@rcsb/rcsb-saguaro-app
Version:
RCSB 1D Saguaro Web App
743 lines (742 loc) • 38.3 kB
JavaScript
"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/lib/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_alignments) === 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_alignments) === 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_alignments);
const exonTracks = this.collectExons(ar.target_alignments, "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_alignments);
e[index] = alignment.target_alignments;
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;