From 53c8ba549fe1af07a33e5524ba68efc93564f5d9 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 28 Feb 2019 09:47:40 +0100
Subject: [PATCH] wip selection model
---
src/examples/proteopedia-wrapper/helpers.ts | 2 -
.../structure/query/queries/combinators.ts | 2 +-
src/mol-model/structure/query/selection.ts | 2 +-
.../structure/query/utils/builders.ts | 2 +-
src/mol-model/structure/structure/element.ts | 7 +
.../structure/structure/structure.ts | 2 +-
src/mol-plugin/util/canvas3d-identify.ts | 4 +-
.../util/selection/structure-element.ts | 115 --------------
.../util/selection/structure-loci.ts | 147 ++++++++++++++++++
src/mol-util/object.ts | 8 +
10 files changed, 168 insertions(+), 123 deletions(-)
delete mode 100644 src/mol-plugin/util/selection/structure-element.ts
create mode 100644 src/mol-plugin/util/selection/structure-loci.ts
diff --git a/src/examples/proteopedia-wrapper/helpers.ts b/src/examples/proteopedia-wrapper/helpers.ts
index d3154f7c1..427fb057e 100644
--- a/src/examples/proteopedia-wrapper/helpers.ts
+++ b/src/examples/proteopedia-wrapper/helpers.ts
@@ -25,8 +25,6 @@ export namespace ModelInfo {
const json = JSON.parse(src);
const data = json && json[id];
- console.log(data);
-
const assemblies = data[0] && data[0].assemblies;
if (!assemblies || !assemblies.length) return void 0;
diff --git a/src/mol-model/structure/query/queries/combinators.ts b/src/mol-model/structure/query/queries/combinators.ts
index 7bd531bd3..a3b060ae6 100644
--- a/src/mol-model/structure/query/queries/combinators.ts
+++ b/src/mol-model/structure/query/queries/combinators.ts
@@ -47,7 +47,7 @@ export function intersect(queries: ArrayLike<StructureQuery>): StructureQuery {
}
ctx.throwIfTimedOut();
- const pivotSet = HashSet<Structure>(s => s.hashCode, Structure.areEqual);
+ const pivotSet = HashSet<Structure>(s => s.hashCode, Structure.areUnitAndIndicesEqual);
StructureSelection.forEach(selections[pivotIndex], s => pivotSet.add(s));
const ret = StructureSelection.UniqueBuilder(ctx.inputStructure);
diff --git a/src/mol-model/structure/query/selection.ts b/src/mol-model/structure/query/selection.ts
index b25717071..901452573 100644
--- a/src/mol-model/structure/query/selection.ts
+++ b/src/mol-model/structure/query/selection.ts
@@ -84,7 +84,7 @@ namespace StructureSelection {
class HashBuilderImpl implements Builder {
private structures: Structure[] = [];
private allSingletons = true;
- private uniqueSets = HashSet(Structure.hashCode, Structure.areEqual);
+ private uniqueSets = HashSet(Structure.hashCode, Structure.areUnitAndIndicesEqual);
add(structure: Structure) {
const atomCount = structure.elementCount;
diff --git a/src/mol-model/structure/query/utils/builders.ts b/src/mol-model/structure/query/utils/builders.ts
index 9da400cba..a47a5354b 100644
--- a/src/mol-model/structure/query/utils/builders.ts
+++ b/src/mol-model/structure/query/utils/builders.ts
@@ -12,7 +12,7 @@ import { StructureSubsetBuilder } from '../../structure/util/subset-builder';
import { ElementIndex } from '../../model';
export class UniqueStructuresBuilder {
- private set = HashSet(Structure.hashCode, Structure.areEqual);
+ private set = HashSet(Structure.hashCode, Structure.areUnitAndIndicesEqual);
private structures: Structure[] = [];
private allSingletons = true;
diff --git a/src/mol-model/structure/structure/element.ts b/src/mol-model/structure/structure/element.ts
index e9287c338..1e4c7ae2e 100644
--- a/src/mol-model/structure/structure/element.ts
+++ b/src/mol-model/structure/structure/element.ts
@@ -117,6 +117,13 @@ namespace StructureElement {
})));
}
+ export function remap(loci: Loci, structure: Structure): Loci {
+ return Loci(structure, loci.elements.map(e => ({
+ unit: structure.unitMap.get(e.unit.id)!,
+ indices: e.indices
+ })));
+ }
+
export function union(xs: Loci, ys: Loci): Loci {
if (xs.structure !== ys.structure) throw new Error(`Can't union Loci of different structures.`);
if (xs.elements.length > ys.elements.length) return union(ys, xs);
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index b86668743..8d45b5146 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -424,7 +424,7 @@ namespace Structure {
return hashString(s.units.map(u => Unit.conformationId(u)).join('|'))
}
- export function areEqual(a: Structure, b: Structure) {
+ export function areUnitAndIndicesEqual(a: Structure, b: Structure) {
if (a.elementCount !== b.elementCount) return false;
const len = a.units.length;
if (len !== b.units.length) return false;
diff --git a/src/mol-plugin/util/canvas3d-identify.ts b/src/mol-plugin/util/canvas3d-identify.ts
index a9fd5e13c..c7e0e64ed 100644
--- a/src/mol-plugin/util/canvas3d-identify.ts
+++ b/src/mol-plugin/util/canvas3d-identify.ts
@@ -6,7 +6,7 @@
import { PluginContext } from '../context';
import { PickingId } from 'mol-geo/geometry/picking';
-import { EmptyLoci, Loci } from 'mol-model/loci';
+import { EmptyLoci } from 'mol-model/loci';
import { Representation } from 'mol-repr/representation';
import { ModifiersKeys, ButtonsType } from 'mol-util/input/input-observer';
@@ -49,7 +49,7 @@ export class Canvas3dIdentifyHelper {
}
const loci = this.ctx.canvas3d.getLoci(this.id);
- if (loci.repr !== this.prevLoci.repr || !Loci.areEqual(loci.loci, this.prevLoci.loci)) {
+ if (!Representation.Loci.areEqual(this.prevLoci, loci)) {
this.ctx.events.canvas3d.highlight.next({ loci, modifiers: this.modifiers });
this.prevLoci = loci;
}
diff --git a/src/mol-plugin/util/selection/structure-element.ts b/src/mol-plugin/util/selection/structure-element.ts
deleted file mode 100644
index 8fda7de0d..000000000
--- a/src/mol-plugin/util/selection/structure-element.ts
+++ /dev/null
@@ -1,115 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { StructureElement, Structure } from 'mol-model/structure';
-import { PluginContext } from '../../context';
-import { Loci, EmptyLoci } from 'mol-model/loci';
-import { PluginStateObject } from 'mol-plugin/state/objects';
-import { State } from 'mol-state';
-
-export { StructureElementSelectionManager }
-
-class StructureElementSelectionManager {
- private entries = new Map<string, Entry>();
-
- // maps structure to a parent StateObjectCell
- private structures = {
- root: new Map<Structure, string>(),
- tracked: new Map<string, Structure>()
- }
-
- private getEntry(s: Structure) {
- if (!this.structures.root.has(s)) return;
- const key = this.structures.root.get(s)!;
- if (!this.entries.has(key)) {
- const entry: Entry = {
- selection: StructureElement.Loci(s, []),
- highlight: StructureElement.Loci(s, []),
- };
- this.entries.set(key, entry);
- return entry;
- }
-
- return this.entries.get(key)!;
- }
-
- add(loci: StructureElement.Loci | Structure.Loci, type: 'selection' | 'highlight'): Loci {
- const entry = this.getEntry(loci.structure);
- if (!entry) return EmptyLoci;
- entry[type] = Structure.isLoci(loci) ? StructureElement.Loci.all(loci.structure) : StructureElement.Loci.union(entry[type], loci);
- return entry[type];
- }
-
- remove(loci: StructureElement.Loci | Structure.Loci, type: 'selection' | 'highlight'): Loci {
- const entry = this.getEntry(loci.structure);
- if (!entry) return EmptyLoci;
- entry[type] = Structure.isLoci(loci) ? StructureElement.Loci(loci.structure, []) : StructureElement.Loci.subtract(entry[type], loci);
- return entry[type].elements.length === 0 ? EmptyLoci : entry[type];
- }
-
- set(loci: StructureElement.Loci | Structure.Loci, type: 'selection' | 'highlight'): Loci {
- const entry = this.getEntry(loci.structure);
- if (!entry) return EmptyLoci;
- entry[type] = Structure.isLoci(loci) ? StructureElement.Loci.all(loci.structure) : loci;
- return entry[type].elements.length === 0 ? EmptyLoci : entry[type];
- }
-
- private prevHighlight: StructureElement.Loci | undefined = void 0;
-
- accumulateInteractiveHighlight(loci: StructureElement.Loci) {
- if (this.prevHighlight) {
- this.prevHighlight = StructureElement.Loci.union(this.prevHighlight, loci);
- } else {
- this.prevHighlight = loci;
- }
- return this.prevHighlight;
- }
-
- clearInteractiveHighlight() {
- const ret = this.prevHighlight;
- this.prevHighlight = void 0;
- return ret || EmptyLoci;
- }
-
- private trackCell(state: State, ref: string) {
- const cell = state.cells.get(ref);
- if (!cell || !cell.obj || !PluginStateObject.Molecule.Structure.is(cell.obj)) return;
- const parent = state.selectQ(q => q.byRef(cell.transform.ref).rootOfType([PluginStateObject.Molecule.Structure]))[0];
- this.structures.tracked.set(cell.transform.ref, cell.obj.data);
- if (!parent) {
- this.structures.root.set(cell.obj.data, cell.transform.ref);
- } else {
- this.structures.root.set(cell.obj.data, parent.transform.ref);
- }
- }
-
- private untrackCell(state: State, ref: string) {
- if (!this.structures.tracked.has(ref)) return;
- const s = this.structures.tracked.get(ref)!;
- this.structures.tracked.delete(ref);
- this.structures.root.delete(s);
- }
-
- constructor(plugin: PluginContext) {
- plugin.state.dataState.events.object.created.subscribe(e => {
- this.trackCell(e.state, e.ref);
- });
-
- plugin.state.dataState.events.object.removed.subscribe(e => {
- this.untrackCell(e.state, e.ref);
- });
-
- plugin.state.dataState.events.object.updated.subscribe(e => {
- this.untrackCell(e.state, e.ref);
- this.trackCell(e.state, e.ref);
- });
- }
-}
-
-interface Entry {
- selection: StructureElement.Loci,
- highlight: StructureElement.Loci
-}
diff --git a/src/mol-plugin/util/selection/structure-loci.ts b/src/mol-plugin/util/selection/structure-loci.ts
new file mode 100644
index 000000000..b7613c10b
--- /dev/null
+++ b/src/mol-plugin/util/selection/structure-loci.ts
@@ -0,0 +1,147 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { StructureElement, Structure } from 'mol-model/structure';
+import { PluginContext } from '../../context';
+import { Loci, EmptyLoci } from 'mol-model/loci';
+import { PluginStateObject } from 'mol-plugin/state/objects';
+import { State, StateSelection, StateObject } from 'mol-state';
+import { mapObjectMap } from 'mol-util/object';
+
+export { StructureLociManager }
+
+class StructureLociManager {
+ private entries = new Map<string, SelectionEntry>();
+
+ // maps structure to a parent StateObjectCell
+ private mapping = {
+ root: new Map<Structure, string>(),
+ tracked: new Map<string, Structure>()
+ };
+
+ private getEntry(s: Structure) {
+ if (!this.mapping.root.has(s)) return;
+ const key = this.mapping.root.get(s)!;
+ if (!this.entries.has(key)) {
+ const entry = SelectionEntry(s);
+ this.entries.set(key, entry);
+ return entry;
+ }
+
+ return this.entries.get(key)!;
+ }
+
+ add(loci: StructureElement.Loci | Structure.Loci, type: 'selection' | 'highlight'): Loci {
+ const entry = this.getEntry(loci.structure);
+ if (!entry) return EmptyLoci;
+ const xs = entry.elements;
+ xs[type] = Structure.isLoci(loci) ? StructureElement.Loci.all(loci.structure) : StructureElement.Loci.union(xs[type], loci);
+ return xs[type];
+ }
+
+ remove(loci: StructureElement.Loci | Structure.Loci, type: 'selection' | 'highlight'): Loci {
+ const entry = this.getEntry(loci.structure);
+ if (!entry) return EmptyLoci;
+ const xs = entry.elements;
+ xs[type] = Structure.isLoci(loci) ? StructureElement.Loci(loci.structure, []) : StructureElement.Loci.subtract(xs[type], loci);
+ return xs[type].elements.length === 0 ? EmptyLoci : xs[type];
+ }
+
+ set(loci: StructureElement.Loci | Structure.Loci, type: 'selection' | 'highlight'): Loci {
+ const entry = this.getEntry(loci.structure);
+ if (!entry) return EmptyLoci;
+ const xs = entry.elements;
+ xs[type] = Structure.isLoci(loci) ? StructureElement.Loci.all(loci.structure) : loci;
+ return xs[type].elements.length === 0 ? EmptyLoci : xs[type];
+ }
+
+ private prevHighlight: StructureElement.Loci | undefined = void 0;
+
+ accumulateInteractiveHighlight(loci: StructureElement.Loci) {
+ if (this.prevHighlight) {
+ this.prevHighlight = StructureElement.Loci.union(this.prevHighlight, loci);
+ } else {
+ this.prevHighlight = loci;
+ }
+ return this.prevHighlight;
+ }
+
+ clearInteractiveHighlight() {
+ const ret = this.prevHighlight;
+ this.prevHighlight = void 0;
+ return ret || EmptyLoci;
+ }
+
+ private addMapping(state: State, ref: string, obj: StateObject) {
+ if (!PluginStateObject.Molecule.Structure.is(obj)) return;
+ const parent = state.select(StateSelection.Generators.byRef(ref).rootOfType([PluginStateObject.Molecule.Structure]))[0];
+ this.mapping.tracked.set(ref, obj.data);
+ if (!parent) {
+ this.mapping.root.set(obj.data, ref);
+ } else {
+ this.mapping.root.set(obj.data, parent.transform.ref);
+ }
+ }
+
+ private removeMapping(ref: string) {
+ if (!this.mapping.tracked.has(ref)) return;
+ const s = this.mapping.tracked.get(ref)!;
+ this.mapping.tracked.delete(ref);
+ const root = this.mapping.root.get(s);
+ this.mapping.root.delete(s);
+ if (root === ref) this.entries.delete(ref);
+ }
+
+ private updateMapping(state: State, ref: string, oldObj: StateObject | undefined, obj: StateObject) {
+ if (!PluginStateObject.Molecule.Structure.is(obj)) return;
+
+ if (this.entries.has(ref)) {
+ if (!PluginStateObject.Molecule.Structure.is(oldObj) || oldObj === obj || oldObj.data === obj.data) return;
+
+ // remap the old selection to be related to the new object if possible.
+ if (Structure.areUnitAndIndicesEqual(oldObj.data, obj.data)) {
+ this.entries.set(ref, remapSelectionEntry(this.entries.get(ref)!, obj.data));
+ return;
+ }
+
+ // clear the selection
+ this.entries.set(ref, SelectionEntry(obj.data));
+ } else {
+ this.removeMapping(ref);
+ this.addMapping(state, ref, obj);
+ }
+ }
+
+ constructor(plugin: PluginContext) {
+ plugin.state.dataState.events.object.created.subscribe(e => {
+ this.addMapping(e.state, e.ref, e.obj);
+ });
+
+ plugin.state.dataState.events.object.removed.subscribe(e => {
+ this.removeMapping(e.ref);
+ });
+
+ plugin.state.dataState.events.object.updated.subscribe(e => {
+ this.updateMapping(e.state, e.ref, e.oldObj, e.obj);
+ });
+ }
+}
+
+interface SelectionEntry {
+ elements: { [category: string]: StructureElement.Loci }
+}
+
+function SelectionEntry(s: Structure): SelectionEntry {
+ return {
+ elements: { }
+ };
+}
+
+function remapSelectionEntry(e: SelectionEntry, s: Structure): SelectionEntry {
+ return {
+ elements: mapObjectMap(e.elements, (l: StructureElement.Loci) => StructureElement.Loci.remap(l, s))
+ };
+}
\ No newline at end of file
diff --git a/src/mol-util/object.ts b/src/mol-util/object.ts
index a88d70325..bfb4824f5 100644
--- a/src/mol-util/object.ts
+++ b/src/mol-util/object.ts
@@ -82,4 +82,12 @@ export function deepClone<T>(source: T): T {
}
throw new Error(`Can't clone, type "${typeof source}" unsupported`);
+}
+
+export function mapObjectMap<O extends { [k: string]: T }, T, S>(o: O, f: (v: T) => S): { [k: string]: S } {
+ const ret: any = { };
+ for (const k of Object.keys(o)) {
+ ret[k] = f((o as any)[k]);
+ }
+ return ret;
}
\ No newline at end of file
--
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