From 6afe8085558c8f4a0f9f53931aa09dc1b3a3516a Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Tue, 17 Jul 2018 19:38:06 +0200
Subject: [PATCH] wip mol-model/query
---
src/mol-model/structure/query.ts | 4 +-
src/mol-model/structure/query/context.ts | 18 ++++-
.../structure/query/queries/combinators.ts | 5 ++
.../structure/query/queries/filters.ts | 41 ++++++++++
.../query/{ => queries}/generators.ts | 34 ++++-----
.../query/{ => queries}/modifiers.ts | 24 +++---
src/perf-tests/tasks.ts | 76 +++++++++++++++++--
7 files changed, 161 insertions(+), 41 deletions(-)
create mode 100644 src/mol-model/structure/query/queries/combinators.ts
create mode 100644 src/mol-model/structure/query/queries/filters.ts
rename src/mol-model/structure/query/{ => queries}/generators.ts (86%)
rename src/mol-model/structure/query/{ => queries}/modifiers.ts (79%)
diff --git a/src/mol-model/structure/query.ts b/src/mol-model/structure/query.ts
index e4f3190a4..775112fbc 100644
--- a/src/mol-model/structure/query.ts
+++ b/src/mol-model/structure/query.ts
@@ -7,8 +7,8 @@
import { StructureSelection } from './query/selection'
import { StructureQuery } from './query/query'
export * from './query/context'
-import * as generators from './query/generators'
-import * as modifiers from './query/modifiers'
+import * as generators from './query/queries/generators'
+import * as modifiers from './query/queries/modifiers'
import pred from './query/predicates'
export const Queries = {
diff --git a/src/mol-model/structure/query/context.ts b/src/mol-model/structure/query/context.ts
index eedd8d3e3..5c94becb6 100644
--- a/src/mol-model/structure/query/context.ts
+++ b/src/mol-model/structure/query/context.ts
@@ -9,16 +9,19 @@ import { Structure, StructureElement } from '../structure';
export interface QueryContextView {
readonly element: StructureElement;
+ readonly currentStructure: Structure;
}
export class QueryContext implements QueryContextView {
private currentStack: StructureElement[] = [];
+ private currentLocked = false;
- readonly structure: Structure;
+ readonly inputStructure: Structure;
readonly taskCtx: RuntimeContext;
/** Current element */
readonly element: StructureElement = StructureElement.create();
+ readonly currentStructure: Structure = void 0 as any;
pushCurrentElement(): StructureElement {
this.currentStack[this.currentStack.length] = this.element;
@@ -30,8 +33,19 @@ export class QueryContext implements QueryContextView {
(this.element as StructureElement) = this.currentStack.pop()!;
}
+ lockCurrentStructure(structure: Structure) {
+ if (this.currentLocked) throw new Error('Current structure already locked.');
+ this.currentLocked = true;
+ (this.currentStructure as Structure) = structure;
+ }
+
+ unlockCurrentStructure() {
+ this.currentLocked = false;
+ (this.currentStructure as any) = void 0;
+ }
+
constructor(structure: Structure, taskCtx: RuntimeContext) {
- this.structure = structure;
+ this.inputStructure = structure;
this.taskCtx = taskCtx;
}
}
diff --git a/src/mol-model/structure/query/queries/combinators.ts b/src/mol-model/structure/query/queries/combinators.ts
new file mode 100644
index 000000000..de7200ac1
--- /dev/null
+++ b/src/mol-model/structure/query/queries/combinators.ts
@@ -0,0 +1,5 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
diff --git a/src/mol-model/structure/query/queries/filters.ts b/src/mol-model/structure/query/queries/filters.ts
new file mode 100644
index 000000000..9bd5a50d2
--- /dev/null
+++ b/src/mol-model/structure/query/queries/filters.ts
@@ -0,0 +1,41 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+// import { StructureQuery } from '../query'
+// import { StructureSelection } from '../selection'
+// import { Unit, StructureProperties as P, Structure } from '../../structure'
+// import { Segmentation, SortedArray } from 'mol-data/int'
+// import { LinearGroupingBuilder } from '../utils/builders';
+// import { QueryPredicate, QueryFn, QueryContextView } from '../context';
+
+// export function pick(query: StructureQuery, pred: QueryPredicate): StructureQuery {
+// return async ctx => {
+// const sel = await query(ctx);
+
+// if (StructureSelection.isSingleton(sel)) {
+// const ret = StructureSelection.LinearBuilder(ctx.inputStructure);
+// for (const unit of ctx.inputStructure.units) {
+// const { elements } = unit;
+// for (let i = 0, _i = elements.length; i < _i; i++) {
+// // TODO: optimize this somehow???
+// const s = Structure.create([unit.getChild(SortedArray.ofSingleton(elements[i]))]);
+// ctx.lockCurrentStructure(s);
+// if (pred(ctx)) ret.add(s);
+// ctx.unlockCurrentStructure();
+// }
+// }
+// return ret.getSelection();
+// } else {
+// const ret = StructureSelection.LinearBuilder(ctx.inputStructure);
+// for (const s of sel.structures) {
+// ctx.lockCurrentStructure(s);
+// if (pred(ctx)) ret.add(s);
+// ctx.unlockCurrentStructure();
+// }
+// return ret.getSelection();
+// }
+// };
+// }
diff --git a/src/mol-model/structure/query/generators.ts b/src/mol-model/structure/query/queries/generators.ts
similarity index 86%
rename from src/mol-model/structure/query/generators.ts
rename to src/mol-model/structure/query/queries/generators.ts
index 01f16cccb..8454c781f 100644
--- a/src/mol-model/structure/query/generators.ts
+++ b/src/mol-model/structure/query/queries/generators.ts
@@ -4,14 +4,14 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { StructureQuery } from './query'
-import { StructureSelection } from './selection'
-import { Unit, StructureProperties as P } from '../structure'
+import { StructureQuery } from '../query'
+import { StructureSelection } from '../selection'
+import { Unit, StructureProperties as P } from '../../structure'
import { Segmentation } from 'mol-data/int'
-import { LinearGroupingBuilder } from './utils/builders';
-import { QueryPredicate, QueryFn, QueryContextView } from './context';
+import { LinearGroupingBuilder } from '../utils/builders';
+import { QueryPredicate, QueryFn, QueryContextView } from '../context';
-export const all: StructureQuery = async (ctx) => StructureSelection.Singletons(ctx.structure, ctx.structure);
+export const all: StructureQuery = async (ctx) => StructureSelection.Singletons(ctx.inputStructure, ctx.inputStructure);
export interface AtomsQueryParams {
entityTest: QueryPredicate,
@@ -45,10 +45,10 @@ export function atoms(params?: Partial<AtomsQueryParams>): StructureQuery {
function atomGroupsLinear(atomTest: QueryPredicate): StructureQuery {
return async (ctx) => {
- const { structure } = ctx;
- const { units } = structure;
+ const { inputStructure } = ctx;
+ const { units } = inputStructure;
const l = ctx.pushCurrentElement();
- const builder = structure.subsetBuilder(true);
+ const builder = inputStructure.subsetBuilder(true);
let progress = 0;
for (const unit of units) {
@@ -66,16 +66,16 @@ function atomGroupsLinear(atomTest: QueryPredicate): StructureQuery {
if (ctx.taskCtx.shouldUpdate) await ctx.taskCtx.update({ message: 'Atom Groups', current: progress, max: units.length });
}
ctx.popCurrentElement();
- return StructureSelection.Singletons(structure, builder.getStructure());
+ return StructureSelection.Singletons(inputStructure, builder.getStructure());
};
}
function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: AtomsQueryParams): StructureQuery {
return async (ctx) => {
- const { structure } = ctx;
- const { units } = structure;
+ const { inputStructure } = ctx;
+ const { units } = inputStructure;
const l = ctx.pushCurrentElement();
- const builder = structure.subsetBuilder(true);
+ const builder = inputStructure.subsetBuilder(true);
let progress = 0;
for (const unit of units) {
@@ -115,16 +115,16 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A
if (ctx.taskCtx.shouldUpdate) await ctx.taskCtx.update({ message: 'Atom Groups', current: progress, max: units.length });
}
ctx.popCurrentElement();
- return StructureSelection.Singletons(structure, builder.getStructure());
+ return StructureSelection.Singletons(inputStructure, builder.getStructure());
};
}
function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, groupBy }: AtomsQueryParams): StructureQuery {
return async (ctx) => {
- const { structure } = ctx;
- const { units } = structure;
+ const { inputStructure } = ctx;
+ const { units } = inputStructure;
const l = ctx.pushCurrentElement();
- const builder = new LinearGroupingBuilder(structure);
+ const builder = new LinearGroupingBuilder(inputStructure);
let progress = 0;
for (const unit of units) {
diff --git a/src/mol-model/structure/query/modifiers.ts b/src/mol-model/structure/query/queries/modifiers.ts
similarity index 79%
rename from src/mol-model/structure/query/modifiers.ts
rename to src/mol-model/structure/query/queries/modifiers.ts
index 42dea2f05..7943e9e7f 100644
--- a/src/mol-model/structure/query/modifiers.ts
+++ b/src/mol-model/structure/query/queries/modifiers.ts
@@ -6,11 +6,11 @@
import { Segmentation } from 'mol-data/int';
import { RuntimeContext } from 'mol-task';
-import { Structure, Unit } from '../structure';
-import { StructureQuery } from './query';
-import { StructureSelection } from './selection';
-import { UniqueStructuresBuilder } from './utils/builders';
-import { StructureUniqueSubsetBuilder } from '../structure/util/unique-subset-builder';
+import { Structure, Unit } from '../../structure';
+import { StructureQuery } from '../query';
+import { StructureSelection } from '../selection';
+import { UniqueStructuresBuilder } from '../utils/builders';
+import { StructureUniqueSubsetBuilder } from '../../structure/util/unique-subset-builder';
function getWholeResidues(ctx: RuntimeContext, source: Structure, structure: Structure) {
const builder = source.subsetBuilder(true);
@@ -41,12 +41,12 @@ export function wholeResidues(query: StructureQuery, isFlat: boolean): Structure
return async (ctx) => {
const inner = await query(ctx);
if (StructureSelection.isSingleton(inner)) {
- return StructureSelection.Singletons(ctx.structure, getWholeResidues(ctx.taskCtx, ctx.structure, inner.structure));
+ return StructureSelection.Singletons(ctx.inputStructure, getWholeResidues(ctx.taskCtx, ctx.inputStructure, inner.structure));
} else {
- const builder = new UniqueStructuresBuilder(ctx.structure);
+ const builder = new UniqueStructuresBuilder(ctx.inputStructure);
let progress = 0;
for (const s of inner.structures) {
- builder.add(getWholeResidues(ctx.taskCtx, ctx.structure, s));
+ builder.add(getWholeResidues(ctx.taskCtx, ctx.inputStructure, s));
progress++;
if (ctx.taskCtx.shouldUpdate) await ctx.taskCtx.update({ message: 'Whole Residues', current: progress, max: inner.structures.length });
}
@@ -87,13 +87,13 @@ export function includeSurroundings(query: StructureQuery, params: IncludeSurrou
return async (ctx) => {
const inner = await query(ctx);
if (StructureSelection.isSingleton(inner)) {
- const surr = await getIncludeSurroundings(ctx.taskCtx, ctx.structure, inner.structure, params);
- const ret = StructureSelection.Singletons(ctx.structure, surr);
+ const surr = await getIncludeSurroundings(ctx.taskCtx, ctx.inputStructure, inner.structure, params);
+ const ret = StructureSelection.Singletons(ctx.inputStructure, surr);
return ret;
} else {
- const builder = new UniqueStructuresBuilder(ctx.structure);
+ const builder = new UniqueStructuresBuilder(ctx.inputStructure);
for (const s of inner.structures) {
- builder.add(await getIncludeSurroundings(ctx.taskCtx, ctx.structure, s, params));
+ builder.add(await getIncludeSurroundings(ctx.taskCtx, ctx.inputStructure, s, params));
}
return builder.getSelection();
}
diff --git a/src/perf-tests/tasks.ts b/src/perf-tests/tasks.ts
index c1fa6c9c9..f0c0eb86b 100644
--- a/src/perf-tests/tasks.ts
+++ b/src/perf-tests/tasks.ts
@@ -98,20 +98,80 @@ export namespace Tasks {
.on('cycle', (e: any) => console.log(String(e.target)))
.run();
}
+
+ function add(x: number, y: number) {
+ return x + y;
+ }
+
+ // async function addAs(x: number, y: number) {
+ // return x + y;
+ // }
+
+ async function opAsync(n: number) {
+ let ret = 0;
+ for (let i = 0; i < n; i++) {
+ const v = add(i, i + 1);
+ ret += (v as any).then ? await v : v;
+ }
+ return ret;
+ }
+
+ function opNormal(n: number) {
+ let ret = 0;
+ for (let i = 0; i < n; i++) {
+ ret += add(i, i + 1);
+ }
+ return ret;
+ }
+
+ export async function awaitF() {
+ const N = 10000000;
+
+ console.time('async');
+ console.log(await opAsync(N));
+ console.timeEnd('async');
+
+ console.time('async');
+ console.log(await opAsync(N));
+ console.timeEnd('async');
+
+ console.time('async');
+ console.log(await opAsync(N));
+ console.timeEnd('async');
+
+ console.time('normal');
+ console.log(opNormal(N));
+ console.timeEnd('normal');
+ console.time('normal');
+ console.log(opNormal(N));
+ console.timeEnd('normal');
+ console.time('normal');
+ console.log(opNormal(N));
+ console.timeEnd('normal');
+
+ // const suite = new B.Suite();
+ // suite
+ // .add(`async`, async () => { return await opAsync(100000); })
+ // .add(`normal`, () => { return opNormal(100000); })
+ // .on('cycle', (e: any) => console.log(String(e.target)))
+ // .run();
+ }
}
(async function() {
// await Tasks.testImmediate();
// await Tasks.testImmediate();
- await Tasks.baseline();
- await Tasks.yielding();
- await Tasks.yielding1();
- await Tasks.testYielding();
- await Tasks.baseline();
- await Tasks.yielding();
- await Tasks.yielding1();
- await Tasks.testYielding();
+ // await Tasks.baseline();
+ // await Tasks.yielding();
+ // await Tasks.yielding1();
+ // await Tasks.testYielding();
+ // await Tasks.baseline();
+ // await Tasks.yielding();
+ // await Tasks.yielding1();
+ // await Tasks.testYielding();
+
+ await Tasks.awaitF();
}())
// console.time('test')
--
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