@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationBlockManager.js

@@ -1,98 +0,0 @@
-import { __awaiter } from "tslib";
-import { Assertions } from "../../../../RcsbUtils/Helpers/Assertions";
-var assertDefined = Assertions.assertDefined;
-export class AnnotationBlockManager {
-    constructor(trackManagerFactory, rcsbAnnotationConfig, polymerEntityInstanceTranslator) {
-        this.annotationTracks = new Map();
-        this.trackManagerFactory = trackManagerFactory;
-        this.rcsbAnnotationConfig = rcsbAnnotationConfig;
-        this.polymerEntityInstanceTranslator = polymerEntityInstanceTranslator;
-    }
-    setData(requestConfig, data) {
-        return __awaiter(this, void 0, void 0, function* () {
-            yield this.processAnnotations(requestConfig, data);
-            this.mergeTracks();
-        });
-    }
-    getTracks() {
-        var _a;
-        return (_a = this.orderedTypes()
-            .filter(type => { var _a, _b; return this.has(type) && ((_b = (_a = this.annotationTracks.get(type)) === null || _a === void 0 ? void 0 : _a.size()) !== null && _b !== void 0 ? _b : 0) > 0; })
-            .map(type => this.annotationTracks.get(type))
-            .filter((track) => track != null)) !== null && _a !== void 0 ? _a : [];
-    }
-    has(type) {
-        return this.annotationTracks.has(type);
-    }
-    orderedTypes() {
-        return [
-            this.rcsbAnnotationConfig.instanceOrder(),
-            this.rcsbAnnotationConfig.entityOrder(),
-            this.rcsbAnnotationConfig.uniprotOrder(),
-            Array.from(this.annotationTracks.keys()).filter(type => !this.rcsbAnnotationConfig.allTypes().has(type))
-        ].flat();
-    }
-    processAnnotations(requestConfig, data) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b;
-            yield Promise.all(data.map(ann => {
-                var _a, _b;
-                return (_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.map((feature) => __awaiter(this, void 0, void 0, function* () {
-                    if (feature)
-                        return yield this.addFeature(requestConfig, ann, feature);
-                }))) !== null && _b !== void 0 ? _b : [];
-            }).flat());
-            (_b = (_a = requestConfig.annotationProcessing) === null || _a === void 0 ? void 0 : _a.computeAnnotationValue) === null || _b === void 0 ? void 0 : _b.call(_a, this.annotationTracks);
-        });
-    }
-    addFeature(requestConfig, ann, feature) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e;
-            if (feature.type && ((_a = this.rcsbAnnotationConfig.getConfig(feature.type)) === null || _a === void 0 ? void 0 : _a.ignore))
-                return;
-            const type = yield this.rcsbAnnotationConfig.getAnnotationType(requestConfig, ann, feature);
-            if (!this.annotationTracks.has(type)) {
-                const o = (_b = this.rcsbAnnotationConfig.getConfig(type)) !== null && _b !== void 0 ? _b : {
-                    type: type,
-                    display: "block" /* RcsbFvDisplayTypes.BLOCK */,
-                    title: type,
-                    provenanceList: new Set()
-                };
-                assertDefined(o, `Unknown type: ${type}`);
-                this.annotationTracks.set(type, this.trackManagerFactory.getTrackManager(type, o, this.polymerEntityInstanceTranslator));
-            }
-            const queryId = (_c = requestConfig.queryId) !== null && _c !== void 0 ? _c : requestConfig.groupId;
-            assertDefined(queryId, "undefined queryId or groupId");
-            assertDefined(ann.source, "undefined source");
-            assertDefined(ann.target_id, "undefined target_id");
-            (_d = this.annotationTracks.get(type)) === null || _d === void 0 ? void 0 : _d.addFeature({
-                reference: (_e = requestConfig.reference) !== null && _e !== void 0 ? _e : undefined,
-                queryId: queryId,
-                source: ann.source,
-                targetId: ann.target_id,
-                feature: feature
-            }, requestConfig.annotationProcessing);
-        });
-    }
-    mergeTracks() {
-        const typeList = Array.from(this.annotationTracks.keys());
-        typeList.forEach((type) => {
-            var _a, _b, _c, _d, _e;
-            if (this.rcsbAnnotationConfig.isMergedType(type)) {
-                const newType = (_a = this.rcsbAnnotationConfig.getMergeConfig(type)) === null || _a === void 0 ? void 0 : _a.type;
-                assertDefined(newType);
-                const color = (_b = this.rcsbAnnotationConfig.getConfig(type)) === null || _b === void 0 ? void 0 : _b.color;
-                if (!this.annotationTracks.has(newType)) {
-                    const o = this.rcsbAnnotationConfig.getConfig(newType);
-                    assertDefined(o);
-                    this.annotationTracks.set(newType, this.trackManagerFactory.getTrackManager(newType, o, this.polymerEntityInstanceTranslator));
-                }
-                const o = this.annotationTracks.get(type);
-                if (o && typeof color === "string")
-                    (_c = this.annotationTracks.get(newType)) === null || _c === void 0 ? void 0 : _c.addAll(o, color);
-                this.rcsbAnnotationConfig.addMultipleProvenance(newType, Array.from((_e = (_d = this.annotationTracks.get(newType)) === null || _d === void 0 ? void 0 : _d.getTrackProvenance()) !== null && _e !== void 0 ? _e : []));
-                this.annotationTracks.delete(type);
-            }
-        });
-    }
-}

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationTrackManager.d.ts

@@ -1,11 +0,0 @@
-import { RcsbFvTrackDataElementGapInterface } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
-import { FeaturePosition } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { RcsbAnnotationConfigInterface } from "../../../../RcsbAnnotationConfig/AnnotationConfigInterface";
-import { TrackManagerFactoryInterface, TrackManagerInterface } from "./TrackManagerInterface";
-export interface FeaturePositionGaps extends FeaturePosition {
-    gaps?: Array<RcsbFvTrackDataElementGapInterface>;
-}
-export declare class AnnotationTrackManagerFactory implements TrackManagerFactoryInterface<[string, RcsbAnnotationConfigInterface, PolymerEntityInstanceTranslate]> {
-    getTrackManager(trackId: string, annotationConfig: RcsbAnnotationConfigInterface, entityInstanceTranslator?: PolymerEntityInstanceTranslate): TrackManagerInterface;
-}

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

@@ -1,241 +0,0 @@
-import { Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { TrackUtils } from "../../RcsbFvTrackFactory/TrackFactoryImpl/Helper/TrackUtils";
-import { Assertions } from "../../../../RcsbUtils/Helpers/Assertions";
-var assertElementListDefined = Assertions.assertElementListDefined;
-var assertDefined = Assertions.assertDefined;
-import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
-export class AnnotationTrackManagerFactory {
-    getTrackManager(trackId, annotationConfig, entityInstanceTranslator) {
-        return new AnnotationTrackManager(trackId, annotationConfig, entityInstanceTranslator);
-    }
-}
-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 == Source.PdbInstance && this.entityInstanceTranslator != null ?
-            TagDelimiter.parseInstance(targetId).entryId + TagDelimiter.instance + this.entityInstanceTranslator.translateAsymToAuth(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.transformSourceFromTarget(targetId, source),
-            provenanceName: provenance,
-            provenanceColor: 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/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/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/BlockManagerInterface.js

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

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

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

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

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

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

@@ -1,128 +0,0 @@
-import { __awaiter } from "tslib";
-import { FeatureTools } from "../../../../RcsbCollectTools/FeatureTools/FeatureTools";
-import { SequenceTrackFactory } from "./SequenceTrackFactory";
-import { AlignmentTrackTitleFactory } from "../TrackTitleFactoryImpl/AlignmentTrackTitleFactory";
-import { TrackUtils } from "./Helper/TrackUtils";
-import { Assertions } from "../../../../RcsbUtils/Helpers/Assertions";
-var assertDefined = Assertions.assertDefined;
-export class AlignmentTrackFactory {
-    constructor(entityInstanceTranslator, trackTitleFactory) {
-        this.sequenceTrackFactory = new SequenceTrackFactory(entityInstanceTranslator);
-        this.trackTitleFactory = trackTitleFactory !== null && trackTitleFactory !== void 0 ? trackTitleFactory : new AlignmentTrackTitleFactory(entityInstanceTranslator);
-    }
-    getTrack(alignmentRequestContext, targetAlignment, alignedRegionToTrackElementList) {
-        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" /* 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.transformSourceFromTarget(alignmentContext.targetId, alignmentContext.to),
-                        provenanceName: TrackUtils.getProvenanceConfigFormTarget(alignmentContext.targetId, alignmentQueryContext.to).name,
-                        provenanceColor: TrackUtils.getProvenanceConfigFormTarget(alignmentContext.targetId, alignmentQueryContext.to).color,
-                        type: "MISMATCH",
-                        title: "MISMATCH"
-                    }, alignmentContext));
-                });
-        });
-        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.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"
-            }, 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);
-            }
-        }
-    }
-    else {
-        console.error("Find alignment missmatch failed. Sequence regions of different length");
-    }
-    return out;
-}

package/lib/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>;
-}