diff --git a/src/mol-base/collections/_spec/column.spec.ts b/src/mol-base/collections/_spec/column.spec.ts
index 5449d7d8ea2f7b925776e98630b64c25880906a9..6f1aa50b6f38997b6608adeb40a511c5d0b2ac95 100644
--- a/src/mol-base/collections/_spec/column.spec.ts
+++ b/src/mol-base/collections/_spec/column.spec.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Column, { isTypedArray } from '../column.1'
+import Column, { isTypedArray } from '../column'
describe('column', () => {
const cc = Column.ofConst(10, 2, Column.Type.int);
@@ -14,6 +14,8 @@ describe('column', () => {
const typed = Column.ofArray({ array: new Int32Array([1, 2, 3, 4]), type: Column.Type.int });
const typedWindow = Column.window(typed, 1, 3);
+ const numStr = Column.ofArray({ array: [1, 2] as any, type: Column.Type.str });
+
it('constant', () => {
expect(cc.rowCount).toBe(2);
expect(cc.value(0)).toBe(10);
@@ -31,4 +33,9 @@ describe('column', () => {
expect(typedWindow.rowCount).toBe(2);
expect(isTypedArray(typedWindow.toArray())).toBe(true);
});
+
+ it('numStr', () => {
+ expect(numStr.value(0)).toBe('1');
+ expect(numStr.toArray()).toEqual(['1', '2']);
+ });
})
\ No newline at end of file
diff --git a/src/mol-base/collections/column.1.ts b/src/mol-base/collections/column.1.ts
deleted file mode 100644
index d851a7c753996599df824a0dbbe9778ed3c074c4..0000000000000000000000000000000000000000
--- a/src/mol-base/collections/column.1.ts
+++ /dev/null
@@ -1,191 +0,0 @@
-/**
- * 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 4aec52f9e8767f6bf9bf32a232a33d99fb92519c..6139a04f42e12f47dbd34c44e7d3751ddacc24d6 100644
--- a/src/mol-base/collections/column.ts
+++ b/src/mol-base/collections/column.ts
@@ -4,94 +4,119 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-export type ColumnType = typeof ColumnType.str | typeof ColumnType.pooledStr | typeof ColumnType.int | typeof ColumnType.float | typeof ColumnType.vector | typeof ColumnType.matrix
-
-export namespace ColumnType {
- export const str = { '@type': '' as string, kind: 'str' as 'str', isScalar: false, isString: true };
- export const pooledStr = { '@type': '' as string, kind: 'pooled-str' as 'pooled-str', isScalar: false, isString: true };
- export const int = { '@type': 0 as number, kind: 'int' as 'int', isScalar: true, isString: false };
- export const float = { '@type': 0 as number, kind: 'float' as 'float', isScalar: true, isString: false };
- export const vector = { '@type': [] as number[], kind: 'vector' as 'vector', isScalar: false, isString: false };
- export const matrix = { '@type': [] as number[][], kind: 'matrix' as 'matrix', isScalar: false, isString: false };
-}
-
-export interface ToArrayParams {
- array?: { new(size: number): ArrayLike<number> },
- /** First row */
- start?: number,
- /** Last row (exclusive) */
- end?: number
-}
+interface Column<T> {
+ readonly '@type': Column.Type,
+ readonly '@array': ArrayLike<any> | undefined,
-export interface Column<T> {
- readonly '@type': ColumnType,
readonly isDefined: boolean,
readonly rowCount: number,
value(row: number): T,
- isValueDefined(row: number): boolean,
- toArray(params?: ToArrayParams): ReadonlyArray<T>,
+ valueKind(row: number): Column.ValueKind,
+ toArray(params?: Column.ToArrayParams): ReadonlyArray<T>,
stringEquals(row: number, value: string): boolean,
areValuesEqual(rowA: number, rowB: number): boolean
}
-export function UndefinedColumn<T extends ColumnType>(rowCount: number, type: T): Column<T['@type']> {
- const v = type.isString ? '' : 0;
- const value: Column<T['@type']>['value'] = type.isString ? row => '' : row => 0;
- return {
- '@type': type,
- isDefined: false,
- rowCount,
- value,
- isValueDefined: row => false,
- toArray: params => {
- const { array } = createArray(rowCount, params);
- for (let i = 0, _i = array.length; i < _i; i++) array[i] = v;
- return array;
- },
- stringEquals: (row, value) => !value,
- areValuesEqual: (rowA, rowB) => true
+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 = 0, NotPresent = 1, Unknown = 2 }
+
+ 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 function ConstColumn<T extends ColumnType>(v: T['@type'], rowCount: number, type: T): Column<T['@type']> {
+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,
- isDefined: true,
+ '@array': void 0,
+ isDefined: valueKind === Column.ValueKind.Present,
rowCount,
value,
- isValueDefined: row => false,
+ 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.isString
+ stringEquals: type.kind === 'str'
? (row, value) => value === v
- : type.isScalar
- ? (row, value) => +value === v
- : (row, value) => false,
+ : type.kind === 'float' || type.kind === 'int'
+ ? (row, value) => +value === v
+ : (row, value) => false,
areValuesEqual: (rowA, rowB) => true
}
}
-export interface ArrayColumnSpec<T extends ColumnType> {
- array: ArrayLike<T['@type']>,
- type: T,
- isValueDefined?: (row: number) => boolean
-}
-
-export function ArrayColumn<T extends ColumnType>({ array, type, isValueDefined }: ArrayColumnSpec<T>): Column<T['@type']> {
+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 value: Column<T['@type']>['value'] = type.kind === 'str'
+ ? row => { const v = array[row]; return typeof v === 'string' ? v : '' + v; }
+ : row => array[row];
+
const isTyped = isTypedArray(array);
return {
'@type': type,
+ '@array': array,
isDefined: true,
rowCount,
value,
- isValueDefined: isValueDefined ? isValueDefined : row => true,
- toArray: isTyped
+ valueKind: valueKind ? valueKind : row => Column.ValueKind.Present,
+ toArray: type.kind === 'str'
+ ? params => {
+ const { start, end } = getArrayBounds(rowCount, params);
+ 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++) {
+ const v = array[start + i];
+ ret[i] = typeof v === 'string' ? v : '' + v;
+ }
+ return ret;
+ }
+ : isTyped
? params => typedArrayWindow(array, params) as any as ReadonlyArray<T>
: params => {
const { start, end } = getArrayBounds(rowCount, params);
@@ -100,30 +125,56 @@ export function ArrayColumn<T extends ColumnType>({ array, type, isValueDefined
for (let i = 0, _i = end - start; i < _i; i++) ret[i] = array[start + i];
return ret;
},
- stringEquals: type.isScalar
+ stringEquals: type.kind === 'int' || type.kind === 'float'
? (row, value) => (array as any)[row] === +value
- : type.isString
- ? (row, value) => array[row] === value
+ : type.kind === 'str'
+ ? (row, value) => { const v = array[row]; return typeof v === 'string' ? v === value : +v === +value; }
: (row, value) => false,
areValuesEqual: (rowA, rowB) => array[rowA] === array[rowB]
}
}
-/** Makes the column backned by an array. Useful for columns that accessed often. */
-export function toArrayColumn<T>(c: Column<T>): Column<T> {
- if (!c.isDefined) return UndefinedColumn(c.rowCount, c['@type']) as any as Column<T>;
- return ArrayColumn({ array: c.toArray(), type: c['@type'] as any, isValueDefined: c.isValueDefined });
+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?: ToArrayParams) {
+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?: ToArrayParams) {
+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 };
@@ -136,16 +187,16 @@ export function fillArrayValues(value: (row: number) => any, target: any[], star
}
/** A helped function for Column.toArray */
-export function createAndFillArray(rowCount: number, value: (row: number) => any, params?: ToArrayParams) {
+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) {
- return data.buffer && typeof data.byteLength === 'number' && data.BYTES_PER_ELEMENT;
+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?: ToArrayParams): ReadonlyArray<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;
diff --git a/src/mol-io/reader/_spec/column.spec.ts b/src/mol-io/reader/_spec/column.spec.ts
index de51bde201a6d04aa24e1ea169213372a4845aeb..7ce9499de04be3eb1ca50cc9bfa18f3b291cd007 100644
--- a/src/mol-io/reader/_spec/column.spec.ts
+++ b/src/mol-io/reader/_spec/column.spec.ts
@@ -7,7 +7,7 @@
import FixedColumn from '../common/text/column/fixed'
import TokenColumn from '../common/text/column/token'
-import { ColumnType, typedArrayWindow } from '../../../mol-base/collections/column'
+import Column, { typedArrayWindow } from '../../../mol-base/collections/column'
const lines = [
'1.123 abc',
@@ -32,8 +32,8 @@ const linesTokens = (function () {
describe('fixed text column', () => {
const col = FixedColumn({ data: linesData, indices: linesTokens, count: lines.length });
- const col1 = col(0, 5, ColumnType.float);
- const col2 = col(5, 4, ColumnType.str);
+ const col1 = col(0, 5, Column.Type.float);
+ const col2 = col(5, 4, Column.Type.str);
it('number', () => {
expect(col1.value(0)).toBe(1.123);
expect(col1.value(1)).toBe(1.0);
@@ -53,7 +53,7 @@ describe('fixed text column', () => {
describe('token text column', () => {
const tokensData = '321';
const col = TokenColumn({ data: tokensData, indices: [0, 1, 1, 2, 2, 3], count: 3 });
- const col1 = col(ColumnType.int);
+ const col1 = col(Column.Type.int);
it('number', () => {
expect(col1.value(0)).toBe(3);
expect(col1.value(1)).toBe(2);
diff --git a/src/mol-io/reader/cif/binary/field.ts b/src/mol-io/reader/cif/binary/field.ts
index d1d1c035a7e3a52d14919815beb1e9cf8047e1cb..1fc47f4a65ce91f06ba752e7097323aef7f36f7e 100644
--- a/src/mol-io/reader/cif/binary/field.ts
+++ b/src/mol-io/reader/cif/binary/field.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import * as Column from '../../../../mol-base/collections/column'
+import Column, { isTypedArray, createAndFillArray, typedArrayWindow } from '../../../../mol-base/collections/column'
import * as Data from '../data-model'
import { EncodedColumn } from './encoding'
import decode from './decoder'
@@ -13,14 +13,14 @@ import { parseInt as fastParseInt, parseFloat as fastParseFloat } from '../../co
export default function Field(column: EncodedColumn): Data.Field {
const mask = column.mask ? decode(column.mask) as number[] : void 0;
const data = decode(column.data);
- const isNumeric = Column.isTypedArray(data);
+ const isNumeric = isTypedArray(data);
const str: Data.Field['str'] = isNumeric
? mask
- ? row => mask[row] === Data.ValuePresence.Present ? '' + data[row] : ''
+ ? row => mask[row] === Column.ValueKind.Present ? '' + data[row] : ''
: row => '' + data[row]
: mask
- ? row => mask[row] === Data.ValuePresence.Present ? data[row] : ''
+ ? row => mask[row] === Column.ValueKind.Present ? data[row] : ''
: row => data[row];
const int: Data.Field['int'] = isNumeric
@@ -31,27 +31,28 @@ export default function Field(column: EncodedColumn): Data.Field {
? row => data[row]
: row => { const v = data[row]; return fastParseFloat(v, 0, v.length); };
- const presence: Data.Field['presence'] = mask
+ const valueKind: Data.Field['valueKind'] = mask
? row => mask[row]
- : row => Data.ValuePresence.Present;
+ : row => Column.ValueKind.Present;
const rowCount = data.length;
return {
+ '@array': data,
isDefined: true,
rowCount,
str,
int,
float,
- presence,
+ valueKind,
areValuesEqual: (rowA, rowB) => data[rowA] === data[rowB],
stringEquals: (row, v) => str(row) === v,
- toStringArray: params => Column.createAndFillArray(rowCount, str, params),
+ toStringArray: params => createAndFillArray(rowCount, str, params),
toIntArray: isNumeric
- ? params => Column.typedArrayWindow(data, params)
- : params => Column.createAndFillArray(rowCount, int, params),
+ ? params => typedArrayWindow(data, params)
+ : params => createAndFillArray(rowCount, int, params),
toFloatArray: isNumeric
- ? params => Column.typedArrayWindow(data, params)
- : params => Column.createAndFillArray(rowCount, float, params)
+ ? params => typedArrayWindow(data, params)
+ : params => createAndFillArray(rowCount, float, params)
};
}
\ No newline at end of file
diff --git a/src/mol-io/reader/cif/data-model.ts b/src/mol-io/reader/cif/data-model.ts
index e396f71b7e3bfe8f9bd83d5920321508d7c3db80..2de58e8ad0682bff11e9281e9c64bb4e75cbd431 100644
--- a/src/mol-io/reader/cif/data-model.ts
+++ b/src/mol-io/reader/cif/data-model.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import * as Column from '../../../mol-base/collections/column'
+import Column, { createArray } from '../../../mol-base/collections/column'
export interface File {
readonly name?: string,
@@ -50,12 +50,6 @@ export namespace Category {
export const Empty: Category = { rowCount: 0, getField(name: string) { return void 0; } };
}
-export const enum ValuePresence {
- Present = 0,
- NotSpecified = 1,
- Unknown = 2
-}
-
/**
* Implementation note:
* Always implement this as a "plain" object so that the functions are "closures"
@@ -63,6 +57,7 @@ export const enum ValuePresence {
* additional closures.
*/
export interface Field {
+ readonly '@array': ArrayLike<any> | undefined
readonly isDefined: boolean,
readonly rowCount: number,
@@ -70,7 +65,7 @@ export interface Field {
int(row: number): number,
float(row: number): number,
- presence(row: number): ValuePresence,
+ valueKind(row: number): Column.ValueKind,
areValuesEqual(rowA: number, rowB: number): boolean,
stringEquals(row: number, value: string): boolean,
@@ -82,19 +77,20 @@ export interface Field {
export function DefaultUndefinedField(rowCount: number): Field {
return {
+ '@array': void 0,
isDefined: false,
rowCount,
str: row => '',
int: row => 0,
float: row => 0,
- presence: row => ValuePresence.NotSpecified,
+ valueKind: row => Column.ValueKind.NotPresent,
areValuesEqual: (rowA, rowB) => true,
stringEquals: (row, value) => value === null,
- toStringArray: (p) => Column.createArray(rowCount, p).array,
- toIntArray: (p) => Column.createArray(rowCount, p).array,
- toFloatArray: (p) => Column.createArray(rowCount, p).array
+ toStringArray: (p) => createArray(rowCount, p).array,
+ toIntArray: (p) => createArray(rowCount, p).array,
+ toFloatArray: (p) => createArray(rowCount, p).array
};
}
diff --git a/src/mol-io/reader/cif/schema.ts b/src/mol-io/reader/cif/schema.ts
index b391d05b994ac565ee93517c55a8c3f540c2d320..7d603fc73f3710f279c20c33c7952860768b5087 100644
--- a/src/mol-io/reader/cif/schema.ts
+++ b/src/mol-io/reader/cif/schema.ts
@@ -5,8 +5,7 @@
*/
import * as Data from './data-model'
-import * as Column from '../../../mol-base/collections/column'
-import StringPool from '../../utils/short-string-pool'
+import Column, { createAndFillArray } from '../../../mol-base/collections/column'
/**
* A schema defines the shape of categories and fields.
@@ -45,60 +44,53 @@ export type TypedCategory<Schema extends CategorySchema> = {
readonly _rowCount: number,
readonly _isDefined: boolean,
readonly _category: Data.Category
-} & { [F in keyof Schema]: Column.Column<Schema[F]['T']> }
+} & { [F in keyof Schema]: Column<Schema[F]['T']> }
export namespace Field {
- export interface Schema<T> { T: T, ctor: (field: Data.Field, category: Data.Category, key: string) => Column.Column<T>, undefinedField: (c: number) => Data.Field, alias?: string };
+ export interface Schema<T> { T: T, ctor: (field: Data.Field, category: Data.Category, key: string) => Column<T>, undefinedField: (c: number) => Data.Field, alias?: string };
export interface Spec { undefinedField?: (c: number) => Data.Field, alias?: string }
export function alias(name: string): Schema<any> { return { alias: name } as any; }
- export function pooledStr(spec?: Spec) { return createSchema(spec, PooledStr); }
export function str(spec?: Spec) { return createSchema(spec, Str); }
export function int(spec?: Spec) { return createSchema(spec, Int); }
export function float(spec?: Spec) { return createSchema(spec, Float); }
export function vector(rows: number, spec?: Spec) { return createSchema(spec, Vector(rows)); }
export function matrix(rows: number, cols: number, spec?: Spec) { return createSchema(spec, Matrix(rows, cols)); }
- function create<T>(type: Column.ColumnType, field: Data.Field, value: (row: number) => T, toArray: Column.Column<T>['toArray']): Column.Column<T> {
- const presence = field.presence;
+ function create<T>(type: Column.Type, field: Data.Field, value: (row: number) => T, toArray: Column<T>['toArray']): Column<T> {
return {
'@type': type,
+ '@array': field['@array'],
isDefined: field.isDefined,
rowCount: field.rowCount,
value,
- isValueDefined: row => presence(row) === Data.ValuePresence.Present,
+ valueKind: field.valueKind,
stringEquals: field.stringEquals,
areValuesEqual: field.areValuesEqual,
toArray
};
}
- function PooledStr(field: Data.Field) {
- const pool = StringPool.create();
- const value = (row: number) => StringPool.get(pool, field.str(row));
- const array = (params?: Column.ToArrayParams) => Column.createAndFillArray(field.rowCount, value, params);
- return create<string>(Column.ColumnType.str, field, value, array);
- }
- function Str(field: Data.Field) { return create(Column.ColumnType.str, field, field.str, field.toStringArray); }
- function Int(field: Data.Field) { return create(Column.ColumnType.int, field, field.int, field.toIntArray); }
- function Float(field: Data.Field) { return create(Column.ColumnType.float, field, field.float, field.toFloatArray); }
+ function Str(field: Data.Field) { return create(Column.Type.str, field, field.str, field.toStringArray); }
+ function Int(field: Data.Field) { return create(Column.Type.int, field, field.int, field.toIntArray); }
+ function Float(field: Data.Field) { return create(Column.Type.float, field, field.float, field.toFloatArray); }
function Vector(rows: number) {
return function(field: Data.Field, category: Data.Category, key: string) {
const value = (row: number) => Data.getVector(category, key, rows, row);
- return create(Column.ColumnType.vector, field, value, params => Column.createAndFillArray(field.rowCount, value, params));
+ return create(Column.Type.vector, field, value, params => createAndFillArray(field.rowCount, value, params));
}
}
function Matrix(rows: number, cols: number) {
return function(field: Data.Field, category: Data.Category, key: string) {
const value = (row: number) => Data.getMatrix(category, key, rows, cols, row);
- return create(Column.ColumnType.matrix, field, value, params => Column.createAndFillArray(field.rowCount, value, params));
+ return create(Column.Type.matrix, field, value, params => createAndFillArray(field.rowCount, value, params));
}
}
// spec argument is to allow for specialised implementation for undefined fields
- function createSchema<T>(spec: Spec | undefined, ctor: (field: Data.Field, category: Data.Category, key: string) => Column.Column<T>): Schema<T> {
+ function createSchema<T>(spec: Spec | undefined, ctor: (field: Data.Field, category: Data.Category, key: string) => Column<T>): Schema<T> {
return { T: 0 as any, ctor, undefinedField: (spec && spec.undefinedField) || Data.DefaultUndefinedField, alias: spec && spec.alias };
}
}
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index 45f31a003d75608660acc7a369a83496caca9605..b317a628481b7292b353517ebdc4f9f04c47b42d 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -6,7 +6,6 @@
import { Field, TypedFrame } from '../schema'
-const pooledStr = Field.pooledStr();
const str = Field.str();
const int = Field.int();
const float = Field.float();
@@ -58,19 +57,19 @@ const struct_conf = {
conf_type_id: str,
id: str,
pdbx_PDB_helix_id: int,
- beg_label_comp_id: pooledStr,
- beg_label_asym_id: pooledStr,
+ beg_label_comp_id: str,
+ beg_label_asym_id: str,
beg_label_seq_id: int,
- pdbx_beg_PDB_ins_code: pooledStr,
- end_label_comp_id: pooledStr,
- end_label_asym_id: pooledStr,
+ pdbx_beg_PDB_ins_code: str,
+ end_label_comp_id: str,
+ end_label_asym_id: str,
end_label_seq_id: int,
- pdbx_end_PDB_ins_code: pooledStr,
- beg_auth_comp_id: pooledStr,
- beg_auth_asym_id: pooledStr,
+ pdbx_end_PDB_ins_code: str,
+ beg_auth_comp_id: str,
+ beg_auth_asym_id: str,
beg_auth_seq_id: int,
- end_auth_comp_id: pooledStr,
- end_auth_asym_id: pooledStr,
+ end_auth_comp_id: str,
+ end_auth_asym_id: str,
end_auth_seq_id: int,
pdbx_PDB_helix_class: int,
details: str,
@@ -78,21 +77,21 @@ const struct_conf = {
}
const struct_sheet_range = {
- sheet_id: pooledStr,
+ sheet_id: str,
id: int,
- beg_label_comp_id: pooledStr,
- beg_label_asym_id: pooledStr,
+ beg_label_comp_id: str,
+ beg_label_asym_id: str,
beg_label_seq_id: int,
- pdbx_beg_PDB_ins_code: pooledStr,
- end_label_comp_id: pooledStr,
- end_label_asym_id: pooledStr,
+ pdbx_beg_PDB_ins_code: str,
+ end_label_comp_id: str,
+ end_label_asym_id: str,
end_label_seq_id: int,
- pdbx_end_PDB_ins_code: pooledStr,
- beg_auth_comp_id: pooledStr,
- beg_auth_asym_id: pooledStr,
+ pdbx_end_PDB_ins_code: str,
+ beg_auth_comp_id: str,
+ beg_auth_asym_id: str,
beg_auth_seq_id: int,
- end_auth_comp_id: pooledStr,
- end_auth_asym_id: pooledStr,
+ end_auth_comp_id: str,
+ end_auth_asym_id: str,
end_auth_seq_id: int
}
@@ -116,38 +115,38 @@ type BondValueOrder =
const struct_conn = {
id: str,
- conn_type_id: pooledStr as Field.Schema<StructConnTypeId>,
+ conn_type_id: str as Field.Schema<StructConnTypeId>,
pdbx_PDB_id: str,
- ptnr1_label_asym_id: pooledStr,
- ptnr1_label_comp_id: pooledStr,
+ ptnr1_label_asym_id: str,
+ ptnr1_label_comp_id: str,
ptnr1_label_seq_id: int,
- ptnr1_label_atom_id: pooledStr,
- pdbx_ptnr1_label_alt_id: pooledStr,
- pdbx_ptnr1_PDB_ins_code: pooledStr,
- pdbx_ptnr1_standard_comp_id: pooledStr,
- ptnr1_symmetry: pooledStr,
- ptnr2_label_asym_id: pooledStr,
- ptnr2_label_comp_id: pooledStr,
+ ptnr1_label_atom_id: str,
+ pdbx_ptnr1_label_alt_id: str,
+ pdbx_ptnr1_PDB_ins_code: str,
+ pdbx_ptnr1_standard_comp_id: str,
+ ptnr1_symmetry: str,
+ ptnr2_label_asym_id: str,
+ ptnr2_label_comp_id: str,
ptnr2_label_seq_id: int,
- ptnr2_label_atom_id: pooledStr,
- pdbx_ptnr2_label_alt_id: pooledStr,
- pdbx_ptnr2_PDB_ins_code: pooledStr,
- ptnr1_auth_asym_id: pooledStr,
- ptnr1_auth_comp_id: pooledStr,
+ ptnr2_label_atom_id: str,
+ pdbx_ptnr2_label_alt_id: str,
+ pdbx_ptnr2_PDB_ins_code: str,
+ ptnr1_auth_asym_id: str,
+ ptnr1_auth_comp_id: str,
ptnr1_auth_seq_id: int,
- ptnr2_auth_asym_id: pooledStr,
- ptnr2_auth_comp_id: pooledStr,
+ ptnr2_auth_asym_id: str,
+ ptnr2_auth_comp_id: str,
ptnr2_auth_seq_id: int,
- ptnr2_symmetry: pooledStr,
- pdbx_ptnr3_label_atom_id: pooledStr,
+ ptnr2_symmetry: str,
+ pdbx_ptnr3_label_atom_id: str,
pdbx_ptnr3_label_seq_id: int,
- pdbx_ptnr3_label_comp_id: pooledStr,
- pdbx_ptnr3_label_asym_id: pooledStr,
- pdbx_ptnr3_label_alt_id: pooledStr,
- pdbx_ptnr3_PDB_ins_code: pooledStr,
- details: pooledStr,
+ pdbx_ptnr3_label_comp_id: str,
+ pdbx_ptnr3_label_asym_id: str,
+ pdbx_ptnr3_label_alt_id: str,
+ pdbx_ptnr3_PDB_ins_code: str,
+ details: str,
pdbx_dist_value: float,
- pdbx_value_order: pooledStr as Field.Schema<BondValueOrder>
+ pdbx_value_order: str as Field.Schema<BondValueOrder>
}
const struct_conn_type = {
@@ -157,13 +156,13 @@ const struct_conn_type = {
}
const chem_comp_bond = {
- comp_id: pooledStr,
- pdbx_stereo_config: pooledStr,
+ comp_id: str,
+ pdbx_stereo_config: str,
pdbx_ordinal: int,
- pdbx_aromatic_flag: pooledStr as Field.Schema<'Y' | 'N'>,
- atom_id_1: pooledStr,
- atom_id_2: pooledStr,
- value_order: pooledStr as Field.Schema<BondValueOrder>
+ pdbx_aromatic_flag: str as Field.Schema<'Y' | 'N'>,
+ atom_id_1: str,
+ atom_id_2: str,
+ value_order: str as Field.Schema<BondValueOrder>
}
const pdbx_struct_assembly = {
@@ -191,37 +190,37 @@ const pdbx_struct_oper_list = {
const pdbx_struct_mod_residue = {
id: int,
- label_asym_id: pooledStr,
+ label_asym_id: str,
label_seq_id: int,
- label_comp_id: pooledStr,
- auth_asym_id: pooledStr,
+ label_comp_id: str,
+ auth_asym_id: str,
auth_seq_id: int,
- auth_comp_id: pooledStr,
- PDB_ins_code: pooledStr,
- parent_comp_id: pooledStr,
+ auth_comp_id: str,
+ PDB_ins_code: str,
+ parent_comp_id: str,
details: str
}
const atom_site = {
- group_PDB: pooledStr,
+ group_PDB: str,
id: int,
- type_symbol: pooledStr,
- label_atom_id: pooledStr,
- label_alt_id: pooledStr,
- label_comp_id: pooledStr,
- label_asym_id: pooledStr,
- label_entity_id: pooledStr,
+ type_symbol: str,
+ label_atom_id: str,
+ label_alt_id: str,
+ label_comp_id: str,
+ label_asym_id: str,
+ label_entity_id: str,
label_seq_id: int,
- pdbx_PDB_ins_code: pooledStr,
- pdbx_formal_charge: pooledStr,
+ pdbx_PDB_ins_code: str,
+ pdbx_formal_charge: str,
Cartn_x: float,
Cartn_y: float,
Cartn_z: float,
occupancy: float,
B_iso_or_equiv: float,
- auth_atom_id: pooledStr,
- auth_comp_id: pooledStr,
- auth_asym_id: pooledStr,
+ auth_atom_id: str,
+ auth_comp_id: str,
+ auth_asym_id: str,
auth_seq_id: int,
pdbx_PDB_model_num: int
}
diff --git a/src/mol-io/reader/cif/text/field.ts b/src/mol-io/reader/cif/text/field.ts
index 338bc327ddbffa062d7c7183410e916e14df435b..17454c0d791461a5b81926ed4d30a6b1c48f6930 100644
--- a/src/mol-io/reader/cif/text/field.ts
+++ b/src/mol-io/reader/cif/text/field.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import * as Column from '../../../../mol-base/collections/column'
+import Column, { createAndFillArray } from '../../../../mol-base/collections/column'
import * as TokenColumn from '../../common/text/column/token'
import { Tokens } from '../../common/text/tokenizer'
import * as Data from '../data-model'
@@ -27,27 +27,28 @@ export default function CifTextField(tokens: Tokens, rowCount: number): Data.Fie
return fastParseFloat(data, indices[2 * row], indices[2 * row + 1]) || 0;
};
- const presence: Data.Field['presence'] = row => {
+ const valueKind: Data.Field['valueKind'] = row => {
const s = indices[2 * row];
- if (indices[2 * row + 1] - s !== 1) return Data.ValuePresence.Present;
+ if (indices[2 * row + 1] - s !== 1) return Column.ValueKind.Present;
const v = data.charCodeAt(s);
- if (v === 46 /* . */) return Data.ValuePresence.NotSpecified;
- if (v === 63 /* ? */) return Data.ValuePresence.Unknown;
- return Data.ValuePresence.Present;
+ if (v === 46 /* . */) return Column.ValueKind.NotPresent;
+ if (v === 63 /* ? */) return Column.ValueKind.Unknown;
+ return Column.ValueKind.Present;
};
return {
+ '@array': void 0,
isDefined: true,
rowCount,
str,
int,
float,
- presence,
+ valueKind,
areValuesEqual: TokenColumn.areValuesEqualProvider(tokens),
stringEquals: (row, v) => {
const s = indices[2 * row];
const value = v || '';
- if (!value && presence(row) !== Data.ValuePresence.Present) return true;
+ if (!value && valueKind(row) !== Column.ValueKind.Present) return true;
const len = value.length;
if (len !== indices[2 * row + 1] - s) return false;
for (let i = 0; i < len; i++) {
@@ -55,8 +56,8 @@ export default function CifTextField(tokens: Tokens, rowCount: number): Data.Fie
}
return true;
},
- toStringArray: params => Column.createAndFillArray(rowCount, str, params),
- toIntArray: params => Column.createAndFillArray(rowCount, int, params),
- toFloatArray: params => Column.createAndFillArray(rowCount, float, params)
+ toStringArray: params => createAndFillArray(rowCount, str, params),
+ toIntArray: params => createAndFillArray(rowCount, int, params),
+ toFloatArray: params => createAndFillArray(rowCount, float, params)
}
}
\ No newline at end of file
diff --git a/src/mol-io/reader/common/text/column/fixed.ts b/src/mol-io/reader/common/text/column/fixed.ts
index 0a384f8a46508f89ec4c27d3fe53e9b3e1186b00..26d1c969d0e6dfe57d8f8b36e4435898b6eeb966 100644
--- a/src/mol-io/reader/common/text/column/fixed.ts
+++ b/src/mol-io/reader/common/text/column/fixed.ts
@@ -4,21 +4,19 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Column, ColumnType, createAndFillArray } from '../../../../../mol-base/collections/column'
+import Column, { createAndFillArray } from '../../../../../mol-base/collections/column'
import { trimStr, Tokens } from '../tokenizer'
import { parseIntSkipLeadingWhitespace, parseFloatSkipLeadingWhitespace } from '../number-parser'
-import StringPool from '../../../../utils/short-string-pool'
export default function FixedColumnProvider(lines: Tokens) {
- return function<T extends ColumnType>(offset: number, width: number, type: T) {
+ return function<T extends Column.Type>(offset: number, width: number, type: T) {
return FixedColumn(lines, offset, width, type);
}
}
-export function FixedColumn<T extends ColumnType>(lines: Tokens, offset: number, width: number, type: T): Column<T['@type']> {
+export function FixedColumn<T extends Column.Type>(lines: Tokens, offset: number, width: number, type: T): Column<T['@type']> {
const { data, indices, count: rowCount } = lines;
const { kind } = type;
- const pool = kind === 'pooled-str' ? StringPool.create() : void 0;
const value: Column<T['@type']>['value'] = kind === 'str' ? row => {
let s = indices[2 * row] + offset, le = indices[2 * row + 1];
@@ -26,12 +24,6 @@ export function FixedColumn<T extends ColumnType>(lines: Tokens, offset: number,
let e = s + width;
if (e > le) e = le;
return trimStr(data, s, e);
- } : kind === 'pooled-str' ? row => {
- let s = indices[2 * row] + offset, le = indices[2 * row + 1];
- if (s >= le) return '';
- let e = s + width;
- if (e > le) e = le;
- return StringPool.get(pool!, trimStr(data, s, e));
} : kind === 'int' ? row => {
const s = indices[2 * row] + offset;
if (s > indices[2 * row + 1]) return 0;
@@ -43,10 +35,11 @@ export function FixedColumn<T extends ColumnType>(lines: Tokens, offset: number,
};
return {
'@type': type,
+ '@array': void 0,
isDefined: true,
rowCount,
value,
- isValueDefined: row => true,
+ valueKind: row => Column.ValueKind.Present,
toArray: params => createAndFillArray(rowCount, value, params),
stringEquals: (row, v) => value(row) === v,
areValuesEqual: (rowA, rowB) => value(rowA) === value(rowB)
diff --git a/src/mol-io/reader/common/text/column/token.ts b/src/mol-io/reader/common/text/column/token.ts
index 0b8d732b99f6081c99f99007fe7ccdee3cd44815..447752cc195ebccb7db44e0fa74ed1e889ce48ac 100644
--- a/src/mol-io/reader/common/text/column/token.ts
+++ b/src/mol-io/reader/common/text/column/token.ts
@@ -4,37 +4,34 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Column, ColumnType, createAndFillArray } from '../../../../../mol-base/collections/column'
+import Column, { createAndFillArray } from '../../../../../mol-base/collections/column'
import { Tokens } from '../tokenizer'
import { parseInt as fastParseInt, parseFloat as fastParseFloat } from '../number-parser'
-import StringPool from '../../../../utils/short-string-pool'
export default function TokenColumnProvider(tokens: Tokens) {
- return function<T extends ColumnType>(type: T) {
+ return function<T extends Column.Type>(type: T) {
return TokenColumn(tokens, type);
}
}
-export function TokenColumn<T extends ColumnType>(tokens: Tokens, type: T): Column<T['@type']> {
+export function TokenColumn<T extends Column.Type>(tokens: Tokens, type: T): Column<T['@type']> {
const { data, indices, count: rowCount } = tokens;
const { kind } = type;
- const pool = kind === 'pooled-str' ? StringPool.create() : void 0;
const value: Column<T['@type']>['value'] =
kind === 'str'
? row => data.substring(indices[2 * row], indices[2 * row + 1])
- : kind === 'pooled-str'
- ? row => StringPool.get(pool!, data.substring(indices[2 * row], indices[2 * row + 1]))
: kind === 'int'
? row => fastParseInt(data, indices[2 * row], indices[2 * row + 1]) || 0
: row => fastParseFloat(data, indices[2 * row], indices[2 * row + 1]) || 0;
return {
'@type': type,
+ '@array': void 0,
isDefined: true,
rowCount,
value,
- isValueDefined: row => true,
+ valueKind: row => Column.ValueKind.Present,
toArray: params => createAndFillArray(rowCount, value, params),
stringEquals: (row, v) => {
const s = indices[2 * row];
diff --git a/src/mol-io/reader/gro/parser.ts b/src/mol-io/reader/gro/parser.ts
index f4d28e4b0045270a4287d6942cefd83848f5a5ee..7a849ccc371fa1618955d4a8705700614195564f 100644
--- a/src/mol-io/reader/gro/parser.ts
+++ b/src/mol-io/reader/gro/parser.ts
@@ -7,7 +7,7 @@
import Tokenizer from '../common/text/tokenizer'
import FixedColumn from '../common/text/column/fixed'
-import { ColumnType, UndefinedColumn } from '../../../mol-base/collections/column'
+import Column from '../../../mol-base/collections/column'
import * as Schema from './schema'
import Result from '../result'
import Computation from '../../../mol-base/computation'
@@ -106,20 +106,20 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
const vW = state.header.precision.velocity + 4;
const col = FixedColumn(lines);
- const undef = UndefinedColumn(state.numberOfAtoms, ColumnType.float);
+ const undef = Column.Undefined(state.numberOfAtoms, Column.Type.float);
const ret = {
count: state.numberOfAtoms,
- residueNumber: col(0, 5, ColumnType.int),
- residueName: col(5, 5, ColumnType.pooledStr),
- atomName: col(10, 5, ColumnType.pooledStr),
- atomNumber: col(15, 5, ColumnType.int),
- x: col(pO, pW, ColumnType.float),
- y: col(pO + pW, pW, ColumnType.float),
- z: col(pO + 2 * pW, pW, ColumnType.float),
- vx: hasVelocities ? col(vO, vW, ColumnType.float) : undef,
- vy: hasVelocities ? col(vO + vW, vW, ColumnType.float) : undef,
- vz: hasVelocities ? col(vO + 2 * vW, vW, ColumnType.float) : undef,
+ residueNumber: col(0, 5, Column.Type.int),
+ residueName: col(5, 5, Column.Type.str),
+ atomName: col(10, 5, Column.Type.str),
+ atomNumber: col(15, 5, Column.Type.int),
+ x: col(pO, pW, Column.Type.float),
+ y: col(pO + pW, pW, Column.Type.float),
+ z: col(pO + 2 * pW, pW, Column.Type.float),
+ vx: hasVelocities ? col(vO, vW, Column.Type.float) : undef,
+ vy: hasVelocities ? col(vO + vW, vW, Column.Type.float) : undef,
+ vz: hasVelocities ? col(vO + 2 * vW, vW, Column.Type.float) : undef,
};
return ret;
diff --git a/src/mol-io/reader/gro/schema.d.ts b/src/mol-io/reader/gro/schema.d.ts
index 981d2906aa620cd40898719bdb9181a47d672fbf..a32f34ee1ecc5ca3c2b5df1bb222b175c023026f 100644
--- a/src/mol-io/reader/gro/schema.d.ts
+++ b/src/mol-io/reader/gro/schema.d.ts
@@ -5,7 +5,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Column } from '../../../mol-base/collections/column'
+import Column from '../../../mol-base/collections/column'
export interface Header {
title: string,
diff --git a/src/mol-io/reader/mol2/schema.d.ts b/src/mol-io/reader/mol2/schema.d.ts
index 8284c6f05d565a51b73a580713df5b52046050cd..15a2ca7afff455774e7bed56b72a7914c4a48dda 100644
--- a/src/mol-io/reader/mol2/schema.d.ts
+++ b/src/mol-io/reader/mol2/schema.d.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Column } from '../../../mol-base/collections/column'
+import Column from '../../../mol-base/collections/column'
// Full format http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
// there are many records but for now ignore (pass over) all but the following