@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

package/lib/RcsbUtils/Groups/GroupProvenanceToAggregationType.d.ts

@@ -1,6 +0,0 @@
-import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
-import { ReturnType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
-interface GroupProvenanceToReturnType extends Record<GroupProvenanceId, ReturnType> {
-}
-export declare const groupProvenanceToReturnType: GroupProvenanceToReturnType;
-export {};

package/lib/RcsbUtils/Groups/GroupProvenanceToAggregationType.js

@@ -1,7 +0,0 @@
-import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
-import { ReturnType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
-export const groupProvenanceToReturnType = {
-    [GroupProvenanceId.ProvenanceMatchingDepositGroupId]: ReturnType.Entry,
-    [GroupProvenanceId.ProvenanceMatchingUniprotAccession]: ReturnType.PolymerEntity,
-    [GroupProvenanceId.ProvenanceSequenceIdentity]: ReturnType.PolymerEntity,
-};

package/lib/RcsbUtils/Helpers/Assertions.d.ts

@@ -1,5 +0,0 @@
-export declare namespace Assertions {
-    function assertDefined<T>(x: T, message?: string): asserts x is NonNullable<T>;
-    function assertElementListDefined<T>(x: (T | undefined | null)[] | undefined | null, message?: string): asserts x is NonNullable<T>[];
-    function assertElementMatrixDefined<T>(x: ((T | undefined | null)[] | undefined | null)[] | undefined | null, message?: string): asserts x is NonNullable<T>[][];
-}

package/lib/RcsbUtils/Helpers/Assertions.js

@@ -1,26 +0,0 @@
-export var Assertions;
-(function (Assertions) {
-    function assertDefined(x, message) {
-        if (x === null || x === undefined)
-            throw message ? new Error(message) : new Error(`Undefined value`);
-    }
-    Assertions.assertDefined = assertDefined;
-    function assertElementListDefined(x, message) {
-        if (x === null || x === undefined)
-            throw new Error(`Undefined list`);
-        x.forEach((e, n) => {
-            if (e === null || x === undefined)
-                throw message ? new Error(`${message} in index ${n}`) : new Error(`Undefined value in index ${n}`);
-        });
-    }
-    Assertions.assertElementListDefined = assertElementListDefined;
-    function assertElementMatrixDefined(x, message) {
-        if (x === null || x === undefined)
-            throw new Error(`Undefined list`);
-        x.flat().forEach((e, n) => {
-            if (e === null || x === undefined)
-                throw message ? new Error(`${message} in index ${n}`) : new Error(`Undefined value in index ${n}`);
-        });
-    }
-    Assertions.assertElementMatrixDefined = assertElementMatrixDefined;
-})(Assertions || (Assertions = {}));

package/lib/RcsbUtils/Helpers/DataContainer.d.ts

@@ -1,9 +0,0 @@
-export declare class DataContainer<T> {
-    private data;
-    constructor(data?: T);
-    get(): T | undefined;
-    set(data: T | undefined): void;
-}
-export interface DataContainerReader<T> {
-    get(): T | undefined;
-}

package/lib/RcsbUtils/Helpers/DataContainer.js

@@ -1,12 +0,0 @@
-export class DataContainer {
-    constructor(data) {
-        this.data = undefined;
-        this.data = data;
-    }
-    get() {
-        return this.data;
-    }
-    set(data) {
-        this.data = data;
-    }
-}

package/lib/RcsbUtils/Helpers/ObservableHelper.d.ts

@@ -1,4 +0,0 @@
-import { Subject } from "rxjs";
-export declare class ObservableHelper {
-    static oneTimeSubscription<T>(resolve: (x: T) => void, subject: Subject<T>, resolveCondition?: (x: T) => boolean): void;
-}

package/lib/RcsbUtils/Helpers/ObservableHelper.js

@@ -1,12 +0,0 @@
-export class ObservableHelper {
-    static oneTimeSubscription(resolve, subject, resolveCondition) {
-        const s = subject.subscribe({
-            next(x) {
-                if (!resolveCondition || resolveCondition(x)) {
-                    resolve(x);
-                    s.unsubscribe();
-                }
-            }
-        });
-    }
-}

package/lib/RcsbUtils/Helpers/Operator.d.ts

@@ -1,5 +0,0 @@
-export declare class Operator {
-    static uniqueValues<T>(array: Array<T>): T[];
-    static arrayChunk<T>(array: Array<T>, size: number): Array<Array<T>>;
-    static digitGrouping(x: string | number): string;
-}

package/lib/RcsbUtils/Helpers/Operator.js

@@ -1,15 +0,0 @@
-export class Operator {
-    static uniqueValues(array) {
-        return Array.from(new Set(array));
-    }
-    static arrayChunk(array, size) {
-        const out = new Array();
-        for (let i = 0; i < array.length; i += size) {
-            out.push(array.slice(i, i + size));
-        }
-        return out;
-    }
-    static digitGrouping(x) {
-        return parseFloat(x).toLocaleString('en-US');
-    }
-}

package/lib/RcsbUtils/Helpers/SingletonMap.d.ts

@@ -1,4 +0,0 @@
-export declare class SingletonMap {
-    private static readonly map;
-    static update(key: string, obj: any): void;
-}

package/lib/RcsbUtils/Helpers/SingletonMap.js

@@ -1,11 +0,0 @@
-export class SingletonMap {
-    static update(key, obj) {
-        if (SingletonMap.map.has(key)) {
-            Object.assign(SingletonMap.map.get(key), obj);
-        }
-        else {
-            SingletonMap.map.set(key, obj);
-        }
-    }
-}
-SingletonMap.map = new Map();

package/lib/RcsbUtils/Helpers/UrlTools.d.ts

@@ -1,11 +0,0 @@
-export declare namespace UrlTools {
-    function encodeUrlParameterList(paramList: {
-        key: string;
-        value: any;
-    }[]): void;
-    function encodeUrlParameter(key: string, value: any): void;
-    function decodeUrlParameters(): {
-        key: string;
-        value: any;
-    }[] | undefined;
-}

package/lib/RcsbUtils/Helpers/UrlTools.js

@@ -1,31 +0,0 @@
-export var UrlTools;
-(function (UrlTools) {
-    function encodeUrlParameterList(paramList) {
-        const urlParams = [];
-        paramList.filter(p => p.value).forEach(p => {
-            urlParams.push(`${p.key}=${encode(p.value)}`);
-        });
-        globalThis === null || globalThis === void 0 ? void 0 : globalThis.history.replaceState(null, "", "?" + urlParams.join("&"));
-    }
-    UrlTools.encodeUrlParameterList = encodeUrlParameterList;
-    function encodeUrlParameter(key, value) {
-        globalThis === null || globalThis === void 0 ? void 0 : globalThis.history.replaceState(null, "", "?" + (value ? `${key}=${encode(value)}` : ""));
-    }
-    UrlTools.encodeUrlParameter = encodeUrlParameter;
-    function decodeUrlParameters() {
-        var _a;
-        return (_a = parseUrlParameters()) === null || _a === void 0 ? void 0 : _a.map(param => ({ key: param.key, value: JSON.parse(decodeURIComponent(param.value)) }));
-    }
-    UrlTools.decodeUrlParameters = decodeUrlParameters;
-    function parseUrlParameters() {
-        if (globalThis.window.location.search.length === 0)
-            return;
-        return globalThis.window.location.search.substring(1)
-            .split("&")
-            .map((param) => (param.split("=")))
-            .map((param) => ({ key: param[0], value: param[1] }));
-    }
-    function encode(p) {
-        return encodeURIComponent(JSON.stringify(p));
-    }
-})(UrlTools || (UrlTools = {}));

package/lib/RcsbUtils/PairwiseAlignmentTools/AlignmentReference.d.ts

@@ -1,17 +0,0 @@
-import { AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-type AlignmentRefType = (number | undefined)[];
-export declare class AlignmentReference {
-    private readonly alignmentRefMap;
-    private readonly refId;
-    private readonly alignmentRefGaps;
-    private readonly memberRefList;
-    constructor(refId: string, targetId: string, alignment: AlignmentRefType, target: AlignmentRefType);
-    addAlignment(id: string, alignment: AlignmentRefType, target: AlignmentRefType): void;
-    buildAlignments(): AlignmentResponse;
-    private addRef;
-    private addEnd;
-    private addBeg;
-    private addGap;
-    private extendGap;
-}
-export {};

package/lib/RcsbUtils/PairwiseAlignmentTools/AlignmentReference.js

@@ -1,165 +0,0 @@
-import { cloneDeep } from "lodash";
-export class AlignmentReference {
-    constructor(refId, targetId, alignment, target) {
-        this.memberRefList = [];
-        this.alignmentRefMap = cloneDeep(alignment);
-        this.alignmentRefGaps = findGaps(alignment);
-        if (alignment.length != target.length)
-            throw new Error("Alignment and target length error");
-        this.refId = refId;
-        this.memberRefList.push({
-            id: targetId,
-            map: alignment.map((v, n) => n),
-            ref: cloneDeep(alignment),
-            target
-        });
-    }
-    addAlignment(id, alignment, target) {
-        const gaps = findGaps(alignment);
-        for (const gapBeg in gaps) {
-            if (this.alignmentRefGaps[gapBeg])
-                this.extendGap(parseInt(gapBeg), gaps[gapBeg]);
-            else
-                this.addGap(parseInt(gapBeg), gaps[gapBeg]);
-        }
-        const beg = alignment.filter(a => (a && this.alignmentRefMap[0] && a < this.alignmentRefMap[0]));
-        if (beg.length > 0)
-            this.addBeg(beg);
-        const n = this.alignmentRefMap[this.alignmentRefMap.length - 1];
-        const end = alignment.filter(a => (a && n && a > n));
-        if (end.length > 0)
-            this.addEnd(end);
-        this.addRef(id, alignment, target);
-    }
-    buildAlignments() {
-        return buildAlignments(this.refId, this.alignmentRefMap, this.memberRefList);
-    }
-    addRef(id, alignment, target) {
-        const map = Array(this.alignmentRefMap.length).fill(undefined);
-        alignment.forEach((v, n) => {
-            if (typeof v === "undefined")
-                return;
-            const index = this.alignmentRefMap.findIndex(e => e === v);
-            if (index >= 0)
-                map[index] = n;
-        });
-        const gaps = findGaps(alignment);
-        for (const gapBeg in gaps) {
-            const index = this.alignmentRefMap.findIndex(v => v === parseInt(gapBeg));
-            for (let i = 1; i <= gaps[gapBeg]; i++) {
-                map[index + i] = map[index] + i;
-            }
-        }
-        this.memberRefList.push({
-            id,
-            map,
-            ref: cloneDeep(alignment),
-            target: cloneDeep(target)
-        });
-    }
-    addEnd(indexList) {
-        const last = this.alignmentRefMap.length;
-        this.alignmentRefMap.splice(last, 0, ...indexList);
-        this.memberRefList.forEach(mr => {
-            mr.map.splice(last, 0, ...Array(indexList.length).fill(undefined));
-        });
-    }
-    addBeg(indexList) {
-        this.alignmentRefMap.splice(0, 0, ...indexList);
-        this.memberRefList.forEach(mr => {
-            mr.map.splice(0, 0, ...Array(indexList.length).fill(undefined));
-        });
-    }
-    addGap(gapBeg, gapLength) {
-        this.alignmentRefGaps[gapBeg] = gapLength;
-        const i = this.alignmentRefMap.findIndex((v) => v === gapBeg) + 1;
-        this.alignmentRefMap.splice(i, 0, ...Array(gapLength).fill(undefined));
-        this.memberRefList.forEach(mr => {
-            mr.map.splice(i, 0, ...Array(gapLength).fill(undefined));
-        });
-    }
-    extendGap(gapBeg, gapLength) {
-        if (!this.alignmentRefGaps[gapBeg] || this.alignmentRefGaps[gapBeg] >= gapLength)
-            return;
-        const delta = gapLength - this.alignmentRefGaps[gapBeg];
-        this.alignmentRefGaps[gapBeg] += delta;
-        const i = this.alignmentRefMap.findIndex((v) => v === gapBeg) + 1;
-        this.alignmentRefMap.splice(i, 0, ...Array(delta).fill(undefined));
-        this.memberRefList.forEach(mr => {
-            mr.map.splice(i, 0, ...Array(delta).fill(undefined));
-        });
-    }
-}
-function buildAlignments(refId, alignmentRefMap, alignmentMembers) {
-    const out = {};
-    out.target_alignment = [];
-    out.target_alignment.push({
-        aligned_regions: buildRegions(alignmentRefMap),
-        target_id: refId
-    });
-    alignmentMembers.forEach(am => {
-        var _a;
-        (_a = out.target_alignment) === null || _a === void 0 ? void 0 : _a.push({
-            target_id: am.id,
-            aligned_regions: buildRegions(am.map.map((v, n) => typeof v === "number" ? am.target[v] : undefined))
-        });
-    });
-    return out;
-}
-function buildRegions(alignment) {
-    const out = [];
-    let begIndex = 0;
-    let begPos = 0;
-    alignment.forEach((v, n) => {
-        if (!v) {
-            if (begIndex > 0) {
-                out.push({
-                    query_begin: begIndex,
-                    target_begin: begPos,
-                    query_end: n,
-                    target_end: alignment[n - 1]
-                });
-                begIndex = 0;
-                begPos = 0;
-            }
-        }
-        else {
-            if (begIndex == 0) {
-                begIndex = n + 1;
-                begPos = v;
-            }
-        }
-    });
-    if (begPos > 0) {
-        const n = alignment.length;
-        out.push({
-            query_begin: begIndex,
-            target_begin: begPos,
-            query_end: n,
-            target_end: alignment[n - 1]
-        });
-    }
-    return out;
-}
-function findGaps(alignment) {
-    const out = {};
-    let gapBeg = 0;
-    let gapLength = 0;
-    alignment.forEach((v, n) => {
-        if (!v) {
-            if (gapBeg == 0)
-                gapBeg = alignment[n - 1];
-            gapLength++;
-        }
-        else {
-            if (gapLength > 0) {
-                out[gapBeg] = gapLength;
-                gapBeg = 0;
-                gapLength = 0;
-            }
-        }
-    });
-    if (gapLength > 0)
-        out[gapBeg] = gapLength;
-    return out;
-}

package/lib/RcsbUtils/PairwiseAlignmentTools/PairwiseAlignmentBuilder.d.ts

@@ -1,37 +0,0 @@
-import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-export interface PairwiseAlignmentInterface {
-    querySequence: string;
-    targetSequence: string;
-    queryAlignment: string;
-    targetAlignment: string;
-    queryBegin: number;
-    queryEnd: number;
-    targetBegin: number;
-    targetEnd: number;
-    targetId: string;
-    queryId: string;
-    sequenceId: number;
-    isQueryExternal: boolean;
-    isTargetExternal: boolean;
-    pairwiseView?: boolean;
-}
-export declare class PairwiseAlignmentBuilder {
-    private querySequence;
-    private targetSequence;
-    private queryAlignment;
-    private targetAlignment;
-    private readonly queryBegin;
-    private readonly targetBegin;
-    private readonly alignmentLength;
-    private readonly targetId;
-    private readonly queryId;
-    private sequenceId;
-    private readonly isQueryExternal;
-    private readonly isTargetExternal;
-    private readonly pairwiseView;
-    constructor(paI: PairwiseAlignmentInterface);
-    getLength(): number;
-    buildReferenceAlignment(): Array<RcsbFvRowConfigInterface>;
-    buildPairwiseAlignment(): Array<RcsbFvRowConfigInterface>;
-    private addBlockTerminalTags;
-}