diff --git a/src/mol-data/int/map.ts b/src/mol-data/int/map.ts
index 4d75644ed6f43ff7f6c801358745438c91f88c3b..30725a89c49238468e858c85cb88c65f3b3062e4 100644
--- a/src/mol-data/int/map.ts
+++ b/src/mol-data/int/map.ts
@@ -28,16 +28,6 @@ namespace IntMap {
return iterableToArray(map.keys());
}
- export function ofObj<T>(obj: { [key: number]: T }): IntMap<T> {
- const keys = Object.keys(obj);
- const ret = new Map<number, T>();
- for (let i = 0, _i = keys.length; i < _i; i++) {
- const k = keys[i];
- ret.set(+k, obj[k as any]);
- }
- return ret as IntMap<T>;
- }
-
export function Mutable<T>(): Mutable<T> {
return new Map<number, T>() as Mutable<T>;
}
@@ -45,6 +35,27 @@ namespace IntMap {
export function asImmutable<T>(map: IntMap<T>): IntMap<T> {
return map;
}
+
+ export function copy<T>(map: IntMap<T>): Mutable<T> {
+ const ret = Mutable<T>();
+ const it = map.keys();
+ while (true) {
+ const { done, value } = it.next();
+ if (done) break;
+ ret.set(value, map.get(value));
+ }
+ return ret;
+ }
+
+ export function addFrom<T>(map: Mutable<T>, src: IntMap<T>) {
+ const it = src.keys();
+ while (true) {
+ const { done, value } = it.next();
+ if (done) break;
+ map.set(value, src.get(value));
+ }
+ return map;
+ }
}
export default IntMap;
\ No newline at end of file
diff --git a/src/mol-model/structure/query/generators.ts b/src/mol-model/structure/query/generators.ts
index 305488104df685fbfc81f9779cc712d0970e7bc2..e8d8ab6469692124e43ac8eaf7a846b612e4ac2f 100644
--- a/src/mol-model/structure/query/generators.ts
+++ b/src/mol-model/structure/query/generators.ts
@@ -45,7 +45,7 @@ function atomGroupsLinear(atomTest: Atom.Predicate): Query {
for (let i = 0, _i = unitIds.length; i < _i; i++) {
const unitId = unitIds[i];
- l.unit = units[unitId];
+ l.unit = units.get(unitId);
const set = AtomSet.unitGetByIndex(atoms, i);
builder.beginUnit();
@@ -69,7 +69,7 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A
for (let i = 0, _i = unitIds.length; i < _i; i++) {
const unitId = unitIds[i];
- const unit = units[unitId];
+ const unit = units.get(unitId);
l.unit = unit;
const set = AtomSet.unitGetByIndex(atoms, i);
@@ -160,7 +160,7 @@ function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, group
for (let i = 0, _i = unitIds.length; i < _i; i++) {
const unitId = unitIds[i];
- const unit = units[unitId];
+ const unit = units.get(unitId);
l.unit = unit;
const set = AtomSet.unitGetByIndex(atoms, i);
diff --git a/src/mol-model/structure/query/query.ts b/src/mol-model/structure/query/query.ts
index 20c569b6d96b66351c2aca3fb2837f056bb47c49..001f1e0e79b3082011d3b60baecfa2a67e88befa 100644
--- a/src/mol-model/structure/query/query.ts
+++ b/src/mol-model/structure/query/query.ts
@@ -7,5 +7,7 @@
import { Structure } from '../structure'
import Selection from './selection'
+// TODO: Query { (s: Structure): Computation<Selection> }
+
interface Query { (s: Structure): Selection }
export default Query
\ No newline at end of file
diff --git a/src/mol-model/structure/query/selection.ts b/src/mol-model/structure/query/selection.ts
index c1e0f9fb179d72184e14e492c440bf7d60e6c0b5..8aec9b363f73b2d7e3db98e7732f6dff4ba861eb 100644
--- a/src/mol-model/structure/query/selection.ts
+++ b/src/mol-model/structure/query/selection.ts
@@ -6,6 +6,7 @@
import Iterator from 'mol-data/iterator'
import { HashSet } from 'mol-data/util'
+import { IntMap } from 'mol-data/int'
import { Structure, Atom, AtomSet } from '../structure'
type Selection =
@@ -105,20 +106,18 @@ export default Selection
function unionUnits(xs: Structure[]): Structure['units'] {
let prev = xs[0].units;
- let sameModel = true;
+ let sameUnits = true;
for (let i = 1, _i = xs.length; i < _i; i++) {
- if (xs[i].units !== prev) sameModel = false;
+ if (xs[i].units !== prev) sameUnits = false;
}
- if (sameModel) return prev;
+ if (sameUnits) return prev;
- let ret: any = { ...prev };
+ const ret = IntMap.copy(prev);
for (let i = 1, _i = xs.length; i < _i; i++) {
const units = xs[i].units;
- if (units !== prev) {
- const keys = Object.keys(units);
- for (let j = 0; j < keys.length; j++) ret[keys[j]] = (units as any)[keys[j]];
- }
- prev = xs[i];
+ if (units !== prev) IntMap.addFrom(ret, units);
+ prev = units;
}
+
return ret;
}
diff --git a/src/mol-model/structure/structure/atom.ts b/src/mol-model/structure/structure/atom.ts
index 217bbb1eb581c5d869c3c91f70d100e8c598fa8f..55a88dcb633af95e0242d38dae0750397e6c708a 100644
--- a/src/mol-model/structure/structure/atom.ts
+++ b/src/mol-model/structure/structure/atom.ts
@@ -29,7 +29,7 @@ namespace Atom {
export interface Predicate extends Property<boolean> { }
export function updateLocation(structure: Structure, l: Location, atom: Atom) {
- l.unit = structure.units[unit(atom)];
+ l.unit = structure.units.get(unit(atom));
l.atom = index(atom);
return l;
}
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 0434bcf8a300b761c7c046fee0410497d641010f..42b97a86832f85524aaa7a63fd4b0008559d0295 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { OrderedSet, Iterator } from 'mol-data/int'
+import { OrderedSet, Iterator, IntMap } from 'mol-data/int'
import { UniqueArray } from 'mol-data/util'
import SymmetryOperator from 'mol-math/geometry/symmetry-operator'
import { Model, Format } from '../model'
@@ -14,14 +14,14 @@ import Atom from './atom'
interface Structure extends Readonly<{
- units: { readonly [id: number]: Unit },
+ units: IntMap<Unit>,
atoms: AtomSet
}> { }
namespace Structure {
- export const Empty = { units: {}, atoms: AtomSet.Empty };
+ export const Empty: Structure = { units: IntMap.Empty, atoms: AtomSet.Empty };
- export function create(units: Structure['units'], atoms: AtomSet): Structure {
+ export function create(units: IntMap<Unit>, atoms: AtomSet): Structure {
return { units, atoms };
}
@@ -36,8 +36,7 @@ namespace Structure {
for (let c = 0; c < chains.count; c++) {
const unit = Unit.create(model, SymmetryOperator.Default);
- builder.addUnit(unit);
- builder.setAtoms(unit.id, OrderedSet.ofBounds(chains.segments[c], chains.segments[c + 1]));
+ builder.add(unit, OrderedSet.ofBounds(chains.segments[c], chains.segments[c + 1]));
}
return builder.getStructure();
@@ -52,12 +51,12 @@ namespace Structure {
}
class BuilderImpl implements Builder {
- private units = Object.create(null);
+ private units = IntMap.Mutable<Unit>();
private atoms = AtomSet.Generator();
atomCount = 0;
add(unit: Unit, atoms: OrderedSet) { this.addUnit(unit); this.setAtoms(unit.id, atoms); }
- addUnit(unit: Unit) { this.units[unit.id] = unit; }
+ addUnit(unit: Unit) { this.units.set(unit.id, unit); }
setAtoms(unitId: number, atoms: OrderedSet) { this.atoms.add(unitId, atoms); this.atomCount += OrderedSet.size(atoms); }
getStructure(): Structure { return this.atomCount > 0 ? Structure.create(this.units, this.atoms.getSet()) : Empty; }
}
@@ -72,9 +71,11 @@ namespace Structure {
}
export function getModels(s: Structure) {
+ const { units, atoms } = s;
const arr = UniqueArray.create<Model['id'], Model>();
- for (const k of Object.keys(s.units)) {
- const u = s.units[+k];
+ const ids = AtomSet.unitIds(atoms);
+ for (let i = 0; i < ids.length; i++) {
+ const u = units.get(ids[i]);
UniqueArray.add(arr, u.model.id, u.model);
}
return arr.array;
diff --git a/src/mol-model/structure/structure/symmetry.ts b/src/mol-model/structure/structure/symmetry.ts
index fa1ca3ab1749e4d88b8a6742c04885be94f9e639..ec8de5d4d65548816e97c02f2e7b965ab1237d7b 100644
--- a/src/mol-model/structure/structure/symmetry.ts
+++ b/src/mol-model/structure/structure/symmetry.ts
@@ -34,7 +34,7 @@ function buildAssemblyImpl(structure: Structure, name: string) {
for (const oper of g.operators) {
for (let uI = 0, _uI = unitIds.length; uI < _uI; uI++) {
- const unit = units[unitIds[uI]];
+ const unit = units.get(unitIds[uI]);
assembler.add(Unit.create(unit.model, oper), AtomSet.unitGetByIndex(atoms, uI));
}
}
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index d0f9286bcfa152dfd8dc521708c4659546d53e0a..204ac9df92c9617de2cf7bb227e0d7d7d9b33208 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -74,7 +74,7 @@ export namespace PropertyAccess {
let s = 0;
for (let i = 0, _i = unitIds.length; i < _i; i++) {
- l.unit = units[unitIds[i]];
+ l.unit = units.get(unitIds[i]);
const set = AtomSet.unitGetByIndex(atoms, i);
@@ -96,7 +96,7 @@ export namespace PropertyAccess {
let vA = 0, cC = 0, rC = 0;
for (let i = 0, _i = unitIds.length; i < _i; i++) {
- const unit = units[unitIds[i]];
+ const unit = units.get(unitIds[i]);
l.unit = unit;
const set = AtomSet.unitGetByIndex(atoms, i);
@@ -134,7 +134,7 @@ export namespace PropertyAccess {
let s = 0;
for (let i = 0, _i = unitIds.length; i < _i; i++) {
- const unit = units[unitIds[i]];
+ const unit = units.get(unitIds[i]);
l.unit = unit;
const set = AtomSet.unitGetByIndex(atoms, i);
const residuesIt = Segmentation.transientSegments(unit.hierarchy.residueSegments, set);
@@ -155,7 +155,7 @@ export namespace PropertyAccess {
const l = Atom.Location();
while (atomsIt.hasNext) {
const a = atomsIt.move();
- l.unit = units[Atom.unit(a)];
+ l.unit = units.get(Atom.unit(a));
l.atom = Atom.index(a);
s += p(l);
}
@@ -200,7 +200,7 @@ export namespace PropertyAccess {
for (let i = 0, _i = unitIds.length; i < _i; i++) {
const unitId = unitIds[i];
- const unit = units[unitId];
+ const unit = units.get(unitId);
const set = AtomSet.unitGetByIndex(atoms, i);
//const { residueIndex, chainIndex } = unit;
const p = unit.conformation.atomId.value;