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Commit c5b1b84e authored by David Sehnal's avatar David Sehnal
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Data model improvements

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src/reader/cif/data-model.ts
+ 22
− 4
View file @ c5b1b84e
...@@ -60,9 +60,27 @@ export interface Field { ...@@ -60,9 +60,27 @@ export interface Field {
presence(row: number): ValuePresence, presence(row: number): ValuePresence,
areValuesEqual(rowA: number, rowB: number): boolean, areValuesEqual(rowA: number, rowB: number): boolean,
stringEquals(row: number, value: string | null): boolean, stringEquals(row: number, value: string): boolean,
toStringArray(ctor?: (size: number) => Column.ArrayType, startRow?: number, endRowExclusive?: number): ReadonlyArray<string>, toStringArray(params?: Column.ToArrayParams): ReadonlyArray<string>,
toIntArray(ctor?: (size: number) => Column.ArrayType, startRow?: number, endRowExclusive?: number): ReadonlyArray<number>, toIntArray(params?: Column.ToArrayParams): ReadonlyArray<number>,
toFloatArray(ctor?: (size: number) => Column.ArrayType, startRow?: number, endRowExclusive?: number): ReadonlyArray<number> toFloatArray(params?: Column.ToArrayParams): ReadonlyArray<number>
}
export function DefaultUndefinedField(rowCount: number): Field {
return {
isDefined: false,
rowCount,
str: row => '',
int: row => 0,
float: row => 0,
presence: row => ValuePresence.NotSpecified,
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
};
} }
\ No newline at end of file
src/reader/cif/schema.ts
+ 23
− 33
View file @ c5b1b84e
...@@ -48,55 +48,45 @@ export type Category<Fields> = Fields & { ...@@ -48,55 +48,45 @@ export type Category<Fields> = Fields & {
export namespace Category { export namespace Category {
export type Schema = { '@alias'?: string } & { [field: string]: Field.Schema<any> } export type Schema = { '@alias'?: string } & { [field: string]: Field.Schema<any> }
export type Instance<T extends Schema> = Category<{ [F in keyof T]: Field<T[F]['type']> }> export type Instance<T extends Schema> = Category<{ [F in keyof T]: Column.Column<T[F]['type']> }>
} }
export interface Field<T> { // export interface Field<T> {
readonly isDefined: boolean, // readonly isDefined: boolean,
value(row: number): T, // value(row: number): T,
presence(row: number): Data.ValuePresence, // presence(row: number): Data.ValuePresence,
areValuesEqual(rowA: number, rowB: number): boolean, // areValuesEqual(rowA: number, rowB: number): boolean,
stringEquals(row: number, value: string | null): boolean, // stringEquals(row: number, value: string | null): boolean,
/** Converts the selected row range to an array. ctor might or might not be called depedning on the source data format. */ // /** Converts the selected row range to an array. ctor might or might not be called depedning on the source data format. */
toArray(ctor?: (size: number) => Column.ArrayType, startRow?: number, endRowExclusive?: number): ReadonlyArray<T> | undefined // toArray(params?: Column.ToArrayParams): ReadonlyArray<T>
} // }
export namespace Field { export namespace Field {
export interface Schema<T> { type: T, ctor: (field: Data.Field) => Field<T>, undefinedField: (c: number) => Data.Field, alias?: string }; export interface Schema<T> { type: T, ctor: (field: Data.Field) => Column.Column<T>, undefinedField: (c: number) => Data.Field, alias?: string };
export interface Spec { undefinedField?: (c: number) => Data.Field, alias?: string } export interface Spec { undefinedField?: (c: number) => Data.Field, alias?: string }
export function str(spec?: Spec) { return createSchema(spec, Str); } export function str(spec?: Spec) { return createSchema(spec, Str); }
export function int(spec?: Spec) { return createSchema(spec, Int); } export function int(spec?: Spec) { return createSchema(spec, Int); }
export function float(spec?: Spec) { return createSchema(spec, Float); } export function float(spec?: Spec) { return createSchema(spec, Float); }
function create<T>(field: Data.Field, value: (row: number) => T, toArray: Field<T>['toArray']): Field<T> { function create<T>(field: Data.Field, value: (row: number) => T, toArray: Column.Column<T>['toArray']): Column.Column<T> {
return { isDefined: field.isDefined, value, presence: field.presence, areValuesEqual: field.areValuesEqual, stringEquals: field.stringEquals, toArray }; const presence = field.presence;
return {
isDefined: field.isDefined,
rowCount: field.rowCount,
value,
isValueDefined: row => presence(row) === Data.ValuePresence.Present,
areValuesEqual: field.areValuesEqual,
toArray
};
} }
function Str(field: Data.Field) { return create(field, field.str, field.toStringArray); } function Str(field: Data.Field) { return create(field, field.str, field.toStringArray); }
function Int(field: Data.Field) { return create(field, field.int, field.toIntArray); } function Int(field: Data.Field) { return create(field, field.int, field.toIntArray); }
function Float(field: Data.Field) { return create(field, field.float, field.toFloatArray); } function Float(field: Data.Field) { return create(field, field.float, field.toFloatArray); }
function defaultUndefined(rowCount: number): Data.Field { function createSchema<T>(spec: Spec | undefined, ctor: (field: Data.Field) => Column.Column<T>): Schema<T> {
return { return { type: 0 as any, ctor, undefinedField: (spec && spec.undefinedField) || Data.DefaultUndefinedField, alias: spec && spec.alias };
isDefined: false,
rowCount,
str: row => '',
int: row => 0,
float: row => 0,
presence: row => Data.ValuePresence.NotSpecified,
areValuesEqual: (rowA, rowB) => true,
stringEquals: (row, value) => value === null,
toStringArray: (ctor, s, e) => Column.createArray(rowCount, ctor, s, e).array,
toIntArray: (ctor, s, e) => Column.createArray(rowCount, ctor, s, e).array,
toFloatArray: (ctor, s, e) => Column.createArray(rowCount, ctor, s, e).array
};
}
function createSchema<T>(spec: Spec | undefined, ctor: (field: Data.Field) => Field<T>): Schema<T> {
return { type: 0 as any, ctor, undefinedField: (spec && spec.undefinedField) || defaultUndefined, alias: spec && spec.alias };
} }
} }
......
src/reader/cif/text-field.ts
+ 8
− 8
View file @ c5b1b84e
...@@ -42,7 +42,7 @@ export default function CifTextField(data: string, tokens: ArrayLike<number>, ro ...@@ -42,7 +42,7 @@ export default function CifTextField(data: string, tokens: ArrayLike<number>, ro
int, int,
float, float,
presence, presence,
areValuesEqual: (rowA, rowB) => { areValuesEqual(rowA, rowB) {
const aS = tokens[2 * rowA], bS = tokens[2 * rowB]; const aS = tokens[2 * rowA], bS = tokens[2 * rowB];
const len = tokens[2 * rowA + 1] - aS; const len = tokens[2 * rowA + 1] - aS;
if (len !== tokens[2 * rowB + 1] - bS) return false; if (len !== tokens[2 * rowB + 1] - bS) return false;
...@@ -53,7 +53,7 @@ export default function CifTextField(data: string, tokens: ArrayLike<number>, ro ...@@ -53,7 +53,7 @@ export default function CifTextField(data: string, tokens: ArrayLike<number>, ro
} }
return true; return true;
}, },
stringEquals: (row, value) => { stringEquals(row, value) {
const s = tokens[2 * row]; const s = tokens[2 * row];
if (!value) return presence(row) !== Data.ValuePresence.Present; if (!value) return presence(row) !== Data.ValuePresence.Present;
const len = value.length; const len = value.length;
...@@ -63,16 +63,16 @@ export default function CifTextField(data: string, tokens: ArrayLike<number>, ro ...@@ -63,16 +63,16 @@ export default function CifTextField(data: string, tokens: ArrayLike<number>, ro
} }
return true; return true;
}, },
toStringArray: (ctor, s, e) => { toStringArray(params) {
const { array, start } = Column.createArray(rowCount, ctor, s, e); const { array, start } = Column.createArray(rowCount, params);
return fillArrayValues(str, array, start); return fillArrayValues(str, array, start);
}, },
toIntArray: (ctor, s, e) => { toIntArray(params) {
const { array, start } = Column.createArray(rowCount, ctor, s, e); const { array, start } = Column.createArray(rowCount, params);
return fillArrayValues(int, array, start); return fillArrayValues(int, array, start);
}, },
toFloatArray: (ctor, s, e) => { toFloatArray(params) {
const { array, start } = Column.createArray(rowCount, ctor, s, e); const { array, start } = Column.createArray(rowCount, params);
return fillArrayValues(float, array, start); return fillArrayValues(float, array, start);
} }
} }
......
src/reader/common/column.ts
+ 20
− 8
View file @ c5b1b84e
...@@ -4,7 +4,6 @@ ...@@ -4,7 +4,6 @@
* @author David Sehnal <david.sehnal@gmail.com> * @author David Sehnal <david.sehnal@gmail.com>
*/ */
export type ArrayType = string[] | number[] | Float32Array | Float64Array | Int8Array | Int16Array | Int32Array | Uint8Array | Uint16Array | Uint32Array
export type ColumnType = typeof ColumnType.str | typeof ColumnType.pooledStr | typeof ColumnType.int | typeof ColumnType.float export type ColumnType = typeof ColumnType.str | typeof ColumnType.pooledStr | typeof ColumnType.int | typeof ColumnType.float
export namespace ColumnType { export namespace ColumnType {
...@@ -14,11 +13,21 @@ export namespace ColumnType { ...@@ -14,11 +13,21 @@ export namespace ColumnType {
export const float = { '@type': 0 as number, kind: 'float' as 'float' }; export const float = { '@type': 0 as number, kind: 'float' as 'float' };
} }
export interface ToArrayParams {
array?: { new(size: number): ArrayLike<number> },
/** First row */
start?: number,
/** Last row (exclusive) */
end?: number
}
export interface Column<T> { export interface Column<T> {
readonly isDefined: boolean, readonly isDefined: boolean,
readonly rowCount: number, readonly rowCount: number,
value(row: number): T, value(row: number): T,
toArray(ctor?: (size: number) => ArrayType, startRow?: number, endRowExclusive?: number): ReadonlyArray<T> isValueDefined(row: number): boolean,
toArray(params?: ToArrayParams): ReadonlyArray<T>,
areValuesEqual(rowA: number, rowB: number): boolean
} }
export function UndefinedColumn<T extends ColumnType>(rowCount: number, type: T): Column<T['@type']> { export function UndefinedColumn<T extends ColumnType>(rowCount: number, type: T): Column<T['@type']> {
...@@ -27,18 +36,21 @@ export function UndefinedColumn<T extends ColumnType>(rowCount: number, type: T) ...@@ -27,18 +36,21 @@ export function UndefinedColumn<T extends ColumnType>(rowCount: number, type: T)
isDefined: false, isDefined: false,
rowCount, rowCount,
value, value,
toArray(ctor, s, e) { isValueDefined(row) { return false; },
const { array } = createArray(rowCount, ctor, s, e); toArray(params) {
const { array } = createArray(rowCount, params);
for (let i = 0, _i = array.length; i < _i; i++) array[i] = value(0) for (let i = 0, _i = array.length; i < _i; i++) array[i] = value(0)
return array; return array;
} },
areValuesEqual() { return true; }
} }
} }
/** A helped function for Column.toArray */ /** A helped function for Column.toArray */
export function createArray(rowCount: number, ctor?: (size: number) => ArrayType, start?: number, end?: number) { export function createArray(rowCount: number, params?: ToArrayParams) {
const c = typeof ctor !== 'undefined' ? ctor : (s: number) => new Array(s); const { array, start, end } = params || ({} as ToArrayParams);
const c = typeof array !== 'undefined' ? array : Array;
const s = typeof start !== 'undefined' ? Math.max(Math.min(start, rowCount - 1), 0) : 0; const s = typeof start !== 'undefined' ? Math.max(Math.min(start, rowCount - 1), 0) : 0;
const e = typeof end !== 'undefined' ? Math.min(end, rowCount) : rowCount; const e = typeof end !== 'undefined' ? Math.min(end, rowCount) : rowCount;
return { array: c(e - s) as any[], start: s, end: e }; return { array: new c(e - s) as any[], start: s, end: e };
} }
\ No newline at end of file
src/reader/common/text/column/fixed.ts
+ 17
− 19
View file @ c5b1b84e
...@@ -5,19 +5,13 @@ ...@@ -5,19 +5,13 @@
*/ */
import { Column, ColumnType, createArray } from '../../column' import { Column, ColumnType, createArray } from '../../column'
import { trimStr } from '../tokenizer' import { trimStr, Lines } from '../tokenizer'
import { parseIntSkipLeadingWhitespace, parseFloatSkipLeadingWhitespace } from '../number-parser' import { parseIntSkipLeadingWhitespace, parseFloatSkipLeadingWhitespace } from '../number-parser'
import StringPool from '../../../../utils/short-string-pool' import StringPool from '../../../../utils/short-string-pool'
export interface FixedColumnInfo { export default function FixedColumnProvider(lines: Lines) {
data: string,
lines: ArrayLike<number>,
rowCount: number
}
export default function FixedColumnProvider(info: FixedColumnInfo) {
return function<T extends ColumnType>(offset: number, width: number, type: T) { return function<T extends ColumnType>(offset: number, width: number, type: T) {
return FixedColumn(info, offset, width, type); return FixedColumn(lines, offset, width, type);
} }
} }
...@@ -26,39 +20,43 @@ function fillArrayValues(value: (row: number) => any, target: any[], start: numb ...@@ -26,39 +20,43 @@ function fillArrayValues(value: (row: number) => any, target: any[], start: numb
return target; return target;
} }
export function FixedColumn<T extends ColumnType>(info: FixedColumnInfo, offset: number, width: number, type: T): Column<T['@type']> { export function FixedColumn<T extends ColumnType>(lines: Lines, offset: number, width: number, type: T): Column<T['@type']> {
const { data, lines, rowCount } = info; const { data, tokens, count: rowCount } = lines;
const { kind } = type; const { kind } = type;
const pool = kind === 'pooled-str' ? StringPool.create() : void 0; const pool = kind === 'pooled-str' ? StringPool.create() : void 0;
const value: Column<T['@type']>['value'] = kind === 'str' ? row => { const value: Column<T['@type']>['value'] = kind === 'str' ? row => {
let s = lines[2 * row] + offset, le = lines[2 * row + 1]; let s = tokens[2 * row] + offset, le = tokens[2 * row + 1];
if (s >= le) return ''; if (s >= le) return '';
let e = s + width; let e = s + width;
if (e > le) e = le; if (e > le) e = le;
return trimStr(data, s, e); return trimStr(data, s, e);
} : kind === 'pooled-str' ? row => { } : kind === 'pooled-str' ? row => {
let s = lines[2 * row] + offset, le = lines[2 * row + 1]; let s = tokens[2 * row] + offset, le = tokens[2 * row + 1];
if (s >= le) return ''; if (s >= le) return '';
let e = s + width; let e = s + width;
if (e > le) e = le; if (e > le) e = le;
return StringPool.get(pool!, trimStr(data, s, e)); return StringPool.get(pool!, trimStr(data, s, e));
} : kind === 'int' ? row => { } : kind === 'int' ? row => {
const s = lines[2 * row] + offset; const s = tokens[2 * row] + offset;
if (s > lines[2 * row + 1]) return 0; if (s > tokens[2 * row + 1]) return 0;
return parseIntSkipLeadingWhitespace(data, s, s + width); return parseIntSkipLeadingWhitespace(data, s, s + width);
} : row => { } : row => {
const s = lines[2 * row] + offset; const s = tokens[2 * row] + offset;
if (s > lines[2 * row + 1]) return 0; if (s > tokens[2 * row + 1]) return 0;
return parseFloatSkipLeadingWhitespace(data, s, s + width); return parseFloatSkipLeadingWhitespace(data, s, s + width);
}; };
return { return {
isDefined: true, isDefined: true,
rowCount, rowCount,
value, value,
toArray(ctor, s, e) { isValueDefined(row) { return true; },
const { array, start } = createArray(rowCount, ctor, s, e); toArray(params) {
const { array, start } = createArray(rowCount, params);
return fillArrayValues(value, array, start); return fillArrayValues(value, array, start);
},
areValuesEqual(rowA, rowB) {
return value(rowA) === value(rowB);
} }
}; };
} }
\ No newline at end of file
src/reader/common/text/tokenizer.ts
+ 118
− 104
View file @ c5b1b84e
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de> * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/ */
export interface State<TokenType = any> { export interface Tokenizer {
data: string data: string
position: number position: number
...@@ -15,132 +15,150 @@ export interface State<TokenType = any> { ...@@ -15,132 +15,150 @@ export interface State<TokenType = any> {
currentLineNumber: number currentLineNumber: number
currentTokenStart: number currentTokenStart: number
currentTokenEnd: number currentTokenEnd: number
}
currentTokenType: TokenType export interface Lines {
data: string,
count: number,
tokens: ArrayLike<number>
} }
export function State<TokenType>(data: string, initialTokenType?: TokenType): State<TokenType> { export function Tokenizer(data: string): Tokenizer {
return { return {
data, data,
position: 0, position: 0,
length: data.length, length: data.length,
currentLineNumber: 1, currentLineNumber: 1,
currentTokenStart: 0, currentTokenStart: 0,
currentTokenEnd: 0, currentTokenEnd: 0
currentTokenType: initialTokenType!
}; };
} }
export function getTokenString(state: State) { export namespace Tokenizer {
return state.data.substring(state.currentTokenStart, state.currentTokenEnd);
}
/** export function getTokenString(state: Tokenizer) {
* Eat everything until a newline occurs. return state.data.substring(state.currentTokenStart, state.currentTokenEnd);
*/ }
export function eatLine(state: State) {
const { data } = state; /**
while (state.position < state.length) { * Eat everything until a newline occurs.
switch (data.charCodeAt(state.position)) { */
case 10: // \n export function eatLine(state: Tokenizer) {
state.currentTokenEnd = state.position; const { data } = state;
++state.position; while (state.position < state.length) {
++state.currentLineNumber; switch (data.charCodeAt(state.position)) {
return; case 10: // \n
case 13: // \r state.currentTokenEnd = state.position;
state.currentTokenEnd = state.position; ++state.position;
++state.position; ++state.currentLineNumber;
++state.currentLineNumber; return;
if (data.charCodeAt(state.position) === 10) { case 13: // \r
state.currentTokenEnd = state.position;
++state.position;
++state.currentLineNumber;
if (data.charCodeAt(state.position) === 10) {
++state.position;
}
return;
default:
++state.position; ++state.position;
} break;
return; }
default:
++state.position;
break;
} }
state.currentTokenEnd = state.position;
} }
state.currentTokenEnd = state.position;
}
/** Sets the current token start to the current position */ /** Sets the current token start to the current position */
export function markStart(state: State) { export function markStart(state: Tokenizer) {
state.currentTokenStart = state.position; state.currentTokenStart = state.position;
} }
/** Sets the current token start to current position and moves to the next line. */ /** Sets the current token start to current position and moves to the next line. */
export function markLine(state: State) { export function markLine(state: Tokenizer) {
state.currentTokenStart = state.position; state.currentTokenStart = state.position;
eatLine(state); eatLine(state);
} }
/** /** Advance the state by the given number of lines and return line starts/ends as tokens. */
* Eat everything until a whitespace/newline occurs. export function readLines(state: Tokenizer, count: number): Lines {
*/ const lineTokens = Tokens.create(count * 2);
export function eatValue(state: State) {
while (state.position < state.length) { for (let i = 0; i < count; i++) {
switch (state.data.charCodeAt(state.position)) { markLine(state);
case 9: // \t Tokens.addUnchecked(lineTokens, state.currentTokenStart, state.currentTokenEnd);
case 10: // \n }
case 13: // \r
case 32: // ' ' return { data: state.data, count, tokens: lineTokens.indices };
state.currentTokenEnd = state.position; }
return;
default: /**
++state.position; * Eat everything until a whitespace/newline occurs.
break; */
export function eatValue(state: Tokenizer) {
while (state.position < state.length) {
switch (state.data.charCodeAt(state.position)) {
case 9: // \t
case 10: // \n
case 13: // \r
case 32: // ' '
state.currentTokenEnd = state.position;
return;
default:
++state.position;
break;
}
} }
state.currentTokenEnd = state.position;
} }
state.currentTokenEnd = state.position;
}
/** /**
* Skips all the whitespace - space, tab, newline, CR * Skips all the whitespace - space, tab, newline, CR
* Handles incrementing line count. * Handles incrementing line count.
*/ */
export function skipWhitespace(state: State): number { export function skipWhitespace(state: Tokenizer): number {
let prev = 10; let prev = 10;
while (state.position < state.length) { while (state.position < state.length) {
let c = state.data.charCodeAt(state.position); let c = state.data.charCodeAt(state.position);
switch (c) { switch (c) {
case 9: // '\t' case 9: // '\t'
case 32: // ' ' case 32: // ' '
prev = c; prev = c;
++state.position; ++state.position;
break; break;
case 10: // \n case 10: // \n
// handle \r\n // handle \r\n
if (prev !== 13) { if (prev !== 13) {
++state.currentLineNumber;
}
prev = c;
++state.position;
break;
case 13: // \r
prev = c;
++state.position;
++state.currentLineNumber; ++state.currentLineNumber;
} break;
prev = c; default:
++state.position; return prev;
break; }
case 13: // \r
prev = c;
++state.position;
++state.currentLineNumber;
break;
default:
return prev;
} }
return prev;
} }
return prev;
}
/** Trims spaces and tabs */ /** Trims spaces and tabs */
export function trim(state: State, start: number, end: number) { export function trim(state: Tokenizer, start: number, end: number) {
const { data } = state; const { data } = state;
let s = start, e = end - 1; let s = start, e = end - 1;
let c = data.charCodeAt(s); let c = data.charCodeAt(s);
while ((c === 9 || c === 32) && s <= e) c = data.charCodeAt(++s); while ((c === 9 || c === 32) && s <= e) c = data.charCodeAt(++s);
c = data.charCodeAt(e); c = data.charCodeAt(e);
while ((c === 9 || c === 32) && e >= s) c = data.charCodeAt(--e); while ((c === 9 || c === 32) && e >= s) c = data.charCodeAt(--e);
state.currentTokenStart = s; state.currentTokenStart = s;
state.currentTokenEnd = e + 1; state.currentTokenEnd = e + 1;
state.position = end; state.position = end;
}
} }
export function trimStr(data: string, start: number, end: number) { export function trimStr(data: string, start: number, end: number) {
...@@ -189,8 +207,4 @@ export namespace Tokens { ...@@ -189,8 +207,4 @@ export namespace Tokens {
} }
} }
export default Tokenizer
/** \ No newline at end of file
* A helper for building a typed array of token indices.
*/
export default Tokens
\ No newline at end of file
src/reader/gro/parser.ts
+ 17
− 22
View file @ c5b1b84e
...@@ -5,14 +5,14 @@ ...@@ -5,14 +5,14 @@
* @author David Sehnal <david.sehnal@gmail.com> * @author David Sehnal <david.sehnal@gmail.com>
*/ */
import { State as TokenizerState, Tokens, markLine, getTokenString } from '../common/text/tokenizer' import Tokenizer from '../common/text/tokenizer'
import FixedColumn from '../common/text/column/fixed' import FixedColumn from '../common/text/column/fixed'
import { ColumnType, UndefinedColumn } from '../common/column' import { ColumnType, UndefinedColumn } from '../common/column'
import * as Schema from './schema' import * as Schema from './schema'
import Result from '../result' import Result from '../result'
interface State { interface State {
tokenizer: TokenizerState, tokenizer: Tokenizer,
header: Schema.Header, header: Schema.Header,
numberOfAtoms: number, numberOfAtoms: number,
} }
...@@ -27,7 +27,7 @@ function createEmptyHeader(): Schema.Header { ...@@ -27,7 +27,7 @@ function createEmptyHeader(): Schema.Header {
}; };
} }
function createState(tokenizer: TokenizerState): State { function State(tokenizer: Tokenizer): State {
return { return {
tokenizer, tokenizer,
header: createEmptyHeader(), header: createEmptyHeader(),
...@@ -40,14 +40,14 @@ function createState(tokenizer: TokenizerState): State { ...@@ -40,14 +40,14 @@ function createState(tokenizer: TokenizerState): State {
*/ */
function handleTitleString(state: State) { function handleTitleString(state: State) {
const { tokenizer, header } = state; const { tokenizer, header } = state;
markLine(tokenizer); Tokenizer.markLine(tokenizer);
let line = getTokenString(tokenizer); let line = Tokenizer.getTokenString(tokenizer);
// skip potential empty lines... // skip potential empty lines...
if (line.trim().length === 0) { if (line.trim().length === 0) {
markLine(tokenizer); Tokenizer.markLine(tokenizer);
line = getTokenString(tokenizer); line = Tokenizer.getTokenString(tokenizer);
} }
const timeOffset = line.lastIndexOf('t='); const timeOffset = line.lastIndexOf('t=');
...@@ -67,8 +67,8 @@ function handleTitleString(state: State) { ...@@ -67,8 +67,8 @@ function handleTitleString(state: State) {
*/ */
function handleNumberOfAtoms(state: State) { function handleNumberOfAtoms(state: State) {
const { tokenizer } = state; const { tokenizer } = state;
markLine(tokenizer); Tokenizer.markLine(tokenizer);
const line = getTokenString(tokenizer); const line = Tokenizer.getTokenString(tokenizer);
state.numberOfAtoms = parseInt(line); state.numberOfAtoms = parseInt(line);
} }
...@@ -90,17 +90,12 @@ function handleNumberOfAtoms(state: State) { ...@@ -90,17 +90,12 @@ function handleNumberOfAtoms(state: State) {
*/ */
function handleAtoms(state: State): Schema.Atoms { function handleAtoms(state: State): Schema.Atoms {
const { tokenizer, numberOfAtoms } = state; const { tokenizer, numberOfAtoms } = state;
const lineTokens = Tokens.create(numberOfAtoms * 2); const lines = Tokenizer.readLines(tokenizer, numberOfAtoms);
for (let i = 0; i < numberOfAtoms; i++) { const positionSample = tokenizer.data.substring(lines.tokens[0], lines.tokens[1]).substring(20);
markLine(tokenizer);
Tokens.addUnchecked(lineTokens, tokenizer.currentTokenStart, tokenizer.currentTokenEnd);
}
const lines = lineTokens.indices;
const positionSample = tokenizer.data.substring(lines[0], lines[1]).substring(20);
const precisions = positionSample.match(/\.\d+/g)!; const precisions = positionSample.match(/\.\d+/g)!;
const hasVelocities = precisions.length === 6; const hasVelocities = precisions.length === 6;
state.header.hasVelocities = hasVelocities; state.header.hasVelocities = hasVelocities;
state.header.precision.position = precisions[0].length - 1; state.header.precision.position = precisions[0].length - 1;
state.header.precision.velocity = hasVelocities ? precisions[3].length - 1 : 0; state.header.precision.velocity = hasVelocities ? precisions[3].length - 1 : 0;
...@@ -110,7 +105,7 @@ function handleAtoms(state: State): Schema.Atoms { ...@@ -110,7 +105,7 @@ function handleAtoms(state: State): Schema.Atoms {
const vO = pO + 3 * pW; const vO = pO + 3 * pW;
const vW = state.header.precision.velocity + 4; const vW = state.header.precision.velocity + 4;
const col = FixedColumn({ data: tokenizer.data, lines, rowCount: state.numberOfAtoms }); const col = FixedColumn(lines);
const undef = UndefinedColumn(state.numberOfAtoms, ColumnType.float); const undef = UndefinedColumn(state.numberOfAtoms, ColumnType.float);
const ret = { const ret = {
...@@ -138,17 +133,17 @@ function handleAtoms(state: State): Schema.Atoms { ...@@ -138,17 +133,17 @@ function handleAtoms(state: State): Schema.Atoms {
*/ */
function handleBoxVectors(state: State) { function handleBoxVectors(state: State) {
const { tokenizer } = state; const { tokenizer } = state;
markLine(tokenizer); Tokenizer.markLine(tokenizer);
const values = getTokenString(tokenizer).trim().split(/\s+/g); const values = Tokenizer.getTokenString(tokenizer).trim().split(/\s+/g);
state.header.box = [+values[0], +values[1], +values[2]]; state.header.box = [+values[0], +values[1], +values[2]];
} }
function parseInternal(data: string): Result<Schema.File> { function parseInternal(data: string): Result<Schema.File> {
const tokenizer = TokenizerState(data); const tokenizer = Tokenizer(data);
const structures: Schema.Structure[] = []; const structures: Schema.Structure[] = [];
while (tokenizer.position < data.length) { while (tokenizer.position < data.length) {
const state = createState(tokenizer); const state = State(tokenizer);
handleTitleString(state); handleTitleString(state);
handleNumberOfAtoms(state); handleNumberOfAtoms(state);
const atoms = handleAtoms(state); const atoms = handleAtoms(state);
......
src/reader/spec/cif.spec.ts
+ 1
− 1
View file @ c5b1b84e
...@@ -34,7 +34,7 @@ describe('schema', () => { ...@@ -34,7 +34,7 @@ describe('schema', () => {
}); });
it('toArray', () => { it('toArray', () => {
const ret = data.atoms.x.toArray(s => new Int32Array(s))!; const ret = data.atoms.x.toArray({ array: Int32Array });
expect(ret.length).toBe(3); expect(ret.length).toBe(3);
expect(ret[0]).toBe(1); expect(ret[0]).toBe(1);
expect(ret[1]).toBe(2); expect(ret[1]).toBe(2);
......
src/reader/spec/fixed-column.spec.ts
+ 1
− 1
View file @ c5b1b84e
...@@ -30,7 +30,7 @@ const linesTokens = (function () { ...@@ -30,7 +30,7 @@ const linesTokens = (function () {
}()); }());
describe('fixed text column', () => { describe('fixed text column', () => {
const col = FixedColumn({ data, lines: linesTokens, rowCount: lines.length }); const col = FixedColumn({ data, tokens: linesTokens, count: lines.length });
const col1 = col(0, 5, ColumnType.float); const col1 = col(0, 5, ColumnType.float);
const col2 = col(5, 4, ColumnType.str); const col2 = col(5, 4, ColumnType.str);
it('number', () => { it('number', () => {
......
src/script.ts
+ 4
− 4
View file @ c5b1b84e
...@@ -51,22 +51,22 @@ export function _gro() { ...@@ -51,22 +51,22 @@ export function _gro() {
console.log('rowCount', n) console.log('rowCount', n)
console.time('getFloatArray x') console.time('getFloatArray x')
const x = atoms.x.toArray(x => new Float32Array(x))! const x = atoms.x.toArray({ array: Float32Array })
console.timeEnd('getFloatArray x') console.timeEnd('getFloatArray x')
console.log(x.length, x[0], x[x.length - 1]) console.log(x.length, x[0], x[x.length - 1])
console.time('getFloatArray y') console.time('getFloatArray y')
const y = atoms.y.toArray(x => new Float32Array(x))! const y = atoms.y.toArray({ array: Float32Array })
console.timeEnd('getFloatArray y') console.timeEnd('getFloatArray y')
console.log(y.length, y[0], y[y.length - 1]) console.log(y.length, y[0], y[y.length - 1])
console.time('getFloatArray z') console.time('getFloatArray z')
const z = atoms.z.toArray(x => new Float32Array(x))! const z = atoms.z.toArray({ array: Float32Array })
console.timeEnd('getFloatArray z') console.timeEnd('getFloatArray z')
console.log(z.length, z[0], z[z.length - 1]) console.log(z.length, z[0], z[z.length - 1])
console.time('getIntArray residueNumber') console.time('getIntArray residueNumber')
const residueNumber = atoms.residueNumber.toArray(x => new Int32Array(x))! const residueNumber = atoms.residueNumber.toArray({ array: Int32Array })
console.timeEnd('getIntArray residueNumber') console.timeEnd('getIntArray residueNumber')
console.log(residueNumber.length, residueNumber[0], residueNumber[residueNumber.length - 1]) console.log(residueNumber.length, residueNumber[0], residueNumber[residueNumber.length - 1])
}); });
......
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