From 19d9439955ec6fb9683657c9c65e236a5728c5fa Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 2 Nov 2017 14:12:59 +0100
Subject: [PATCH] Simplified some modules
---
.../collections/_spec/iterators.spec.ts | 1 +
src/mol-base/collections/integer.ts | 14 +++++
src/mol-base/collections/iterator.ts | 33 +++++++++--
src/mol-data/_spec/atom-set.spec.ts | 4 +-
src/mol-data/model/builders/mmcif.ts | 3 +-
src/mol-data/model/properties/computed.ts | 1 -
src/mol-data/model/properties/hierarchy.ts | 6 +-
src/mol-data/model/utils/hierarchy-keys.ts | 3 +-
src/mol-data/query.ts | 2 +-
src/mol-data/query/generators.ts | 10 +++-
src/mol-data/query/query.ts | 11 ++++
src/mol-data/query/selection.ts | 4 +-
src/mol-data/structure.ts | 24 ++------
src/mol-data/structure/atom.ts | 4 +-
.../structure/{atom-set.ts => atom/set.ts} | 50 ++++++++--------
.../{atom-set => atom/set}/builder.ts | 6 +-
.../{atom-set/base.ts => atom/set/impl.ts} | 11 ++--
.../{atom-set => atom/set}/properties.ts | 0
src/mol-data/structure/base.ts | 37 ------------
src/mol-data/structure/structure.ts | 58 +++++++++++++++++++
src/perf-tests/sets.ts | 6 +-
src/perf-tests/structure.ts | 7 +--
22 files changed, 172 insertions(+), 123 deletions(-)
create mode 100644 src/mol-base/collections/integer.ts
create mode 100644 src/mol-data/query/query.ts
rename src/mol-data/structure/{atom-set.ts => atom/set.ts} (54%)
rename src/mol-data/structure/{atom-set => atom/set}/builder.ts (91%)
rename src/mol-data/structure/{atom-set/base.ts => atom/set/impl.ts} (97%)
rename src/mol-data/structure/{atom-set => atom/set}/properties.ts (100%)
delete mode 100644 src/mol-data/structure/base.ts
create mode 100644 src/mol-data/structure/structure.ts
diff --git a/src/mol-base/collections/_spec/iterators.spec.ts b/src/mol-base/collections/_spec/iterators.spec.ts
index 8df989242..7c8cabe4a 100644
--- a/src/mol-base/collections/_spec/iterators.spec.ts
+++ b/src/mol-base/collections/_spec/iterators.spec.ts
@@ -27,4 +27,5 @@ describe('basic iterators', () => {
check('array', Iterator.Array([1, 2, 3]), [1, 2, 3]);
check('range', Iterator.Range(0, 3), [0, 1, 2, 3]);
check('map', Iterator.map(Iterator.Range(0, 1), x => x + 1), [1, 2]);
+ check('filter', Iterator.filter(Iterator.Range(0, 3), x => x >= 2), [2, 3]);
});
\ No newline at end of file
diff --git a/src/mol-base/collections/integer.ts b/src/mol-base/collections/integer.ts
new file mode 100644
index 000000000..a7ca91076
--- /dev/null
+++ b/src/mol-base/collections/integer.ts
@@ -0,0 +1,14 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import Interval from './integer/interval'
+import OrderedSet from './integer/ordered-set'
+import Segmentation from './integer/segmentation'
+import SortedArray from './integer/sorted-array'
+import Tuple from './integer/tuple'
+import Iterator from './iterator'
+
+export { Interval, OrderedSet, Segmentation, SortedArray, Tuple, Iterator }
\ No newline at end of file
diff --git a/src/mol-base/collections/iterator.ts b/src/mol-base/collections/iterator.ts
index 50ad41cec..02f302d82 100644
--- a/src/mol-base/collections/iterator.ts
+++ b/src/mol-base/collections/iterator.ts
@@ -21,7 +21,7 @@ class ArrayIteratorImpl<T> implements Iterator<T> {
private length: number = 0;
private lastValue: T;
- hasNext: boolean;
+ hasNext: boolean = false;
move() {
++this.index;
@@ -41,9 +41,8 @@ class ArrayIteratorImpl<T> implements Iterator<T> {
}
class RangeIteratorImpl implements Iterator<number> {
- private value: number;
-
- hasNext: boolean;
+ private value: number = 0;
+ hasNext: boolean = false;
move() {
++this.value;
@@ -64,7 +63,7 @@ class ValueIterator<T> implements Iterator<T> {
}
class MapIteratorImpl<T, R> implements Iterator<R> {
- hasNext: boolean;
+ hasNext: boolean = false;
move() {
const v = this.f(this.base.move());
@@ -77,12 +76,36 @@ class MapIteratorImpl<T, R> implements Iterator<R> {
}
}
+class FilterIteratorImpl<T> implements Iterator<T> {
+ private next: T;
+ hasNext: boolean;
+
+ move() {
+ const ret = this.next;
+ this.hasNext = this.findNext();
+ return ret;
+ }
+
+ private findNext() {
+ while (this.base.hasNext) {
+ this.next = this.base.move();
+ if (this.p(this.next)) return true;
+ }
+ return false;
+ }
+
+ constructor(private base: Iterator<T>, private p: (v: T) => boolean) {
+ this.hasNext = this.findNext();
+ }
+}
+
namespace Iterator {
export const Empty: Iterator<any> = new RangeIteratorImpl(0, -1);
export function Array<T>(xs: ArrayLike<T>): Iterator<T> { return new ArrayIteratorImpl<T>(xs); }
export function Value<T>(value: T): Iterator<T> { return new ValueIterator(value); }
export function Range(min: number, max: number): Iterator<number> { return new RangeIteratorImpl(min, max); }
export function map<T, R>(base: Iterator<T>, f: (v: T) => R): Iterator<R> { return new MapIteratorImpl(base, f); }
+ export function filter<T>(base: Iterator<T>, p: (v: T) => boolean): Iterator<T> { return new FilterIteratorImpl(base, p); }
}
export default Iterator
\ No newline at end of file
diff --git a/src/mol-data/_spec/atom-set.spec.ts b/src/mol-data/_spec/atom-set.spec.ts
index 375e5ed37..62e5ea804 100644
--- a/src/mol-data/_spec/atom-set.spec.ts
+++ b/src/mol-data/_spec/atom-set.spec.ts
@@ -4,8 +4,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import OrderedSet from '../../mol-base/collections/integer/ordered-set'
-import AtomSet from '../structure/atom-set'
+import { OrderedSet } from '../../mol-base/collections/integer'
+import AtomSet from '../structure/atom/set'
import Atom from '../structure/atom'
describe('atom set', () => {
diff --git a/src/mol-data/model/builders/mmcif.ts b/src/mol-data/model/builders/mmcif.ts
index 5890965b0..240e1e503 100644
--- a/src/mol-data/model/builders/mmcif.ts
+++ b/src/mol-data/model/builders/mmcif.ts
@@ -9,8 +9,7 @@ import { Frame as mmCIF } from '../../../mol-io/reader/cif/schema/mmcif'
import Model from '../../model'
import Column from '../../../mol-base/collections/column'
import Table from '../../../mol-base/collections/table'
-import Interval from '../../../mol-base/collections/integer/interval'
-import Segmentation from '../../../mol-base/collections/integer/segmentation'
+import { Interval, Segmentation } from '../../../mol-base/collections/integer'
import { newUUID } from '../../../mol-base/utils/uuid'
import * as Hierarchy from '../properties/hierarchy'
import Conformation from '../properties/conformation'
diff --git a/src/mol-data/model/properties/computed.ts b/src/mol-data/model/properties/computed.ts
index 72b082ec5..0cb9039cc 100644
--- a/src/mol-data/model/properties/computed.ts
+++ b/src/mol-data/model/properties/computed.ts
@@ -8,7 +8,6 @@
// secondary structure is also a computed property
// import { SecondaryStructureType } from '../constants'
-// import Segmentation from '../../../mol-base/collections/integer/segmentation'
// interface SecondaryStructure {
diff --git a/src/mol-data/model/properties/hierarchy.ts b/src/mol-data/model/properties/hierarchy.ts
index ac0c96fa3..e86fc8983 100644
--- a/src/mol-data/model/properties/hierarchy.ts
+++ b/src/mol-data/model/properties/hierarchy.ts
@@ -6,7 +6,7 @@
import Column from '../../../mol-base/collections/column'
import Table from '../../../mol-base/collections/table'
-import IntervalSegmentation from '../../../mol-base/collections/integer/segmentation'
+import { Segmentation } from '../../../mol-base/collections/integer'
import { Schema as mmCIF } from '../../../mol-io/reader/cif/schema/mmcif'
const _esCache = Object.create(null);
@@ -59,8 +59,8 @@ export interface Data {
}
export interface Segments {
- residueSegments: IntervalSegmentation,
- chainSegments: IntervalSegmentation
+ residueSegments: Segmentation,
+ chainSegments: Segmentation
}
export interface Keys {
diff --git a/src/mol-data/model/utils/hierarchy-keys.ts b/src/mol-data/model/utils/hierarchy-keys.ts
index ae9f9a176..6bc5a4a8c 100644
--- a/src/mol-data/model/utils/hierarchy-keys.ts
+++ b/src/mol-data/model/utils/hierarchy-keys.ts
@@ -6,8 +6,7 @@
import Column from '../../../mol-base/collections/column'
import { Data, Segments, Keys } from '../properties/hierarchy'
-import Segmentation from '../../../mol-base/collections/integer/segmentation'
-import Interval from '../../../mol-base/collections/integer/interval'
+import { Interval, Segmentation } from '../../../mol-base/collections/integer'
function getResidueId(comp_id: string, seq_id: number, ins_code: string) {
return `${comp_id} ${seq_id} ${ins_code}`;
diff --git a/src/mol-data/query.ts b/src/mol-data/query.ts
index 89aaef1c2..e5684e1bd 100644
--- a/src/mol-data/query.ts
+++ b/src/mol-data/query.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Structure from './structure'
+import { Structure } from './structure'
import Selection from './query/selection'
interface Query { (s: Structure): Selection }
diff --git a/src/mol-data/query/generators.ts b/src/mol-data/query/generators.ts
index 28ce9a001..d91aad5eb 100644
--- a/src/mol-data/query/generators.ts
+++ b/src/mol-data/query/generators.ts
@@ -2,4 +2,12 @@
* Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
- */
\ No newline at end of file
+ */
+
+// import Selection from './selection'
+// import AtomSet from '../structure/atom-set'
+// import Atom from '../structure/atom'
+
+// class LinearGroupingBuilder {
+
+// }
\ No newline at end of file
diff --git a/src/mol-data/query/query.ts b/src/mol-data/query/query.ts
new file mode 100644
index 000000000..f3bd96b69
--- /dev/null
+++ b/src/mol-data/query/query.ts
@@ -0,0 +1,11 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Structure } from '../structure'
+import Selection from './selection'
+
+interface Query { (s: Structure): Selection }
+export default Query
\ No newline at end of file
diff --git a/src/mol-data/query/selection.ts b/src/mol-data/query/selection.ts
index 762c304ac..d2ef57dff 100644
--- a/src/mol-data/query/selection.ts
+++ b/src/mol-data/query/selection.ts
@@ -6,9 +6,7 @@
import Iterator from '../../mol-base/collections/iterator'
import HashSet from '../../mol-base/collections/hash-set'
-import Structure from './../structure'
-import Atom from './../structure/atom'
-import AtomSet from './../structure/atom-set'
+import { Structure, Atom, AtomSet } from '../structure'
type Selection =
| Structure // each atom is interpreted as a singleton structure
diff --git a/src/mol-data/structure.ts b/src/mol-data/structure.ts
index cab016bb1..cc8bf49f3 100644
--- a/src/mol-data/structure.ts
+++ b/src/mol-data/structure.ts
@@ -4,24 +4,10 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-//import { Vec3 } from '../mol-base/math/linear-algebra'
-import AtomSet from './structure/atom-set'
+import Atom from './structure/atom'
+import AtomSet from './structure/atom/set'
+import Structure from './structure/structure'
+import Operator from './structure/operator'
import Unit from './structure/unit'
-import * as Base from './structure/base'
-//import Model from './model'
-//import Operator from './structure/operator'
-// TODO: do "single model" version of the structure?
-interface Structure extends Readonly<{
- units: { readonly [id: number]: Unit },
- atoms: AtomSet
-}> { }
-
-namespace Structure {
- export const Empty = Base.Empty;
- export const ofModel = Base.ofModel;
- // TODO: "lift" atom set operators
- // TODO: "diff"
-}
-
-export default Structure
\ No newline at end of file
+export { Atom, AtomSet, Structure, Operator, Unit }
\ No newline at end of file
diff --git a/src/mol-data/structure/atom.ts b/src/mol-data/structure/atom.ts
index 5dfb6d5da..30f5f60f1 100644
--- a/src/mol-data/structure/atom.ts
+++ b/src/mol-data/structure/atom.ts
@@ -4,9 +4,9 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Tuple from '../../mol-base/collections/integer/tuple'
+import { Tuple } from '../../mol-base/collections/integer'
import Unit from './unit'
-import Structure from '../structure'
+import Structure from './structure'
/** Atom pointer */
interface Atom { '@type': Tuple['@type'] }
diff --git a/src/mol-data/structure/atom-set.ts b/src/mol-data/structure/atom/set.ts
similarity index 54%
rename from src/mol-data/structure/atom-set.ts
rename to src/mol-data/structure/atom/set.ts
index 1e654f113..92a04dc70 100644
--- a/src/mol-data/structure/atom-set.ts
+++ b/src/mol-data/structure/atom/set.ts
@@ -4,41 +4,39 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import SortedArray from '../../mol-base/collections/integer/sorted-array'
-import OrderedSet from '../../mol-base/collections/integer/ordered-set'
-import Iterator from '../../mol-base/collections/iterator'
-import Atom from './atom'
-import * as Base from './atom-set/base'
-import createBuilder from './atom-set/builder'
+import { OrderedSet, SortedArray, Iterator } from '../../../mol-base/collections/integer'
+import Atom from '../atom'
+import * as Impl from './set/impl'
+import createBuilder from './set/builder'
/** A map-like representation of grouped atom set */
namespace AtomSet {
- export const Empty: AtomSet = Base.Empty as any;
+ export const Empty: AtomSet = Impl.Empty as any;
- export const create: (data: Atom | ArrayLike<Atom> | { [unitId: number]: OrderedSet }) => AtomSet = Base.create as any;
+ export const create: (data: Atom | ArrayLike<Atom> | { [unitId: number]: OrderedSet }) => AtomSet = Impl.create as any;
- export const unitCount: (set: AtomSet) => number = Base.keyCount as any;
- export const unitIds: (set: AtomSet) => SortedArray = Base.getKeys as any;
- export const unitHas: (set: AtomSet, id: number) => boolean = Base.hasKey as any;
- export const unitGetId: (set: AtomSet, i: number) => number = Base.getKey as any;
+ export const unitCount: (set: AtomSet) => number = Impl.keyCount as any;
+ export const unitIds: (set: AtomSet) => SortedArray = Impl.getKeys as any;
+ export const unitHas: (set: AtomSet, id: number) => boolean = Impl.hasKey as any;
+ export const unitGetId: (set: AtomSet, i: number) => number = Impl.getKey as any;
- export const unitGetById: (set: AtomSet, key: number) => OrderedSet = Base.getByKey as any;
- export const unitGetByIndex: (set: AtomSet, i: number) => OrderedSet = Base.getByIndex as any;
+ export const unitGetById: (set: AtomSet, key: number) => OrderedSet = Impl.getByKey as any;
+ export const unitGetByIndex: (set: AtomSet, i: number) => OrderedSet = Impl.getByIndex as any;
- export const atomCount: (set: AtomSet) => number = Base.size as any;
- export const atomHas: (set: AtomSet, x: Atom) => boolean = Base.hasAtom as any;
- export const atomIndexOf: (set: AtomSet, x: Atom) => number = Base.indexOf as any;
- export const atomGetAt: (set: AtomSet, i: number) => Atom = Base.getAt as any;
- export const atoms: (set: AtomSet) => Iterator<Atom> = Base.values as any;
+ export const atomCount: (set: AtomSet) => number = Impl.size as any;
+ export const atomHas: (set: AtomSet, x: Atom) => boolean = Impl.hasAtom as any;
+ export const atomIndexOf: (set: AtomSet, x: Atom) => number = Impl.indexOf as any;
+ export const atomGetAt: (set: AtomSet, i: number) => Atom = Impl.getAt as any;
+ export const atoms: (set: AtomSet) => Iterator<Atom> = Impl.values as any;
- export const hashCode: (set: AtomSet) => number = Base.hashCode as any;
- export const areEqual: (a: AtomSet, b: AtomSet) => boolean = Base.areEqual as any;
- export const areIntersecting: (a: AtomSet, b: AtomSet) => boolean = Base.areIntersecting as any;
+ export const hashCode: (set: AtomSet) => number = Impl.hashCode as any;
+ export const areEqual: (a: AtomSet, b: AtomSet) => boolean = Impl.areEqual as any;
+ export const areIntersecting: (a: AtomSet, b: AtomSet) => boolean = Impl.areIntersecting as any;
- export const union: (a: AtomSet, b: AtomSet) => AtomSet = Base.union as any;
- export const unionMany: (sets: AtomSet[]) => AtomSet = Base.unionMany as any;
- export const intersect: (a: AtomSet, b: AtomSet) => AtomSet = Base.intersect as any;
- export const subtract: (a: AtomSet, b: AtomSet) => AtomSet = Base.subtract as any;
+ export const union: (a: AtomSet, b: AtomSet) => AtomSet = Impl.union as any;
+ export const unionMany: (sets: AtomSet[]) => AtomSet = Impl.unionMany as any;
+ export const intersect: (a: AtomSet, b: AtomSet) => AtomSet = Impl.intersect as any;
+ export const subtract: (a: AtomSet, b: AtomSet) => AtomSet = Impl.subtract as any;
export function SortedBuilder(parent: AtomSet) { return createBuilder(parent, true); }
export function Builder(parent: AtomSet) { return createBuilder(parent, false); }
diff --git a/src/mol-data/structure/atom-set/builder.ts b/src/mol-data/structure/atom/set/builder.ts
similarity index 91%
rename from src/mol-data/structure/atom-set/builder.ts
rename to src/mol-data/structure/atom/set/builder.ts
index e566c30dc..d79afeb79 100644
--- a/src/mol-data/structure/atom-set/builder.ts
+++ b/src/mol-data/structure/atom/set/builder.ts
@@ -4,9 +4,9 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import AtomSet from '../atom-set'
-import OrderedSet from '../../../mol-base/collections/integer/ordered-set'
-import { sortArray } from '../../../mol-base/collections/sort'
+import AtomSet from '../set'
+import { OrderedSet } from '../../../../mol-base/collections/integer'
+import { sortArray } from '../../../../mol-base/collections/sort'
class Builder {
private keys: number[] = [];
diff --git a/src/mol-data/structure/atom-set/base.ts b/src/mol-data/structure/atom/set/impl.ts
similarity index 97%
rename from src/mol-data/structure/atom-set/base.ts
rename to src/mol-data/structure/atom/set/impl.ts
index d8be533e7..fab4133aa 100644
--- a/src/mol-data/structure/atom-set/base.ts
+++ b/src/mol-data/structure/atom/set/impl.ts
@@ -4,13 +4,10 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import OrderedSet from '../../../mol-base/collections/integer/ordered-set'
-import SortedArray from '../../../mol-base/collections/integer/sorted-array'
-import Iterator from '../../../mol-base/collections/iterator'
-import Interval from '../../../mol-base/collections/integer/interval'
-import { sortArray } from '../../../mol-base/collections/sort'
-import { hash1 } from '../../../mol-base/collections/hash-functions'
-import Atom from '../atom'
+import { SortedArray, Interval, Iterator, OrderedSet } from '../../../../mol-base/collections/integer'
+import { sortArray } from '../../../../mol-base/collections/sort'
+import { hash1 } from '../../../../mol-base/collections/hash-functions'
+import Atom from '../../atom'
/** Long and painful implementation starts here */
diff --git a/src/mol-data/structure/atom-set/properties.ts b/src/mol-data/structure/atom/set/properties.ts
similarity index 100%
rename from src/mol-data/structure/atom-set/properties.ts
rename to src/mol-data/structure/atom/set/properties.ts
diff --git a/src/mol-data/structure/base.ts b/src/mol-data/structure/base.ts
deleted file mode 100644
index 210c7dcd5..000000000
--- a/src/mol-data/structure/base.ts
+++ /dev/null
@@ -1,37 +0,0 @@
-/**
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import Model from '../model'
-import Structure from '../structure'
-import Unit from './unit'
-import Operator from './operator'
-import AtomSet from './atom-set'
-import OrderedSet from '../../mol-base/collections/integer/ordered-set'
-
-export class StructureBuilder {
- private units = Object.create(null);
- private atoms = Object.create(null);
-
- addUnit(unit: Unit) { this.units[unit.id] = unit; }
- addAtoms(unitId: number, atoms: OrderedSet) { this.atoms[unitId] = atoms; }
-
- getStructure(): Structure { return { units: this.units, atoms: AtomSet.create(this.atoms) }; }
-}
-
-export const Empty: Structure = { units: {}, atoms: AtomSet.Empty };
-
-export function ofModel(model: Model): Structure {
- const chains = model.hierarchy.chainSegments;
- const builder = new StructureBuilder();
-
- for (let c = 0; c < chains.count; c++) {
- const unit = Unit.create(model, Operator.Identity);
- builder.addUnit(unit);
- builder.addAtoms(unit.id, OrderedSet.ofBounds(chains.segments[c], chains.segments[c + 1]));
- }
-
- return builder.getStructure();
-}
\ No newline at end of file
diff --git a/src/mol-data/structure/structure.ts b/src/mol-data/structure/structure.ts
new file mode 100644
index 000000000..fcfb15a9d
--- /dev/null
+++ b/src/mol-data/structure/structure.ts
@@ -0,0 +1,58 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import Model from '../model'
+import Unit from './unit'
+import Operator from './operator'
+import AtomSet from './atom/set'
+import { OrderedSet } from '../../mol-base/collections/integer'
+
+interface Structure extends Readonly<{
+ units: { readonly [id: number]: Unit },
+ atoms: AtomSet
+}> { }
+
+namespace Structure {
+ export const Empty = { units: {}, atoms: AtomSet.Empty };
+
+ export function ofModel(model: Model): Structure {
+ const chains = model.hierarchy.chainSegments;
+ const builder = Builder();
+
+ for (let c = 0; c < chains.count; c++) {
+ const unit = Unit.create(model, Operator.Identity);
+ builder.addUnit(unit);
+ builder.addAtoms(unit.id, OrderedSet.ofBounds(chains.segments[c], chains.segments[c + 1]));
+ }
+
+ return builder.getStructure();
+ }
+
+ export interface Builder {
+ addUnit(unit: Unit): void,
+ addAtoms(unitId: number, atoms: OrderedSet): void,
+ getStructure(): Structure,
+ readonly atomCount: number
+ }
+
+ class BuilderImpl implements Builder {
+ private units = Object.create(null);
+ private atoms = Object.create(null);
+ atomCount = 0;
+
+ addUnit(unit: Unit) { this.units[unit.id] = unit; }
+ addAtoms(unitId: number, atoms: OrderedSet) { this.atoms[unitId] = atoms; this.atomCount += OrderedSet.size(atoms); }
+ getStructure(): Structure { return this.atomCount > 0 ? { units: this.units, atoms: AtomSet.create(this.atoms) } : Empty; }
+ }
+
+ export function Builder(): Builder { return new BuilderImpl(); }
+
+
+ // TODO: "lift" atom set operators?
+ // TODO: "diff"
+}
+
+export default Structure
\ No newline at end of file
diff --git a/src/perf-tests/sets.ts b/src/perf-tests/sets.ts
index b94f63786..e4f067085 100644
--- a/src/perf-tests/sets.ts
+++ b/src/perf-tests/sets.ts
@@ -1,8 +1,6 @@
import * as B from 'benchmark'
-import Tuple from '../mol-base/collections/integer/tuple'
-import OrdSet from '../mol-base/collections/integer/ordered-set'
-import AtomSet from '../mol-data/structure/atom-set'
-import Segmentation from '../mol-base/collections/integer/segmentation'
+import { Tuple, Segmentation, OrderedSet as OrdSet } from '../mol-base/collections/integer'
+import { AtomSet } from '../mol-data/structure'
export namespace Iteration {
const U = 1000, V = 2500;
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index 31488d2e3..6549e7e16 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -11,11 +11,8 @@ import * as fs from 'fs'
import CIF from '../mol-io/reader/cif'
import Model from '../mol-data/Model'
-import Structure from '../mol-data/structure'
-import OrdSet from '../mol-base/collections/integer/ordered-set'
-import Atom from '../mol-data/structure/atom'
-import AtomSet from '../mol-data/structure/atom-set'
-import Segmentation from '../mol-base/collections/integer/segmentation'
+import { Structure, Atom, AtomSet } from '../mol-data/structure'
+import { OrderedSet as OrdSet, Segmentation } from '../mol-base/collections/integer'
require('util.promisify').shim();
const readFileAsync = util.promisify(fs.readFile);
--
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