@rcsb/rcsb-saguaro-app 6.0.0-development.1 → 6.0.0-development.3

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

@@ -0,0 +1,742 @@
+"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) {
+        var _c, _d;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            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() {
+        var _c, _d, _e, _f, _g, _h, _j;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            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() {
+        var _c, _d, _e, _f;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            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;