From 727a75ee6a61075b24857b828e7c7b7944f30088 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Tue, 7 Nov 2017 23:49:00 +0100
Subject: [PATCH] ability to specify default value in column schema
---
src/mol-data/db/column.ts | 18 +++++++++++++-----
src/mol-io/reader/cif/schema/mmcif.ts | 16 ++++++++--------
src/mol-model/structure/model/formats/mmcif.ts | 2 +-
.../structure/model/properties/hierarchy.ts | 2 +-
4 files changed, 23 insertions(+), 15 deletions(-)
diff --git a/src/mol-data/db/column.ts b/src/mol-data/db/column.ts
index b65e45d0c..54fe666de 100644
--- a/src/mol-data/db/column.ts
+++ b/src/mol-data/db/column.ts
@@ -25,6 +25,8 @@ namespace Column {
export type Schema<T = any> = Schema.Str | Schema.Int | Schema.Float | Schema.Coordinate | Schema.Aliased<T> | Schema.Tensor
export namespace Schema {
+ // T also serves as a default value for undefined columns
+
type Base<T extends string> = { valueType: T }
export type Str = { '@type': 'str', T: string } & Base<'str'>
export type Int = { '@type': 'int', T: number } & Base<'int'>
@@ -39,11 +41,17 @@ namespace Column {
export const coord: Coordinate = { '@type': 'coord', T: 0, valueType: 'float' };
export const float: Float = { '@type': 'float', T: 0, valueType: 'float' };
- export function tensor(space: Tensors.Space): Tensor { return { '@type': 'tensor', T: space.create(), space, valueType: 'tensor' }; }
- export function vector(dim: number): Tensor { return tensor(Tensors.Vector(dim)); }
- export function matrix(rows: number, cols: number): Tensor { return tensor(Tensors.ColumnMajorMatrix(rows, cols)); }
-
- export function aliased<T>(t: Str | Int): Aliased<T> { return t as any as Aliased<T>; }
+ export function Str(defaultValue = ''): Str { return { '@type': 'str', T: defaultValue, valueType: 'str' } };
+ export function Int(defaultValue = 0): Int { return { '@type': 'int', T: defaultValue, valueType: 'int' } };
+ export function Float(defaultValue = 0): Float { return { '@type': 'float', T: defaultValue, valueType: 'float' } };
+ export function Tensor(space: Tensors.Space): Tensor { return { '@type': 'tensor', T: space.create(), space, valueType: 'tensor' }; }
+ export function Vector(dim: number): Tensor { return Tensor(Tensors.Vector(dim)); }
+ export function Matrix(rows: number, cols: number): Tensor { return Tensor(Tensors.ColumnMajorMatrix(rows, cols)); }
+
+ export function Aliased<T>(t: Str | Int, defaultValue?: T): Aliased<T> {
+ if (typeof defaultValue !== 'undefined') return { ...t, T: defaultValue } as any as Aliased<T>;
+ return t as any as Aliased<T>;
+ }
}
export interface ToArrayParams<T> {
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index 13ff7ade9..62f3a395c 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -20,7 +20,7 @@ type EntityType = 'polymer' | 'non-polymer' | 'water' | 'macrolide'
const entity = {
id: str,
- type: Schema.aliased<EntityType>(str),
+ type: Schema.Aliased<EntityType>(str),
src_method: str,
pdbx_description: str,
formula_weight: float,
@@ -119,7 +119,7 @@ type BondValueOrder =
const struct_conn = {
id: str,
- conn_type_id: Schema.aliased<StructConnTypeId>(str),
+ conn_type_id: Schema.Aliased<StructConnTypeId>(str),
pdbx_PDB_id: str,
ptnr1_label_asym_id: str,
ptnr1_label_comp_id: str,
@@ -150,11 +150,11 @@ const struct_conn = {
pdbx_ptnr3_PDB_ins_code: str,
details: str,
pdbx_dist_value: float,
- pdbx_value_order: Schema.aliased<BondValueOrder>(str)
+ pdbx_value_order: Schema.Aliased<BondValueOrder>(str)
}
const struct_conn_type = {
- id: Schema.aliased<StructConnTypeId>(str),
+ id: Schema.Aliased<StructConnTypeId>(str),
criteria: str,
reference: str
}
@@ -163,10 +163,10 @@ const chem_comp_bond = {
comp_id: str,
pdbx_stereo_config: str,
pdbx_ordinal: int,
- pdbx_aromatic_flag: Schema.aliased<'Y' | 'N'>(str),
+ pdbx_aromatic_flag: Schema.Aliased<'Y' | 'N'>(str),
atom_id_1: str,
atom_id_2: str,
- value_order: Schema.aliased<BondValueOrder>(str)
+ value_order: Schema.Aliased<BondValueOrder>(str)
}
const pdbx_struct_assembly = {
@@ -188,8 +188,8 @@ const pdbx_struct_oper_list = {
type: str,
name: str,
symmetry_operation: str,
- matrix: Schema.matrix(3, 3),
- vector: Schema.vector(3)
+ matrix: Schema.Matrix(3, 3),
+ vector: Schema.Vector(3)
}
const pdbx_struct_mod_residue = {
diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index aca855e52..b0f421ca8 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -48,7 +48,7 @@ function createHierarchyData({ data }: mmCIF_Format, bounds: Interval, offsets:
const { atom_site } = data;
const start = Interval.start(bounds), end = Interval.end(bounds);
const atoms = Table.ofColumns(Hierarchy.AtomsSchema, {
- type_symbol: Column.ofArray({ array: Column.mapToArray(Column.window(atom_site.type_symbol, start, end), ElementSymbol), schema: Column.Schema.aliased<ElementSymbol>(Column.Schema.str) }),
+ type_symbol: Column.ofArray({ array: Column.mapToArray(Column.window(atom_site.type_symbol, start, end), ElementSymbol), schema: Column.Schema.Aliased<ElementSymbol>(Column.Schema.str) }),
label_atom_id: Column.window(atom_site.label_atom_id, start, end),
auth_atom_id: Column.window(atom_site.auth_atom_id, start, end),
label_alt_id: Column.window(atom_site.label_alt_id, start, end),
diff --git a/src/mol-model/structure/model/properties/hierarchy.ts b/src/mol-model/structure/model/properties/hierarchy.ts
index f3bec187d..92d5f006a 100644
--- a/src/mol-model/structure/model/properties/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/hierarchy.ts
@@ -10,7 +10,7 @@ import { mmCIF_Schema as mmCIF } from 'mol-io/reader/cif/schema/mmcif'
import { ElementSymbol} from '../types'
export const AtomsSchema = {
- type_symbol: Column.Schema.aliased<ElementSymbol>(mmCIF.atom_site.type_symbol),
+ type_symbol: Column.Schema.Aliased<ElementSymbol>(mmCIF.atom_site.type_symbol),
label_atom_id: mmCIF.atom_site.label_atom_id,
auth_atom_id: mmCIF.atom_site.auth_atom_id,
label_alt_id: mmCIF.atom_site.label_alt_id,
--
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