diff --git a/src/mol-plugin/behavior/dynamic/animation.ts b/src/mol-plugin/behavior/dynamic/animation.ts
index d54e53db816499d74d497d28afd9e842eb6a386f..2b3a1cee14b172862acd3a79390ce0b660ef8c41 100644
--- a/src/mol-plugin/behavior/dynamic/animation.ts
+++ b/src/mol-plugin/behavior/dynamic/animation.ts
@@ -64,7 +64,7 @@ export const StructureAnimation = PluginBehavior.create<StructureAnimationProps>
rotate(rad: number) {
this.updatedUnitTransforms.clear()
const state = this.ctx.state.dataState
- const reprs = state.select(q => q.rootsOfType(PluginStateObject.Molecule.Representation3D))
+ const reprs = state.selectQ(q => q.rootsOfType(PluginStateObject.Molecule.Representation3D))
Mat4.rotate(this.rotMat, this.tmpMat, rad, this.rotVec)
for (const r of reprs) {
if (!SO.isRepresentation3D(r.obj)) return
@@ -112,7 +112,7 @@ export const StructureAnimation = PluginBehavior.create<StructureAnimationProps>
explode(p: number) {
this.updatedUnitTransforms.clear()
const state = this.ctx.state.dataState
- const reprs = state.select(q => q.rootsOfType(PluginStateObject.Molecule.Representation3D));
+ const reprs = state.selectQ(q => q.rootsOfType(PluginStateObject.Molecule.Representation3D));
for (const r of reprs) {
if (!SO.isRepresentation3D(r.obj)) return
const structure = getRootStructure(r, state)
@@ -187,5 +187,5 @@ export const StructureAnimation = PluginBehavior.create<StructureAnimationProps>
//
function getRootStructure(root: StateObjectCell, state: State) {
- return state.query(StateSelection.Generators.byValue(root).rootOfType([PluginStateObject.Molecule.Structure]))[0];
+ return state.select(StateSelection.Generators.byValue(root).rootOfType([PluginStateObject.Molecule.Structure]))[0];
}
\ No newline at end of file
diff --git a/src/mol-plugin/behavior/dynamic/labels.ts b/src/mol-plugin/behavior/dynamic/labels.ts
index f30f4464e52091c277f7cdcf9531faf4f5d5a5c5..0faa3ffbd84254fac455c412c2e153fd3da2938f 100644
--- a/src/mol-plugin/behavior/dynamic/labels.ts
+++ b/src/mol-plugin/behavior/dynamic/labels.ts
@@ -112,7 +112,7 @@ export const SceneLabels = PluginBehavior.create<SceneLabelsProps>({
/** Update structures to be labeled, returns true if changed */
private updateStructures(p: SceneLabelsProps) {
const state = this.ctx.state.dataState
- const structures = state.select(q => q.rootsOfType(PluginStateObject.Molecule.Structure));
+ const structures = state.selectQ(q => q.rootsOfType(PluginStateObject.Molecule.Structure));
const rootStructures = new Set<SO.Molecule.Structure>()
for (const s of structures) {
const rootStructure = getRootStructure(s, state)
diff --git a/src/mol-plugin/behavior/static/state.ts b/src/mol-plugin/behavior/static/state.ts
index f3d852d82e218b3cc1455ea579b70bd88032dae4..2e53ede8c6ae73956b50ce2fc5061749bfd8a3a1 100644
--- a/src/mol-plugin/behavior/static/state.ts
+++ b/src/mol-plugin/behavior/static/state.ts
@@ -51,17 +51,17 @@ export function SetCurrentObject(ctx: PluginContext) {
}
export function Update(ctx: PluginContext) {
- PluginCommands.State.Update.subscribe(ctx, ({ state, tree }) => ctx.runTask(state.update(tree)));
+ PluginCommands.State.Update.subscribe(ctx, ({ state, tree }) => ctx.runTask(state.updateTree(tree)));
}
export function ApplyAction(ctx: PluginContext) {
- PluginCommands.State.ApplyAction.subscribe(ctx, ({ state, action, ref }) => ctx.runTask(state.apply(action.action, action.params, ref)));
+ PluginCommands.State.ApplyAction.subscribe(ctx, ({ state, action, ref }) => ctx.runTask(state.applyAction(action.action, action.params, ref)));
}
export function RemoveObject(ctx: PluginContext) {
PluginCommands.State.RemoveObject.subscribe(ctx, ({ state, ref }) => {
const tree = state.tree.build().delete(ref).getTree();
- return ctx.runTask(state.update(tree));
+ return ctx.runTask(state.updateTree(tree));
});
}
diff --git a/src/mol-plugin/command/base.ts b/src/mol-plugin/command/base.ts
index fcf1980a4e158b1dc29f27a7c085b5c187327095..d58e5e1b709d80b1e28a530f9e681d0b28d2af24 100644
--- a/src/mol-plugin/command/base.ts
+++ b/src/mol-plugin/command/base.ts
@@ -42,7 +42,7 @@ namespace PluginCommand {
unsubscribe(): void
}
- export type Action<T> = (params: T) => void | Promise<void>
+ export type Action<T> = (params: T) => unknown | Promise<unknown>
type Instance = { cmd: PluginCommand<any>, params: any, resolve: () => void, reject: (e: any) => void }
export class Manager {
diff --git a/src/mol-plugin/context.ts b/src/mol-plugin/context.ts
index 2749c5eee811344b9646c7a403a3cbb11eed5b72..f841c936382c7a440fa7f935db19cf6de87b1af0 100644
--- a/src/mol-plugin/context.ts
+++ b/src/mol-plugin/context.ts
@@ -152,7 +152,7 @@ export class PluginContext {
tree.toRoot().apply(b.transformer, b.defaultParams, { ref: b.transformer.id });
}
- await this.runTask(this.state.behaviorState.update(tree, true));
+ await this.runTask(this.state.behaviorState.updateTree(tree, true));
}
initDataActions() {
@@ -181,9 +181,6 @@ export class PluginContext {
this.lociLabels = new LociLabelManager(this);
- // TODO: find a better solution for this.
- setTimeout(() => this.log.message(`Mol* Plugin ${PLUGIN_VERSION} [${PLUGIN_VERSION_DATE.toLocaleString()}]`), 500);
+ this.log.message(`Mol* Plugin ${PLUGIN_VERSION} [${PLUGIN_VERSION_DATE.toLocaleString()}]`);
}
-
- // settings = ;
}
\ No newline at end of file
diff --git a/src/mol-plugin/state/actions/basic.ts b/src/mol-plugin/state/actions/basic.ts
index e2be44425b97f00504319e7623a88291115aa0ee..bd45155cf267a0497daea4a7533707855a3b87be 100644
--- a/src/mol-plugin/state/actions/basic.ts
+++ b/src/mol-plugin/state/actions/basic.ts
@@ -74,7 +74,7 @@ const DownloadStructure = StateAction.build({
}
const data = b.toRoot().apply(StateTransforms.Data.Download, downloadParams);
- return state.update(createStructureTree(ctx, data, params.source.params.supportProps));
+ return state.updateTree(createStructureTree(ctx, data, params.source.params.supportProps));
});
export const OpenStructure = StateAction.build({
@@ -84,7 +84,7 @@ export const OpenStructure = StateAction.build({
})(({ params, state }, ctx: PluginContext) => {
const b = state.build();
const data = b.toRoot().apply(StateTransforms.Data.ReadFile, { file: params.file, isBinary: /\.bcif$/i.test(params.file.name) });
- return state.update(createStructureTree(ctx, data, false));
+ return state.updateTree(createStructureTree(ctx, data, false));
});
function createStructureTree(ctx: PluginContext, b: StateTreeBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>, supportProps: boolean): StateTree {
@@ -123,7 +123,7 @@ export const CreateComplexRepresentation = StateAction.build({
})(({ ref, state }, ctx: PluginContext) => {
const root = state.build().to(ref);
complexRepresentation(ctx, root);
- return state.update(root.getTree());
+ return state.updateTree(root.getTree());
});
export const UpdateTrajectory = StateAction.build({
@@ -133,7 +133,7 @@ export const UpdateTrajectory = StateAction.build({
by: PD.makeOptional(PD.Numeric(1, { min: -1, max: 1, step: 1 }))
}
})(({ params, state }) => {
- const models = state.select(q => q.rootsOfType(PluginStateObject.Molecule.Model)
+ const models = state.selectQ(q => q.rootsOfType(PluginStateObject.Molecule.Model)
.filter(c => c.transform.transformer === StateTransforms.Model.ModelFromTrajectory));
const update = state.build();
@@ -157,7 +157,7 @@ export const UpdateTrajectory = StateAction.build({
}
}
- return state.update(update);
+ return state.updateTree(update);
});
//
@@ -175,15 +175,13 @@ function getVolumeData(format: VolumeFormat, b: StateTreeBuilder.To<PluginStateO
}
function createVolumeTree(format: VolumeFormat, ctx: PluginContext, b: StateTreeBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>): StateTree {
-
- const root = getVolumeData(format, b)
+ return getVolumeData(format, b)
.apply(StateTransforms.Representation.VolumeRepresentation3D,
- VolumeRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'isosurface'));
-
- return root.getTree();
+ VolumeRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'isosurface'))
+ .getTree();
}
-function getFileFormat(format: VolumeFormat | 'auto', file: FileInput): VolumeFormat {
+function getFileFormat(format: VolumeFormat | 'auto', file: FileInput, data?: Uint8Array): VolumeFormat {
if (format === 'auto') {
const fileFormat = getFileInfo(file).ext
if (fileFormat in VolumeFormats) {
@@ -205,11 +203,20 @@ export const OpenVolume = StateAction.build({
['auto', 'Automatic'], ['ccp4', 'CCP4'], ['mrc', 'MRC'], ['map', 'MAP'], ['dsn6', 'DSN6'], ['brix', 'BRIX']
]),
}
-})(({ params, state }, ctx: PluginContext) => {
- const b = state.build();
- const data = b.toRoot().apply(StateTransforms.Data.ReadFile, { file: params.file, isBinary: true });
- const format = getFileFormat(params.format, params.file)
- return state.update(createVolumeTree(format, ctx, data));
+})(async ({ params, state }, ctx: PluginContext) => {
+ const dataTree = state.build().toRoot().apply(StateTransforms.Data.ReadFile, { file: params.file, isBinary: true });
+ const volumeData = await ctx.runTask(state.updateTree(dataTree));
+
+ // Alternative for more complex states where the builder is not a simple StateTreeBuilder.To<>:
+ /*
+ const dataRef = dataTree.ref;
+ await ctx.runTask(state.updateTree(dataTree));
+ const dataCell = state.select(dataRef)[0];
+ */
+
+ const format = getFileFormat(params.format, params.file, volumeData.data as Uint8Array)
+ const volumeTree = state.build().to(dataTree.ref);
+ return state.updateTree(createVolumeTree(format, ctx, volumeTree));
});
export { DownloadDensity };
@@ -276,5 +283,5 @@ const DownloadDensity = StateAction.build({
}
const data = b.toRoot().apply(StateTransforms.Data.Download, downloadParams);
- return state.update(createVolumeTree(format, ctx, data));
+ return state.updateTree(createVolumeTree(format, ctx, data));
});
\ No newline at end of file
diff --git a/src/mol-state/action.ts b/src/mol-state/action.ts
index 1b178246fbc2fe31d421b4c116db744492117813..53b41b53b66b1727944f135ebdb4baf9176350be 100644
--- a/src/mol-state/action.ts
+++ b/src/mol-state/action.ts
@@ -71,7 +71,7 @@ namespace StateAction {
params: def.params as Transformer.Definition<Transformer.From<T>, any, Transformer.Params<T>>['params'],
run({ cell, state, params }) {
const tree = state.build().to(cell.transform.ref).apply(transformer, params);
- return state.update(tree);
+ return state.updateTree(tree) as Task<void>;
}
})
}
diff --git a/src/mol-state/object.ts b/src/mol-state/object.ts
index 495206df1f0a9ae667baf3b5e10c2eb463b78a97..3e2df3343df0b95b85698bbbbdabcfbda6dbbbd6 100644
--- a/src/mol-state/object.ts
+++ b/src/mol-state/object.ts
@@ -105,7 +105,7 @@ export class StateObjectTracker<T extends StateObject> {
}
update() {
- const cell = this.state.query(this.query)[0];
+ const cell = this.state.select(this.query)[0];
const version = cell ? cell.transform.version : void 0;
const changed = this.cell !== cell || this.version !== version;
this.cell = cell;
diff --git a/src/mol-state/state.ts b/src/mol-state/state.ts
index 9733c06add1823d77dcef5785eb3dfe878783532..586321e8957c77a65bd6e08320ff5f206e5e6f55 100644
--- a/src/mol-state/state.ts
+++ b/src/mol-state/state.ts
@@ -33,7 +33,7 @@ class State {
readonly globalContext: unknown = void 0;
readonly events = {
cell: {
- stateUpdated: this.ev<State.ObjectEvent & { cellState: StateObjectCell.State}>(),
+ stateUpdated: this.ev<State.ObjectEvent & { cellState: StateObjectCell.State }>(),
created: this.ev<State.ObjectEvent & { cell: StateObjectCell }>(),
removed: this.ev<State.ObjectEvent & { parent: Transform.Ref }>(),
},
@@ -67,7 +67,7 @@ class State {
setSnapshot(snapshot: State.Snapshot) {
const tree = StateTree.fromJSON(snapshot.tree);
- return this.update(tree);
+ return this.updateTree(tree);
}
setCurrent(ref: Transform.Ref) {
@@ -89,26 +89,28 @@ class State {
}
/**
- * Select Cells by ref or a query generated on the fly.
- * @example state.select('test')
- * @example state.select(q => q.byRef('test').subtree())
+ * Select Cells using the provided selector.
+ * @example state.query(StateSelection.Generators.byRef('test').ancestorOfType([type]))
+ * @example state.query('test')
*/
- select(selector: Transform.Ref | ((q: typeof StateSelection.Generators) => StateSelection.Selector)) {
- if (typeof selector === 'string') return StateSelection.select(selector, this);
- return StateSelection.select(selector(StateSelection.Generators), this)
+ select(selector: StateSelection.Selector) {
+ return StateSelection.select(selector, this)
}
/**
- * Select Cells using the provided selector.
- * @example state.select('test')
+ * Select Cells by building a query generated on the fly.
* @example state.select(q => q.byRef('test').subtree())
*/
- query(selector: StateSelection.Selector) {
- return StateSelection.select(selector, this)
+ selectQ(selector: (q: typeof StateSelection.Generators) => StateSelection.Selector) {
+ if (typeof selector === 'string') return StateSelection.select(selector, this);
+ return StateSelection.select(selector(StateSelection.Generators), this)
}
- /** If no ref is specified, apply to root */
- apply<A extends StateAction>(action: A, params: StateAction.Params<A>, ref: Transform.Ref = Transform.RootRef): Task<void> {
+ /**
+ * Creates a Task that applies the specified StateAction (i.e. must use run* on the result)
+ * If no ref is specified, apply to root.
+ */
+ applyAction<A extends StateAction>(action: A, params: StateAction.Params<A>, ref: Transform.Ref = Transform.RootRef): Task<void> {
return Task.create('Apply Action', ctx => {
const cell = this.cells.get(ref);
if (!cell) throw new Error(`'${ref}' does not exist.`);
@@ -118,41 +120,59 @@ class State {
});
}
- update(tree: StateTree | StateTreeBuilder, silent: boolean = false): Task<void> {
- const _tree = (StateTreeBuilder.is(tree) ? tree.getTree() : tree).asTransient();
+ /**
+ * Reconcialites the existing state tree with the new version.
+ *
+ * If the tree is StateTreeBuilder.To<T>, the corresponding StateObject is returned by the task.
+ * @param tree Tree instance or a tree builder instance
+ * @param doNotReportTiming Indicates whether to log timing of the individual transforms
+ */
+ updateTree<T extends StateObject>(tree: StateTree | StateTreeBuilder | StateTreeBuilder.To<T>, doNotLogTiming?: boolean): Task<T>
+ updateTree(tree: StateTree | StateTreeBuilder, doNotLogTiming?: boolean): Task<void>
+ updateTree(tree: StateTree | StateTreeBuilder, doNotLogTiming: boolean = false): Task<any> {
return Task.create('Update Tree', async taskCtx => {
let updated = false;
try {
- const oldTree = this._tree;
- this._tree = _tree;
+ const ctx = this.updateTreeAndCreateCtx(tree, taskCtx, doNotLogTiming);
+ updated = await update(ctx);
+ if (StateTreeBuilder.isTo(tree)) {
+ const cell = this.select(tree.ref)[0];
+ return cell && cell.obj;
+ }
+ } finally {
+ if (updated) this.events.changed.next();
+ }
+ });
+ }
+
+ private updateTreeAndCreateCtx(tree: StateTree | StateTreeBuilder, taskCtx: RuntimeContext, doNotLogTiming: boolean) {
+ const _tree = (StateTreeBuilder.is(tree) ? tree.getTree() : tree).asTransient();
+ const oldTree = this._tree;
+ this._tree = _tree;
- const ctx: UpdateContext = {
- parent: this,
- editInfo: StateTreeBuilder.is(tree) ? tree.editInfo : void 0,
+ const ctx: UpdateContext = {
+ parent: this,
+ editInfo: StateTreeBuilder.is(tree) ? tree.editInfo : void 0,
- errorFree: this.errorFree,
- taskCtx,
- oldTree,
- tree: _tree,
- cells: this.cells as Map<Transform.Ref, StateObjectCell>,
- transformCache: this.transformCache,
+ errorFree: this.errorFree,
+ taskCtx,
+ oldTree,
+ tree: _tree,
+ cells: this.cells as Map<Transform.Ref, StateObjectCell>,
+ transformCache: this.transformCache,
- results: [],
+ results: [],
- silent,
+ silent: doNotLogTiming,
- changed: false,
- hadError: false,
- newCurrent: void 0
- };
+ changed: false,
+ hadError: false,
+ newCurrent: void 0
+ };
- this.errorFree = true;
- // TODO: handle "cancelled" error? Or would this be handled automatically?
- updated = await update(ctx);
- } finally {
- if (updated) this.events.changed.next();
- }
- });
+ this.errorFree = true;
+
+ return ctx;
}
constructor(rootObject: StateObject, params?: { globalContext?: unknown }) {
@@ -167,8 +187,8 @@ class State {
version: root.version,
errorText: void 0,
params: {
- definition: { },
- values: { }
+ definition: {},
+ values: {}
}
});
@@ -311,7 +331,7 @@ async function update(ctx: UpdateContext) {
const current = ctx.parent.current;
const currentCell = ctx.cells.get(current);
if (currentCell && (
- currentCell.obj === StateObject.Null
+ currentCell.obj === StateObject.Null
|| (currentCell.status === 'error' && currentCell.errorText === ParentNullErrorText))) {
newCurrent = findNewCurrent(ctx.oldTree, current, [], ctx.cells);
ctx.parent.setCurrent(newCurrent);
@@ -523,7 +543,7 @@ async function updateSubtree(ctx: UpdateContext, root: Ref) {
function resolveParams(ctx: UpdateContext, transform: Transform, src: StateObject) {
const prms = transform.transformer.definition.params;
- const definition = prms ? prms(src, ctx.parent.globalContext) : { };
+ const definition = prms ? prms(src, ctx.parent.globalContext) : {};
const values = transform.params ? transform.params : ParamDefinition.getDefaultValues(definition);
return { definition, values };
}
diff --git a/src/mol-state/tree/builder.ts b/src/mol-state/tree/builder.ts
index 2eb22efd86b5797c1845f75603646ca94af8ff79..0cd0faa0b36088c79de318bd233bdba057a07c59 100644
--- a/src/mol-state/tree/builder.ts
+++ b/src/mol-state/tree/builder.ts
@@ -33,6 +33,10 @@ namespace StateTreeBuilder {
return !!obj && typeof (obj as StateTreeBuilder).getTree === 'function';
}
+ export function isTo(obj: any): obj is StateTreeBuilder.To<any> {
+ return !!obj && typeof (obj as StateTreeBuilder).getTree === 'function' && typeof (obj as StateTreeBuilder.To<any>).ref === 'string';
+ }
+
export class Root implements StateTreeBuilder {
private state: State;
get editInfo() { return this.state.editInfo; }