From f16c699d3bfc5c2b92ddbfdc4aa890bc86cbe7d9 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Fri, 8 Dec 2017 17:21:36 +0100
Subject: [PATCH] Added linked list to mol-data, refactoring
---
src/mol-data/generic.ts | 9 ++
.../generic/_spec/linked-list.spec.ts | 63 ++++++++++
src/mol-data/{util => generic}/hash-set.ts | 0
src/mol-data/generic/linked-list.ts | 119 ++++++++++++++++++
.../{util => generic}/unique-array.ts | 0
src/mol-data/index.ts | 3 +-
src/mol-data/util.ts | 2 -
src/mol-data/util/array.ts | 2 +-
src/mol-model/structure/query/selection.ts | 2 +-
.../structure/structure/structure.ts | 2 +-
src/mol-task/computation.ts | 2 +-
src/mol-task/execution/observable.ts | 55 +++++++-
src/mol-task/index.ts | 3 +-
src/mol-task/task.ts | 13 +-
src/mol-task/util/chunked.ts | 0
src/mol-task/util/multistep.ts | 0
src/mol-task/{time.ts => util/now.ts} | 0
17 files changed, 257 insertions(+), 18 deletions(-)
create mode 100644 src/mol-data/generic.ts
create mode 100644 src/mol-data/generic/_spec/linked-list.spec.ts
rename src/mol-data/{util => generic}/hash-set.ts (100%)
create mode 100644 src/mol-data/generic/linked-list.ts
rename src/mol-data/{util => generic}/unique-array.ts (100%)
create mode 100644 src/mol-task/util/chunked.ts
create mode 100644 src/mol-task/util/multistep.ts
rename src/mol-task/{time.ts => util/now.ts} (100%)
diff --git a/src/mol-data/generic.ts b/src/mol-data/generic.ts
new file mode 100644
index 000000000..d837d1060
--- /dev/null
+++ b/src/mol-data/generic.ts
@@ -0,0 +1,9 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+export * from './generic/hash-set'
+export * from './generic/linked-list'
+export * from './generic/unique-array'
\ No newline at end of file
diff --git a/src/mol-data/generic/_spec/linked-list.spec.ts b/src/mol-data/generic/_spec/linked-list.spec.ts
new file mode 100644
index 000000000..cb439b3da
--- /dev/null
+++ b/src/mol-data/generic/_spec/linked-list.spec.ts
@@ -0,0 +1,63 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { LinkedList } from '../linked-list'
+
+describe('linked list', () => {
+
+ function toArray<T>(list: LinkedList<T>) {
+ const ret: T[] = [];
+ for (let t = list.first; !!t; t = t.next) {
+ ret[ret.length] = t.value;
+ }
+ return ret;
+ }
+
+ function create<T>(xs: T[]) {
+ const list = LinkedList<T>();
+ for (const x of xs) list.addLast(x);
+ return list;
+ }
+
+ it('add', () => {
+ const list = LinkedList<number>();
+ list.addFirst(1);
+ list.addLast(2);
+ list.addFirst(3);
+ list.addFirst(4);
+ list.addLast(5);
+ expect(toArray(list)).toEqual([4, 3, 1, 2, 5]);
+ expect(list.count).toBe(5);
+ });
+
+ it ('remove', () => {
+ const list = create([1, 2, 3, 4]);
+ let fst = list.removeFirst();
+ expect(fst).toBe(1);
+ expect(list.last!.value).toBe(4);
+ expect(list.count).toBe(3);
+ expect(toArray(list)).toEqual([2, 3, 4]);
+
+ let last = list.removeLast();
+ expect(last).toBe(4);
+ expect(list.last!.value).toBe(3);
+ expect(list.count).toBe(2);
+ expect(toArray(list)).toEqual([2, 3]);
+
+ let n3 = list.find(3)!;
+ list.remove(n3);
+ expect(list.first!.value).toBe(2);
+ expect(list.last!.value).toBe(2);
+ expect(list.count).toBe(1);
+ expect(toArray(list)).toEqual([2]);
+
+ list.removeFirst();
+ expect(list.first).toBe(null);
+ expect(list.last).toBe(null);
+ expect(list.count).toBe(0);
+ expect(toArray(list)).toEqual([]);
+ })
+});
\ No newline at end of file
diff --git a/src/mol-data/util/hash-set.ts b/src/mol-data/generic/hash-set.ts
similarity index 100%
rename from src/mol-data/util/hash-set.ts
rename to src/mol-data/generic/hash-set.ts
diff --git a/src/mol-data/generic/linked-list.ts b/src/mol-data/generic/linked-list.ts
new file mode 100644
index 000000000..3f5422699
--- /dev/null
+++ b/src/mol-data/generic/linked-list.ts
@@ -0,0 +1,119 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+interface LinkedList<T> {
+ readonly count: number,
+ readonly first: LinkedList.Node<T> | null,
+ readonly last: LinkedList.Node<T> | null,
+ addFirst(value: T): LinkedList.Node<T>,
+ addLast(value: T): LinkedList.Node<T>,
+ remove(node: LinkedList.Node<T>): void,
+ removeFirst(): T | undefined,
+ removeLast(): T | undefined,
+ find(value: T): LinkedList.Node<T> | undefined
+}
+
+function LinkedList<T>(): LinkedList<T> {
+ return new LinkedListImpl();
+}
+
+namespace LinkedList {
+ export interface Node<T> {
+ previous: Node<T> | null,
+ next: Node<T> | null,
+ inList: boolean,
+ value: T
+ }
+}
+
+function createListNode<T>(value: T): LinkedList.Node<T> {
+ return { previous: null, next: null, inList: true, value };
+}
+
+class LinkedListImpl<T> implements LinkedList<T> {
+ count: number = 0;
+ first: LinkedList.Node<T> | null = null;
+ last: LinkedList.Node<T> | null = null;
+
+ addFirst(value: T) {
+ const node = createListNode(value);
+ node.inList = true;
+ if (this.first) this.first.previous = node;
+ node.next = this.first;
+ this.first = node;
+ this.count++;
+ if (!this.last) this.last = node;
+ return node;
+ }
+
+ addLast(value: T) {
+ const node = createListNode(value);
+ if (this.last !== null) {
+ this.last.next = node;
+ }
+ node.previous = this.last;
+ this.last = node;
+ if (this.first === null) {
+ this.first = node;
+ }
+ node.inList = true;
+ this.count++;
+ return node;
+ }
+
+ removeFirst(): T | undefined {
+ const fst = this.first;
+ if (fst) {
+ this.remove(fst);
+ return fst.value;
+ }
+ return void 0;
+ }
+
+ removeLast(): T | undefined {
+ const last = this.last;
+ if (last) {
+ this.remove(last);
+ return last.value;
+ }
+ return void 0;
+ }
+
+ remove(node: LinkedList.Node<T>) {
+ if (!node.inList) return;
+
+ node.inList = false;
+
+ if (node.previous !== null) {
+ node.previous.next = node.next;
+ }
+ else if (/*first == item*/ node.previous === null) {
+ this.first = node.next;
+ }
+
+ if (node.next !== null) {
+ node.next.previous = node.previous;
+ }
+ else if (/*last == item*/ node.next === null) {
+ this.last = node.previous;
+ }
+
+ node.next = null;
+ node.previous = null;
+ this.count--;
+ }
+
+ find(value: T): LinkedList.Node<T> | undefined {
+ let current = this.first;
+ while (current !== null) {
+ if (current.value === value) return current;
+ current = current.next;
+ }
+ return void 0;
+ }
+}
+
+export { LinkedList }
\ No newline at end of file
diff --git a/src/mol-data/util/unique-array.ts b/src/mol-data/generic/unique-array.ts
similarity index 100%
rename from src/mol-data/util/unique-array.ts
rename to src/mol-data/generic/unique-array.ts
diff --git a/src/mol-data/index.ts b/src/mol-data/index.ts
index 1db90c26e..b1d250084 100644
--- a/src/mol-data/index.ts
+++ b/src/mol-data/index.ts
@@ -8,5 +8,6 @@ import * as DB from './db'
import * as Int from './int'
import Iterator from './iterator'
import * as Util from './util'
+import * as Generic from './generic'
-export { DB, Int, Iterator, Util }
\ No newline at end of file
+export { DB, Int, Iterator, Util, Generic }
\ No newline at end of file
diff --git a/src/mol-data/util.ts b/src/mol-data/util.ts
index 629b3b517..c541a1e9e 100644
--- a/src/mol-data/util.ts
+++ b/src/mol-data/util.ts
@@ -5,8 +5,6 @@
*/
export * from './util/chunked-array'
-export * from './util/unique-array'
-export * from './util/hash-set'
export * from './util/equivalence-classes'
export * from './util/hash-functions'
export * from './util/sort'
diff --git a/src/mol-data/util/array.ts b/src/mol-data/util/array.ts
index 664138327..93707e797 100644
--- a/src/mol-data/util/array.ts
+++ b/src/mol-data/util/array.ts
@@ -14,7 +14,7 @@ export function arrayFind<T>(array: ArrayLike<T>, f: (v: T) => boolean): T | und
export function iterableToArray<T>(it: IterableIterator<T>): T[] {
if (Array.from) return Array.from(it);
-
+
const ret = [];
while (true) {
const { done, value } = it.next();
diff --git a/src/mol-model/structure/query/selection.ts b/src/mol-model/structure/query/selection.ts
index 2d8467e07..5b317240a 100644
--- a/src/mol-model/structure/query/selection.ts
+++ b/src/mol-model/structure/query/selection.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { HashSet } from 'mol-data/util'
+import { HashSet } from 'mol-data/generic'
import { Structure, AtomSet } from '../structure'
// A selection is a pair of a Structure and a sequence of unique AtomSets
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 6cac5a7b8..dfd764e47 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -5,7 +5,7 @@
*/
import { OrderedSet, Iterator } from 'mol-data/int'
-import { UniqueArray } from 'mol-data/util'
+import { UniqueArray } from 'mol-data/generic'
import SymmetryOperator from 'mol-math/geometry/symmetry-operator'
import { Model, Format } from '../model'
import Unit from './unit'
diff --git a/src/mol-task/computation.ts b/src/mol-task/computation.ts
index 3d956de70..b4b1c9d13 100644
--- a/src/mol-task/computation.ts
+++ b/src/mol-task/computation.ts
@@ -6,7 +6,7 @@
*/
import Scheduler from './scheduler'
-import timeNow from './time'
+import timeNow from './util/now'
interface Computation<A> {
(ctx?: Computation.Context): Promise<A>
diff --git a/src/mol-task/execution/observable.ts b/src/mol-task/execution/observable.ts
index f06abbf0c..44fa65170 100644
--- a/src/mol-task/execution/observable.ts
+++ b/src/mol-task/execution/observable.ts
@@ -7,10 +7,38 @@
import Task from '../task'
import RuntimeContext from './runtime-context'
import Progress from './progress'
+import now from '../util/now'
+
+function defaultProgress(rootTaskId: number, task: Task<any>): Task.Progress {
+ return {
+ rootTaskId,
+ taskId: task.id,
+ taskName: task.name,
+ message: 'Running...',
+ elapsedMs: { real: 0, cpu: 0 },
+ canAbort: true,
+ isIndeterminate: true,
+ current: 0,
+ max: 0
+ };
+}
+
+class ProgressInfo {
+ taskId: number;
+ elapsedMs: { real: number, cpu: number };
+ tree: Progress.Node;
+ tryAbort?: (reason?: string) => void;
+
+ snapshot(): Progress {
+ return 0 as any;
+ }
+}
class ObservableExecutor {
+ progressInfo: ProgressInfo;
+
async run<T>(task: Task<T>): Promise<T> {
- const ctx = new ObservableRuntimeContext();
+ const ctx = new ObservableRuntimeContext(task.id, task, 0);
if (!task.__onAbort) return task.__f(ctx);
try {
@@ -27,14 +55,35 @@ class ObservableExecutor {
}
class ObservableRuntimeContext implements RuntimeContext {
- id: number = 0;
- requiresUpdate: boolean = false;
+ elapsedCpuMs: number;
+ lastScheduledTime: number;
+
+ started: number;
+ taskId: number;
+ taskName: string;
+ progress: Task.Progress;
+ updateRateMs: number;
+
+ get requiresUpdate(): boolean {
+ return now() - this.started > this.updateRateMs;
+ }
+
update(progress: Partial<RuntimeContext.ProgressUpdate>): Promise<void> {
return 0 as any;
}
+
runChild<T>(progress: Partial<RuntimeContext.ProgressUpdate>, task: Task<T>): Promise<T> {
return 0 as any;
}
+
+ constructor(parentId: number, task: Task<any>, updateRateMs: number) {
+ this.started = now();
+ this.lastScheduledTime = this.started;
+ this.taskId = task.id;
+ this.taskName = task.name;
+ this.progress = defaultProgress(parentId, task);
+ this.updateRateMs = updateRateMs;
+ }
}
function ExecuteObservable<T>(task: Task<T>, observer: Progress.Observer, updateRateMs = 250) {
diff --git a/src/mol-task/index.ts b/src/mol-task/index.ts
index d9626148c..6367cb572 100644
--- a/src/mol-task/index.ts
+++ b/src/mol-task/index.ts
@@ -9,6 +9,7 @@ import RuntimeContext from './execution/runtime-context'
import ExecuteSynchronous from './execution/synchronous'
import ExecuteObservable from './execution/observable'
import Progress from './execution/progress'
+import now from './util/now'
function Run<T>(task: Task<T>): Promise<T>;
function Run<T>(task: Task<T>, observer: Progress.Observer, updateRateMs?: number): Promise<T>;
@@ -17,4 +18,4 @@ function Run<T>(task: Task<T>, observer?: Progress.Observer, updateRateMs?: numb
return ExecuteSynchronous(task);
}
-export { Task, RuntimeContext, Progress, Run }
\ No newline at end of file
+export { Task, RuntimeContext, Progress, Run, now }
\ No newline at end of file
diff --git a/src/mol-task/task.ts b/src/mol-task/task.ts
index e0e5174a9..8f6a700c3 100644
--- a/src/mol-task/task.ts
+++ b/src/mol-task/task.ts
@@ -35,18 +35,17 @@ namespace Task {
return ret;
}
- export type Progress = IndeterminateProgress | DeterminateProgress
-
- interface ProgressBase {
+ export interface Progress {
rootTaskId: number,
taskId: number,
+ taskName: string,
message: string,
elapsedMs: { real: number, cpu: number },
- canAbort: boolean
+ canAbort: boolean,
+ isIndeterminate: boolean,
+ current: number,
+ max: number
}
-
- export interface IndeterminateProgress extends ProgressBase { isIndeterminate: true }
- export interface DeterminateProgress extends ProgressBase { isIndeterminate: false, current: number, max: number }
}
export default Task
\ No newline at end of file
diff --git a/src/mol-task/util/chunked.ts b/src/mol-task/util/chunked.ts
new file mode 100644
index 000000000..e69de29bb
diff --git a/src/mol-task/util/multistep.ts b/src/mol-task/util/multistep.ts
new file mode 100644
index 000000000..e69de29bb
diff --git a/src/mol-task/time.ts b/src/mol-task/util/now.ts
similarity index 100%
rename from src/mol-task/time.ts
rename to src/mol-task/util/now.ts
--
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