From 1057caaada7fc924f1df3be6bcc7c4cfaee71691 Mon Sep 17 00:00:00 2001
From: David Sehnal <dave@Davids-MacBook-Pro.local>
Date: Wed, 4 Apr 2018 14:04:15 -0700
Subject: [PATCH] Chunked array
---
package-lock.json | Bin 242118 -> 430838 bytes
src/mol-data/util/_spec/chunked-array.spec.ts | 24 +
src/mol-data/util/chunked-array.ts | 37 +-
src/mol-geo/util/marching-cubes/algorithm.ts | 0
src/mol-geo/util/marching-cubes/tables.ts | 420 ++++++++++++++++++
src/mol-io/common/binary-cif/array-encoder.ts | 2 +-
src/perf-tests/chunked-array-vs-native.ts | 4 +-
7 files changed, 469 insertions(+), 18 deletions(-)
create mode 100644 src/mol-data/util/_spec/chunked-array.spec.ts
create mode 100644 src/mol-geo/util/marching-cubes/algorithm.ts
create mode 100644 src/mol-geo/util/marching-cubes/tables.ts
diff --git a/package-lock.json b/package-lock.json
index b17cb5bffca40761c12d75553813608f5fedc15d..30e5e6dcabee5841e3d7f44234f68549cde793fe 100644
GIT binary patch
delta 63707
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zC!XO{$qDpLn|ANrORT9SM@;o6Q`Xmv#iiC$2?q>IdY(Wpenjh7n}RdclfpQU_4Jh^
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zp^i%OTk!hb{qW!?VCu^|nq0g01Vq2*_6ZFvgbcDdAi{fuJTB6-_n;S2+LIGq_bmF+
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z)&ed>HOqiR@ZCfn41FyJl>ys6?Xk&|zj-E^U~@^Sm~(k5R)b<JnIdI~wu)wt!_gT=
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IOuO&@0)Ejo&;S4c
delta 1190
zcmXw%eN2{R6vlV%``pj_!u#@qf{EygVJg!?L?lNcL`~5tnse321*RgDVTvn1mzXp(
zP~uUJ;dcnjltdr5%de#(N{FDO1`6g!NiLe$RyN$yUjFExvvaPU>$mG{=TTL}`Cojs
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zy05UafTEPp6Te}an?hs<Oq{&_1=UNx5;}_1GCD+v{)&DMK*HX>gFdUKXEoaQ(-Dn~
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z<&)xbDpl6ZVYh7CWO*?miw^{#EstXe&SE~PP_m4tF}_>PVIDkM&sBu363)<=U&bXq
zL|1dli^ys7$H0#rJjRXjUA#aetef{Jr1fxlC|t&52TSz;(}C^?^CS?b<4rrkJHaH9
ztTxIm)8qZc|GHkO9cx$~7MeJ_bTVUAipjGOlV-ZKJf3P=aBGIC93got%sDAsW6ogc
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diff --git a/src/mol-data/util/_spec/chunked-array.spec.ts b/src/mol-data/util/_spec/chunked-array.spec.ts
new file mode 100644
index 000000000..ded69465d
--- /dev/null
+++ b/src/mol-data/util/_spec/chunked-array.spec.ts
@@ -0,0 +1,24 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { ChunkedArray } from '../chunked-array'
+
+describe('Chunked Array', () => {
+ it('creation', () => {
+ const arr = ChunkedArray.create<number>(_ => [], 2, 2);
+ ChunkedArray.add2(arr, 1, 2);
+ ChunkedArray.add2(arr, 3, 4);
+ expect(ChunkedArray.compact(arr)).toEqual([1, 2, 3, 4]);
+ });
+
+ it('initial', () => {
+ const arr = ChunkedArray.create<number>(s => new Int32Array(s), 2, 6, new Int32Array([1, 2, 3, 4]));
+ ChunkedArray.add2(arr, 4, 3);
+ ChunkedArray.add2(arr, 2, 1);
+ ChunkedArray.add2(arr, 5, 6);
+ expect(ChunkedArray.compact(arr)).toEqual(new Int32Array([4, 3, 2, 1, 5, 6]));
+ });
+});
\ No newline at end of file
diff --git a/src/mol-data/util/chunked-array.ts b/src/mol-data/util/chunked-array.ts
index f9b977571..8ac4ba715 100644
--- a/src/mol-data/util/chunked-array.ts
+++ b/src/mol-data/util/chunked-array.ts
@@ -16,9 +16,7 @@ interface ChunkedArray<T> {
ctor: (size: number) => any,
elementSize: number,
- linearGrowth: boolean,
-
- initialSize: number,
+ growBy: number,
allocatedSize: number,
elementCount: number,
@@ -26,20 +24,16 @@ interface ChunkedArray<T> {
currentChunk: any,
currentIndex: number,
- chunks: any[]
+ chunks: any[][]
}
-// TODO: better api, write tests
namespace ChunkedArray {
export function is(x: any): x is ChunkedArray<any> {
return x.creator && x.chunkSize;
}
function allocateNext(array: ChunkedArray<any>) {
- let nextSize = !array.allocatedSize || array.linearGrowth
- ? array.initialSize * array.elementSize
- : Math.max(Math.ceil(0.61 * array.allocatedSize), 1);
- if (nextSize % array.elementSize !== 0) nextSize += nextSize % array.elementSize;
+ let nextSize = array.growBy * array.elementSize;
array.currentSize = nextSize;
array.currentIndex = 0;
array.currentChunk = array.ctor(nextSize);
@@ -89,7 +83,11 @@ namespace ChunkedArray {
return chunks[0];
}
- const ret = ctor(array.elementSize * array.elementCount);
+ let size = 0;
+ for (let i = 0, _i = chunks.length - 1; i < _i; i++) size += chunks[i].length;
+ size += array.currentIndex;
+
+ const ret = ctor(size);
let offset = 0;
if (ret.buffer) {
@@ -115,13 +113,12 @@ namespace ChunkedArray {
return ret;
}
- export function create<T>(ctor: (size: number) => any, elementSize: number, initialSize: number, linearGrowth: boolean): ChunkedArray<T> {
- return {
+ export function create<T>(ctor: (size: number) => any, elementSize: number, growBy: number, initialChunk?: ArrayLike<T>): ChunkedArray<T> {
+ const ret: ChunkedArray<T> = {
ctor,
elementSize,
- linearGrowth,
- initialSize,
+ growBy,
allocatedSize: 0,
elementCount: 0,
@@ -130,7 +127,17 @@ namespace ChunkedArray {
currentIndex: 0,
chunks: []
- } as ChunkedArray<T>;
+ };
+
+ if (!initialChunk) return ret;
+
+ if (initialChunk.length % elementSize !== 0) throw new Error('initialChunk length must be a multiple of the element size.');
+ ret.currentChunk = initialChunk;
+ ret.allocatedSize = initialChunk.length;
+ ret.currentSize = initialChunk.length;
+ ret.chunks[0] = initialChunk as any;
+
+ return ret;
}
}
diff --git a/src/mol-geo/util/marching-cubes/algorithm.ts b/src/mol-geo/util/marching-cubes/algorithm.ts
new file mode 100644
index 000000000..e69de29bb
diff --git a/src/mol-geo/util/marching-cubes/tables.ts b/src/mol-geo/util/marching-cubes/tables.ts
new file mode 100644
index 000000000..b363f2370
--- /dev/null
+++ b/src/mol-geo/util/marching-cubes/tables.ts
@@ -0,0 +1,420 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+export interface Index { i: number, j: number, k: number }
+export function Index(i: number, j: number, k: number): Index { return { i, j, k }; }
+
+export interface IndexPair { a: Index, b: Index }
+export function IndexPair(a: Index, b: Index): IndexPair { return { a, b }; }
+
+export const EdgesXY = [
+ [],
+ [0, 3],
+ [0, 1],
+ [1, 3],
+ [1, 2],
+
+ [0, 1, 1, 2, 2, 3, 0, 3],
+
+ [0, 2],
+ [2, 3],
+ [2, 3],
+ [0, 2],
+
+ [0, 1, 1, 2, 2, 3, 0, 3],
+
+ [1, 2],
+ [1, 3],
+ [0, 1],
+ [0, 3],
+ []
+];
+
+export const EdgesXZ = [
+ [],
+ [0, 8],
+ [0, 9],
+ [9, 8],
+ [9, 4],
+
+ [0, 9, 9, 4, 4, 8, 0, 8],
+
+ [0, 4],
+ [4, 8],
+ [4, 8],
+ [0, 4],
+
+ [0, 9, 9, 4, 4, 8, 0, 8],
+
+ [9, 4],
+ [9, 8],
+ [0, 9],
+ [0, 8],
+ []
+];
+
+export const EdgesYZ = [
+ [],
+ [3, 8],
+ [3, 11],
+ [11, 8],
+ [11, 7],
+
+ [3, 11, 11, 7, 7, 8, 3, 8],
+
+ [3, 7],
+ [7, 8],
+ [7, 8],
+ [3, 7],
+
+ [3, 11, 11, 7, 7, 8, 3, 8],
+
+ [11, 7],
+ [11, 8],
+ [3, 11],
+ [3, 8],
+ []
+];
+
+export const CubeVertices = [
+ Index(0, 0, 0), // a
+ Index(1, 0, 0), // b
+ Index(1, 1, 0), // c
+ Index(0, 1, 0), // d
+ Index(0, 0, 1), // e
+ Index(1, 0, 1), // f
+ Index(1, 1, 1), // g
+ Index(0, 1, 1), // h
+];
+
+export const CubeEdges = [
+ IndexPair(CubeVertices[0], CubeVertices[1]),
+ IndexPair(CubeVertices[1], CubeVertices[2]),
+ IndexPair(CubeVertices[2], CubeVertices[3]),
+ IndexPair(CubeVertices[3], CubeVertices[0]),
+
+ IndexPair(CubeVertices[4], CubeVertices[5]),
+ IndexPair(CubeVertices[5], CubeVertices[6]),
+ IndexPair(CubeVertices[6], CubeVertices[7]),
+ IndexPair(CubeVertices[7], CubeVertices[4]),
+
+ IndexPair(CubeVertices[0], CubeVertices[4]),
+ IndexPair(CubeVertices[1], CubeVertices[5]),
+ IndexPair(CubeVertices[2], CubeVertices[6]),
+ IndexPair(CubeVertices[3], CubeVertices[7]),
+];
+
+export const EdgeIdInfo = [
+ { i: 0, j: 0, k: 0, e: 0 },
+ { i: 1, j: 0, k: 0, e: 1 },
+ { i: 0, j: 1, k: 0, e: 0 },
+ { i: 0, j: 0, k: 0, e: 1 },
+
+ { i: 0, j: 0, k: 1, e: 0 },
+ { i: 1, j: 0, k: 1, e: 1 },
+ { i: 0, j: 1, k: 1, e: 0 },
+ { i: 0, j: 0, k: 1, e: 1 },
+
+ { i: 0, j: 0, k: 0, e: 2 },
+ { i: 1, j: 0, k: 0, e: 2 },
+ { i: 1, j: 1, k: 0, e: 2 },
+ { i: 0, j: 1, k: 0, e: 2 }
+];
+
+// Tables EdgeTable and TriTable taken from http://paulbourke.net/geometry/polygonise/
+export const EdgeTable = [
+ 0x0, 0x109, 0x203, 0x30a, 0x406, 0x50f, 0x605, 0x70c,
+ 0x80c, 0x905, 0xa0f, 0xb06, 0xc0a, 0xd03, 0xe09, 0xf00,
+ 0x190, 0x99, 0x393, 0x29a, 0x596, 0x49f, 0x795, 0x69c,
+ 0x99c, 0x895, 0xb9f, 0xa96, 0xd9a, 0xc93, 0xf99, 0xe90,
+ 0x230, 0x339, 0x33, 0x13a, 0x636, 0x73f, 0x435, 0x53c,
+ 0xa3c, 0xb35, 0x83f, 0x936, 0xe3a, 0xf33, 0xc39, 0xd30,
+ 0x3a0, 0x2a9, 0x1a3, 0xaa, 0x7a6, 0x6af, 0x5a5, 0x4ac,
+ 0xbac, 0xaa5, 0x9af, 0x8a6, 0xfaa, 0xea3, 0xda9, 0xca0,
+ 0x460, 0x569, 0x663, 0x76a, 0x66, 0x16f, 0x265, 0x36c,
+ 0xc6c, 0xd65, 0xe6f, 0xf66, 0x86a, 0x963, 0xa69, 0xb60,
+ 0x5f0, 0x4f9, 0x7f3, 0x6fa, 0x1f6, 0xff, 0x3f5, 0x2fc,
+ 0xdfc, 0xcf5, 0xfff, 0xef6, 0x9fa, 0x8f3, 0xbf9, 0xaf0,
+ 0x650, 0x759, 0x453, 0x55a, 0x256, 0x35f, 0x55, 0x15c,
+ 0xe5c, 0xf55, 0xc5f, 0xd56, 0xa5a, 0xb53, 0x859, 0x950,
+ 0x7c0, 0x6c9, 0x5c3, 0x4ca, 0x3c6, 0x2cf, 0x1c5, 0xcc,
+ 0xfcc, 0xec5, 0xdcf, 0xcc6, 0xbca, 0xac3, 0x9c9, 0x8c0,
+ 0x8c0, 0x9c9, 0xac3, 0xbca, 0xcc6, 0xdcf, 0xec5, 0xfcc,
+ 0xcc, 0x1c5, 0x2cf, 0x3c6, 0x4ca, 0x5c3, 0x6c9, 0x7c0,
+ 0x950, 0x859, 0xb53, 0xa5a, 0xd56, 0xc5f, 0xf55, 0xe5c,
+ 0x15c, 0x55, 0x35f, 0x256, 0x55a, 0x453, 0x759, 0x650,
+ 0xaf0, 0xbf9, 0x8f3, 0x9fa, 0xef6, 0xfff, 0xcf5, 0xdfc,
+ 0x2fc, 0x3f5, 0xff, 0x1f6, 0x6fa, 0x7f3, 0x4f9, 0x5f0,
+ 0xb60, 0xa69, 0x963, 0x86a, 0xf66, 0xe6f, 0xd65, 0xc6c,
+ 0x36c, 0x265, 0x16f, 0x66, 0x76a, 0x663, 0x569, 0x460,
+ 0xca0, 0xda9, 0xea3, 0xfaa, 0x8a6, 0x9af, 0xaa5, 0xbac,
+ 0x4ac, 0x5a5, 0x6af, 0x7a6, 0xaa, 0x1a3, 0x2a9, 0x3a0,
+ 0xd30, 0xc39, 0xf33, 0xe3a, 0x936, 0x83f, 0xb35, 0xa3c,
+ 0x53c, 0x435, 0x73f, 0x636, 0x13a, 0x33, 0x339, 0x230,
+ 0xe90, 0xf99, 0xc93, 0xd9a, 0xa96, 0xb9f, 0x895, 0x99c,
+ 0x69c, 0x795, 0x49f, 0x596, 0x29a, 0x393, 0x99, 0x190,
+ 0xf00, 0xe09, 0xd03, 0xc0a, 0xb06, 0xa0f, 0x905, 0x80c,
+ 0x70c, 0x605, 0x50f, 0x406, 0x30a, 0x203, 0x109, 0x0
+];
+
+export const TriTable = [
+ [],
+ [0, 8, 3],
+ [0, 1, 9],
+ [1, 8, 3, 9, 8, 1],
+ [1, 2, 10],
+ [0, 8, 3, 1, 2, 10],
+ [9, 2, 10, 0, 2, 9],
+ [2, 8, 3, 2, 10, 8, 10, 9, 8],
+ [3, 11, 2],
+ [0, 11, 2, 8, 11, 0],
+ [1, 9, 0, 2, 3, 11],
+ [1, 11, 2, 1, 9, 11, 9, 8, 11],
+ [3, 10, 1, 11, 10, 3],
+ [0, 10, 1, 0, 8, 10, 8, 11, 10],
+ [3, 9, 0, 3, 11, 9, 11, 10, 9],
+ [9, 8, 10, 10, 8, 11],
+ [4, 7, 8],
+ [4, 3, 0, 7, 3, 4],
+ [0, 1, 9, 8, 4, 7],
+ [4, 1, 9, 4, 7, 1, 7, 3, 1],
+ [1, 2, 10, 8, 4, 7],
+ [3, 4, 7, 3, 0, 4, 1, 2, 10],
+ [9, 2, 10, 9, 0, 2, 8, 4, 7],
+ [2, 10, 9, 2, 9, 7, 2, 7, 3, 7, 9, 4],
+ [8, 4, 7, 3, 11, 2],
+ [11, 4, 7, 11, 2, 4, 2, 0, 4],
+ [9, 0, 1, 8, 4, 7, 2, 3, 11],
+ [4, 7, 11, 9, 4, 11, 9, 11, 2, 9, 2, 1],
+ [3, 10, 1, 3, 11, 10, 7, 8, 4],
+ [1, 11, 10, 1, 4, 11, 1, 0, 4, 7, 11, 4],
+ [4, 7, 8, 9, 0, 11, 9, 11, 10, 11, 0, 3],
+ [4, 7, 11, 4, 11, 9, 9, 11, 10],
+ [9, 5, 4],
+ [9, 5, 4, 0, 8, 3],
+ [0, 5, 4, 1, 5, 0],
+ [8, 5, 4, 8, 3, 5, 3, 1, 5],
+ [1, 2, 10, 9, 5, 4],
+ [3, 0, 8, 1, 2, 10, 4, 9, 5],
+ [5, 2, 10, 5, 4, 2, 4, 0, 2],
+ [2, 10, 5, 3, 2, 5, 3, 5, 4, 3, 4, 8],
+ [9, 5, 4, 2, 3, 11],
+ [0, 11, 2, 0, 8, 11, 4, 9, 5],
+ [0, 5, 4, 0, 1, 5, 2, 3, 11],
+ [2, 1, 5, 2, 5, 8, 2, 8, 11, 4, 8, 5],
+ [10, 3, 11, 10, 1, 3, 9, 5, 4],
+ [4, 9, 5, 0, 8, 1, 8, 10, 1, 8, 11, 10],
+ [5, 4, 0, 5, 0, 11, 5, 11, 10, 11, 0, 3],
+ [5, 4, 8, 5, 8, 10, 10, 8, 11],
+ [9, 7, 8, 5, 7, 9],
+ [9, 3, 0, 9, 5, 3, 5, 7, 3],
+ [0, 7, 8, 0, 1, 7, 1, 5, 7],
+ [1, 5, 3, 3, 5, 7],
+ [9, 7, 8, 9, 5, 7, 10, 1, 2],
+ [10, 1, 2, 9, 5, 0, 5, 3, 0, 5, 7, 3],
+ [8, 0, 2, 8, 2, 5, 8, 5, 7, 10, 5, 2],
+ [2, 10, 5, 2, 5, 3, 3, 5, 7],
+ [7, 9, 5, 7, 8, 9, 3, 11, 2],
+ [9, 5, 7, 9, 7, 2, 9, 2, 0, 2, 7, 11],
+ [2, 3, 11, 0, 1, 8, 1, 7, 8, 1, 5, 7],
+ [11, 2, 1, 11, 1, 7, 7, 1, 5],
+ [9, 5, 8, 8, 5, 7, 10, 1, 3, 10, 3, 11],
+ [5, 7, 0, 5, 0, 9, 7, 11, 0, 1, 0, 10, 11, 10, 0],
+ [11, 10, 0, 11, 0, 3, 10, 5, 0, 8, 0, 7, 5, 7, 0],
+ [11, 10, 5, 7, 11, 5],
+ [10, 6, 5],
+ [0, 8, 3, 5, 10, 6],
+ [9, 0, 1, 5, 10, 6],
+ [1, 8, 3, 1, 9, 8, 5, 10, 6],
+ [1, 6, 5, 2, 6, 1],
+ [1, 6, 5, 1, 2, 6, 3, 0, 8],
+ [9, 6, 5, 9, 0, 6, 0, 2, 6],
+ [5, 9, 8, 5, 8, 2, 5, 2, 6, 3, 2, 8],
+ [2, 3, 11, 10, 6, 5],
+ [11, 0, 8, 11, 2, 0, 10, 6, 5],
+ [0, 1, 9, 2, 3, 11, 5, 10, 6],
+ [5, 10, 6, 1, 9, 2, 9, 11, 2, 9, 8, 11],
+ [6, 3, 11, 6, 5, 3, 5, 1, 3],
+ [0, 8, 11, 0, 11, 5, 0, 5, 1, 5, 11, 6],
+ [3, 11, 6, 0, 3, 6, 0, 6, 5, 0, 5, 9],
+ [6, 5, 9, 6, 9, 11, 11, 9, 8],
+ [5, 10, 6, 4, 7, 8],
+ [4, 3, 0, 4, 7, 3, 6, 5, 10],
+ [1, 9, 0, 5, 10, 6, 8, 4, 7],
+ [10, 6, 5, 1, 9, 7, 1, 7, 3, 7, 9, 4],
+ [6, 1, 2, 6, 5, 1, 4, 7, 8],
+ [1, 2, 5, 5, 2, 6, 3, 0, 4, 3, 4, 7],
+ [8, 4, 7, 9, 0, 5, 0, 6, 5, 0, 2, 6],
+ [7, 3, 9, 7, 9, 4, 3, 2, 9, 5, 9, 6, 2, 6, 9],
+ [3, 11, 2, 7, 8, 4, 10, 6, 5],
+ [5, 10, 6, 4, 7, 2, 4, 2, 0, 2, 7, 11],
+ [0, 1, 9, 4, 7, 8, 2, 3, 11, 5, 10, 6],
+ [9, 2, 1, 9, 11, 2, 9, 4, 11, 7, 11, 4, 5, 10, 6],
+ [8, 4, 7, 3, 11, 5, 3, 5, 1, 5, 11, 6],
+ [5, 1, 11, 5, 11, 6, 1, 0, 11, 7, 11, 4, 0, 4, 11],
+ [0, 5, 9, 0, 6, 5, 0, 3, 6, 11, 6, 3, 8, 4, 7],
+ [6, 5, 9, 6, 9, 11, 4, 7, 9, 7, 11, 9],
+ [10, 4, 9, 6, 4, 10],
+ [4, 10, 6, 4, 9, 10, 0, 8, 3],
+ [10, 0, 1, 10, 6, 0, 6, 4, 0],
+ [8, 3, 1, 8, 1, 6, 8, 6, 4, 6, 1, 10],
+ [1, 4, 9, 1, 2, 4, 2, 6, 4],
+ [3, 0, 8, 1, 2, 9, 2, 4, 9, 2, 6, 4],
+ [0, 2, 4, 4, 2, 6],
+ [8, 3, 2, 8, 2, 4, 4, 2, 6],
+ [10, 4, 9, 10, 6, 4, 11, 2, 3],
+ [0, 8, 2, 2, 8, 11, 4, 9, 10, 4, 10, 6],
+ [3, 11, 2, 0, 1, 6, 0, 6, 4, 6, 1, 10],
+ [6, 4, 1, 6, 1, 10, 4, 8, 1, 2, 1, 11, 8, 11, 1],
+ [9, 6, 4, 9, 3, 6, 9, 1, 3, 11, 6, 3],
+ [8, 11, 1, 8, 1, 0, 11, 6, 1, 9, 1, 4, 6, 4, 1],
+ [3, 11, 6, 3, 6, 0, 0, 6, 4],
+ [6, 4, 8, 11, 6, 8],
+ [7, 10, 6, 7, 8, 10, 8, 9, 10],
+ [0, 7, 3, 0, 10, 7, 0, 9, 10, 6, 7, 10],
+ [10, 6, 7, 1, 10, 7, 1, 7, 8, 1, 8, 0],
+ [10, 6, 7, 10, 7, 1, 1, 7, 3],
+ [1, 2, 6, 1, 6, 8, 1, 8, 9, 8, 6, 7],
+ [2, 6, 9, 2, 9, 1, 6, 7, 9, 0, 9, 3, 7, 3, 9],
+ [7, 8, 0, 7, 0, 6, 6, 0, 2],
+ [7, 3, 2, 6, 7, 2],
+ [2, 3, 11, 10, 6, 8, 10, 8, 9, 8, 6, 7],
+ [2, 0, 7, 2, 7, 11, 0, 9, 7, 6, 7, 10, 9, 10, 7],
+ [1, 8, 0, 1, 7, 8, 1, 10, 7, 6, 7, 10, 2, 3, 11],
+ [11, 2, 1, 11, 1, 7, 10, 6, 1, 6, 7, 1],
+ [8, 9, 6, 8, 6, 7, 9, 1, 6, 11, 6, 3, 1, 3, 6],
+ [0, 9, 1, 11, 6, 7],
+ [7, 8, 0, 7, 0, 6, 3, 11, 0, 11, 6, 0],
+ [7, 11, 6],
+ [7, 6, 11],
+ [3, 0, 8, 11, 7, 6],
+ [0, 1, 9, 11, 7, 6],
+ [8, 1, 9, 8, 3, 1, 11, 7, 6],
+ [10, 1, 2, 6, 11, 7],
+ [1, 2, 10, 3, 0, 8, 6, 11, 7],
+ [2, 9, 0, 2, 10, 9, 6, 11, 7],
+ [6, 11, 7, 2, 10, 3, 10, 8, 3, 10, 9, 8],
+ [7, 2, 3, 6, 2, 7],
+ [7, 0, 8, 7, 6, 0, 6, 2, 0],
+ [2, 7, 6, 2, 3, 7, 0, 1, 9],
+ [1, 6, 2, 1, 8, 6, 1, 9, 8, 8, 7, 6],
+ [10, 7, 6, 10, 1, 7, 1, 3, 7],
+ [10, 7, 6, 1, 7, 10, 1, 8, 7, 1, 0, 8],
+ [0, 3, 7, 0, 7, 10, 0, 10, 9, 6, 10, 7],
+ [7, 6, 10, 7, 10, 8, 8, 10, 9],
+ [6, 8, 4, 11, 8, 6],
+ [3, 6, 11, 3, 0, 6, 0, 4, 6],
+ [8, 6, 11, 8, 4, 6, 9, 0, 1],
+ [9, 4, 6, 9, 6, 3, 9, 3, 1, 11, 3, 6],
+ [6, 8, 4, 6, 11, 8, 2, 10, 1],
+ [1, 2, 10, 3, 0, 11, 0, 6, 11, 0, 4, 6],
+ [4, 11, 8, 4, 6, 11, 0, 2, 9, 2, 10, 9],
+ [10, 9, 3, 10, 3, 2, 9, 4, 3, 11, 3, 6, 4, 6, 3],
+ [8, 2, 3, 8, 4, 2, 4, 6, 2],
+ [0, 4, 2, 4, 6, 2],
+ [1, 9, 0, 2, 3, 4, 2, 4, 6, 4, 3, 8],
+ [1, 9, 4, 1, 4, 2, 2, 4, 6],
+ [8, 1, 3, 8, 6, 1, 8, 4, 6, 6, 10, 1],
+ [10, 1, 0, 10, 0, 6, 6, 0, 4],
+ [4, 6, 3, 4, 3, 8, 6, 10, 3, 0, 3, 9, 10, 9, 3],
+ [10, 9, 4, 6, 10, 4],
+ [4, 9, 5, 7, 6, 11],
+ [0, 8, 3, 4, 9, 5, 11, 7, 6],
+ [5, 0, 1, 5, 4, 0, 7, 6, 11],
+ [11, 7, 6, 8, 3, 4, 3, 5, 4, 3, 1, 5],
+ [9, 5, 4, 10, 1, 2, 7, 6, 11],
+ [6, 11, 7, 1, 2, 10, 0, 8, 3, 4, 9, 5],
+ [7, 6, 11, 5, 4, 10, 4, 2, 10, 4, 0, 2],
+ [3, 4, 8, 3, 5, 4, 3, 2, 5, 10, 5, 2, 11, 7, 6],
+ [7, 2, 3, 7, 6, 2, 5, 4, 9],
+ [9, 5, 4, 0, 8, 6, 0, 6, 2, 6, 8, 7],
+ [3, 6, 2, 3, 7, 6, 1, 5, 0, 5, 4, 0],
+ [6, 2, 8, 6, 8, 7, 2, 1, 8, 4, 8, 5, 1, 5, 8],
+ [9, 5, 4, 10, 1, 6, 1, 7, 6, 1, 3, 7],
+ [1, 6, 10, 1, 7, 6, 1, 0, 7, 8, 7, 0, 9, 5, 4],
+ [4, 0, 10, 4, 10, 5, 0, 3, 10, 6, 10, 7, 3, 7, 10],
+ [7, 6, 10, 7, 10, 8, 5, 4, 10, 4, 8, 10],
+ [6, 9, 5, 6, 11, 9, 11, 8, 9],
+ [3, 6, 11, 0, 6, 3, 0, 5, 6, 0, 9, 5],
+ [0, 11, 8, 0, 5, 11, 0, 1, 5, 5, 6, 11],
+ [6, 11, 3, 6, 3, 5, 5, 3, 1],
+ [1, 2, 10, 9, 5, 11, 9, 11, 8, 11, 5, 6],
+ [0, 11, 3, 0, 6, 11, 0, 9, 6, 5, 6, 9, 1, 2, 10],
+ [11, 8, 5, 11, 5, 6, 8, 0, 5, 10, 5, 2, 0, 2, 5],
+ [6, 11, 3, 6, 3, 5, 2, 10, 3, 10, 5, 3],
+ [5, 8, 9, 5, 2, 8, 5, 6, 2, 3, 8, 2],
+ [9, 5, 6, 9, 6, 0, 0, 6, 2],
+ [1, 5, 8, 1, 8, 0, 5, 6, 8, 3, 8, 2, 6, 2, 8],
+ [1, 5, 6, 2, 1, 6],
+ [1, 3, 6, 1, 6, 10, 3, 8, 6, 5, 6, 9, 8, 9, 6],
+ [10, 1, 0, 10, 0, 6, 9, 5, 0, 5, 6, 0],
+ [0, 3, 8, 5, 6, 10],
+ [10, 5, 6],
+ [11, 5, 10, 7, 5, 11],
+ [11, 5, 10, 11, 7, 5, 8, 3, 0],
+ [5, 11, 7, 5, 10, 11, 1, 9, 0],
+ [10, 7, 5, 10, 11, 7, 9, 8, 1, 8, 3, 1],
+ [11, 1, 2, 11, 7, 1, 7, 5, 1],
+ [0, 8, 3, 1, 2, 7, 1, 7, 5, 7, 2, 11],
+ [9, 7, 5, 9, 2, 7, 9, 0, 2, 2, 11, 7],
+ [7, 5, 2, 7, 2, 11, 5, 9, 2, 3, 2, 8, 9, 8, 2],
+ [2, 5, 10, 2, 3, 5, 3, 7, 5],
+ [8, 2, 0, 8, 5, 2, 8, 7, 5, 10, 2, 5],
+ [9, 0, 1, 5, 10, 3, 5, 3, 7, 3, 10, 2],
+ [9, 8, 2, 9, 2, 1, 8, 7, 2, 10, 2, 5, 7, 5, 2],
+ [1, 3, 5, 3, 7, 5],
+ [0, 8, 7, 0, 7, 1, 1, 7, 5],
+ [9, 0, 3, 9, 3, 5, 5, 3, 7],
+ [9, 8, 7, 5, 9, 7],
+ [5, 8, 4, 5, 10, 8, 10, 11, 8],
+ [5, 0, 4, 5, 11, 0, 5, 10, 11, 11, 3, 0],
+ [0, 1, 9, 8, 4, 10, 8, 10, 11, 10, 4, 5],
+ [10, 11, 4, 10, 4, 5, 11, 3, 4, 9, 4, 1, 3, 1, 4],
+ [2, 5, 1, 2, 8, 5, 2, 11, 8, 4, 5, 8],
+ [0, 4, 11, 0, 11, 3, 4, 5, 11, 2, 11, 1, 5, 1, 11],
+ [0, 2, 5, 0, 5, 9, 2, 11, 5, 4, 5, 8, 11, 8, 5],
+ [9, 4, 5, 2, 11, 3],
+ [2, 5, 10, 3, 5, 2, 3, 4, 5, 3, 8, 4],
+ [5, 10, 2, 5, 2, 4, 4, 2, 0],
+ [3, 10, 2, 3, 5, 10, 3, 8, 5, 4, 5, 8, 0, 1, 9],
+ [5, 10, 2, 5, 2, 4, 1, 9, 2, 9, 4, 2],
+ [8, 4, 5, 8, 5, 3, 3, 5, 1],
+ [0, 4, 5, 1, 0, 5],
+ [8, 4, 5, 8, 5, 3, 9, 0, 5, 0, 3, 5],
+ [9, 4, 5],
+ [4, 11, 7, 4, 9, 11, 9, 10, 11],
+ [0, 8, 3, 4, 9, 7, 9, 11, 7, 9, 10, 11],
+ [1, 10, 11, 1, 11, 4, 1, 4, 0, 7, 4, 11],
+ [3, 1, 4, 3, 4, 8, 1, 10, 4, 7, 4, 11, 10, 11, 4],
+ [4, 11, 7, 9, 11, 4, 9, 2, 11, 9, 1, 2],
+ [9, 7, 4, 9, 11, 7, 9, 1, 11, 2, 11, 1, 0, 8, 3],
+ [11, 7, 4, 11, 4, 2, 2, 4, 0],
+ [11, 7, 4, 11, 4, 2, 8, 3, 4, 3, 2, 4],
+ [2, 9, 10, 2, 7, 9, 2, 3, 7, 7, 4, 9],
+ [9, 10, 7, 9, 7, 4, 10, 2, 7, 8, 7, 0, 2, 0, 7],
+ [3, 7, 10, 3, 10, 2, 7, 4, 10, 1, 10, 0, 4, 0, 10],
+ [1, 10, 2, 8, 7, 4],
+ [4, 9, 1, 4, 1, 7, 7, 1, 3],
+ [4, 9, 1, 4, 1, 7, 0, 8, 1, 8, 7, 1],
+ [4, 0, 3, 7, 4, 3],
+ [4, 8, 7],
+ [9, 10, 8, 10, 11, 8],
+ [3, 0, 9, 3, 9, 11, 11, 9, 10],
+ [0, 1, 10, 0, 10, 8, 8, 10, 11],
+ [3, 1, 10, 11, 3, 10],
+ [1, 2, 11, 1, 11, 9, 9, 11, 8],
+ [3, 0, 9, 3, 9, 11, 1, 2, 9, 2, 11, 9],
+ [0, 2, 11, 8, 0, 11],
+ [3, 2, 11],
+ [2, 3, 8, 2, 8, 10, 10, 8, 9],
+ [9, 10, 2, 0, 9, 2],
+ [2, 3, 8, 2, 8, 10, 0, 1, 8, 1, 10, 8],
+ [1, 10, 2],
+ [1, 3, 8, 9, 1, 8],
+ [0, 9, 1],
+ [0, 3, 8],
+ []
+];
\ No newline at end of file
diff --git a/src/mol-io/common/binary-cif/array-encoder.ts b/src/mol-io/common/binary-cif/array-encoder.ts
index 67a9084ca..d5c1e76a7 100644
--- a/src/mol-io/common/binary-cif/array-encoder.ts
+++ b/src/mol-io/common/binary-cif/array-encoder.ts
@@ -357,7 +357,7 @@ export namespace ArrayEncoding {
let map: any = Object.create(null);
let strings: string[] = [];
let accLength = 0;
- let offsets = ChunkedArray.create<number>(s => new Int32Array(s), 1, 1024, true)
+ let offsets = ChunkedArray.create<number>(s => new Int32Array(s), 1, 1024)
let output = new Int32Array(data.length);
ChunkedArray.add(offsets, 0);
diff --git a/src/perf-tests/chunked-array-vs-native.ts b/src/perf-tests/chunked-array-vs-native.ts
index e7843412a..7b620294f 100644
--- a/src/perf-tests/chunked-array-vs-native.ts
+++ b/src/perf-tests/chunked-array-vs-native.ts
@@ -8,13 +8,13 @@ function testNative(size: number) {
}
function testChunkedTyped(size: number, chunk: number, linear: boolean) {
- const xs = ChunkedArray.create(s => new Int32Array(s), 1, chunk, linear);
+ const xs = ChunkedArray.create(s => new Int32Array(s), 1, chunk);
for (let i = 0; i < size; i++) ChunkedArray.add(xs, i * i);
return ChunkedArray.compact(xs);
}
function testChunkedNative(size: number, chunk: number) {
- const xs = ChunkedArray.create(s => [], 1, chunk, false);
+ const xs = ChunkedArray.create(s => [], 1, chunk);
for (let i = 0; i < size; i++) ChunkedArray.add(xs, i * i);
return ChunkedArray.compact(xs);
}
--
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