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Commit f52ee9db authored by David Sehnal's avatar David Sehnal
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Structure and selection cosntruction updates

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with 233 additions and 163 deletions
src/mol-data/int/_spec/sorted-array.spec.ts
+ 11
− 0
View file @ f52ee9db
......@@ -16,6 +16,11 @@ describe('sortedArray', () => {
it(name, () => expect(a).toEqual(b));
}
function compareArrays(a: ArrayLike<number>, b: ArrayLike<number>) {
expect(a.length).toBe(b.length);
for (let i = 0; i < a.length; i++) expect(a[i]).toBe(b[i]);
}
const a1234 = SortedArray.ofSortedArray([1, 2, 3, 4]);
const a2468 = SortedArray.ofSortedArray([2, 4, 6, 8]);
......@@ -48,6 +53,12 @@ describe('sortedArray', () => {
testI('findRange', SortedArray.findRange(a2468, 2, 4), Interval.ofRange(0, 1));
it('deduplicate', () => {
compareArrays(SortedArray.deduplicate(SortedArray.ofSortedArray([1, 1, 1, 1])), [1]);
compareArrays(SortedArray.deduplicate(SortedArray.ofSortedArray([1, 1, 2, 2, 3, 4])), [1, 2, 3, 4]);
compareArrays(SortedArray.deduplicate(SortedArray.ofSortedArray([1, 2, 3])), [1, 2, 3]);
});
// console.log(Interval.findPredecessorIndexInInterval(Interval.ofBounds(0, 3), 2, Interval.ofBounds(0, 3)))
// console.log(SortedArray.findPredecessorIndexInInterval(SortedArray.ofSortedArray([0, 1, 2]), 2, Interval.ofBounds(0, 3)))
});
\ No newline at end of file
src/mol-data/int/impl/sorted-array.ts
+ 16
− 0
View file @ f52ee9db
......@@ -273,6 +273,22 @@ export function subtract(a: Nums, b: Nums) {
return ofSortedArray(indices);
}
export function deduplicate(xs: Nums) {
if (xs.length < 2) return xs;
let count = 1;
for (let i = 0, _i = xs.length - 1; i < _i; i++) {
if (xs[i] !== xs[i + 1]) count++;
}
if (count === xs.length) return xs;
const ret = new Int32Array(count);
let o = 0;
for (let i = 0, _i = xs.length - 1; i < _i; i++) {
if (xs[i] !== xs[i + 1]) ret[o++] = xs[i];
}
ret[o] = xs[xs.length - 1];
return ret;
}
const _maxIntRangeRet = { startI: 0, startJ: 0, endI: 0, endJ: 0 };
// for small sets, just gets the whole range, for large sets does a bunch of binary searches
function getSuitableIntersectionRange(a: Nums, b: Nums) {
......
src/mol-data/int/sorted-array.ts
+ 2
− 0
View file @ f52ee9db
......@@ -40,6 +40,8 @@ namespace SortedArray {
export const findPredecessorIndex: (array: SortedArray, x: number) => number = Impl.findPredecessorIndex as any;
export const findPredecessorIndexInInterval: (array: SortedArray, x: number, bounds: Interval) => number = Impl.findPredecessorIndexInInterval as any;
export const findRange: (array: SortedArray, min: number, max: number) => Interval = Impl.findRange as any;
export const deduplicate: (arrat: SortedArray) => SortedArray = Impl.deduplicate as any;
}
interface SortedArray extends ArrayLike<number> { '@type': 'int-sorted-array' }
......
src/mol-model/structure/query/generators.ts
+ 2
− 50
View file @ f52ee9db
......@@ -7,8 +7,9 @@
import Query from './query'
import Selection from './selection'
import P from './properties'
import { Structure, Element, Unit } from '../structure'
import { Element, Unit } from '../structure'
import { OrderedSet, Segmentation } from 'mol-data/int'
import { LinearGroupingBuilder } from './utils/builders';
export const all: Query.Provider = async (s, ctx) => Selection.Singletons(s, s);
......@@ -113,55 +114,6 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A
};
}
class LinearGroupingBuilder {
private builders: Structure.SubsetBuilder[] = [];
private builderMap = new Map<string, Structure.SubsetBuilder>();
add(key: any, unit: number, element: number) {
let b = this.builderMap.get(key);
if (!b) {
b = this.source.subsetBuilder(true);
this.builders[this.builders.length] = b;
this.builderMap.set(key, b);
}
b.addToUnit(unit, element);
}
private allSingletons() {
for (let i = 0, _i = this.builders.length; i < _i; i++) {
if (this.builders[i].elementCount > 1) return false;
}
return true;
}
private singletonSelection(): Selection {
const builder = this.source.subsetBuilder(true);
const loc = Element.Location();
for (let i = 0, _i = this.builders.length; i < _i; i++) {
this.builders[i].setSingletonLocation(loc);
builder.addToUnit(loc.unit.id, loc.element);
}
return Selection.Singletons(this.source, builder.getStructure());
}
private fullSelection() {
const structures: Structure[] = new Array(this.builders.length);
for (let i = 0, _i = this.builders.length; i < _i; i++) {
structures[i] = this.builders[i].getStructure();
}
return Selection.Sequence(this.source, structures);
}
getSelection(): Selection {
const len = this.builders.length;
if (len === 0) return Selection.Empty(this.source);
if (this.allSingletons()) return this.singletonSelection();
return this.fullSelection();
}
constructor(private source: Structure) { }
}
function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, groupBy }: AtomGroupsQueryParams): Query.Provider {
return async (structure, ctx) => {
const { units } = structure;
......
src/mol-model/structure/query/selection.ts
+ 3
− 3
View file @ f52ee9db
......@@ -6,7 +6,7 @@
import { HashSet } from 'mol-data/generic'
import { Structure } from '../structure'
import { StructureUtils } from './utils';
import { structureUnion } from './utils/structure';
// A selection is a pair of a Structure and a sequence of unique AtomSets
type Selection = Selection.Singletons | Selection.Sequence
......@@ -31,7 +31,7 @@ namespace Selection {
export function unionStructure(sel: Selection): Structure {
if (isEmpty(sel)) return Structure.Empty;
if (isSingleton(sel)) return sel.structure;
return StructureUtils.union(sel.source, sel.structures);
return structureUnion(sel.source, sel.structures);
}
export interface Builder {
......@@ -42,7 +42,7 @@ namespace Selection {
function getSelection(source: Structure, structures: Structure[], allSingletons: boolean) {
const len = structures.length;
if (len === 0) return Empty(source);
if (allSingletons) return Singletons(source, StructureUtils.union(source, structures));
if (allSingletons) return Singletons(source, structureUnion(source, structures));
return Sequence(source, structures);
}
......
src/mol-model/structure/query/utils.ts deleted 100644 → 0
+ 0
− 107
View file @ 59f5f0ca
/**
* Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { Structure, Unit } from '../structure'
import { SortedArray } from 'mol-data/int';
namespace StructureUtils {
export function union(source: Structure, structures: Structure[]) {
if (structures.length === 0) return Structure.Empty;
if (structures.length === 1) return structures[0];
const unitMap = new Map<number, SortedArray>();
const fullUnits = new Set<number>();
for (const { units } of structures) {
for (let i = 0, _i = units.length; i < _i; i++) {
const u = units[i];
if (unitMap.has(u.id)) {
// check if there is anything more to union in this particual unit.
if (fullUnits.has(u.id)) continue;
const merged = SortedArray.union(unitMap.get(u.id)!, u.elements);
unitMap.set(u.id, merged);
if (merged.length === source.unitMap.get(u.id).elements.length) fullUnits.add(u.id);
} else {
unitMap.set(u.id, u.elements);
if (u.elements.length === source.unitMap.get(u.id).elements.length) fullUnits.add(u.id);
}
}
}
const builder = source.subsetBuilder(true);
unitMap.forEach(buildUnion, builder);
return builder.getStructure();
}
function buildUnion(this: Structure.SubsetBuilder, elements: SortedArray, id: number) {
this.setUnit(id, elements);
}
export function areIntersecting(sA: Structure, sB: Structure): boolean {
if (sA === sB) return true;
let a, b;
if (sA.units.length < sB.units.length) { a = sA; b = sB; }
else { a = sB; b = sA; }
const aU = a.units, bU = b.unitMap;
for (let i = 0, _i = aU.length; i < _i; i++) {
const u = aU[i];
if (!bU.has(u.id)) continue;
const v = bU.get(u.id);
if (SortedArray.areIntersecting(u.elements, v.elements)) return true;
}
return false;
}
export function intersect(sA: Structure, sB: Structure): Structure {
if (sA === sB) return sA;
if (!areIntersecting(sA, sB)) return Structure.Empty;
let a, b;
if (sA.units.length < sB.units.length) { a = sA; b = sB; }
else { a = sB; b = sA; }
const aU = a.units, bU = b.unitMap;
const units: Unit[] = [];
for (let i = 0, _i = aU.length; i < _i; i++) {
const u = aU[i];
if (!bU.has(u.id)) continue;
const v = bU.get(u.id);
if (SortedArray.areIntersecting(u.elements, v.elements)) {
const int = SortedArray.intersect(u.elements, v.elements);
units[units.length] = u.getChild(int);
}
}
return Structure.create(units);
}
export function subtract(a: Structure, b: Structure): Structure {
if (a === b) return Structure.Empty;
if (!areIntersecting(a, b)) return a;
const aU = a.units, bU = b.unitMap;
const units: Unit[] = [];
for (let i = 0, _i = aU.length; i < _i; i++) {
const u = aU[i];
if (!bU.has(u.id)) continue;
const v = bU.get(u.id);
const sub = SortedArray.intersect(u.elements, v.elements);
if (sub.length > 0) {
units[units.length] = u.getChild(sub);
}
}
return Structure.create(units);
}
}
export { StructureUtils }
\ No newline at end of file
src/mol-model/structure/query/utils/builders.ts 0 → 100644
+ 81
− 0
View file @ f52ee9db
/**
* Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { Element, Structure } from '../../structure';
import Selection from '../selection';
import { HashSet } from 'mol-data/generic';
import { structureUnion } from './structure';
export class UniqueStructuresBuilder {
private set = HashSet(Structure.hashCode, Structure.areEqual);
private structures: Structure[] = [];
private allSingletons = true;
add(s: Structure) {
if (!s.elementCount) return;
if (s.elementCount !== 1) this.allSingletons = false;
if (this.set.add(s)) {
this.structures[this.structures.length] = s;
}
}
getSelection() {
if (this.allSingletons) return Selection.Singletons(this.source, structureUnion(this.source, this.structures));
return Selection.Sequence(this.source, this.structures);
}
constructor(private source: Structure) {
}
}
export class LinearGroupingBuilder {
private builders: Structure.SubsetBuilder[] = [];
private builderMap = new Map<string, Structure.SubsetBuilder>();
add(key: any, unit: number, element: number) {
let b = this.builderMap.get(key);
if (!b) {
b = this.source.subsetBuilder(true);
this.builders[this.builders.length] = b;
this.builderMap.set(key, b);
}
b.addToUnit(unit, element);
}
private allSingletons() {
for (let i = 0, _i = this.builders.length; i < _i; i++) {
if (this.builders[i].elementCount > 1) return false;
}
return true;
}
private singletonSelection(): Selection {
const builder = this.source.subsetBuilder(true);
const loc = Element.Location();
for (let i = 0, _i = this.builders.length; i < _i; i++) {
this.builders[i].setSingletonLocation(loc);
builder.addToUnit(loc.unit.id, loc.element);
}
return Selection.Singletons(this.source, builder.getStructure());
}
private fullSelection() {
const structures: Structure[] = new Array(this.builders.length);
for (let i = 0, _i = this.builders.length; i < _i; i++) {
structures[i] = this.builders[i].getStructure();
}
return Selection.Sequence(this.source, structures);
}
getSelection(): Selection {
const len = this.builders.length;
if (len === 0) return Selection.Empty(this.source);
if (this.allSingletons()) return this.singletonSelection();
return this.fullSelection();
}
constructor(private source: Structure) { }
}
\ No newline at end of file
src/mol-model/structure/query/utils/structure.ts 0 → 100644
+ 103
− 0
View file @ f52ee9db
/**
* Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { Structure, Unit } from '../../structure'
import { SortedArray } from 'mol-data/int';
export function structureUnion(source: Structure, structures: Structure[]) {
if (structures.length === 0) return Structure.Empty;
if (structures.length === 1) return structures[0];
const unitMap = new Map<number, SortedArray>();
const fullUnits = new Set<number>();
for (const { units } of structures) {
for (let i = 0, _i = units.length; i < _i; i++) {
const u = units[i];
if (unitMap.has(u.id)) {
// check if there is anything more to union in this particual unit.
if (fullUnits.has(u.id)) continue;
const merged = SortedArray.union(unitMap.get(u.id)!, u.elements);
unitMap.set(u.id, merged);
if (merged.length === source.unitMap.get(u.id).elements.length) fullUnits.add(u.id);
} else {
unitMap.set(u.id, u.elements);
if (u.elements.length === source.unitMap.get(u.id).elements.length) fullUnits.add(u.id);
}
}
}
const builder = source.subsetBuilder(true);
unitMap.forEach(buildUnion, builder);
return builder.getStructure();
}
function buildUnion(this: Structure.SubsetBuilder, elements: SortedArray, id: number) {
this.setUnit(id, elements);
}
export function structureAreIntersecting(sA: Structure, sB: Structure): boolean {
if (sA === sB) return true;
let a, b;
if (sA.units.length < sB.units.length) { a = sA; b = sB; }
else { a = sB; b = sA; }
const aU = a.units, bU = b.unitMap;
for (let i = 0, _i = aU.length; i < _i; i++) {
const u = aU[i];
if (!bU.has(u.id)) continue;
const v = bU.get(u.id);
if (SortedArray.areIntersecting(u.elements, v.elements)) return true;
}
return false;
}
export function structureIntersect(sA: Structure, sB: Structure): Structure {
if (sA === sB) return sA;
if (!structureAreIntersecting(sA, sB)) return Structure.Empty;
let a, b;
if (sA.units.length < sB.units.length) { a = sA; b = sB; }
else { a = sB; b = sA; }
const aU = a.units, bU = b.unitMap;
const units: Unit[] = [];
for (let i = 0, _i = aU.length; i < _i; i++) {
const u = aU[i];
if (!bU.has(u.id)) continue;
const v = bU.get(u.id);
if (SortedArray.areIntersecting(u.elements, v.elements)) {
const int = SortedArray.intersect(u.elements, v.elements);
units[units.length] = u.getChild(int);
}
}
return Structure.create(units);
}
export function structureSubtract(a: Structure, b: Structure): Structure {
if (a === b) return Structure.Empty;
if (!structureAreIntersecting(a, b)) return a;
const aU = a.units, bU = b.unitMap;
const units: Unit[] = [];
for (let i = 0, _i = aU.length; i < _i; i++) {
const u = aU[i];
if (!bU.has(u.id)) continue;
const v = bU.get(u.id);
const sub = SortedArray.intersect(u.elements, v.elements);
if (sub.length > 0) {
units[units.length] = u.getChild(sub);
}
}
return Structure.create(units);
}
\ No newline at end of file
src/mol-model/structure/structure/structure.ts
+ 15
− 3
View file @ f52ee9db
......@@ -181,7 +181,7 @@ namespace Structure {
this.elementCount += elements.length;
}
getStructure(): Structure {
private _getStructure(deduplicateElements: boolean): Structure {
if (this.isEmpty) return Structure.Empty;
const newUnits: Unit[] = [];
......@@ -193,7 +193,15 @@ namespace Structure {
const id = this.ids[i];
const parent = this.parent.unitMap.get(id);
const unit = this.unitMap.get(id);
let unit: ArrayLike<number> = this.unitMap.get(id);
let sorted = false;
if (deduplicateElements) {
if (!this.isSorted) sortArray(unit);
unit = SortedArray.deduplicate(SortedArray.ofSortedArray(this.currentUnit));
sorted = true;
}
const l = unit.length;
// if the length is the same, just copy the old unit.
......@@ -203,7 +211,7 @@ namespace Structure {
continue;
}
if (!this.isSorted && l > 1) sortArray(unit);
if (!this.isSorted && !sorted && l > 1) sortArray(unit);
let child = parent.getChild(SortedArray.ofSortedArray(unit));
const pivot = symmGroups.add(child.id, child);
......@@ -214,6 +222,10 @@ namespace Structure {
return create(newUnits);
}
getStructure(deduplicateElements = false) {
return this._getStructure(deduplicateElements);
}
setSingletonLocation(location: Element.Location) {
const id = this.ids[0];
location.unit = this.parent.unitMap.get(id);
......
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