molstar
Version:
A comprehensive macromolecular library.
80 lines (79 loc) • 3.15 kB
JavaScript
;
/**
* Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Adam Midlik <midlik@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.ElementSequenceWrapper = void 0;
const int_1 = require("../../mol-data/int");
const structure_1 = require("../../mol-model/structure");
const names_1 = require("../../mol-util/color/names");
const wrapper_1 = require("./wrapper");
class ElementSequenceWrapper extends wrapper_1.SequenceWrapper {
residueLabel(seqIdx) {
return 'X';
}
residueColor(seqIdx) {
return names_1.ColorNames.black;
}
residueClass(seqIdx) {
return 'msp-sequence-present';
}
getSeqIndices(loci) {
const { structure, units } = this.data;
if (structure_1.StructureElement.Loci.is(loci)) {
if (!structure_1.Structure.areRootsEquivalent(loci.structure, structure))
return int_1.Interval.Empty;
loci = structure_1.StructureElement.Loci.remap(loci, structure);
for (const e of loci.elements) {
const indices = this.unitIndices.get(e.unit.id);
if (indices) {
if (int_1.OrderedSet.isSubset(indices, e.indices)) {
// this assumes this SequnceWrapper has only a single unit, otherwise we'd need to collect indices from all units and apply offsets
return e.indices;
}
}
}
}
else if (structure_1.Structure.isLoci(loci)) {
if (!structure_1.Structure.areRootsEquivalent(loci.structure, structure))
return int_1.Interval.Empty;
for (let i = 0, il = units.length; i < il; ++i) {
const indices = this.unitIndices.get(units[i].id);
return indices;
}
}
return int_1.Interval.Empty;
}
getLoci(seqIdx) {
const { units } = this.data;
const lociElements = [];
let offset = 0;
for (let i = 0, il = units.length; i < il; ++i) {
const unit = units[i];
if (seqIdx < offset + unit.elements.length) {
lociElements.push({ unit, indices: int_1.Interval.ofSingleton(seqIdx - offset) });
break;
}
offset += unit.elements.length;
}
return structure_1.StructureElement.Loci(this.data.structure, lociElements);
}
constructor(data) {
let length = 0;
const unitIndices = new Map();
const lociElements = [];
for (let i = 0, il = data.units.length; i < il; ++i) {
const unit = data.units[i];
length += unit.elements.length;
const indices = int_1.Interval.ofBounds(0, unit.elements.length);
unitIndices.set(unit.id, indices);
lociElements.push({ unit, indices });
}
super(data, length);
this.unitIndices = unitIndices;
}
}
exports.ElementSequenceWrapper = ElementSequenceWrapper;