npm - @rcsb/rcsb-saguaro-app - Versions diffs - 6.3.2 → 6.3.4 - Mend

@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

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Files changed (834) hide show

package/lib/RcsbFvExamples/ExternalDataProvider.js DELETED Viewed

@@ -1,951 +0,0 @@
-import { __awaiter } from "tslib";
-import { SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { buildDataProviderFv } from "../RcsbFvWeb/RcsbFvBuilder";
-import { rcsbRequestCtxManager } from "../RcsbRequest/RcsbRequestContextManager";
-import { Assertions } from "../RcsbUtils/Helpers/Assertions";
-var assertElementListDefined = Assertions.assertElementListDefined;
-import { AlignmentReference } from "../RcsbUtils/PairwiseAlignmentTools/AlignmentReference";
-const alignment = {
-    "info": {
-        "uuid": "e6e216de-c650-4ad5-bd81-45e75dfbe180",
-        "status": "COMPLETE"
-    },
-    "meta": {
-        "alignment_mode": "pairwise",
-        "alignment_method": "fatcat-rigid"
-    },
-    "results": [
-        {
-            "structures": [
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-                    "selection": {
-                        "asym_id": "A"
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-                },
-                {
-                    "entry_id": "1ASH",
-                    "selection": {
-                        "asym_id": "A"
-                    }
-                }
-            ],
-            "structure_alignment": [
-                {
-                    "regions": [
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-            "sequence_alignment": [
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-class RcsbStructuralAlignmentProvider {
-    constructor(alignment) {
-        this.alignmentResponse = undefined;
-        this.alignment = alignment;
-    }
-    data() {
-        return __awaiter(this, void 0, void 0, function* () {
-            if (this.alignmentResponse)
-                return this.alignmentResponse;
-            return new Promise((resolve) => {
-                alignmentTransform(this.alignment).then(ar => {
-                    this.alignmentResponse = ar;
-                    resolve(ar);
-                });
-            });
-        });
-    }
-    collect(requestConfig, filter) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return new Promise((resolve) => __awaiter(this, void 0, void 0, function* () {
-                resolve(yield this.data());
-            }));
-        });
-    }
-    getTargets() {
-        return __awaiter(this, void 0, void 0, function* () {
-            return new Promise((resolve) => __awaiter(this, void 0, void 0, function* () {
-                var _a, _b;
-                resolve((_b = (_a = (yield this.data()).target_alignment) === null || _a === void 0 ? void 0 : _a.map(ta => { var _a; return (_a = ta === null || ta === void 0 ? void 0 : ta.target_id) !== null && _a !== void 0 ? _a : "NA"; })) !== null && _b !== void 0 ? _b : []);
-            }));
-        });
-    }
-    getAlignmentLength() {
-        return __awaiter(this, void 0, void 0, function* () {
-            return new Promise((resolve) => __awaiter(this, void 0, void 0, function* () {
-                var _a;
-                const ends = (_a = (yield this.data()).target_alignment) === null || _a === void 0 ? void 0 : _a.map(ta => { var _a, _b, _c; return (_c = (_a = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _a === void 0 ? void 0 : _a[((_b = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _b === void 0 ? void 0 : _b.length) - 1]) === null || _c === void 0 ? void 0 : _c.query_end; });
-                assertElementListDefined(ends);
-                resolve(Math.max(...ends));
-            }));
-        });
-    }
-    getAlignment() {
-        return __awaiter(this, void 0, void 0, function* () {
-            return new Promise((resolve) => __awaiter(this, void 0, void 0, function* () {
-                resolve(this.data());
-            }));
-        });
-    }
-}
-function alignmentTransform(alignment) {
-    return __awaiter(this, void 0, void 0, function* () {
-        var _a, _b;
-        const alignmentRef = mergeAlignments(alignment.results);
-        const out = alignmentRef.buildAlignments();
-        const instance_ids = (_a = out.target_alignment) === null || _a === void 0 ? void 0 : _a.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id);
-        assertElementListDefined(instance_ids);
-        const seqs = yield rcsbRequestCtxManager.getInstanceSequences(instance_ids);
-        (_b = out.target_alignment) === null || _b === void 0 ? void 0 : _b.forEach(ta => {
-            var _a;
-            const seq = (_a = seqs.find(s => s.rcsbId === (ta === null || ta === void 0 ? void 0 : ta.target_id))) === null || _a === void 0 ? void 0 : _a.sequence;
-            if (seq && ta)
-                ta.target_sequence = seq;
-        });
-        return out;
-    });
-}
-function app() {
-    return __awaiter(this, void 0, void 0, function* () {
-        yield buildDataProviderFv("pfv", {
-            alignments: {
-                collector: new RcsbStructuralAlignmentProvider(alignment),
-                context: {
-                    queryId: "structural-alignment",
-                    to: SequenceReference.PdbInstance
-                }
-            }
-        }, {
-            boardConfig: {
-                rowTitleWidth: 100
-            }
-        });
-    });
-}
-app().then(() => {
-});
-function mergeAlignments(results) {
-    const result = results[0];
-    if (!result)
-        throw "Results not available";
-    const alignmentRef = new AlignmentReference(getInstanceId(result, 0), getInstanceId(result), transformToGapedDomain(result.sequence_alignment[0].regions), transformToGapedDomain(result.sequence_alignment[1].regions));
-    results.slice(1).forEach(result => {
-        alignmentRef.addAlignment(getInstanceId(result), transformToGapedDomain(result.sequence_alignment[0].regions), transformToGapedDomain(result.sequence_alignment[1].regions));
-    });
-    return alignmentRef;
-}
-function getInstanceId(result, index = 1) {
-    return `${result.structures[index].entry_id}.${result.structures[index].selection.asym_id}`;
-}
-function transformToGapedDomain(regions) {
-    const out = [];
-    let prevRegionEnd = 0;
-    regions.forEach(region => {
-        const beg = region.beg_index + 1;
-        const end = region.beg_index + region.length;
-        if (beg > (prevRegionEnd + 1)) {
-            const nGaps = beg - (prevRegionEnd + 1);
-            out.push(...Array(nGaps).fill(undefined));
-        }
-        prevRegionEnd = end;
-        const seqBeg = region.beg_seq_id;
-        const seqEnd = region.beg_seq_id + region.length - 1;
-        for (let i = seqBeg; i <= seqEnd; i++) {
-            out.push(i);
-        }
-    });
-    return out;
-}