From fe572f89d9bc12b1265618545215f3d7ba4f6a59 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Sat, 28 Oct 2017 18:54:41 +0200
Subject: [PATCH] refactoring column part 1
---
src/mol-base/collections/_spec/column.spec.ts | 34 ++++
src/mol-base/collections/column.1.ts | 191 ++++++++++++++++++
src/mol-base/collections/column.ts | 2 +-
.../{ => integer}/_spec/interval.spec.ts | 2 +-
.../{ => integer}/_spec/ordered-set.spec.ts | 4 +-
.../{ => integer}/_spec/segmentation.spec.ts | 8 +-
.../{ => integer}/_spec/sorted-array.spec.ts | 4 +-
.../_spec/tuple.spec.ts} | 2 +-
.../collections/integer/segmentation.ts | 3 +-
src/mol-data/model.ts | 12 +-
src/mol-data/model/builders/mmcif.ts | 4 +-
src/mol-data/structure.ts | 1 +
src/perf-tests/sets.ts | 2 +-
13 files changed, 248 insertions(+), 21 deletions(-)
create mode 100644 src/mol-base/collections/_spec/column.spec.ts
create mode 100644 src/mol-base/collections/column.1.ts
rename src/mol-base/collections/{ => integer}/_spec/interval.spec.ts (98%)
rename src/mol-base/collections/{ => integer}/_spec/ordered-set.spec.ts (99%)
rename src/mol-base/collections/{ => integer}/_spec/segmentation.spec.ts (86%)
rename src/mol-base/collections/{ => integer}/_spec/sorted-array.spec.ts (95%)
rename src/mol-base/collections/{_spec/int-tuple.spec.ts => integer/_spec/tuple.spec.ts} (92%)
diff --git a/src/mol-base/collections/_spec/column.spec.ts b/src/mol-base/collections/_spec/column.spec.ts
new file mode 100644
index 000000000..5449d7d8e
--- /dev/null
+++ b/src/mol-base/collections/_spec/column.spec.ts
@@ -0,0 +1,34 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import Column, { isTypedArray } from '../column.1'
+
+describe('column', () => {
+ const cc = Column.ofConst(10, 2, Column.Type.int);
+ const arr = Column.ofArray({ array: [1, 2, 3, 4], type: Column.Type.int });
+ const arrWindow = Column.window(arr, 1, 3);
+
+ const typed = Column.ofArray({ array: new Int32Array([1, 2, 3, 4]), type: Column.Type.int });
+ const typedWindow = Column.window(typed, 1, 3);
+
+ it('constant', () => {
+ expect(cc.rowCount).toBe(2);
+ expect(cc.value(0)).toBe(10);
+ });
+
+ it('arr', () => {
+ expect(arr.rowCount).toBe(4);
+ expect(arr.value(1)).toBe(2);
+ expect(arrWindow.value(0)).toBe(2);
+ expect(arrWindow.rowCount).toBe(2);
+ });
+
+ it('typed', () => {
+ expect(typedWindow.value(0)).toBe(2);
+ expect(typedWindow.rowCount).toBe(2);
+ expect(isTypedArray(typedWindow.toArray())).toBe(true);
+ });
+})
\ No newline at end of file
diff --git a/src/mol-base/collections/column.1.ts b/src/mol-base/collections/column.1.ts
new file mode 100644
index 000000000..d851a7c75
--- /dev/null
+++ b/src/mol-base/collections/column.1.ts
@@ -0,0 +1,191 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+interface Column<T> {
+ readonly '@type': Column.Type,
+ readonly '@array': ArrayLike<any> | undefined,
+
+ readonly isDefined: boolean,
+ readonly rowCount: number,
+ value(row: number): T,
+ valueKind(row: number): Column.ValueKind,
+ toArray(params?: Column.ToArrayParams): ReadonlyArray<T>,
+ stringEquals(row: number, value: string): boolean,
+ areValuesEqual(rowA: number, rowB: number): boolean
+}
+
+namespace Column {
+ export type Type = typeof Type.str | typeof Type.int | typeof Type.float | typeof Type.vector | typeof Type.matrix
+
+ export namespace Type {
+ export const str = { '@type': '' as string, kind: 'str' as 'str' };
+ export const int = { '@type': 0 as number, kind: 'int' as 'int' };
+ export const float = { '@type': 0 as number, kind: 'float' as 'float' };
+ export const vector = { '@type': [] as number[], kind: 'vector' as 'vector' };
+ export const matrix = { '@type': [] as number[][], kind: 'matrix' as 'matrix' };
+ }
+
+ export interface ToArrayParams {
+ array?: { new(size: number): ArrayLike<number> },
+ start?: number,
+ /** Last row (exclusive) */
+ end?: number
+ }
+
+ export interface ArraySpec<T extends Type> {
+ array: ArrayLike<T['@type']>,
+ type: T,
+ valueKind?: (row: number) => ValueKind
+ }
+
+ export const enum ValueKind { Present, NotPresent, Unknown }
+
+ export function Undefined<T extends Type>(rowCount: number, type: T): Column<T['@type']> {
+ return constColumn(type['@type'], rowCount, type, ValueKind.NotPresent);
+ }
+
+ export function ofConst<T extends Type>(v: T['@type'], rowCount: number, type: T): Column<T['@type']> {
+ return constColumn(v, rowCount, type, ValueKind.Present);
+ }
+
+ export function ofArray<T extends Column.Type>(spec: Column.ArraySpec<T>): Column<T['@type']> {
+ return arrayColumn(spec);
+ }
+
+ export function window<T>(column: Column<T>, start: number, end: number) {
+ return windowColumn(column, start, end);
+ }
+
+ /** Makes the column backned by an array. Useful for columns that accessed often. */
+ export function asArrayColumn<T>(c: Column<T>, array?: ToArrayParams['array']): Column<T> {
+ if (c['@array']) return c;
+ if (!c.isDefined) return Undefined(c.rowCount, c['@type']) as any as Column<T>;
+ return arrayColumn({ array: c.toArray({ array }), type: c['@type'] as any, valueKind: c.valueKind });
+ }
+}
+
+export default Column;
+
+function constColumn<T extends Column.Type>(v: T['@type'], rowCount: number, type: T, valueKind: Column.ValueKind): Column<T['@type']> {
+ const value: Column<T['@type']>['value'] = row => v;
+ return {
+ '@type': type,
+ '@array': void 0,
+ isDefined: valueKind === Column.ValueKind.Present,
+ rowCount,
+ value,
+ valueKind: row => valueKind,
+ toArray: params => {
+ const { array } = createArray(rowCount, params);
+ for (let i = 0, _i = array.length; i < _i; i++) array[i] = v;
+ return array;
+ },
+ stringEquals: type.kind === 'str'
+ ? (row, value) => value === v
+ : type.kind === 'float' || type.kind === 'int'
+ ? (row, value) => +value === v
+ : (row, value) => false,
+ areValuesEqual: (rowA, rowB) => true
+ }
+}
+
+function arrayColumn<T extends Column.Type>({ array, type, valueKind }: Column.ArraySpec<T>): Column<T['@type']> {
+ const rowCount = array.length;
+ const value: Column<T['@type']>['value'] = row => array[row];
+ const isTyped = isTypedArray(array);
+ return {
+ '@type': type,
+ '@array': array,
+ isDefined: true,
+ rowCount,
+ value,
+ valueKind: valueKind ? valueKind : row => Column.ValueKind.Present,
+ toArray: isTyped
+ ? params => typedArrayWindow(array, params) as any as ReadonlyArray<T>
+ : params => {
+ const { start, end } = getArrayBounds(rowCount, params);
+ if (start === 0 && end === array.length) return array as ReadonlyArray<T['@type']>;
+ const ret = new (params && typeof params.array !== 'undefined' ? params.array : (array as any).constructor)(end - start) as any;
+ for (let i = 0, _i = end - start; i < _i; i++) ret[i] = array[start + i];
+ return ret;
+ },
+ stringEquals: type.kind === 'int' || type.kind === 'float'
+ ? (row, value) => (array as any)[row] === +value
+ : type.kind === 'str'
+ ? (row, value) => array[row] === value
+ : (row, value) => false,
+ areValuesEqual: (rowA, rowB) => array[rowA] === array[rowB]
+ }
+}
+
+function windowColumn<T>(column: Column<T>, start: number, end: number) {
+ if (!column.isDefined) return Column.Undefined(end - start, column['@type']);
+ if (column['@array'] && isTypedArray(column['@array'])) return windowTyped(column, start, end);
+ return windowFull(column, start, end);
+}
+
+function windowTyped<T>(c: Column<T>, start: number, end: number): Column<T> {
+ const array = typedArrayWindow(c['@array'], { start, end });
+ return arrayColumn({ array, type: c['@type'], valueKind: c.valueKind }) as any;
+}
+
+function windowFull<T>(c: Column<T>, start: number, end: number): Column<T> {
+ const v = c.value, vk = c.valueKind, se = c.stringEquals, ave = c.areValuesEqual;
+ const value: Column<T>['value'] = start > 0 ? v : row => v(row + start);
+ const rowCount = end - start;
+ return {
+ '@type': c['@type'],
+ '@array': void 0,
+ isDefined: c.isDefined,
+ rowCount,
+ value,
+ valueKind: start > 0 ? vk : row => vk(row + start),
+ toArray: params => {
+ const { array } = createArray(rowCount, params);
+ for (let i = 0, _i = array.length; i < _i; i++) array[i] = v(i + start);
+ return array;
+ },
+ stringEquals: start > 0 ? se : (row, value) => se(row + start, value),
+ areValuesEqual: start > 0 ? ave : (rowA, rowB) => ave(rowA + start, rowB + start)
+ };
+}
+
+/** A helped function for Column.toArray */
+export function getArrayBounds(rowCount: number, params?: Column.ToArrayParams) {
+ const start = params && typeof params.start !== 'undefined' ? Math.max(Math.min(params.start, rowCount - 1), 0) : 0;
+ const end = params && typeof params.end !== 'undefined' ? Math.min(params.end, rowCount) : rowCount;
+ return { start, end };
+}
+
+/** A helped function for Column.toArray */
+export function createArray(rowCount: number, params?: Column.ToArrayParams) {
+ const c = params && typeof params.array !== 'undefined' ? params.array : Array;
+ const { start, end } = getArrayBounds(rowCount, params);
+ return { array: new c(end - start) as any[], start, end };
+}
+
+/** A helped function for Column.toArray */
+export function fillArrayValues(value: (row: number) => any, target: any[], start: number) {
+ for (let i = 0, _e = target.length; i < _e; i++) target[i] = value(start + i);
+ return target;
+}
+
+/** A helped function for Column.toArray */
+export function createAndFillArray(rowCount: number, value: (row: number) => any, params?: Column.ToArrayParams) {
+ const { array, start } = createArray(rowCount, params);
+ return fillArrayValues(value, array, start);
+}
+
+export function isTypedArray(data: any): boolean {
+ return !!data.buffer && typeof data.byteLength === 'number' && typeof data.BYTES_PER_ELEMENT === 'number';
+}
+
+export function typedArrayWindow(data: any, params?: Column.ToArrayParams): ReadonlyArray<number> {
+ const { constructor, buffer, length, byteOffset, BYTES_PER_ELEMENT } = data;
+ const { start, end } = getArrayBounds(length, params);
+ if (start === 0 && end === length) return data;
+ return new constructor(buffer, byteOffset + BYTES_PER_ELEMENT * start, Math.min(length, end - start));
+}
\ No newline at end of file
diff --git a/src/mol-base/collections/column.ts b/src/mol-base/collections/column.ts
index 0a9ec96f6..4aec52f9e 100644
--- a/src/mol-base/collections/column.ts
+++ b/src/mol-base/collections/column.ts
@@ -53,7 +53,7 @@ export function UndefinedColumn<T extends ColumnType>(rowCount: number, type: T)
}
}
-export function SingleValueColumn<T extends ColumnType>(v: T['@type'], rowCount: number, type: T): Column<T['@type']> {
+export function ConstColumn<T extends ColumnType>(v: T['@type'], rowCount: number, type: T): Column<T['@type']> {
const value: Column<T['@type']>['value'] = row => v;
return {
'@type': type,
diff --git a/src/mol-base/collections/_spec/interval.spec.ts b/src/mol-base/collections/integer/_spec/interval.spec.ts
similarity index 98%
rename from src/mol-base/collections/_spec/interval.spec.ts
rename to src/mol-base/collections/integer/_spec/interval.spec.ts
index 015d54123..cda22df8e 100644
--- a/src/mol-base/collections/_spec/interval.spec.ts
+++ b/src/mol-base/collections/integer/_spec/interval.spec.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Interval from '../integer/interval'
+import Interval from '../interval'
describe('interval', () => {
function testI(name: string, a: Interval, b: Interval) {
diff --git a/src/mol-base/collections/_spec/ordered-set.spec.ts b/src/mol-base/collections/integer/_spec/ordered-set.spec.ts
similarity index 99%
rename from src/mol-base/collections/_spec/ordered-set.spec.ts
rename to src/mol-base/collections/integer/_spec/ordered-set.spec.ts
index 28927b185..41b70f708 100644
--- a/src/mol-base/collections/_spec/ordered-set.spec.ts
+++ b/src/mol-base/collections/integer/_spec/ordered-set.spec.ts
@@ -4,8 +4,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import OrderedSet from '../integer/ordered-set'
-import Interval from '../integer/interval'
+import OrderedSet from '../ordered-set'
+import Interval from '../interval'
describe('ordered set', () => {
function ordSetToArray(set: OrderedSet) {
diff --git a/src/mol-base/collections/_spec/segmentation.spec.ts b/src/mol-base/collections/integer/_spec/segmentation.spec.ts
similarity index 86%
rename from src/mol-base/collections/_spec/segmentation.spec.ts
rename to src/mol-base/collections/integer/_spec/segmentation.spec.ts
index b44766e5f..c77fbb86f 100644
--- a/src/mol-base/collections/_spec/segmentation.spec.ts
+++ b/src/mol-base/collections/integer/_spec/segmentation.spec.ts
@@ -4,9 +4,9 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import OrderedSet from '../integer/ordered-set'
-import Interval from '../integer/interval'
-import Segmentation from '../integer/segmentation'
+import OrderedSet from '../ordered-set'
+import Interval from '../interval'
+import Segmentation from '../segmentation'
describe('segments', () => {
const data = OrderedSet.ofSortedArray([4, 9, 10, 11, 14, 15, 16]);
@@ -27,7 +27,7 @@ describe('segments', () => {
})
it('iteration', () => {
- const it = Segmentation.segments(segs, data);
+ const it = Segmentation.transientSegments(segs, data);
const t = Object.create(null);
while (it.hasNext) {
diff --git a/src/mol-base/collections/_spec/sorted-array.spec.ts b/src/mol-base/collections/integer/_spec/sorted-array.spec.ts
similarity index 95%
rename from src/mol-base/collections/_spec/sorted-array.spec.ts
rename to src/mol-base/collections/integer/_spec/sorted-array.spec.ts
index 7aa731c9d..e3b729523 100644
--- a/src/mol-base/collections/_spec/sorted-array.spec.ts
+++ b/src/mol-base/collections/integer/_spec/sorted-array.spec.ts
@@ -4,8 +4,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Interval from '../integer/interval'
-import SortedArray from '../integer/sorted-array'
+import Interval from '../interval'
+import SortedArray from '../sorted-array'
describe('sortedArray', () => {
function testI(name: string, a: Interval, b: Interval) {
diff --git a/src/mol-base/collections/_spec/int-tuple.spec.ts b/src/mol-base/collections/integer/_spec/tuple.spec.ts
similarity index 92%
rename from src/mol-base/collections/_spec/int-tuple.spec.ts
rename to src/mol-base/collections/integer/_spec/tuple.spec.ts
index 6ff7827c4..45b02a0ef 100644
--- a/src/mol-base/collections/_spec/int-tuple.spec.ts
+++ b/src/mol-base/collections/integer/_spec/tuple.spec.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import IntTuple from '../integer/tuple'
+import IntTuple from '../tuple'
describe('int pair', () => {
it('works', () => {
diff --git a/src/mol-base/collections/integer/segmentation.ts b/src/mol-base/collections/integer/segmentation.ts
index 6ecdbdf27..dda6b63a3 100644
--- a/src/mol-base/collections/integer/segmentation.ts
+++ b/src/mol-base/collections/integer/segmentation.ts
@@ -18,7 +18,8 @@ namespace Segmentation {
export const getSegment: (segs: Segmentation, value: number) => number = Impl.getSegment as any;
export const projectValue: (segs: Segmentation, set: OrderedSet, value: number) => Interval = Impl.projectValue as any;
- export const segments: (segs: Segmentation, set: OrderedSet, range?: Interval) => Iterator<Segment> = Impl.segments as any;
+ // Segment iterator that mutates a single segment object to mark all the segments.
+ export const transientSegments: (segs: Segmentation, set: OrderedSet, range?: Interval) => Iterator<Segment> = Impl.segments as any;
}
interface Segmentation {
diff --git a/src/mol-data/model.ts b/src/mol-data/model.ts
index 54f89ceb9..689b170e5 100644
--- a/src/mol-data/model.ts
+++ b/src/mol-data/model.ts
@@ -14,16 +14,18 @@ import Segmentation from '../mol-base/collections/integer/segmentation'
*
* "Atoms" are integers in the range [0, atomCount).
*/
-interface Model {
+interface Model extends Readonly<{
sourceData: Formats.RawData,
common: CommonInterface,
macromolecule: MacromoleculeInterface
atomCount: number,
- chains: Segmentation,
- residues: Segmentation,
- entities: Segmentation
-}
+ segments: Readonly<{
+ chains: Segmentation,
+ residues: Segmentation,
+ entities: Segmentation
+ }>
+}> { }
export default Model
\ No newline at end of file
diff --git a/src/mol-data/model/builders/mmcif.ts b/src/mol-data/model/builders/mmcif.ts
index 71eff5052..f2318b794 100644
--- a/src/mol-data/model/builders/mmcif.ts
+++ b/src/mol-data/model/builders/mmcif.ts
@@ -57,9 +57,7 @@ function createModel(raw: RawData, data: mmCIF, bounds: Interval): Model {
common: 0 as any,
macromolecule: 0 as any,
atomCount: Interval.size(bounds),
- residues: segments.residues,
- chains: segments.chains,
- entities: segments.entities
+ segments
};
}
diff --git a/src/mol-data/structure.ts b/src/mol-data/structure.ts
index 26059084e..d4488fca5 100644
--- a/src/mol-data/structure.ts
+++ b/src/mol-data/structure.ts
@@ -40,6 +40,7 @@ export interface Unit extends Readonly<{
getPosition(atom: number, slot: Vec3): Vec3
}
+// TODO: do "single model" version of the structure?
export interface Structure extends Readonly<{
units: Readonly<{ [id: number]: Unit }>,
atoms: AtomSet
diff --git a/src/perf-tests/sets.ts b/src/perf-tests/sets.ts
index 4794a55cf..f5d4f394c 100644
--- a/src/perf-tests/sets.ts
+++ b/src/perf-tests/sets.ts
@@ -274,7 +274,7 @@ export namespace Tuples {
export function testSegments() {
const data = OrdSet.ofSortedArray([4, 9, 10, 11, 14, 15, 16]);
const segs = Segmentation.create([0, 4, 10, 12, 13, 15, 25]);
- const it = Segmentation.segments(segs, data);
+ const it = Segmentation.transientSegments(segs, data);
while (it.hasNext) {
const s = it.move();
--
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