@rcsb/rcsb-saguaro-app
Version:
RCSB 1D Saguaro Web App
184 lines • 9.05 kB
JavaScript
import { __awaiter } from "tslib";
import * as acm from "./RcsbAnnotationConfig.ac.json";
import stc from "string-to-color";
import { Assertions } from "../RcsbUtils/Helpers/Assertions";
var assertDefined = Assertions.assertDefined;
import uniqid from "uniqid";
const annotationConfigMap = acm;
export class RcsbAnnotationConfig {
constructor(acm) {
this.annotationMap = new Map();
this.annotationTypes = {
instance: new Map(),
entity: new Map(),
external: new Map()
};
this.mergedTypes = new Map();
this.annotationConfigMap = acm !== null && acm !== void 0 ? acm : annotationConfigMap;
this.annotationConfigMap.config.forEach(m => {
//TODO move provenance list from configuration to TrackManager
m.provenanceList = new Set();
this.annotationMap.set(m.type, m);
});
this.initTypes();
}
getConfig(type) {
return this.annotationMap.get(type);
}
allTypes() {
const concat = this.uniprotOrder().concat(this.instanceOrder()).concat(this.entityOrder());
return new Set(concat);
}
uniprotOrder() {
return Array.from(this.annotationTypes.external.entries()).map(e => e[1].sort((a, b) => a.localeCompare(b))).flat();
}
instanceOrder() {
return Array.from(this.annotationTypes.instance.entries()).map(e => e[1].sort((a, b) => a.localeCompare(b))).flat();
}
entityOrder() {
return Array.from(this.annotationTypes.entity.entries()).map(e => e[1].sort((a, b) => a.localeCompare(b))).flat();
}
//TODO refactor how title and type are defined. Can this be split in two different methods ?
getAnnotationType(requestConfig, ann, feature) {
return __awaiter(this, void 0, void 0, function* () {
var _a, _b, _c;
const trackTitle = typeof requestConfig.trackTitle === "function" ? (yield requestConfig.trackTitle(ann, feature)) : undefined;
const titleSuffix = typeof requestConfig.titleSuffix === "function" ? (yield requestConfig.titleSuffix(ann, feature)) : undefined;
const typeSuffix = typeof requestConfig.typeSuffix === "function" ? (yield requestConfig.typeSuffix(ann, feature)) : undefined;
const type = feature.type;
assertDefined(type);
const a = feature;
const addToTypeSuffix = new ArraySuffix();
const ac = this.annotationMap.get(type);
if (titleSuffix)
addToTypeSuffix.push(titleSuffix);
if (typeSuffix)
addToTypeSuffix.push(typeSuffix);
if (Array.isArray(ac === null || ac === void 0 ? void 0 : ac.addToType)) {
(_a = ac === null || ac === void 0 ? void 0 : ac.addToType) === null || _a === void 0 ? void 0 : _a.forEach(field => {
if (a[field] != null)
addToTypeSuffix.push(a[field]);
});
}
let newType;
if (ac && ac.key != null && a[ac.key]) {
addToTypeSuffix.unshift(a[ac.key]);
newType = type + addToTypeSuffix.join(".");
if (!this.annotationMap.has(newType)) {
const title = a[ac.key] != null ? a[ac.key] : "";
this.annotationMap.set(newType, Object.assign(Object.assign({}, ac), { type: newType, color: typeof ac.color === "string" ? RcsbAnnotationConfig.randomRgba(title) : Object.assign(Object.assign({}, ac.color), { colors: RcsbAnnotationConfig.randomRgba(title) }), prefix: trackTitle !== null && trackTitle !== void 0 ? trackTitle : ac.title, title: title, provenanceList: new Set() }));
this.addNewType(newType, type);
}
}
else if (titleSuffix != null) {
newType = type + addToTypeSuffix.join(".");
if (!this.annotationMap.has(newType)) {
this.annotationMap.set(newType, Object.assign(Object.assign({ display: (_b = ac === null || ac === void 0 ? void 0 : ac.display) !== null && _b !== void 0 ? _b : "block" /* RcsbFvDisplayTypes.BLOCK */ }, ac), { type: newType, prefix: trackTitle !== null && trackTitle !== void 0 ? trackTitle : ac === null || ac === void 0 ? void 0 : ac.title, title: titleSuffix, provenanceList: new Set() }));
this.addNewType(newType, type, titleSuffix);
}
}
else if (trackTitle != null) {
newType = type + addToTypeSuffix.join(".");
if (!this.annotationMap.has(newType)) {
this.annotationMap.set(newType, Object.assign(Object.assign({ display: "block" /* RcsbFvDisplayTypes.BLOCK */, type: uniqid("type-") }, ac), { title: trackTitle, provenanceList: new Set() }));
this.addNewType(newType, type);
}
}
else {
newType = type + addToTypeSuffix.join(".");
if (!this.annotationMap.has(newType) || this.mergedTypes.has(type)) {
this.addNewType(newType, type);
}
}
this.addProvenance(newType, (_c = feature.provenance_source) !== null && _c !== void 0 ? _c : "N/A");
return newType;
});
}
isMergedType(type) {
return this.mergedTypes.has(type);
}
getMergeConfig(type) {
return this.mergedTypes.get(type);
}
addNewType(newType, type, titleSuffix) {
const mt = this.mergedTypes.get(type);
if (mt) {
const mergedType = titleSuffix ? mt.type + "." + titleSuffix : mt.type;
if (newType != type)
this.mergedTypes.set(newType, {
merged_types: mt.merged_types,
display: mt.display,
type: mergedType,
title: mt.title,
});
this.annotationMap.set(mergedType, {
type: mergedType,
display: mt.display,
title: titleSuffix !== null && titleSuffix !== void 0 ? titleSuffix : mt.title,
prefix: titleSuffix ? mt.title : undefined,
provenanceList: new Set()
});
this.checkAndIncludeNewType(mergedType, mt.type);
}
else {
this.checkAndIncludeNewType(newType, type);
}
}
checkAndIncludeNewType(newType, type) {
var _a, _b, _c, _d, _e, _f;
if (type === newType)
return;
if (this.annotationTypes.instance.has(type) && !((_a = this.annotationTypes.instance.get(type)) === null || _a === void 0 ? void 0 : _a.includes(newType)))
(_b = this.annotationTypes.instance.get(type)) === null || _b === void 0 ? void 0 : _b.push(newType);
if (this.annotationTypes.entity.has(type) && !((_c = this.annotationTypes.entity.get(type)) === null || _c === void 0 ? void 0 : _c.includes(newType)))
(_d = this.annotationTypes.entity.get(type)) === null || _d === void 0 ? void 0 : _d.push(newType);
if (this.annotationTypes.external.has(type) && !((_e = this.annotationTypes.external.get(type)) === null || _e === void 0 ? void 0 : _e.includes(newType)))
(_f = this.annotationTypes.external.get(type)) === null || _f === void 0 ? void 0 : _f.push(newType);
}
static randomRgba(str) {
return stc(str);
}
addProvenance(type, provenanceName) {
var _a;
if (this.annotationMap.has(type))
(_a = this.annotationMap.get(type)) === null || _a === void 0 ? void 0 : _a.provenanceList.add(provenanceName);
}
addMultipleProvenance(type, provenanceList) {
provenanceList.forEach(p => {
this.addProvenance(type, p);
});
}
initTypes() {
var _a, _b, _c, _d;
(_a = this.annotationConfigMap.external_data_order) === null || _a === void 0 ? void 0 : _a.forEach(type => {
this.annotationTypes.external.set(type, [type]);
});
(_b = this.annotationConfigMap.instance_order) === null || _b === void 0 ? void 0 : _b.forEach(type => {
this.annotationTypes.instance.set(type, [type]);
});
(_c = this.annotationConfigMap.entity_order) === null || _c === void 0 ? void 0 : _c.forEach(type => {
this.annotationTypes.entity.set(type, [type]);
});
(_d = this.annotationConfigMap.merge) === null || _d === void 0 ? void 0 : _d.forEach(m => {
m.merged_types.forEach(type => {
this.mergedTypes.set(type, m);
});
});
}
}
class ArraySuffix extends Array {
join(separator) {
if (this.length == 0)
return "";
else
return ":" + super.join(separator);
}
push(...items) {
items.forEach(i => {
if (i)
super.push(i);
});
return this.length;
}
}
//# sourceMappingURL=RcsbAnnotationConfig.js.map