From 13e63cedf4566f60846b5682c86bd4385a9a2c19 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Mon, 5 Mar 2018 18:33:33 -0800
Subject: [PATCH] added 'list' column type
TODO handle in writer
---
src/mol-data/db/_spec/table.spec.ts | 12 +++++++++++-
src/mol-data/db/column.ts | 9 +++++++--
src/mol-io/reader/cif/binary/field.ts | 11 +++++++++--
src/mol-io/reader/cif/data-model.ts | 5 ++++-
src/mol-io/reader/cif/schema.ts | 4 +++-
src/mol-io/reader/cif/text/field.ts | 13 +++++++++++--
6 files changed, 45 insertions(+), 9 deletions(-)
diff --git a/src/mol-data/db/_spec/table.spec.ts b/src/mol-data/db/_spec/table.spec.ts
index 51965938a..76aae4de0 100644
--- a/src/mol-data/db/_spec/table.spec.ts
+++ b/src/mol-data/db/_spec/table.spec.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import * as ColumnHelpers from '../column-helpers'
@@ -11,6 +12,8 @@ import Table from '../table'
describe('column', () => {
const cc = Column.ofConst(10, 2, Column.Schema.int);
const arr = Column.ofArray({ array: [1, 2, 3, 4], schema: Column.Schema.int });
+ const arrNumberList = Column.ofArray({ array: [[1, 2], [3, 4], [5, 6]], schema: Column.Schema.List<number>() });
+ const arrStringList = Column.ofArray({ array: [['a', 'b'], ['c', 'd'], ['e', 'f']], schema: Column.Schema.List<string>() });
const arrWindow = Column.window(arr, 1, 3);
const typed = Column.ofArray({ array: new Int32Array([1, 2, 3, 4]), schema: Column.Schema.int });
@@ -30,6 +33,13 @@ describe('column', () => {
expect(arrWindow.rowCount).toBe(2);
});
+ it('arrList', () => {
+ expect(arrNumberList.rowCount).toBe(3);
+ expect(arrNumberList.value(1)).toEqual([3, 4]);
+ expect(arrStringList.rowCount).toBe(3);
+ expect(arrStringList.value(2)).toEqual(['e', 'f']);
+ });
+
it('typed', () => {
expect(typedWindow.value(0)).toBe(2);
expect(typedWindow.rowCount).toBe(2);
diff --git a/src/mol-data/db/column.ts b/src/mol-data/db/column.ts
index d94afadcd..db692ef06 100644
--- a/src/mol-data/db/column.ts
+++ b/src/mol-data/db/column.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import * as ColumnHelpers from './column-helpers'
@@ -22,7 +23,7 @@ interface Column<T> {
namespace Column {
export type ArrayCtor<T> = { new(size: number): ArrayLike<T> }
- export type Schema<T = any> = Schema.Str | Schema.Int | Schema.Float | Schema.Coordinate | Schema.Aliased<T> | Schema.Tensor
+ export type Schema<T = any> = Schema.Str | Schema.Int | Schema.Float | Schema.Coordinate | Schema.Aliased<T> | Schema.Tensor | Schema.List<number|string>
export namespace Schema {
// T also serves as a default value for undefined columns
@@ -35,6 +36,7 @@ namespace Column {
export type Tensor = { '@type': 'tensor', T: Tensors, space: Tensors.Space } & Base<'tensor'>
export type Aliased<T> = { '@type': 'aliased', T: T } & Base<'str' | 'int'>
+ export type List<T extends number|string> = { '@type': 'list', T: T[] } & Base<'list'>
export const str: Str = { '@type': 'str', T: '', valueType: 'str' };
export const int: Int = { '@type': 'int', T: 0, valueType: 'int' };
@@ -52,6 +54,9 @@ namespace Column {
if (typeof defaultValue !== 'undefined') return { ...t, T: defaultValue } as any as Aliased<T>;
return t as any as Aliased<T>;
}
+ export function List<T extends number|string>(defaultValue: T[] = []): List<T> {
+ return { '@type': 'list', T: defaultValue, valueType: 'list' }
+ }
}
export interface ToArrayParams<T> {
diff --git a/src/mol-io/reader/cif/binary/field.ts b/src/mol-io/reader/cif/binary/field.ts
index c3b2ad33f..854eaa550 100644
--- a/src/mol-io/reader/cif/binary/field.ts
+++ b/src/mol-io/reader/cif/binary/field.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Column, ColumnHelpers } from 'mol-data/db'
@@ -30,6 +31,10 @@ export default function Field(column: EncodedColumn): Data.Field {
? row => data[row]
: row => { const v = data[row]; return fastParseFloat(v, 0, v.length); };
+ const list: Data.Field['list'] = mask
+ ? row => mask[row] === Column.ValueKind.Present ? data[row] : []
+ : row => data[row];
+
const valueKind: Data.Field['valueKind'] = mask
? row => mask[row]
: row => Column.ValueKind.Present;
@@ -43,6 +48,7 @@ export default function Field(column: EncodedColumn): Data.Field {
str,
int,
float,
+ list,
valueKind,
areValuesEqual: (rowA, rowB) => data[rowA] === data[rowB],
toStringArray: params => ColumnHelpers.createAndFillArray(rowCount, str, params),
@@ -51,6 +57,7 @@ export default function Field(column: EncodedColumn): Data.Field {
: params => ColumnHelpers.createAndFillArray(rowCount, int, params),
toFloatArray: isNumeric
? params => ColumnHelpers.typedArrayWindow(data, params)
- : params => ColumnHelpers.createAndFillArray(rowCount, float, params)
+ : params => ColumnHelpers.createAndFillArray(rowCount, float, params),
+ toListArray: params => ColumnHelpers.createAndFillArray(rowCount, list, 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 417692342..28299b659 100644
--- a/src/mol-io/reader/cif/data-model.ts
+++ b/src/mol-io/reader/cif/data-model.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Column } from 'mol-data/db'
@@ -67,6 +68,7 @@ export interface Field {
str(row: number): string,
int(row: number): number,
float(row: number): number,
+ list<T extends number|string>(row: number): T[],
valueKind(row: number): Column.ValueKind,
@@ -75,6 +77,7 @@ export interface Field {
toStringArray(params?: Column.ToArrayParams<string>): ReadonlyArray<string>,
toIntArray(params?: Column.ToArrayParams<number>): ReadonlyArray<number>,
toFloatArray(params?: Column.ToArrayParams<number>): ReadonlyArray<number>
+ toListArray<T extends number|string>(params?: Column.ToArrayParams<T[]>): ReadonlyArray<T[]>
}
export function getTensor(category: Category, field: string, space: Tensor.Space, row: number): Tensor {
diff --git a/src/mol-io/reader/cif/schema.ts b/src/mol-io/reader/cif/schema.ts
index 1be7563d4..e3bb62f3e 100644
--- a/src/mol-io/reader/cif/schema.ts
+++ b/src/mol-io/reader/cif/schema.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Database, Table, Column, ColumnHelpers } from 'mol-data/db'
@@ -23,6 +24,7 @@ function getColumnCtor(t: Column.Schema): ColumnCtor {
case 'str': return (f, c, k) => createColumn(t, f, f.str, f.toStringArray);
case 'int': return (f, c, k) => createColumn(t, f, f.int, f.toIntArray);
case 'float': return (f, c, k) => createColumn(t, f, f.float, f.toFloatArray);
+ case 'list': return (f, c, k) => createColumn(t, f, f.list, f.toListArray);
case 'tensor': throw new Error(`Use createTensorColumn instead.`);
}
}
diff --git a/src/mol-io/reader/cif/text/field.ts b/src/mol-io/reader/cif/text/field.ts
index 6d1888494..a1c929cba 100644
--- a/src/mol-io/reader/cif/text/field.ts
+++ b/src/mol-io/reader/cif/text/field.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Column, ColumnHelpers } from 'mol-data/db'
@@ -27,6 +28,12 @@ export default function CifTextField(tokens: Tokens, rowCount: number): Data.Fie
return fastParseFloat(data, indices[2 * row], indices[2 * row + 1]) || 0;
};
+ const list: Data.Field['list'] = <T extends string|number>(row: number) => {
+ const ret = data.substring(indices[2 * row], indices[2 * row + 1]);
+ if (ret === '.' || ret === '?') return [];
+ return ret.split(',') as T[];
+ };
+
const valueKind: Data.Field['valueKind'] = row => {
const s = indices[2 * row];
if (indices[2 * row + 1] - s !== 1) return Column.ValueKind.Present;
@@ -43,10 +50,12 @@ export default function CifTextField(tokens: Tokens, rowCount: number): Data.Fie
str,
int,
float,
+ list,
valueKind,
areValuesEqual: TokenColumn.areValuesEqualProvider(tokens),
toStringArray: params => ColumnHelpers.createAndFillArray(rowCount, str, params),
toIntArray: params => ColumnHelpers.createAndFillArray(rowCount, int, params),
- toFloatArray: params => ColumnHelpers.createAndFillArray(rowCount, float, params)
+ toFloatArray: params => ColumnHelpers.createAndFillArray(rowCount, float, params),
+ toListArray: params => ColumnHelpers.createAndFillArray(rowCount, list, params)
}
}
\ No newline at end of file
--
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