils";
-import { rcsbRequestCtxManager } from "../../../../RcsbRequest/RcsbRequestContextManager";
-import { Assertions } from "../../../../RcsbUtils/Helpers/Assertions";
-var assertDefined = Assertions.assertDefined;
-import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
-export class PlainObservedAlignmentTrackFactory {
-    constructor(entityInstanceTranslator) {
-        this.unObservedResidues = new Map();
-        this.instanceEntityMap = new Map();
-        this.entityInstanceNumberMap = new Map();
-        this.alignmentTrackFactory = new PlainAlignmentTrackFactory(entityInstanceTranslator);
-    }
-    getTrack(alignmentRequestContext, targetAlignment) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return this.alignmentTrackFactory.getTrack(alignmentRequestContext, targetAlignment, this.alignedRegionToTrackElementList.bind(this));
-        });
-    }
-    prepareFeatures(unObservedRegions) {
-        return __awaiter(this, void 0, void 0, function* () {
-            yield this.collectFeatureEntryProperties(unObservedRegions);
-            this.prepareFeaturesAlignmentMap(unObservedRegions);
-        });
-    }
-    collectFeatureEntryProperties(unObservedRegions) {
-        return __awaiter(this, void 0, void 0, function* () {
-            const entryIds = Operator.uniqueValues(unObservedRegions.map(uor => {
-                assertDefined(uor.target_id);
-                return uor.target_id.split(TagDelimiter.instance)[0];
-            }));
-            //TODO define a Translator class for multiple entry entry data
-            const entryProperties = (yield Promise.all(Operator.arrayChunk(entryIds, 100).map(ids => rcsbRequestCtxManager.getEntryProperties(ids)))).flat();
-            entryProperties.forEach(ep => {
-                ep.entityToInstance.forEach((instanceList, entityId) => {
-                    this.entityInstanceNumberMap.set(entityId, instanceList.length);
-                    instanceList.forEach(instanceId => {
-                        this.instanceEntityMap.set(instanceId, entityId);
-                    });
-                });
-            });
-        });
-    }
-    prepareFeaturesAlignmentMap(unObservedRegions) {
-        const uoInstanceFeatureMap = new Map();
-        unObservedRegions.forEach(ur => {
-            var _a;
-            if (!ur.target_id)
-                return;
-            const instanceId = ur.target_id;
-            if (!uoInstanceFeatureMap.has(instanceId))
-                uoInstanceFeatureMap.set(instanceId, new Set());
-            (_a = ur.features) === null || _a === void 0 ? void 0 : _a.forEach(feature => {
-                var _a;
-                (_a = feature === null || feature === void 0 ? void 0 : feature.feature_positions) === null || _a === void 0 ? void 0 : _a.forEach(fp => {
-                    var _a;
-                    if ((fp === null || fp === void 0 ? void 0 : fp.beg_seq_id) && (fp === null || fp === void 0 ? void 0 : fp.end_seq_id))
-                        for (let i = fp.beg_seq_id; i <= fp.end_seq_id; i++) {
-                            (_a = uoInstanceFeatureMap.get(instanceId)) === null || _a === void 0 ? void 0 : _a.add(i);
-                        }
-                });
-            });
-        });
-        const uoEntityFeatureMap = new Map();
-        uoInstanceFeatureMap.forEach((uoSet, instanceId) => {
-            const entityId = this.instanceEntityMap.get(instanceId);
-            if (!entityId)
-                return;
-            if (!uoEntityFeatureMap.has(entityId))
-                uoEntityFeatureMap.set(entityId, new Map());
-            uoSet.forEach(i => {
-                var _a, _b, _c, _d;
-                if ((_a = uoEntityFeatureMap.get(entityId)) === null || _a === void 0 ? void 0 : _a.has(i)) {
-                    const v = (_b = uoEntityFeatureMap.get(entityId)) === null || _b === void 0 ? void 0 : _b.get(i);
-                    if (v)
-                        (_c = uoEntityFeatureMap.get(entityId)) === null || _c === void 0 ? void 0 : _c.set(i, v + 1);
-                }
-                else {
-                    (_d = uoEntityFeatureMap.get(entityId)) === null || _d === void 0 ? void 0 : _d.set(i, 1);
-                }
-            });
-        });
-        uoEntityFeatureMap.forEach((unObservedMap, entityId) => {
-            this.unObservedResidues.set(entityId, Array.from(unObservedMap.entries()).filter(e => (e[1] == this.entityInstanceNumberMap.get(entityId))).map(e => e[0]).sort((a, b) => a - b));
-        });
-    }
-    alignedRegionToTrackElementList(region, alignmentContext) {
-        var _a;
-        if (!this.unObservedResidues.has(alignmentContext.targetId) || ((_a = this.unObservedResidues.get(alignmentContext.targetId)) === null || _a === void 0 ? void 0 : _a.length) == 0)
-            return this.alignmentTrackFactory.alignedRegionToTrackElementList(region, alignmentContext);
-        const unModelledSet = new Set(this.unObservedResidues.get(alignmentContext.targetId));
-        const delta = region.target_begin - region.query_begin;
-        return range(region.query_begin, region.query_end + 1).map((i) => {
-            assertDefined(alignmentContext.to);
-            return this.alignmentTrackFactory.addAuthorResIds({
-                begin: i,
-                oriBegin: i + delta,
-                sourceId: alignmentContext.targetId,
-                source: TrackUtils.transformSourceFromTarget(alignmentContext.targetId, alignmentContext.to),
-                provenanceName: TrackUtils.getProvenanceConfigFormTarget(alignmentContext.targetId, alignmentContext.to).name,
-                provenanceColor: TrackUtils.getProvenanceConfigFormTarget(alignmentContext.targetId, alignmentContext.to).color,
-                type: "ALIGNED_BLOCK",
-                title: unModelledSet.has(i) ? "UNMODELED REGION" : "ALIGNED REGION",
-                value: unModelledSet.has(i) ? 0 : 100
-            }, alignmentContext);
-        });
-    }
-}

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PositionalScoreAlignmentTrackFactory.d.ts

@@ -1,17 +0,0 @@
-import { RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
-import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { AlignedRegion, AnnotationFeatures, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { AlignmentContextInterface, PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { TrackFactoryInterface } from "../TrackFactoryInterface";
-import { AlignmentRequestContextType } from "./AlignmentTrackFactory";
-export declare class PositionalScoreAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
-    private alignmentTrackFactory;
-    private positionalScores;
-    private readonly instanceEntityMap;
-    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignedRegionToTrackElementList?: (region: AlignedRegion, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>): Promise<RcsbFvRowConfigInterface>;
-    prepareFeatures(positionalScores: Array<AnnotationFeatures>): Promise<void>;
-    private collectFeatureEntryProperties;
-    private prepareFeaturesAlignmentMap;
-    private alignedRegionToTrackElementList;
-}

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PositionalScoreAlignmentTrackFactory.js

@@ -1,114 +0,0 @@
-import { __awaiter } from "tslib";
-import { Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { Operator } from "../../../../RcsbUtils/Helpers/Operator";
-import { range } from "lodash";
-import { PlainAlignmentTrackFactory } from "./PlainAlignmentTrackFactory";
-import { TrackUtils } from "./Helper/TrackUtils";
-import { rcsbRequestCtxManager } from "../../../../RcsbRequest/RcsbRequestContextManager";
-import { Assertions } from "../../../../RcsbUtils/Helpers/Assertions";
-var assertDefined = Assertions.assertDefined;
-import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
-export class PositionalScoreAlignmentTrackFactory {
-    constructor(entityInstanceTranslator) {
-        this.positionalScores = new Map();
-        this.instanceEntityMap = new Map();
-        this.alignmentTrackFactory = new PlainAlignmentTrackFactory(entityInstanceTranslator);
-    }
-    getTrack(alignmentRequestContext, targetAlignment, alignedRegionToTrackElementList) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return this.alignmentTrackFactory.getTrack(alignmentRequestContext, targetAlignment, this.alignedRegionToTrackElementList.bind(this), {
-                colors: ["#ff7d45", "#ffdb13", "#65cbf3", "#0053d6"],
-                thresholds: [50, 70, 90]
-            });
-        });
-    }
-    prepareFeatures(positionalScores) {
-        return __awaiter(this, void 0, void 0, function* () {
-            yield this.collectFeatureEntryProperties(positionalScores);
-            this.prepareFeaturesAlignmentMap(positionalScores);
-        });
-    }
-    collectFeatureEntryProperties(unObservedRegions) {
-        return __awaiter(this, void 0, void 0, function* () {
-            const entryIds = Operator.uniqueValues(unObservedRegions.map(uor => {
-                assertDefined(uor.target_id);
-                return uor.target_id.split(TagDelimiter.instance)[0];
-            }));
-            //TODO define a Translator class for multiple entry entry data
-            const entryProperties = (yield Promise.all(Operator.arrayChunk(entryIds, 100).map(ids => rcsbRequestCtxManager.getEntryProperties(ids)))).flat();
-            entryProperties.forEach(ep => {
-                ep.entityToInstance.forEach((instanceList, entityId) => {
-                    instanceList.forEach(instanceId => {
-                        this.instanceEntityMap.set(instanceId, entityId);
-                    });
-                });
-            });
-        });
-    }
-    prepareFeaturesAlignmentMap(positionalScores) {
-        const instancePositionalScores = new Map();
-        positionalScores.forEach(ps => {
-            var _a;
-            if (!ps.target_id)
-                return;
-            const instanceId = ps.target_id;
-            if (!instancePositionalScores.has(instanceId))
-                instancePositionalScores.set(instanceId, new Map());
-            (_a = ps.features) === null || _a === void 0 ? void 0 : _a.forEach(feature => {
-                var _a;
-                (_a = feature === null || feature === void 0 ? void 0 : feature.feature_positions) === null || _a === void 0 ? void 0 : _a.forEach(fp => {
-                    var _a;
-                    (_a = fp === null || fp === void 0 ? void 0 : fp.values) === null || _a === void 0 ? void 0 : _a.forEach((v, n) => {
-                        var _a;
-                        if (fp.beg_seq_id && v)
-                            (_a = instancePositionalScores.get(instanceId)) === null || _a === void 0 ? void 0 : _a.set(fp.beg_seq_id + n, v);
-                    });
-                });
-            });
-        });
-        const entityPositionalScore = new Map();
-        instancePositionalScores.forEach((ips, instanceId) => {
-            const entityId = this.instanceEntityMap.get(instanceId);
-            if (!entityId)
-                return;
-            if (!entityPositionalScore.has(entityId))
-                entityPositionalScore.set(entityId, new Map());
-            const o = entityPositionalScore.get(entityId);
-            assertDefined(o);
-            ips.forEach((score, position) => {
-                var _a;
-                if (!o.has(position)) {
-                    o.set(position, score);
-                }
-                else if (score < ((_a = o.get(position)) !== null && _a !== void 0 ? _a : Number.MIN_SAFE_INTEGER)) {
-                    o.set(position, score);
-                }
-            });
-        });
-        this.positionalScores = entityPositionalScore;
-    }
-    alignedRegionToTrackElementList(region, alignmentContext) {
-        var _a;
-        if (!this.positionalScores.has(alignmentContext.targetId) || ((_a = this.positionalScores.get(alignmentContext.targetId)) === null || _a === void 0 ? void 0 : _a.size) == 0)
-            return this.alignmentTrackFactory.alignedRegionToTrackElementList(region, alignmentContext);
-        const outRegions = [];
-        const entityPositionalScores = this.positionalScores.get(alignmentContext.targetId);
-        if (entityPositionalScores && entityPositionalScores.size > 0) {
-            range(region.query_begin, region.query_end + 1).forEach((p, n) => {
-                if (!alignmentContext.to)
-                    return;
-                outRegions.push(this.alignmentTrackFactory.addAuthorResIds({
-                    begin: p,
-                    oriBegin: region.target_begin + n,
-                    value: entityPositionalScores.get(p),
-                    sourceId: alignmentContext.targetId,
-                    source: TrackUtils.transformSourceFromTarget(alignmentContext.targetId, alignmentContext.to),
-                    provenanceName: TrackUtils.getProvenanceConfigFormTarget(alignmentContext.targetId, alignmentContext.to).name,
-                    provenanceColor: TrackUtils.getProvenanceConfigFormTarget(alignmentContext.targetId, alignmentContext.to).color,
-                    type: Type.MaQaMetricLocalTypeOther,
-                }, alignmentContext));
-            });
-        }
-        return outRegions;
-    }
-}