From 599ab54063ee16dc69ae793c2bdc517faf9c0afd Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Tue, 17 Jul 2018 20:28:47 +0200
Subject: [PATCH] queries are now synchronous due to performance reasons
---
.../ui/visualization/sequence-view.tsx | 4 +-
src/mol-model/structure/query/context.ts | 5 +-
.../structure/query/queries/filters.ts | 65 +++++++++----------
.../structure/query/queries/generators.ts | 20 ++----
.../structure/query/queries/modifiers.ts | 29 ++++-----
src/mol-model/structure/query/query.ts | 11 +---
src/mol-model/structure/structure/symmetry.ts | 4 +-
src/perf-tests/structure.ts | 14 ++--
src/servers/model/server/query.ts | 2 +-
9 files changed, 63 insertions(+), 91 deletions(-)
diff --git a/src/mol-app/ui/visualization/sequence-view.tsx b/src/mol-app/ui/visualization/sequence-view.tsx
index 69a889502..7d9bf1430 100644
--- a/src/mol-app/ui/visualization/sequence-view.tsx
+++ b/src/mol-app/ui/visualization/sequence-view.tsx
@@ -34,14 +34,14 @@ function createQuery(entityId: string, label_seq_id: number) {
// TODO: this is really ineffective and should be done using a canvas.
class EntitySequence extends React.Component<{ ctx: Context, seq: StructureSequence.Entity, structure: Structure }> {
- async raiseInteractityEvent(seqId?: number) {
+ raiseInteractityEvent(seqId?: number) {
if (typeof seqId === 'undefined') {
InteractivityEvents.HighlightLoci.dispatch(this.props.ctx, EmptyLoci);
return;
}
const query = createQuery(this.props.seq.entityId, seqId);
- const loci = StructureSelection.toLoci(await StructureQuery.run(query, this.props.structure));
+ const loci = StructureSelection.toLoci(StructureQuery.run1(query, this.props.structure));
if (loci.elements.length === 0) InteractivityEvents.HighlightLoci.dispatch(this.props.ctx, EmptyLoci);
else InteractivityEvents.HighlightLoci.dispatch(this.props.ctx, loci);
}
diff --git a/src/mol-model/structure/query/context.ts b/src/mol-model/structure/query/context.ts
index 5c94becb6..cefbc8346 100644
--- a/src/mol-model/structure/query/context.ts
+++ b/src/mol-model/structure/query/context.ts
@@ -4,7 +4,6 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { RuntimeContext } from 'mol-task';
import { Structure, StructureElement } from '../structure';
export interface QueryContextView {
@@ -17,7 +16,6 @@ export class QueryContext implements QueryContextView {
private currentLocked = false;
readonly inputStructure: Structure;
- readonly taskCtx: RuntimeContext;
/** Current element */
readonly element: StructureElement = StructureElement.create();
@@ -44,9 +42,8 @@ export class QueryContext implements QueryContextView {
(this.currentStructure as any) = void 0;
}
- constructor(structure: Structure, taskCtx: RuntimeContext) {
+ constructor(structure: Structure) {
this.inputStructure = structure;
- this.taskCtx = taskCtx;
}
}
diff --git a/src/mol-model/structure/query/queries/filters.ts b/src/mol-model/structure/query/queries/filters.ts
index 9bd5a50d2..3bf99a41f 100644
--- a/src/mol-model/structure/query/queries/filters.ts
+++ b/src/mol-model/structure/query/queries/filters.ts
@@ -4,38 +4,37 @@
* @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';
+import { SortedArray } from 'mol-data/int';
+import { Structure } from '../../structure';
+import { QueryPredicate } from '../context';
+import { StructureQuery } from '../query';
+import { StructureSelection } from '../selection';
-// export function pick(query: StructureQuery, pred: QueryPredicate): StructureQuery {
-// return async ctx => {
-// const sel = await query(ctx);
+export function pick(query: StructureQuery, pred: QueryPredicate): StructureQuery {
+ return ctx => {
+ const sel = 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();
-// }
-// };
-// }
+ 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/queries/generators.ts b/src/mol-model/structure/query/queries/generators.ts
index 8454c781f..ef9da1a18 100644
--- a/src/mol-model/structure/query/queries/generators.ts
+++ b/src/mol-model/structure/query/queries/generators.ts
@@ -11,7 +11,7 @@ import { Segmentation } from 'mol-data/int'
import { LinearGroupingBuilder } from '../utils/builders';
import { QueryPredicate, QueryFn, QueryContextView } from '../context';
-export const all: StructureQuery = async (ctx) => StructureSelection.Singletons(ctx.inputStructure, ctx.inputStructure);
+export const all: StructureQuery = ctx => StructureSelection.Singletons(ctx.inputStructure, ctx.inputStructure);
export interface AtomsQueryParams {
entityTest: QueryPredicate,
@@ -44,13 +44,12 @@ export function atoms(params?: Partial<AtomsQueryParams>): StructureQuery {
}
function atomGroupsLinear(atomTest: QueryPredicate): StructureQuery {
- return async (ctx) => {
+ return ctx => {
const { inputStructure } = ctx;
const { units } = inputStructure;
const l = ctx.pushCurrentElement();
const builder = inputStructure.subsetBuilder(true);
- let progress = 0;
for (const unit of units) {
l.unit = unit;
const elements = unit.elements;
@@ -61,9 +60,6 @@ function atomGroupsLinear(atomTest: QueryPredicate): StructureQuery {
if (atomTest(ctx)) builder.addElement(l.element);
}
builder.commitUnit();
-
- progress++;
- if (ctx.taskCtx.shouldUpdate) await ctx.taskCtx.update({ message: 'Atom Groups', current: progress, max: units.length });
}
ctx.popCurrentElement();
return StructureSelection.Singletons(inputStructure, builder.getStructure());
@@ -71,13 +67,12 @@ function atomGroupsLinear(atomTest: QueryPredicate): StructureQuery {
}
function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: AtomsQueryParams): StructureQuery {
- return async (ctx) => {
+ return ctx => {
const { inputStructure } = ctx;
const { units } = inputStructure;
const l = ctx.pushCurrentElement();
const builder = inputStructure.subsetBuilder(true);
- let progress = 0;
for (const unit of units) {
if (unit.kind !== Unit.Kind.Atomic) continue;
@@ -110,9 +105,6 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A
}
}
builder.commitUnit();
-
- progress++;
- if (ctx.taskCtx.shouldUpdate) await ctx.taskCtx.update({ message: 'Atom Groups', current: progress, max: units.length });
}
ctx.popCurrentElement();
return StructureSelection.Singletons(inputStructure, builder.getStructure());
@@ -120,13 +112,12 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A
}
function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, groupBy }: AtomsQueryParams): StructureQuery {
- return async (ctx) => {
+ return ctx => {
const { inputStructure } = ctx;
const { units } = inputStructure;
const l = ctx.pushCurrentElement();
const builder = new LinearGroupingBuilder(inputStructure);
- let progress = 0;
for (const unit of units) {
if (unit.kind !== Unit.Kind.Atomic) continue;
@@ -155,9 +146,6 @@ function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, group
}
}
}
-
- progress++;
- if (ctx.taskCtx.shouldUpdate) await ctx.taskCtx.update({ message: 'Atom Groups', current: progress, max: units.length });
}
ctx.popCurrentElement();
return builder.getSelection();
diff --git a/src/mol-model/structure/query/queries/modifiers.ts b/src/mol-model/structure/query/queries/modifiers.ts
index 7943e9e7f..ba3404e34 100644
--- a/src/mol-model/structure/query/queries/modifiers.ts
+++ b/src/mol-model/structure/query/queries/modifiers.ts
@@ -5,14 +5,13 @@
*/
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';
-function getWholeResidues(ctx: RuntimeContext, source: Structure, structure: Structure) {
+function getWholeResidues(source: Structure, structure: Structure) {
const builder = source.subsetBuilder(true);
for (const unit of structure.units) {
if (unit.kind !== Unit.Kind.Atomic) {
@@ -38,17 +37,14 @@ function getWholeResidues(ctx: RuntimeContext, source: Structure, structure: Str
}
export function wholeResidues(query: StructureQuery, isFlat: boolean): StructureQuery {
- return async (ctx) => {
- const inner = await query(ctx);
+ return ctx => {
+ const inner = query(ctx);
if (StructureSelection.isSingleton(inner)) {
- return StructureSelection.Singletons(ctx.inputStructure, getWholeResidues(ctx.taskCtx, ctx.inputStructure, inner.structure));
+ return StructureSelection.Singletons(ctx.inputStructure, getWholeResidues(ctx.inputStructure, inner.structure));
} else {
const builder = new UniqueStructuresBuilder(ctx.inputStructure);
- let progress = 0;
for (const s of inner.structures) {
- 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 });
+ builder.add(getWholeResidues(ctx.inputStructure, s));
}
return builder.getSelection();
}
@@ -64,12 +60,11 @@ export interface IncludeSurroundingsParams {
wholeResidues?: boolean
}
-async function getIncludeSurroundings(ctx: RuntimeContext, source: Structure, structure: Structure, params: IncludeSurroundingsParams) {
+function getIncludeSurroundings(source: Structure, structure: Structure, params: IncludeSurroundingsParams) {
const builder = new StructureUniqueSubsetBuilder(source);
const lookup = source.lookup3d;
const r = params.radius;
- let progress = 0;
for (const unit of structure.units) {
const { x, y, z } = unit.conformation;
const elements = unit.elements;
@@ -77,23 +72,21 @@ async function getIncludeSurroundings(ctx: RuntimeContext, source: Structure, st
const e = elements[i];
lookup.findIntoBuilder(x(e), y(e), z(e), r, builder);
}
- progress++;
- if (progress % 2500 === 0 && ctx.shouldUpdate) await ctx.update({ message: 'Include Surroudnings', isIndeterminate: true });
}
- return !!params.wholeResidues ? getWholeResidues(ctx, source, builder.getStructure()) : builder.getStructure();
+ return !!params.wholeResidues ? getWholeResidues(source, builder.getStructure()) : builder.getStructure();
}
export function includeSurroundings(query: StructureQuery, params: IncludeSurroundingsParams): StructureQuery {
- return async (ctx) => {
- const inner = await query(ctx);
+ return ctx => {
+ const inner = query(ctx);
if (StructureSelection.isSingleton(inner)) {
- const surr = await getIncludeSurroundings(ctx.taskCtx, ctx.inputStructure, inner.structure, params);
+ const surr = getIncludeSurroundings(ctx.inputStructure, inner.structure, params);
const ret = StructureSelection.Singletons(ctx.inputStructure, surr);
return ret;
} else {
const builder = new UniqueStructuresBuilder(ctx.inputStructure);
for (const s of inner.structures) {
- builder.add(await getIncludeSurroundings(ctx.taskCtx, ctx.inputStructure, s, params));
+ builder.add(getIncludeSurroundings(ctx.inputStructure, s, params));
}
return builder.getSelection();
}
diff --git a/src/mol-model/structure/query/query.ts b/src/mol-model/structure/query/query.ts
index a4c87dc50..acbd39ff6 100644
--- a/src/mol-model/structure/query/query.ts
+++ b/src/mol-model/structure/query/query.ts
@@ -4,19 +4,14 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { RuntimeContext, Task } from 'mol-task'
import { Structure } from '../structure'
import { StructureSelection } from './selection'
import { QueryContext } from './context';
-interface StructureQuery { (ctx: QueryContext): Promise<StructureSelection> }
+interface StructureQuery { (ctx: QueryContext): StructureSelection }
namespace StructureQuery {
- export function run(query: StructureQuery, structure: Structure, ctx?: RuntimeContext) {
- return query(new QueryContext(structure, ctx || RuntimeContext.Synchronous))
- }
-
- export function asTask(query: StructureQuery, structure: Structure) {
- return Task.create('Structure Query', ctx => query(new QueryContext(structure, ctx)));
+ export function run1(query: StructureQuery, structure: Structure) {
+ return query(new QueryContext(structure))
}
}
diff --git a/src/mol-model/structure/structure/symmetry.ts b/src/mol-model/structure/structure/symmetry.ts
index c5f8d2516..227d5c16d 100644
--- a/src/mol-model/structure/structure/symmetry.ts
+++ b/src/mol-model/structure/structure/symmetry.ts
@@ -25,10 +25,10 @@ namespace StructureSymmetry {
const assembler = Structure.Builder();
- const queryCtx = new QueryContext(structure, ctx);
+ const queryCtx = new QueryContext(structure);
for (const g of assembly.operatorGroups) {
- const selection = await g.selector(queryCtx);
+ const selection = g.selector(queryCtx);
if (StructureSelection.structureCount(selection) === 0) {
continue;
}
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index ba9543895..347065088 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -331,7 +331,7 @@ export namespace PropertyAccess {
radius: 5,
wholeResidues: true
});
- const surr = StructureSelection.unionStructure(await StructureQuery.run(q1, a));
+ const surr = StructureSelection.unionStructure(StructureQuery.run1(q1, a));
console.timeEnd('symmetry')
// for (const u of surr.units) {
@@ -372,7 +372,7 @@ export namespace PropertyAccess {
// }
function query(q: StructureQuery, s: Structure) {
- return StructureQuery.run(q, s);
+ return StructureQuery.run1(q, s);
}
export async function run() {
@@ -444,13 +444,13 @@ export namespace PropertyAccess {
//console.log(to_mmCIF('test', Selection.union(q0r)));
console.time('q1')
- await query(q1, structures[0]);
+ query(q1, structures[0]);
console.timeEnd('q1')
console.time('q1')
- await query(q1, structures[0]);
+ query(q1, structures[0]);
console.timeEnd('q1')
console.time('q2')
- const q2r = await query(q2, structures[0]);
+ const q2r = query(q2, structures[0]);
console.timeEnd('q2')
console.log(StructureSelection.structureCount(q2r));
//console.log(q1(structures[0]));
@@ -461,8 +461,8 @@ export namespace PropertyAccess {
//.add('test q', () => q1(structures[0]))
//.add('test q', () => q(structures[0]))
.add('test int', () => sumProperty(structures[0], l => col(l.element)))
- .add('test q1', async () => await query(q1, structures[0]))
- .add('test q3', async () => await query(q3, structures[0]))
+ .add('test q1', async () => query(q1, structures[0]))
+ .add('test q3', async () => query(q3, structures[0]))
// .add('sum residue', () => sumPropertyResidue(structures[0], l => l.unit.hierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.atom])))
// .add('baseline', () => baseline(models[0]))
diff --git a/src/servers/model/server/query.ts b/src/servers/model/server/query.ts
index 4a1049524..4e6866e94 100644
--- a/src/servers/model/server/query.ts
+++ b/src/servers/model/server/query.ts
@@ -69,7 +69,7 @@ export async function resolveRequest(req: Request, writer: Writer) {
? await req.queryDefinition.structureTransform(req.normalizedParams, wrappedStructure.structure)
: wrappedStructure.structure;
const query = req.queryDefinition.query(req.normalizedParams, structure);
- const result = StructureSelection.unionStructure(await StructureQuery.asTask(query, structure).run(abortingObserver, 250));
+ const result = StructureSelection.unionStructure(StructureQuery.run1(query, structure));
perf.end('query');
ConsoleLogger.logId(req.id, 'Query', 'Query finished.');
--
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