Chunked array

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]));
+    });
+});

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;
     }
 }
 

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],
+    []
+];

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);

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);
 }