@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvChromosome.js

@@ -1,742 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.RcsbFvChromosome = void 0;
-const tslib_1 = require("tslib");
-const rxjs_1 = require("rxjs");
-const RcsbDataManager_1 = require("@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager");
-const RcsbFvAbstractModule_1 = require("./RcsbFvAbstractModule");
-const GqlTypes_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes");
-const RcsbAnnotationConstants_1 = require("../../RcsbAnnotationConfig/RcsbAnnotationConstants");
-const RcsbFvAlignmentCollectorQueue_1 = require("../RcsbFvWorkers/RcsbFvAlignmentCollectorQueue");
-const NcbiGenomeSequenceData_1 = require("../../ExternalResources/NcbiData/NcbiGenomeSequenceData");
-const NcbiSummary_1 = require("../../ExternalResources/NcbiData/NcbiSummary");
-const ideogram_1 = tslib_1.__importDefault(require("ideogram"));
-const ObservableHelper_1 = require("../../RcsbUtils/Helpers/ObservableHelper");
-const RcsbClient_1 = require("../../RcsbGraphQL/RcsbClient");
-const Assertions_1 = require("../../RcsbUtils/Helpers/Assertions");
-var assertElementListDefined = Assertions_1.Assertions.assertElementListDefined;
-var assertDefined = Assertions_1.Assertions.assertDefined;
-function sequenceDisplayDynamicUpdate(reference, ranges, trackWidth) {
-    return (where) => {
-        const delta = trackWidth ? trackWidth / (where.to - where.from) : 1000 / (where.to - where.from);
-        if (delta > 4) {
-            const ids = new Array();
-            ranges.forEach((id, r) => {
-                if (!(r[0] > where.to || r[1] < where.from))
-                    ids.push(id);
-            });
-            return Promise.all(ids.map(id => {
-                return RcsbClient_1.rcsbClient.requestAlignment({
-                    queryId: id,
-                    from: reference,
-                    to: GqlTypes_1.SequenceReference.NcbiGenome
-                });
-            })).then(alignments => {
-                const out = new RcsbDataManager_1.RcsbFvTrackData();
-                alignments.forEach((a, n) => {
-                    var _c;
-                    if (a.query_sequence == null)
-                        return;
-                    const sequence = a.query_sequence.split("");
-                    (_c = a.target_alignment) === null || _c === void 0 ? void 0 : _c.forEach(ta => {
-                        var _c;
-                        if (!ta)
-                            return;
-                        const orientation = ta.orientation;
-                        if (!orientation)
-                            return;
-                        (_c = ta.aligned_regions) === null || _c === void 0 ? void 0 : _c.forEach(r => {
-                            if (!r)
-                                return;
-                            const targetIndex = r.target_begin;
-                            const queryIndex = r.query_begin;
-                            const length = r.query_end - r.query_begin + 1;
-                            for (let i = 0; i < length; i++) {
-                                out.push({
-                                    begin: targetIndex + orientation * (1 + 3 * i),
-                                    label: sequence[queryIndex - 1 + i],
-                                    oriBegin: queryIndex + i,
-                                    source: reference.toString(),
-                                    sourceId: ids[n]
-                                });
-                            }
-                        });
-                    });
-                });
-                return out;
-            });
-        }
-        else {
-            return new Promise((resolve, reject) => {
-                resolve([]);
-            });
-        }
-    };
-}
-//TODO This class needs a lot of improvements
-//TODO this Module is not collecting alignments through AlignmentCollector
-class RcsbFvChromosome extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
-    constructor() {
-        super(...arguments);
-        this.targetAlignmentList = new Map([
-            [GqlTypes_1.SequenceReference.NcbiProtein, new Array()],
-            [GqlTypes_1.SequenceReference.Uniprot, new Array()],
-            [GqlTypes_1.SequenceReference.PdbEntity, new Array()]
-        ]);
-        this.maxRange = 0;
-        this.minRange = Number.MAX_SAFE_INTEGER;
-        this.alignmentCollectorQueue = new RcsbFvAlignmentCollectorQueue_1.RcsbFvAlignmentCollectorQueue(12);
-        this.nTasks = 0;
-        this.completeTasks = 0;
-        this.batchSize = 10000000;
-        this.beginView = 0;
-        this.endView = 0;
-        this.entityBegin = 0;
-        this.entityEnd = 0;
-        this.nonExonConfigData = new Array();
-        this.featuresConfigData = new Array();
-        this.targetCoverages = new Map();
-        this.chrSet = new Array();
-        this.targetFilterFlag = true;
-        this.IDEOGRAM_DIV_ID = "chrIdeogramDiv";
-        this.TITLE_CHR_DIV_ID = "chrTitleDiv";
-        this.TITLE_CHR_REGION_ID = "chrTitleRegion";
-        this.currentDisplayedChrId = "";
-        this.buildSubject = new rxjs_1.Subject();
-        this.targetsSubject = new rxjs_1.Subject();
-    }
-    buildPdbGenomeFv(pdbEntityId, chrId) {
-        this.entityId = pdbEntityId;
-        Promise.all([GqlTypes_1.SequenceReference.NcbiProtein, GqlTypes_1.SequenceReference.Uniprot].map(to => {
-            return RcsbClient_1.rcsbClient.requestAlignment({
-                queryId: pdbEntityId,
-                from: GqlTypes_1.SequenceReference.PdbEntity,
-                to: to
-            });
-        })).then(result => {
-            result.forEach(a => {
-                var _c;
-                if (!a)
-                    return;
-                (_c = a.target_alignment) === null || _c === void 0 ? void 0 : _c.forEach(ta => {
-                    if ((ta === null || ta === void 0 ? void 0 : ta.target_id) && (ta === null || ta === void 0 ? void 0 : ta.coverage))
-                        this.targetCoverages.set(ta.target_id, ta.coverage);
-                });
-            });
-            this.alignmentCollectorQueue.sendTask({
-                queryId: pdbEntityId,
-                from: GqlTypes_1.SequenceReference.PdbEntity,
-                to: GqlTypes_1.SequenceReference.NcbiGenome,
-            }, (e) => tslib_1.__awaiter(this, void 0, void 0, function* () {
-                const ar = e;
-                yield this.collectPdbWorkerResults(ar, pdbEntityId, chrId);
-            }));
-        });
-    }
-    buildFullGenomeRangeFv(chrId) {
-        this.plotChromosomeTitle(chrId);
-        this.targetFilterFlag = false;
-        this.genomeSequenceTracks(chrId);
-        this.collectChromosomeAlignments(chrId, GqlTypes_1.SequenceReference.PdbEntity);
-        this.collectChromosomeAlignments(chrId, GqlTypes_1.SequenceReference.Uniprot);
-        this.collectChromosomeAlignments(chrId, GqlTypes_1.SequenceReference.NcbiProtein);
-    }
-    collectPdbWorkerResults(ar, pdbEntityId, chrId) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            var _c, _d;
-            assertElementListDefined(ar.target_alignment);
-            const exonTracks = this.collectExons(ar.target_alignment, "target", RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceColorCode.rcsbPdb, RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceColorCode.rcsbPdb, GqlTypes_1.SequenceReference.PdbEntity, chrId);
-            this.pdbEntityTrack = this.mergeExonTracks(exonTracks, GqlTypes_1.SequenceReference.PdbEntity)[0];
-            (_d = (_c = this.pdbEntityTrack.displayConfig) === null || _c === void 0 ? void 0 : _c[0].displayData) === null || _d === void 0 ? void 0 : _d.forEach(d => {
-                d.description = [pdbEntityId];
-            });
-            this.addSequences([this.pdbEntityTrack], GqlTypes_1.SequenceReference.PdbEntity);
-            this.pdbEntityTrack.rowTitle = {
-                visibleTex: pdbEntityId,
-                style: {
-                    fontWeight: "bold"
-                }
-            };
-            this.pdbEntityTrack.hideEmptyTrackFlag = false;
-            yield this.buildChromosomeFv(chrId !== null && chrId !== void 0 ? chrId : this.chrSet[0]);
-        });
-    }
-    buildChromosomeFv(chrId) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            this.plotChromosomeTitle(chrId);
-            this.genomeSequenceTracks(chrId);
-            this.nonExonConfigData.push(this.pdbEntityTrack);
-            yield this.plot();
-            this.collectChromosomeEntityRegion(chrId);
-        });
-    }
-    plotChromosomeTitle(chrId) {
-        var _c, _d;
-        (_c = document.getElementById(this.IDEOGRAM_DIV_ID)) === null || _c === void 0 ? void 0 : _c.remove();
-        (_d = document.getElementById(this.TITLE_CHR_DIV_ID)) === null || _d === void 0 ? void 0 : _d.remove();
-        this.currentDisplayedChrId = chrId;
-        NcbiSummary_1.NcbiSummary.requestChromosomeData(chrId).then(ncbiChrResult => {
-            var _c, _d;
-            if (chrId == this.currentDisplayedChrId) {
-                const ideogramDiv = document.createElement("div");
-                ideogramDiv.id = this.IDEOGRAM_DIV_ID;
-                const titleDiv = document.createElement("div");
-                titleDiv.style.display = "inline-block";
-                titleDiv.style.marginLeft = "20px";
-                titleDiv.id = this.TITLE_CHR_DIV_ID;
-                const title = document.createElement("span");
-                title.innerHTML = ncbiChrResult.title;
-                titleDiv.append(title);
-                const region = document.createElement("span");
-                region.id = this.TITLE_CHR_REGION_ID;
-                region.innerHTML = " / Region: [" + this.entityBegin + " - " + this.entityEnd + "]";
-                region.style.color = "#666";
-                titleDiv.append(region);
-                (_c = document.getElementById(this.elementSelectId)) === null || _c === void 0 ? void 0 : _c.insertAdjacentElement("afterend", titleDiv);
-                (_d = document.getElementById(this.elementId)) === null || _d === void 0 ? void 0 : _d.insertAdjacentElement("beforebegin", ideogramDiv);
-                this.plotIdeogram(ncbiChrResult);
-            }
-        });
-    }
-    updateChromosomeTitleRegion() {
-        const region = document.getElementById(this.TITLE_CHR_REGION_ID);
-        if (region != null)
-            region.innerHTML = " / Region: [" + this.beginView + " - " + this.endView + "]";
-    }
-    plotIdeogram(ncbiChrResult) {
-        NcbiSummary_1.NcbiSummary.requestTaxonomyData(ncbiChrResult.taxid.toString()).then(ncbiTaxResult => {
-            if (ncbiChrResult.ncbiId == this.currentDisplayedChrId) {
-                const chrName = ncbiChrResult.subname.includes("|") ? ncbiChrResult.subname.split("|").filter(n => {
-                    return (n.match(/^([\dXYxy]+)$/) != null);
-                })[0] : ncbiChrResult.subname;
-                const ideogram = new ideogram_1.default({
-                    rotatable: false,
-                    chrHeight: 1080,
-                    chrWidth: 20,
-                    organism: ncbiTaxResult.scientificname,
-                    chromosomes: [chrName],
-                    orientation: 'horizontal',
-                    container: '#' + this.IDEOGRAM_DIV_ID,
-                    annotationHeight: 8,
-                    showBandLabels: true,
-                    annotations: [{
-                            name: this.entityId,
-                            chr: chrName,
-                            start: this.entityBegin,
-                            stop: this.entityEnd
-                        }],
-                    onLoad: () => {
-                        var _c, _d;
-                        if (!(((_c = ideogram.chromosomesArray) === null || _c === void 0 ? void 0 : _c.length) > 0)) {
-                            (_d = document.getElementById(this.IDEOGRAM_DIV_ID)) === null || _d === void 0 ? void 0 : _d.remove();
-                        }
-                        else {
-                            const e = document.getElementById("_ideogram");
-                            if (e != null)
-                                e.style.padding = "0 0 0 0";
-                        }
-                    }
-                });
-            }
-        });
-    }
-    genomeSequenceTracks(chrId) {
-        var _c, _d, _e, _f;
-        this.nonExonConfigData.push({
-            trackId: "mainSequenceTrack_5_" + chrId,
-            displayType: "sequence" /* RcsbFvDisplayTypes.SEQUENCE */,
-            trackColor: "#F9F9F9",
-            displayColor: "#000000",
-            nonEmptyDisplay: true,
-            rowPrefix: chrId + " ",
-            rowTitle: {
-                visibleTex: "5'",
-                style: {
-                    fontWeight: "bold"
-                },
-            },
-            titleFlagColor: RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceColorCode.external,
-            updateDataOnMove: NcbiGenomeSequenceData_1.NcbiGenomeSequenceData.update(chrId, 1, false, (_d = (_c = this.rcsbFv) === null || _c === void 0 ? void 0 : _c.getBoardConfig()) === null || _d === void 0 ? void 0 : _d.trackWidth)
-        });
-        this.nonExonConfigData.push({
-            trackId: "mainSequenceTrack_3_" + chrId,
-            displayType: "sequence" /* RcsbFvDisplayTypes.SEQUENCE */,
-            trackColor: "#F9F9F9",
-            displayColor: "#000000",
-            rowPrefix: "",
-            nonEmptyDisplay: true,
-            rowTitle: {
-                visibleTex: "3'",
-                style: {
-                    fontWeight: "bold"
-                },
-            },
-            titleFlagColor: RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceColorCode.external,
-            updateDataOnMove: NcbiGenomeSequenceData_1.NcbiGenomeSequenceData.update(chrId, 2, true, (_f = (_e = this.rcsbFv) === null || _e === void 0 ? void 0 : _e.getBoardConfig()) === null || _f === void 0 ? void 0 : _f.trackWidth)
-        });
-    }
-    collectChromosomeEntityRegion(chrId) {
-        var _c, _d, _e, _f;
-        const begin = (_d = (_c = this.pdbEntityTrack.displayConfig) === null || _c === void 0 ? void 0 : _c[0].displayData) === null || _d === void 0 ? void 0 : _d[0].begin;
-        const end = (_f = (_e = this.pdbEntityTrack.displayConfig) === null || _e === void 0 ? void 0 : _e[0].displayData) === null || _f === void 0 ? void 0 : _f[0].end;
-        if (begin && end) {
-            const range = [Math.max(1, begin - 5000000), end + 5000000];
-            this.collectChromosomeAlignments(chrId, GqlTypes_1.SequenceReference.Uniprot, range, 0);
-            this.collectChromosomeAlignments(chrId, GqlTypes_1.SequenceReference.NcbiProtein, range, 0);
-        }
-    }
-    collectChromosomeAlignments(chrId, to, range, index) {
-        if (range != null) {
-            this.nTasks++;
-            this.alignmentCollectorQueue.sendTask({
-                queryId: chrId,
-                from: GqlTypes_1.SequenceReference.NcbiGenome,
-                to: to,
-                range: range
-            }, (e) => tslib_1.__awaiter(this, void 0, void 0, function* () {
-                const ar = e;
-                if (typeof index === "number")
-                    yield this.collectChromosomeWorkerResults(index, to, ar, false);
-            }));
-        }
-        else {
-            for (let i = 0; i < 30; i++) {
-                this.nTasks++;
-                this.alignmentCollectorQueue.sendTask({
-                    queryId: chrId,
-                    from: GqlTypes_1.SequenceReference.NcbiGenome,
-                    to: to,
-                    range: [i * this.batchSize, (i + 1) * this.batchSize]
-                }, (e) => tslib_1.__awaiter(this, void 0, void 0, function* () {
-                    const ar = e;
-                    yield this.collectChromosomeWorkerResults(i, to, ar, false);
-                }));
-            }
-        }
-    }
-    collectChromosomeWorkerResults(index, reference, alignment, forcePlot) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            this.completeTasks++;
-            const e = this.targetAlignmentList.get(reference);
-            assertDefined(e);
-            assertElementListDefined(alignment.target_alignment);
-            e[index] = alignment.target_alignment;
-            console.log("Completed " + Math.floor(this.completeTasks / this.nTasks * 100) + "%");
-            if (forcePlot) {
-                yield this.plot();
-            }
-            else if (this.nTasks == this.completeTasks) {
-                console.log("All Tasks Completed. Starting Rendering");
-                this.alignmentCollectorQueue.terminateWorkers();
-                yield this.plot();
-            }
-        });
-    }
-    collectExons(targetAlignmentList, member, blockColor, flagTitleColor, reference, chrId) {
-        const exonTrackList = new Array();
-        targetAlignmentList.forEach((targetAlignment, i) => {
-            var _c;
-            if (!targetAlignment.target_id)
-                return;
-            if (((_c = targetAlignment.aligned_regions) === null || _c === void 0 ? void 0 : _c.length) == 0 || (member == "query" && this.targetFilterFlag && !this.targetCoverages.has(targetAlignment.target_id)) || (member == "target" && chrId != null && chrId != targetAlignment.target_id))
-                return;
-            exonTrackList.push({ data: [this.normalizeTargetAlignment(targetAlignment, member)], id: targetAlignment.target_id });
-        });
-        const lightTracks = this.simplifyExonTracks(exonTrackList.sort((_a, _b) => {
-            var _c, _d, _e, _f;
-            const a = _a.data;
-            const b = _b.data;
-            if (a[0].begin != b[0].begin)
-                return a[0].begin - b[0].begin;
-            if (b[0].end && a[0].end && b[0].end != a[0].end)
-                return b[0].end - a[0].end;
-            return ((_d = (_c = a[0].gaps) === null || _c === void 0 ? void 0 : _c.map(g => g.end - g.begin).reduce((a, b) => a + b, 0)) !== null && _d !== void 0 ? _d : 0) - ((_f = (_e = b[0].gaps) === null || _e === void 0 ? void 0 : _e.map(g => g.end - g.begin).reduce((a, b) => a + b, 0)) !== null && _f !== void 0 ? _f : 0);
-        }).map(a => {
-            if (member == "target" && !this.chrSet.includes(a.id))
-                this.chrSet.push(a.id);
-            return a.data;
-        }), member, reference);
-        return lightTracks.map((t, index) => {
-            return {
-                trackId: "pdbTracks_" + Math.random().toString(36).substring(2),
-                displayType: "composite" /* RcsbFvDisplayTypes.COMPOSITE */,
-                trackColor: "#F9F9F9",
-                rowTitle: "",
-                titleFlagColor: flagTitleColor,
-                overlap: true,
-                displayConfig: [{
-                        displayType: "block" /* RcsbFvDisplayTypes.BLOCK */,
-                        displayData: t,
-                        displayColor: blockColor,
-                        selectDataInRangeFlag: true,
-                        hideEmptyTrackFlag: true,
-                        minRatio: 1 / 5000
-                    }]
-            };
-        });
-    }
-    normalizeTargetAlignment(targetAlignment, member) {
-        const beginMember = member === "query" ? "query_begin" : "target_begin";
-        const endMember = member === "query" ? "query_end" : "target_end";
-        const ar = targetAlignment.aligned_regions;
-        assertElementListDefined(ar);
-        assertDefined(targetAlignment.target_id), assertDefined(targetAlignment.orientation);
-        const out = {
-            begin: Math.min(ar[0][beginMember], ar[ar.length - 1][endMember]),
-            end: Math.max(ar[0][beginMember], ar[ar.length - 1][endMember]),
-            gaps: [],
-            description: [targetAlignment.target_id],
-            openBegin: targetAlignment.orientation < 0,
-            openEnd: targetAlignment.orientation > 0
-        };
-        if (targetAlignment.orientation > 0) {
-            if (member == "query" && ar[ar.length - 1][endMember] > this.maxRange)
-                this.maxRange = ar[ar.length - 1][endMember];
-            if (member == "query" && ar[0][beginMember] < this.minRange)
-                this.minRange = ar[0][beginMember];
-            ar.forEach((currentExon, n) => {
-                var _c, _d, _e, _f, _g, _h;
-                if ((n + 1) < ar.length) {
-                    const nextExon = ar[n + 1];
-                    let beginGap = currentExon[endMember];
-                    let endGap = nextExon[beginMember];
-                    const exonShift = currentExon.exon_shift ? currentExon.exon_shift.map(e => {
-                        if (!e)
-                            throw new Error(`Undefined exon`);
-                        return e;
-                    }) : [];
-                    if ((exonShift === null || exonShift === void 0 ? void 0 : exonShift.length) == 1) {
-                        if (Math.abs(exonShift[0] - endGap) == 1) {
-                            endGap = exonShift[0];
-                        }
-                        else {
-                            (_c = out.gaps) === null || _c === void 0 ? void 0 : _c.push({
-                                end: exonShift[0],
-                                begin: beginGap,
-                                isConnected: true
-                            });
-                            endGap = exonShift[0];
-                        }
-                    }
-                    else if ((exonShift === null || exonShift === void 0 ? void 0 : exonShift.length) == 2) {
-                        if (Math.abs(exonShift[1] - endGap) == 1 && Math.abs(exonShift[1] - exonShift[0]) == 1) {
-                            endGap = exonShift[0];
-                        }
-                        else if (Math.abs(exonShift[1] - endGap) == 1) {
-                            (_d = out.gaps) === null || _d === void 0 ? void 0 : _d.push({
-                                end: exonShift[0],
-                                begin: beginGap,
-                                isConnected: true
-                            });
-                            beginGap = exonShift[0];
-                            endGap = exonShift[1];
-                        }
-                        else if (Math.abs(exonShift[1] - exonShift[0]) == 1) {
-                            (_e = out.gaps) === null || _e === void 0 ? void 0 : _e.push({
-                                end: exonShift[0],
-                                begin: beginGap,
-                                isConnected: true
-                            });
-                            beginGap = exonShift[1];
-                        }
-                        else {
-                            (_f = out.gaps) === null || _f === void 0 ? void 0 : _f.push({
-                                end: exonShift[0],
-                                begin: beginGap,
-                                isConnected: true
-                            });
-                            beginGap = exonShift[0];
-                            (_g = out.gaps) === null || _g === void 0 ? void 0 : _g.push({
-                                end: exonShift[1],
-                                begin: beginGap,
-                                isConnected: true
-                            });
-                            beginGap = exonShift[1];
-                        }
-                    }
-                    (_h = out.gaps) === null || _h === void 0 ? void 0 : _h.push({
-                        begin: beginGap,
-                        end: endGap,
-                        isConnected: true
-                    });
-                }
-            });
-        }
-        else {
-            if (member == "query" && ar[0][beginMember] > this.maxRange)
-                this.maxRange = ar[0][beginMember];
-            if (member == "query" && ar[ar.length - 1][endMember] < this.minRange)
-                this.minRange = ar[ar.length - 1][endMember];
-            ar.reverse().forEach((currentExon, n) => {
-                var _c, _d, _e, _f, _g, _h;
-                if ((n + 1) < ar.length) {
-                    const nextExon = ar[n + 1];
-                    let beginGap = currentExon[beginMember];
-                    let endGap = nextExon[endMember];
-                    const exonShift = nextExon.exon_shift ? nextExon.exon_shift.map(e => {
-                        if (!e)
-                            throw new Error(`Undefined exon`);
-                        return e;
-                    }) : [];
-                    if ((exonShift === null || exonShift === void 0 ? void 0 : exonShift.length) == 1) {
-                        if (Math.abs(exonShift[0] - beginGap) == 1) {
-                            beginGap = exonShift[0];
-                        }
-                        else {
-                            (_c = out.gaps) === null || _c === void 0 ? void 0 : _c.push({
-                                end: exonShift[0],
-                                begin: beginGap,
-                                isConnected: true
-                            });
-                            beginGap = exonShift[0];
-                        }
-                    }
-                    else if ((exonShift === null || exonShift === void 0 ? void 0 : exonShift.length) == 2) {
-                        if (Math.abs(exonShift[1] - beginGap) == 1 && Math.abs(exonShift[1] - exonShift[0]) == 1) {
-                            beginGap = exonShift[0];
-                        }
-                        else if (Math.abs(exonShift[1] - beginGap) == 1) {
-                            beginGap = exonShift[1];
-                            (_d = out.gaps) === null || _d === void 0 ? void 0 : _d.push({
-                                end: exonShift[0],
-                                begin: beginGap,
-                                isConnected: true
-                            });
-                            beginGap = exonShift[0];
-                        }
-                        else if (Math.abs(exonShift[1] - exonShift[0]) == 1) {
-                            (_e = out.gaps) === null || _e === void 0 ? void 0 : _e.push({
-                                end: exonShift[0],
-                                begin: beginGap,
-                                isConnected: true
-                            });
-                            beginGap = exonShift[1];
-                        }
-                        else {
-                            (_f = out.gaps) === null || _f === void 0 ? void 0 : _f.push({
-                                end: exonShift[0],
-                                begin: beginGap,
-                                isConnected: true
-                            });
-                            beginGap = exonShift[0];
-                            (_g = out.gaps) === null || _g === void 0 ? void 0 : _g.push({
-                                end: exonShift[1],
-                                begin: beginGap,
-                                isConnected: true
-                            });
-                            beginGap = exonShift[1];
-                        }
-                    }
-                    (_h = out.gaps) === null || _h === void 0 ? void 0 : _h.push({
-                        end: endGap,
-                        begin: beginGap,
-                        isConnected: true
-                    });
-                }
-            });
-        }
-        return out;
-    }
-    simplifyExonTracks(tracks, member, reference) {
-        const lightTracks = new Array();
-        tracks.forEach(t => {
-            var _c, _d, _e, _f, _g;
-            const trackBegin = t[0].begin;
-            const trackEnd = t[0].end;
-            if (lightTracks.length == 0) {
-                if ((this.entityBegin > 0 && this.entityEnd > 0) && !(trackBegin > this.entityEnd || (trackEnd && trackEnd < this.entityBegin))) {
-                    if (trackBegin < this.beginView)
-                        this.beginView = trackBegin;
-                    if (trackEnd && trackEnd > this.endView)
-                        this.endView = trackEnd;
-                }
-                lightTracks.push(t);
-            }
-            else {
-                const N = lightTracks.length - 1;
-                const begin = lightTracks[N][0].begin;
-                const end = lightTracks[N][0].end;
-                const trackHash = trackBegin + "." + ((_c = t[0].gaps) === null || _c === void 0 ? void 0 : _c.map((b) => { return b.begin + "." + b.end; }).join(".")) + "." + trackEnd;
-                const ltHash = begin + "." + ((_d = lightTracks[N][0].gaps) === null || _d === void 0 ? void 0 : _d.map((b) => { return b.begin + "." + b.end; }).join(".")) + "." + end;
-                if (trackHash != ltHash) {
-                    if ((this.entityBegin > 0 && this.entityEnd > 0) && !(trackBegin > this.entityEnd || (trackEnd && trackEnd < this.entityBegin))) {
-                        if (trackBegin < this.beginView)
-                            this.beginView = trackBegin;
-                        if (trackEnd && trackEnd > this.endView)
-                            this.endView = trackEnd;
-                    }
-                    lightTracks.push(t);
-                }
-                else {
-                    (_e = lightTracks[N][0].description) === null || _e === void 0 ? void 0 : _e.push((_g = (_f = t[0].description) === null || _f === void 0 ? void 0 : _f[0]) !== null && _g !== void 0 ? _g : "N/A");
-                }
-            }
-        });
-        return lightTracks;
-    }
-    mergeExonTracks(tracks, reference) {
-        const lightTracks = new Array();
-        tracks.forEach(t => {
-            var _c, _d, _e, _f, _g, _h, _j;
-            if (lightTracks.length == 0) {
-                lightTracks.push(t);
-            }
-            else {
-                const trackBegin = (_d = (_c = t.displayConfig) === null || _c === void 0 ? void 0 : _c[0].displayData) === null || _d === void 0 ? void 0 : _d[0].begin;
-                let index = -1;
-                lightTracks.forEach((lT, n) => {
-                    var _c;
-                    const d = (_c = lT.displayConfig) === null || _c === void 0 ? void 0 : _c[0].displayData;
-                    if (!d)
-                        return;
-                    const N = d.length - 1;
-                    const end = d[N].end;
-                    if (trackBegin && end && trackBegin > end && index == -1) {
-                        index = n;
-                    }
-                });
-                if (index >= 0 && ((_f = (_e = t.displayConfig) === null || _e === void 0 ? void 0 : _e[0].displayData) === null || _f === void 0 ? void 0 : _f[0])) {
-                    (_h = (_g = lightTracks[index].displayConfig) === null || _g === void 0 ? void 0 : _g[0].displayData) === null || _h === void 0 ? void 0 : _h.push((_j = t.displayConfig) === null || _j === void 0 ? void 0 : _j[0].displayData[0]);
-                }
-                else if (index == -1) {
-                    lightTracks.push(t);
-                }
-            }
-        });
-        this.addSequences(lightTracks, reference);
-        return lightTracks;
-    }
-    addSequences(lightTracks, reference) {
-        lightTracks.forEach(t => {
-            var _c, _d, _e, _f, _g;
-            const ids = new Map();
-            (_d = (_c = t.displayConfig) === null || _c === void 0 ? void 0 : _c[0].displayData) === null || _d === void 0 ? void 0 : _d.forEach(d => {
-                if (d.end && d.description)
-                    ids.set([d.begin, d.end], d.description[0]);
-            });
-            (_e = t.displayConfig) === null || _e === void 0 ? void 0 : _e.push({
-                displayType: "sequence" /* RcsbFvDisplayTypes.SEQUENCE */,
-                updateDataOnMove: sequenceDisplayDynamicUpdate(reference, ids, (_g = (_f = this.rcsbFv) === null || _f === void 0 ? void 0 : _f.getBoardConfig()) === null || _g === void 0 ? void 0 : _g.trackWidth),
-                displayData: [],
-                hideEmptyTrackFlag: true,
-                minRatio: 1 / 1000
-            });
-        });
-    }
-    setDisplayView() {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            var _c, _d, _e, _f, _g, _h, _j;
-            if (this.entityBegin == 0 && this.entityEnd == 0 && ((_e = (_d = (_c = this.pdbEntityTrack) === null || _c === void 0 ? void 0 : _c.displayConfig) === null || _d === void 0 ? void 0 : _d.length) !== null && _e !== void 0 ? _e : 0) > 0) {
-                const d = (_f = this.pdbEntityTrack.displayConfig) === null || _f === void 0 ? void 0 : _f[0].displayData;
-                if (!d)
-                    return;
-                const lastIndex = d[d.length - 1].end;
-                if (!lastIndex)
-                    return;
-                this.entityBegin = d[0].begin;
-                this.entityEnd = lastIndex;
-                this.beginView = d[0].begin;
-                this.endView = lastIndex;
-                const begin = this.beginView;
-                const end = this.endView;
-                const length = end - begin;
-                this.boardConfigData.range = {
-                    min: begin - Math.ceil(0.05 * length),
-                    max: end + Math.ceil(+0.05 * length)
-                };
-            }
-            else if (((_j = (_h = (_g = this.pdbEntityTrack) === null || _g === void 0 ? void 0 : _g.displayConfig) === null || _h === void 0 ? void 0 : _h.length) !== null && _j !== void 0 ? _j : 0) > 0) {
-                this.beginView = this.minRange;
-                this.endView = this.maxRange;
-                const begin = this.beginView;
-                const end = this.endView;
-                const length = end - begin;
-                this.boardConfigData.range = {
-                    min: begin - Math.ceil(0.05 * length),
-                    max: end + Math.ceil(+0.05 * length)
-                };
-                this.updateChromosomeTitleRegion();
-            }
-            yield this.display();
-            return void 0;
-        });
-    }
-    plot() {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            var _c, _d, _e, _f;
-            console.log("PROCESSING");
-            let tracks = new Array();
-            let ncbiTracks = new Array();
-            (_c = this.targetAlignmentList.get(GqlTypes_1.SequenceReference.NcbiProtein)) === null || _c === void 0 ? void 0 : _c.forEach((tA, index) => {
-                if (tA.length > 0) {
-                    ncbiTracks = ncbiTracks.concat(this.collectExons(tA, "query", "#69b3a2", "#69b3a2", GqlTypes_1.SequenceReference.NcbiProtein));
-                }
-            });
-            ncbiTracks = this.mergeExonTracks(ncbiTracks, GqlTypes_1.SequenceReference.NcbiProtein);
-            let uniprotTracks = new Array();
-            (_d = this.targetAlignmentList.get(GqlTypes_1.SequenceReference.Uniprot)) === null || _d === void 0 ? void 0 : _d.forEach((tA, index) => {
-                if (tA.length > 0)
-                    uniprotTracks = uniprotTracks.concat(this.collectExons(tA, "query", "#cc99ff", "#cc99ff", GqlTypes_1.SequenceReference.Uniprot));
-            });
-            uniprotTracks = this.mergeExonTracks(uniprotTracks, GqlTypes_1.SequenceReference.Uniprot);
-            let entityTracks = new Array();
-            (_e = this.targetAlignmentList.get(GqlTypes_1.SequenceReference.PdbEntity)) === null || _e === void 0 ? void 0 : _e.forEach((tA, index) => {
-                if (tA.length > 0)
-                    entityTracks = entityTracks.concat(this.collectExons(tA, "query", RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceColorCode.rcsbPdb, RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceColorCode.rcsbPdb, GqlTypes_1.SequenceReference.PdbEntity));
-            });
-            entityTracks = this.mergeExonTracks(entityTracks, GqlTypes_1.SequenceReference.PdbEntity);
-            if (ncbiTracks.length > 0) {
-                tracks = tracks.concat(ncbiTracks);
-                ncbiTracks[0].rowTitle = "NCBI PROTEINS";
-            }
-            if (uniprotTracks.length > 0) {
-                tracks = tracks.concat(uniprotTracks);
-                uniprotTracks[0].rowTitle = "UNIPROT PROTEINS";
-            }
-            if (entityTracks.length > 0) {
-                tracks = tracks.concat(entityTracks);
-                entityTracks[0].rowTitle = "PDB ENTITIES";
-            }
-            const headerTracks = ((_f = this.featuresConfigData) === null || _f === void 0 ? void 0 : _f.length) > 0 ? this.nonExonConfigData.concat(this.featuresConfigData) : this.nonExonConfigData;
-            if (tracks.length > 0)
-                this.rowConfigData = headerTracks.concat(tracks);
-            else
-                this.rowConfigData = headerTracks;
-            console.log("RENDERING");
-            this.boardConfigData.hideInnerBorder = true;
-            this.boardConfigData.length = Math.floor(this.maxRange + 0.01 * this.maxRange);
-            this.boardConfigData.includeAxis = true;
-            yield this.setDisplayView();
-            this.buildSubject.next(void 0);
-            this.targetsSubject.next(this.chrSet);
-            return void 0;
-        });
-    }
-    protectedBuild() {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            const buildConfig = this.buildConfig;
-            return new Promise(((resolve, reject) => {
-                ObservableHelper_1.ObservableHelper.oneTimeSubscription(resolve, this.buildSubject);
-                if (buildConfig.elementSelectId)
-                    this.elementSelectId = buildConfig.elementSelectId;
-                if (buildConfig.entityId != null)
-                    this.buildPdbGenomeFv(buildConfig.entityId, buildConfig.chrId);
-                else if (buildConfig.chrId != null)
-                    this.buildFullGenomeRangeFv(buildConfig.chrId);
-            }));
-        });
-    }
-    getTargets() {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            return new Promise((resolve, reject) => {
-                if (this.chrSet.length > 0)
-                    resolve(this.chrSet);
-                else
-                    ObservableHelper_1.ObservableHelper.oneTimeSubscription(resolve, this.targetsSubject);
-            });
-        });
-    }
-    concatAlignmentAndAnnotationTracks() {
-    }
-}
-exports.RcsbFvChromosome = RcsbFvChromosome;