molstar
Version:
A comprehensive macromolecular library.
98 lines (97 loc) • 4.37 kB
JavaScript
;
/**
* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.AlignSequences = void 0;
exports.entityKey = entityKey;
exports.getSequence = getSequence;
const structure_1 = require("../../structure/structure");
const alignment_1 = require("./alignment");
const int_1 = require("../../../mol-data/int");
var AlignSequences;
(function (AlignSequences) {
function createSeqIdIndicesMap(element) {
const seqIds = new Map();
if (structure_1.Unit.isAtomic(element.unit)) {
const { label_seq_id } = element.unit.model.atomicHierarchy.residues;
const { residueIndex } = element.unit;
for (let i = 0, il = int_1.OrderedSet.size(element.indices); i < il; ++i) {
const uI = int_1.OrderedSet.getAt(element.indices, i);
const eI = element.unit.elements[uI];
const seqId = label_seq_id.value(residueIndex[eI]);
if (seqIds.has(seqId))
seqIds.get(seqId).push(uI);
else
seqIds.set(seqId, [uI]);
}
}
else if (structure_1.Unit.isCoarse(element.unit)) {
const { seq_id_begin } = structure_1.Unit.isSpheres(element.unit)
? element.unit.model.coarseHierarchy.spheres
: element.unit.model.coarseHierarchy.gaussians;
for (let i = 0, il = int_1.OrderedSet.size(element.indices); i < il; ++i) {
const uI = int_1.OrderedSet.getAt(element.indices, i);
const eI = element.unit.elements[uI];
const seqId = seq_id_begin.value(eI);
seqIds.set(seqId, [uI]);
}
}
return seqIds;
}
AlignSequences.createSeqIdIndicesMap = createSeqIdIndicesMap;
function compute(input, options = {}) {
const seqA = getSequence(input.a.unit);
const seqB = getSequence(input.b.unit);
const seqIdIndicesA = createSeqIdIndicesMap(input.a);
const seqIdIndicesB = createSeqIdIndicesMap(input.b);
const indicesA = [];
const indicesB = [];
const { aliA, aliB, score } = (0, alignment_1.align)(seqA.code.toArray(), seqB.code.toArray(), options);
let seqIdxA = 0, seqIdxB = 0;
for (let i = 0, il = aliA.length; i < il; ++i) {
if (aliA[i] === '-' || aliB[i] === '-') {
if (aliA[i] !== '-')
seqIdxA += 1;
if (aliB[i] !== '-')
seqIdxB += 1;
continue;
}
const seqIdA = seqA.seqId.value(seqIdxA);
const seqIdB = seqB.seqId.value(seqIdxB);
if (seqIdIndicesA.has(seqIdA) && seqIdIndicesB.has(seqIdB)) {
const iA = seqIdIndicesA.get(seqIdA);
const iB = seqIdIndicesB.get(seqIdB);
// use min length to guard against alternate locations
for (let j = 0, jl = Math.min(iA.length, iB.length); j < jl; ++j) {
indicesA.push(iA[j]);
indicesB.push(iB[j]);
}
}
seqIdxA += 1, seqIdxB += 1;
}
const outA = int_1.OrderedSet.intersect(int_1.OrderedSet.ofSortedArray(indicesA), input.a.indices);
const outB = int_1.OrderedSet.intersect(int_1.OrderedSet.ofSortedArray(indicesB), input.b.indices);
return {
a: { unit: input.a.unit, indices: outA },
b: { unit: input.b.unit, indices: outB },
score
};
}
AlignSequences.compute = compute;
})(AlignSequences || (exports.AlignSequences = AlignSequences = {}));
function entityKey(unit) {
switch (unit.kind) {
case 0 /* Unit.Kind.Atomic */:
return unit.model.atomicHierarchy.index.getEntityFromChain(unit.chainIndex[unit.elements[0]]);
case 1 /* Unit.Kind.Spheres */:
return unit.model.coarseHierarchy.spheres.entityKey[unit.elements[0]];
case 2 /* Unit.Kind.Gaussians */:
return unit.model.coarseHierarchy.gaussians.entityKey[unit.elements[0]];
}
}
function getSequence(unit) {
return unit.model.sequence.byEntityKey[entityKey(unit)].sequence;
}