From 40a35dea8e7b402b1ede3658e0e52cbfcd90075e Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 2 Nov 2017 16:10:41 +0100
Subject: [PATCH] More refactoring, fixed jest
---
package.json | 1 +
src/mol-base/collections/integer.ts | 3 +-
.../{ => integer}/_spec/linked-index.spec.ts | 0
.../collections/{ => integer}/linked-index.ts | 0
src/mol-base/collections/table.ts | 118 +----------------
.../{ => table}/_spec/table.spec.ts | 3 +-
.../collections/table/column-helpers.ts | 40 ++++++
.../collections/{ => table}/column.ts | 37 +-----
src/mol-base/collections/table/table.ts | 121 ++++++++++++++++++
.../structure/model/builders/mmcif.ts | 3 +-
.../model/properties/conformation.ts | 2 +-
.../structure/model/properties/hierarchy.ts | 3 +-
.../structure/model/utils/hierarchy-keys.ts | 2 +-
src/mol-io/reader/_spec/column.spec.ts | 2 +-
src/mol-io/reader/cif/binary/field.ts | 2 +-
src/mol-io/reader/cif/data-model.ts | 2 +-
src/mol-io/reader/cif/schema.ts | 3 +-
src/mol-io/reader/cif/text/field.ts | 2 +-
src/mol-io/reader/common/text/column/fixed.ts | 2 +-
src/mol-io/reader/common/text/column/token.ts | 2 +-
src/mol-io/reader/gro/parser.ts | 2 +-
src/mol-io/reader/gro/schema.d.ts | 2 +-
src/mol-io/reader/mol2/schema.d.ts | 2 +-
src/perf-tests/column.ts | 2 +-
24 files changed, 187 insertions(+), 169 deletions(-)
rename src/mol-base/collections/{ => integer}/_spec/linked-index.spec.ts (100%)
rename src/mol-base/collections/{ => integer}/linked-index.ts (100%)
rename src/mol-base/collections/{ => table}/_spec/table.spec.ts (98%)
create mode 100644 src/mol-base/collections/table/column-helpers.ts
rename src/mol-base/collections/{ => table}/column.ts (86%)
create mode 100644 src/mol-base/collections/table/table.ts
diff --git a/package.json b/package.json
index 02761decc..44965fe03 100644
--- a/package.json
+++ b/package.json
@@ -24,6 +24,7 @@
"transform": {
"\\.ts$": "<rootDir>/node_modules/ts-jest/preprocessor.js"
},
+ "moduleDirectories": ["node_modules", "build/node_modules"],
"testRegex": "\\.spec\\.ts$"
},
"author": "",
diff --git a/src/mol-base/collections/integer.ts b/src/mol-base/collections/integer.ts
index a7ca91076..aba4ca874 100644
--- a/src/mol-base/collections/integer.ts
+++ b/src/mol-base/collections/integer.ts
@@ -9,6 +9,7 @@ import OrderedSet from './integer/ordered-set'
import Segmentation from './integer/segmentation'
import SortedArray from './integer/sorted-array'
import Tuple from './integer/tuple'
+import LinkedIndex from './integer/linked-index'
import Iterator from './iterator'
-export { Interval, OrderedSet, Segmentation, SortedArray, Tuple, Iterator }
\ No newline at end of file
+export { Interval, OrderedSet, Segmentation, SortedArray, Tuple, LinkedIndex, Iterator }
\ No newline at end of file
diff --git a/src/mol-base/collections/_spec/linked-index.spec.ts b/src/mol-base/collections/integer/_spec/linked-index.spec.ts
similarity index 100%
rename from src/mol-base/collections/_spec/linked-index.spec.ts
rename to src/mol-base/collections/integer/_spec/linked-index.spec.ts
diff --git a/src/mol-base/collections/linked-index.ts b/src/mol-base/collections/integer/linked-index.ts
similarity index 100%
rename from src/mol-base/collections/linked-index.ts
rename to src/mol-base/collections/integer/linked-index.ts
diff --git a/src/mol-base/collections/table.ts b/src/mol-base/collections/table.ts
index 32a7b5379..b175419ae 100644
--- a/src/mol-base/collections/table.ts
+++ b/src/mol-base/collections/table.ts
@@ -4,118 +4,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Column from './column'
-import { sortArray } from './sort'
+import Table from './table/table'
+import Column from './table/column'
+import * as ColumnHelpers from './table/column-helpers'
-type Table<Schema extends Table.Schema> = { readonly _rowCount: number, readonly _columns: ReadonlyArray<string> } & Table.Columns<Schema>
-
-/** An immutable table */
-namespace Table {
- export type Schema = { [field: string]: Column.Type }
- export type Columns<S extends Schema> = { [C in keyof S]: Column<S[C]['T']> }
- export type Row<S extends Schema> = { [C in keyof S]: S[C]['T'] }
- export type Arrays<S extends Schema> = { [C in keyof S]: ArrayLike<S[C]['T']> }
- export type PartialTable<S extends Table.Schema> = { readonly _rowCount: number, readonly _columns: ReadonlyArray<string> } & { [C in keyof S]?: Column<S[C]['T']> }
-
- export function pickColumns<S extends Schema>(schema: S, table: PartialTable<S>, guard: Partial<Columns<S>> = {}): Table<S> {
- const ret = Object.create(null);
- const keys = Object.keys(schema);
- ret._rowCount = table._rowCount;
- ret._columns = keys;
- for (const k of keys) {
- if (!!table[k]) ret[k] = table[k];
- else if (!!guard[k]) ret[k] = guard[k];
- else throw Error(`Cannot find column '${k}'.`);
- }
- return ret;
- }
-
- export function ofColumns<S extends Schema, R extends Table<S> = Table<S>>(columns: Columns<S>): R {
- const _columns = Object.keys(columns);
- const _rowCount = columns[_columns[0]].rowCount;
- return { _rowCount, _columns, ...(columns as any) };
- }
-
- export function ofRows<S extends Schema, R extends Table<S> = Table<S>>(schema: Schema, rows: ArrayLike<Row<S>>): R {
- const ret = Object.create(null);
- const rowCount = rows.length;
- const columns = Object.keys(schema);
- ret._rowCount = rowCount;
- ret._columns = columns;
- for (const k of columns) {
- (ret as any)[k] = Column.ofLambda({
- rowCount,
- type: schema[k],
- value: r => rows[r][k],
- valueKind: r => typeof rows[r][k] === 'undefined' ? Column.ValueKind.NotPresent : Column.ValueKind.Present
- })
- }
- return ret as R;
- }
-
- export function ofArrays<S extends Schema, R extends Table<S> = Table<S>>(schema: Schema, arrays: Arrays<S>): R {
- const ret = Object.create(null);
- const columns = Object.keys(schema);
- ret._rowCount = arrays[columns[0]].length;
- ret._columns = columns;
- for (const k of columns) {
- (ret as any)[k] = Column.ofArray({ array: arrays[k], type: schema[k] })
- }
- return ret as R;
- }
-
- export function view<S extends Schema, R extends Schema>(table: Table<S>, schema: R, view: ArrayLike<number>) {
- const ret = Object.create(null);
- const columns = Object.keys(schema);
- ret._rowCount = view.length;
- ret._columns = columns;
- for (const k of columns) {
- (ret as any)[k] = Column.view(table[k], view);
- }
- return ret as Table<R>;
- }
-
- export function columnToArray<S extends Schema>(table: Table<S>, name: keyof S, array?: Column.ArrayCtor<any>) {
- table[name] = Column.asArrayColumn(table[name], array);
- }
-
- /** Sort and return a new table */
- export function sort<T extends Table<S>, S extends Schema>(table: T, cmp: (i: number, j: number) => number) {
- const indices = new Int32Array(table._rowCount);
- for (let i = 0, _i = indices.length; i < _i; i++) indices[i] = i;
- sortArray(indices, (_, i, j) => cmp(i, j));
-
- let isIdentity = true;
- for (let i = 0, _i = indices.length; i < _i; i++) {
- if (indices[i] !== i) {
- isIdentity = false;
- break;
- }
- }
- if (isIdentity) return table;
-
- const ret = Object.create(null);
- ret._rowCount = table._rowCount;
- ret._columns = table._columns;
- for (const c of table._columns) {
- ret[c] = Column.view((table as any)[c], indices, false);
- }
- return ret;
- }
-
- export function areEqual<T extends Table<Schema>>(a: T, b: T) {
- if (a._rowCount !== b._rowCount) return false;
- if (a._columns.length !== b._columns.length) return false;
- for (const c of a._columns) {
- if (!b[c]) return false;
- }
-
- for (const c of a._columns) {
- if (!Column.areEqual(a[c], b[c])) return false;
- }
-
- return true;
- }
-}
-
-export default Table
\ No newline at end of file
+export { Table, Column, ColumnHelpers }
\ No newline at end of file
diff --git a/src/mol-base/collections/_spec/table.spec.ts b/src/mol-base/collections/table/_spec/table.spec.ts
similarity index 98%
rename from src/mol-base/collections/_spec/table.spec.ts
rename to src/mol-base/collections/table/_spec/table.spec.ts
index 4d79f445b..18a49fc54 100644
--- a/src/mol-base/collections/_spec/table.spec.ts
+++ b/src/mol-base/collections/table/_spec/table.spec.ts
@@ -4,7 +4,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Column, { ColumnHelpers } from '../column'
+import * as ColumnHelpers from '../column-helpers'
+import Column from '../column'
import Table from '../table'
describe('column', () => {
diff --git a/src/mol-base/collections/table/column-helpers.ts b/src/mol-base/collections/table/column-helpers.ts
new file mode 100644
index 000000000..b57deec09
--- /dev/null
+++ b/src/mol-base/collections/table/column-helpers.ts
@@ -0,0 +1,40 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import Column from './column'
+
+export function getArrayBounds(rowCount: number, params?: Column.ToArrayParams<any>) {
+ 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 };
+}
+
+export function createArray(rowCount: number, params?: Column.ToArrayParams<any>) {
+ 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 };
+}
+
+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;
+}
+
+export function createAndFillArray(rowCount: number, value: (row: number) => any, params?: Column.ToArrayParams<any>) {
+ 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<any>): 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/table/column.ts
similarity index 86%
rename from src/mol-base/collections/column.ts
rename to src/mol-base/collections/table/column.ts
index 7118f96d0..9f0263306 100644
--- a/src/mol-base/collections/column.ts
+++ b/src/mol-base/collections/table/column.ts
@@ -4,6 +4,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
+import * as ColumnHelpers from './column-helpers'
+
interface Column<T> {
readonly '@type': Column.Type,
readonly '@array': ArrayLike<any> | undefined,
@@ -304,39 +306,4 @@ function areValuesEqual(a: Column<any>, b: Column<any>) {
if (va(i) !== vb(i)) return false;
}
return true;
-}
-
-export namespace ColumnHelpers {
- export function getArrayBounds(rowCount: number, params?: Column.ToArrayParams<any>) {
- 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 };
- }
-
- export function createArray(rowCount: number, params?: Column.ToArrayParams<any>) {
- 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 };
- }
-
- 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;
- }
-
- export function createAndFillArray(rowCount: number, value: (row: number) => any, params?: Column.ToArrayParams<any>) {
- 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<any>): 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/table/table.ts b/src/mol-base/collections/table/table.ts
new file mode 100644
index 000000000..d4e94d985
--- /dev/null
+++ b/src/mol-base/collections/table/table.ts
@@ -0,0 +1,121 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import Column from './column'
+import { sortArray } from '../sort'
+
+type Table<Schema extends Table.Schema> = { readonly _rowCount: number, readonly _columns: ReadonlyArray<string> } & Table.Columns<Schema>
+
+/** An immutable table */
+namespace Table {
+ export type Schema = { [field: string]: Column.Type }
+ export type Columns<S extends Schema> = { [C in keyof S]: Column<S[C]['T']> }
+ export type Row<S extends Schema> = { [C in keyof S]: S[C]['T'] }
+ export type Arrays<S extends Schema> = { [C in keyof S]: ArrayLike<S[C]['T']> }
+ export type PartialTable<S extends Table.Schema> = { readonly _rowCount: number, readonly _columns: ReadonlyArray<string> } & { [C in keyof S]?: Column<S[C]['T']> }
+
+ export function pickColumns<S extends Schema>(schema: S, table: PartialTable<S>, guard: Partial<Columns<S>> = {}): Table<S> {
+ const ret = Object.create(null);
+ const keys = Object.keys(schema);
+ ret._rowCount = table._rowCount;
+ ret._columns = keys;
+ for (const k of keys) {
+ if (!!table[k]) ret[k] = table[k];
+ else if (!!guard[k]) ret[k] = guard[k];
+ else throw Error(`Cannot find column '${k}'.`);
+ }
+ return ret;
+ }
+
+ export function ofColumns<S extends Schema, R extends Table<S> = Table<S>>(columns: Columns<S>): R {
+ const _columns = Object.keys(columns);
+ const _rowCount = columns[_columns[0]].rowCount;
+ return { _rowCount, _columns, ...(columns as any) };
+ }
+
+ export function ofRows<S extends Schema, R extends Table<S> = Table<S>>(schema: Schema, rows: ArrayLike<Row<S>>): R {
+ const ret = Object.create(null);
+ const rowCount = rows.length;
+ const columns = Object.keys(schema);
+ ret._rowCount = rowCount;
+ ret._columns = columns;
+ for (const k of columns) {
+ (ret as any)[k] = Column.ofLambda({
+ rowCount,
+ type: schema[k],
+ value: r => rows[r][k],
+ valueKind: r => typeof rows[r][k] === 'undefined' ? Column.ValueKind.NotPresent : Column.ValueKind.Present
+ })
+ }
+ return ret as R;
+ }
+
+ export function ofArrays<S extends Schema, R extends Table<S> = Table<S>>(schema: Schema, arrays: Arrays<S>): R {
+ const ret = Object.create(null);
+ const columns = Object.keys(schema);
+ ret._rowCount = arrays[columns[0]].length;
+ ret._columns = columns;
+ for (const k of columns) {
+ (ret as any)[k] = Column.ofArray({ array: arrays[k], type: schema[k] })
+ }
+ return ret as R;
+ }
+
+ export function view<S extends Schema, R extends Schema>(table: Table<S>, schema: R, view: ArrayLike<number>) {
+ const ret = Object.create(null);
+ const columns = Object.keys(schema);
+ ret._rowCount = view.length;
+ ret._columns = columns;
+ for (const k of columns) {
+ (ret as any)[k] = Column.view(table[k], view);
+ }
+ return ret as Table<R>;
+ }
+
+ export function columnToArray<S extends Schema>(table: Table<S>, name: keyof S, array?: Column.ArrayCtor<any>) {
+ table[name] = Column.asArrayColumn(table[name], array);
+ }
+
+ /** Sort and return a new table */
+ export function sort<T extends Table<S>, S extends Schema>(table: T, cmp: (i: number, j: number) => number) {
+ const indices = new Int32Array(table._rowCount);
+ for (let i = 0, _i = indices.length; i < _i; i++) indices[i] = i;
+ sortArray(indices, (_, i, j) => cmp(i, j));
+
+ let isIdentity = true;
+ for (let i = 0, _i = indices.length; i < _i; i++) {
+ if (indices[i] !== i) {
+ isIdentity = false;
+ break;
+ }
+ }
+ if (isIdentity) return table;
+
+ const ret = Object.create(null);
+ ret._rowCount = table._rowCount;
+ ret._columns = table._columns;
+ for (const c of table._columns) {
+ ret[c] = Column.view((table as any)[c], indices, false);
+ }
+ return ret;
+ }
+
+ export function areEqual<T extends Table<Schema>>(a: T, b: T) {
+ if (a._rowCount !== b._rowCount) return false;
+ if (a._columns.length !== b._columns.length) return false;
+ for (const c of a._columns) {
+ if (!b[c]) return false;
+ }
+
+ for (const c of a._columns) {
+ if (!Column.areEqual(a[c], b[c])) return false;
+ }
+
+ return true;
+ }
+}
+
+export default Table
\ No newline at end of file
diff --git a/src/mol-data/structure/model/builders/mmcif.ts b/src/mol-data/structure/model/builders/mmcif.ts
index 26591bf4b..40e713590 100644
--- a/src/mol-data/structure/model/builders/mmcif.ts
+++ b/src/mol-data/structure/model/builders/mmcif.ts
@@ -6,8 +6,7 @@
import { mmCIF } from '../data-format'
import Model from '../model'
-import Column from 'mol-base/collections/column'
-import Table from 'mol-base/collections/table'
+import { Column, Table } from 'mol-base/collections/table'
import { Interval, Segmentation } from 'mol-base/collections/integer'
import { newUUID } from 'mol-base/utils/uuid'
import * as Hierarchy from '../properties/hierarchy'
diff --git a/src/mol-data/structure/model/properties/conformation.ts b/src/mol-data/structure/model/properties/conformation.ts
index 9014a0a93..651504d82 100644
--- a/src/mol-data/structure/model/properties/conformation.ts
+++ b/src/mol-data/structure/model/properties/conformation.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Column from 'mol-base/collections/column'
+import { Column } from 'mol-base/collections/table'
import UUID from 'mol-base/utils/uuid'
interface Conformation {
diff --git a/src/mol-data/structure/model/properties/hierarchy.ts b/src/mol-data/structure/model/properties/hierarchy.ts
index fec5de265..c44ca9052 100644
--- a/src/mol-data/structure/model/properties/hierarchy.ts
+++ b/src/mol-data/structure/model/properties/hierarchy.ts
@@ -4,8 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Column from 'mol-base/collections/column'
-import Table from 'mol-base/collections/table'
+import { Column, Table } from 'mol-base/collections/table'
import { Segmentation } from 'mol-base/collections/integer'
import { Schema as mmCIF } from 'mol-io/reader/cif/schema/mmcif'
diff --git a/src/mol-data/structure/model/utils/hierarchy-keys.ts b/src/mol-data/structure/model/utils/hierarchy-keys.ts
index fe4391e42..06aa40957 100644
--- a/src/mol-data/structure/model/utils/hierarchy-keys.ts
+++ b/src/mol-data/structure/model/utils/hierarchy-keys.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Column from 'mol-base/collections/column'
+import { Column } from 'mol-base/collections/table'
import { Data, Segments, Keys } from '../properties/hierarchy'
import { Interval, Segmentation } from 'mol-base/collections/integer'
diff --git a/src/mol-io/reader/_spec/column.spec.ts b/src/mol-io/reader/_spec/column.spec.ts
index a0242c39f..556df5d9f 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 Column, { ColumnHelpers } from 'mol-base/collections/column'
+import { Column, ColumnHelpers } from 'mol-base/collections/table'
const lines = [
'1.123 abc',
diff --git a/src/mol-io/reader/cif/binary/field.ts b/src/mol-io/reader/cif/binary/field.ts
index 1a629ea2f..22165904c 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 Column, { ColumnHelpers } from 'mol-base/collections/column'
+import { Column, ColumnHelpers } from 'mol-base/collections/table'
import * as Data from '../data-model'
import { EncodedColumn } from './encoding'
import decode from './decoder'
diff --git a/src/mol-io/reader/cif/data-model.ts b/src/mol-io/reader/cif/data-model.ts
index bd8cf4ec7..4037ae87c 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 Column from 'mol-base/collections/column'
+import { Column } from 'mol-base/collections/table'
export interface File {
readonly name?: string,
diff --git a/src/mol-io/reader/cif/schema.ts b/src/mol-io/reader/cif/schema.ts
index 7984870d7..abc78e585 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 Column, { ColumnHelpers } from 'mol-base/collections/column'
-import Table from 'mol-base/collections/table'
+import { Table, Column, ColumnHelpers } from 'mol-base/collections/table'
export function toTypedFrame<Schema extends FrameSchema, Frame extends TypedFrame<Schema> = TypedFrame<Schema>>(schema: Schema, frame: Data.Frame): Frame {
return createTypedFrame(schema, frame) as Frame;
diff --git a/src/mol-io/reader/cif/text/field.ts b/src/mol-io/reader/cif/text/field.ts
index b124fed3c..6c1ad0fe4 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 Column, { ColumnHelpers } from 'mol-base/collections/column'
+import { Column, ColumnHelpers } from 'mol-base/collections/table'
import * as TokenColumn from '../../common/text/column/token'
import { Tokens } from '../../common/text/tokenizer'
import * as Data from '../data-model'
diff --git a/src/mol-io/reader/common/text/column/fixed.ts b/src/mol-io/reader/common/text/column/fixed.ts
index 2644ac70a..c9d4aa6a1 100644
--- a/src/mol-io/reader/common/text/column/fixed.ts
+++ b/src/mol-io/reader/common/text/column/fixed.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Column, { ColumnHelpers } from 'mol-base/collections/column'
+import { Column, ColumnHelpers } from 'mol-base/collections/table'
import { trimStr, Tokens } from '../tokenizer'
import { parseIntSkipLeadingWhitespace, parseFloatSkipLeadingWhitespace } from '../number-parser'
diff --git a/src/mol-io/reader/common/text/column/token.ts b/src/mol-io/reader/common/text/column/token.ts
index 21fd44a7a..7ed57ed1e 100644
--- a/src/mol-io/reader/common/text/column/token.ts
+++ b/src/mol-io/reader/common/text/column/token.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Column, { ColumnHelpers } from 'mol-base/collections/column'
+import { Column, ColumnHelpers } from 'mol-base/collections/table'
import { Tokens } from '../tokenizer'
import { parseInt as fastParseInt, parseFloat as fastParseFloat } from '../number-parser'
diff --git a/src/mol-io/reader/gro/parser.ts b/src/mol-io/reader/gro/parser.ts
index 68f05a9df..a257e5020 100644
--- a/src/mol-io/reader/gro/parser.ts
+++ b/src/mol-io/reader/gro/parser.ts
@@ -5,9 +5,9 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
+import { Column } from 'mol-base/collections/table'
import Tokenizer from '../common/text/tokenizer'
import FixedColumn from '../common/text/column/fixed'
-import Column from 'mol-base/collections/column'
import * as Schema from './schema'
import Result from '../result'
import Computation from 'mol-base/computation'
diff --git a/src/mol-io/reader/gro/schema.d.ts b/src/mol-io/reader/gro/schema.d.ts
index d5edb09da..fb2d454b7 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/table'
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 c99074e34..f092b0736 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/table'
// 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
diff --git a/src/perf-tests/column.ts b/src/perf-tests/column.ts
index d43a32a5c..2d0699c71 100644
--- a/src/perf-tests/column.ts
+++ b/src/perf-tests/column.ts
@@ -1,5 +1,5 @@
import * as B from 'benchmark'
-import C from 'mol-base/collections/column'
+import { Column as C } from 'mol-base/collections/table'
export namespace Column {
function createData(n: number) {
--
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