molstar
Version:
A comprehensive macromolecular library.
78 lines (77 loc) • 3.14 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.ChainSequenceWrapper = 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 ChainSequenceWrapper extends wrapper_1.SequenceWrapper {
residueLabel(seqIdx) {
return this.label;
}
residueColor(seqIdx) {
return names_1.ColorNames.black;
}
residueClass(seqIdx) {
return 'msp-sequence-present';
}
getSeqIndices(loci) {
const { structure } = 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)) {
return int_1.Interval.ofSingleton(0);
}
}
}
}
else if (structure_1.Structure.isLoci(loci)) {
if (!structure_1.Structure.areRootsEquivalent(loci.structure, structure))
return int_1.Interval.Empty;
return int_1.Interval.ofSingleton(0);
}
return int_1.Interval.Empty;
}
getLoci(seqIdx) {
return this.loci;
}
constructor(data) {
let residueCount = 0;
let elementCount = 0;
const counts = [];
const l = structure_1.StructureElement.Location.create(data.structure);
const unitIndices = new Map();
const lociElements = [];
for (let i = 0, il = data.units.length; i < il; ++i) {
const unit = data.units[i];
structure_1.StructureElement.Location.set(l, data.structure, unit, unit.elements[0]);
const entitySeq = unit.model.sequence.byEntityKey[structure_1.StructureProperties.entity.key(l)];
if (entitySeq)
residueCount += entitySeq.sequence.length;
elementCount += unit.elements.length;
const indices = int_1.Interval.ofBounds(0, unit.elements.length);
unitIndices.set(unit.id, indices);
lociElements.push({ unit, indices });
}
if (residueCount > 0)
counts.push(`${residueCount} residues`);
counts.push(`${elementCount} elements`);
const length = 1;
super(data, length);
this.label = `Whole Chain (${counts.join(', ')})`;
this.unitIndices = unitIndices;
this.loci = structure_1.StructureElement.Loci(this.data.structure, lociElements);
}
}
exports.ChainSequenceWrapper = ChainSequenceWrapper;