molstar
Version:
A comprehensive macromolecular library.
97 lines • 4.07 kB
JavaScript
;
/**
* Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.getCoarseKeys = void 0;
var sorted_ranges_1 = require("../../../../../mol-data/int/sorted-ranges");
var int_1 = require("../../../../../mol-data/int");
function getElementKey(map, key, counter) {
if (map.has(key))
return map.get(key);
var ret = counter.index++;
map.set(key, ret);
return ret;
}
function getElementSubstructureKeyMap(map, key) {
if (map.has(key))
return map.get(key);
var ret = new Map();
map.set(key, ret);
return ret;
}
function createLookUp(entities, chain, seq) {
var getEntKey = entities.getEntityIndex;
var findChainKey = function (e, c) {
var eKey = getEntKey(e);
if (eKey < 0)
return -1;
var cm = chain.get(eKey);
if (!cm.has(c))
return -1;
return cm.get(c);
};
var findSequenceKey = function (e, c, s) {
var eKey = getEntKey(e);
if (eKey < 0)
return -1;
var cm = chain.get(eKey);
if (cm === undefined)
return -1;
var cKey = cm.get(c);
if (cKey === undefined)
return -1;
var sm = seq.get(cKey);
var elementIndices = sm.elementIndices, seqRanges = sm.seqRanges;
var idx = sorted_ranges_1.SortedRanges.firstIntersectionIndex(seqRanges, int_1.OrderedSet.ofSingleton(s));
return (idx !== -1 ? elementIndices[idx] : -1);
};
return { findChainKey: findChainKey, findSequenceKey: findSequenceKey };
}
function missingEntity(k) {
throw new Error("Missing entity entry for entity id '" + k + "'.");
}
function getCoarseKeys(data, entities) {
var entity_id = data.entity_id, asym_id = data.asym_id, seq_id_begin = data.seq_id_begin, seq_id_end = data.seq_id_end, count = data.count, chainElementSegments = data.chainElementSegments;
var seqMaps = new Map();
var chainMaps = new Map(), chainCounter = { index: 0 };
var chainKey = new Int32Array(count);
var entityKey = new Int32Array(count);
var chainToEntity = new Int32Array(chainElementSegments.count);
for (var i = 0; i < count; i++) {
entityKey[i] = entities.getEntityIndex(entity_id.value(i));
if (entityKey[i] < 0)
missingEntity(entity_id.value(i));
}
for (var cI = 0; cI < chainElementSegments.count; cI++) {
var start = chainElementSegments.offsets[cI];
var end = chainElementSegments.offsets[cI + 1];
var eK = entityKey[start];
chainToEntity[cI] = eK;
var map = getElementSubstructureKeyMap(chainMaps, eK);
var key = getElementKey(map, asym_id.value(start), chainCounter);
for (var i = start; i < end; i++)
chainKey[i] = key;
// create seq_id map for the ranges defined by seq_id_begin and seq_id_end
var elementIndices = [];
var seqRanges = [];
for (var i = start; i < end; i++) {
var seqStart = seq_id_begin.value(i);
var seqEnd = seq_id_end.value(i);
elementIndices.push(i);
seqRanges.push(seqStart, seqEnd);
}
var seqMap = { elementIndices: elementIndices, seqRanges: sorted_ranges_1.SortedRanges.ofSortedRanges(seqRanges) };
seqMaps.set(key, seqMap);
}
var _a = createLookUp(entities, chainMaps, seqMaps), findChainKey = _a.findChainKey, findSequenceKey = _a.findSequenceKey;
var getEntityFromChain = function (c) {
return chainToEntity[c];
};
return { chainKey: chainKey, entityKey: entityKey, findSequenceKey: findSequenceKey, findChainKey: findChainKey, getEntityFromChain: getEntityFromChain };
}
exports.getCoarseKeys = getCoarseKeys;
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