diff --git a/src/mol-io/reader/_spec/gro.spec.ts b/src/mol-io/reader/_spec/gro.spec.ts
index 888f23c83369fa8fc27e4adec486aab86003e7ab..6254be8f9d45d287f643e2d50993e8b62eb11bbe 100644
--- a/src/mol-io/reader/_spec/gro.spec.ts
+++ b/src/mol-io/reader/_spec/gro.spec.ts
@@ -6,6 +6,7 @@
*/
import Gro from '../gro/parser'
+import { Run } from 'mol-task';
const groString = `MD of 2 waters, t= 4.2
6
@@ -26,7 +27,7 @@ const groStringHighPrecision = `Generated by trjconv : 2168 system t= 15.00000
describe('gro reader', () => {
it('basic', async () => {
- const parsed = await Gro(groString)();
+ const parsed = await Run(Gro(groString));
if (parsed.isError) {
console.log(parsed)
@@ -57,7 +58,7 @@ describe('gro reader', () => {
});
it('high precision', async () => {
- const parsed = await Gro(groStringHighPrecision)()
+ const parsed = await Run(Gro(groStringHighPrecision));
if (parsed.isError) {
console.log(parsed)
diff --git a/src/mol-io/reader/_spec/mol2.spec.ts b/src/mol-io/reader/_spec/mol2.spec.ts
index c329f61a4e5c66a28588d8424eb4327dbafb25ff..43244780636af6fbcd75010522ba9405b75ca2ff 100644
--- a/src/mol-io/reader/_spec/mol2.spec.ts
+++ b/src/mol-io/reader/_spec/mol2.spec.ts
@@ -1,5 +1,6 @@
import Mol2 from '../mol2/parser'
+import { Run } from 'mol-task';
const Mol2String = `@<TRIPOS>MOLECULE
5816
@@ -246,7 +247,7 @@ GASTEIGER
describe('mol2 reader', () => {
it('basic', async () => {
- const parsed = await Mol2(Mol2String)();
+ const parsed = await Run(Mol2(Mol2String));
if (parsed.isError) {
throw new Error(parsed.message);
}
@@ -297,7 +298,7 @@ describe('mol2 reader', () => {
});
it('multiblocks', async () => {
- const parsed = await Mol2(Mol2StringMultiBlocks)();
+ const parsed = await Run(Mol2(Mol2StringMultiBlocks));
if (parsed.isError) {
throw new Error(parsed.message);
}
@@ -348,7 +349,7 @@ describe('mol2 reader', () => {
});
it('minimal', async () => {
- const parsed = await Mol2(Mol2StringMinimal)();
+ const parsed = await Run(Mol2(Mol2StringMinimal));
if (parsed.isError) {
throw new Error(parsed.message);
}
diff --git a/src/mol-io/reader/common/text/tokenizer.ts b/src/mol-io/reader/common/text/tokenizer.ts
index 15a8492c74ffd939be708e62e4858a8129291106..60f14c1b135bfca7d215f3a3d8939997b4ec2ae5 100644
--- a/src/mol-io/reader/common/text/tokenizer.ts
+++ b/src/mol-io/reader/common/text/tokenizer.ts
@@ -6,7 +6,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import Computation from 'mol-util/computation'
+import { chunkedSubtask, RuntimeContext } from 'mol-task'
export interface Tokenizer {
data: string,
@@ -109,17 +109,17 @@ export namespace Tokenizer {
}
/** Advance the state by the given number of lines and return line starts/ends as tokens. */
- export async function readLinesAsync(state: Tokenizer, count: number, chunker: Computation.Chunker): Promise<Tokens> {
+ export async function readLinesAsync(state: Tokenizer, count: number, ctx: RuntimeContext, initialLineCount = 100000): Promise<Tokens> {
const { length } = state;
const lineTokens = TokenBuilder.create(state, count * 2);
let linesAlreadyRead = 0;
- await chunker.process(chunkSize => {
+ await chunkedSubtask(ctx, initialLineCount, state, (chunkSize, state) => {
const linesToRead = Math.min(count - linesAlreadyRead, chunkSize);
readLinesChunk(state, linesToRead, lineTokens);
linesAlreadyRead += linesToRead;
return linesToRead;
- }, update => update({ message: 'Parsing...', current: state.position, max: length }));
+ }, (ctx, state) => ctx.update({ message: 'Parsing...', current: state.position, max: length }));
return lineTokens;
}
diff --git a/src/mol-io/reader/gro/parser.ts b/src/mol-io/reader/gro/parser.ts
index d1c71ec315c3f98d47f45692838c9dfa462d4142..eee90135b4a588a565b25ee1f5354f150d987f3b 100644
--- a/src/mol-io/reader/gro/parser.ts
+++ b/src/mol-io/reader/gro/parser.ts
@@ -10,13 +10,13 @@ import Tokenizer from '../common/text/tokenizer'
import FixedColumn from '../common/text/column/fixed'
import * as Schema from './schema'
import Result from '../result'
-import Computation from 'mol-util/computation'
+import { Task, RuntimeContext } from 'mol-task'
interface State {
tokenizer: Tokenizer,
header: Schema.Header,
numberOfAtoms: number,
- chunker: Computation.Chunker
+ runtimeCtx: RuntimeContext
}
function createEmptyHeader(): Schema.Header {
@@ -29,12 +29,12 @@ function createEmptyHeader(): Schema.Header {
};
}
-function State(tokenizer: Tokenizer, ctx: Computation.Context): State {
+function State(tokenizer: Tokenizer, runtimeCtx: RuntimeContext): State {
return {
tokenizer,
header: createEmptyHeader(),
numberOfAtoms: 0,
- chunker: Computation.chunker(ctx, 100000) // 100000 lines is the default chunk size for this reader
+ runtimeCtx
};
}
@@ -90,7 +90,7 @@ function handleNumberOfAtoms(state: State) {
*/
async function handleAtoms(state: State): Promise<Schema.Atoms> {
const { tokenizer, numberOfAtoms } = state;
- const lines = await Tokenizer.readLinesAsync(tokenizer, numberOfAtoms, state.chunker);
+ const lines = await Tokenizer.readLinesAsync(tokenizer, numberOfAtoms, state.runtimeCtx, 100000);
const positionSample = tokenizer.data.substring(lines.indices[0], lines.indices[1]).substring(20);
const precisions = positionSample.match(/\.\d+/g)!;
@@ -137,7 +137,7 @@ function handleBoxVectors(state: State) {
state.header.box = [+values[0], +values[1], +values[2]];
}
-async function parseInternal(data: string, ctx: Computation.Context): Promise<Result<Schema.File>> {
+async function parseInternal(data: string, ctx: RuntimeContext): Promise<Result<Schema.File>> {
const tokenizer = Tokenizer(data);
ctx.update({ message: 'Parsing...', current: 0, max: data.length });
@@ -156,7 +156,7 @@ async function parseInternal(data: string, ctx: Computation.Context): Promise<Re
}
export function parse(data: string) {
- return Computation.create<Result<Schema.File>>(async ctx => {
+ return Task.create<Result<Schema.File>>('Parse GRO', async ctx => {
return await parseInternal(data, ctx);
});
}
diff --git a/src/mol-io/reader/mol2/parser.ts b/src/mol-io/reader/mol2/parser.ts
index f807f4ff7b78d1c3f7a051fbba88a0a69c6216de..32126acb9050dbf33e490f2d9ffed2ca98a5f76c 100644
--- a/src/mol-io/reader/mol2/parser.ts
+++ b/src/mol-io/reader/mol2/parser.ts
@@ -6,7 +6,7 @@
*/
// NOTES
-//When want to created undefined string column, must use
+// When want to created undefined string column, must use
// undefStr = UndefinedColumn(molecule.num_atoms, ColumnType.str)
// but not
// const undefPooledStr = UndefinedColumn(molecule.num_atoms, ColumnType.pooledStr);
@@ -16,14 +16,14 @@ import { TokenBuilder, Tokenizer } from '../common/text/tokenizer'
import TokenColumn from '../common/text/column/token'
import * as Schema from './schema'
import Result from '../result'
-import Computation from 'mol-util/computation'
+import { Task, RuntimeContext, chunkedSubtask } from 'mol-task'
const { skipWhitespace, eatValue, markLine, getTokenString, readLine } = Tokenizer;
interface State {
tokenizer: Tokenizer,
molecule: Schema.Molecule,
- chunker: Computation.Chunker
+ runtimeCtx: RuntimeContext
}
function createEmptyMolecule(): Schema.Molecule {
@@ -36,16 +36,16 @@ function createEmptyMolecule(): Schema.Molecule {
num_sets: 0,
mol_type: '',
charge_type: '',
- status_bits:'',
+ status_bits: '',
mol_comment: ''
};
}
-function State(tokenizer: Tokenizer, ctx: Computation.Context): State {
+function State(tokenizer: Tokenizer, runtimeCtx: RuntimeContext): State {
return {
tokenizer,
molecule: createEmptyMolecule(),
- chunker: Computation.chunker(ctx, 100000)
+ runtimeCtx
};
}
@@ -54,7 +54,7 @@ const reWhitespace = /\s+/g;
function handleMolecule(state: State) {
const { tokenizer, molecule } = state;
- while(getTokenString(tokenizer) !== '@<TRIPOS>MOLECULE'){
+ while (getTokenString(tokenizer) !== '@<TRIPOS>MOLECULE') {
markLine(tokenizer);
}
@@ -84,10 +84,10 @@ function handleMolecule(state: State) {
molecule.mol_comment = getTokenString(tokenizer)
}
-function isStatus_bit(aString: String): Boolean{
- if(aString.includes('DSPMOD') || aString.includes('TYPECOL') || aString.includes('CAP')
- || aString.includes('BACKBONE') || aString.includes('DICT') || aString.includes('ESSENTIAL')
- || aString.includes('WATER') || aString.includes('DIRECT')){
+function isStatus_bit(aString: String): Boolean {
+ if (aString.includes('DSPMOD') || aString.includes('TYPECOL') || aString.includes('CAP')
+ || aString.includes('BACKBONE') || aString.includes('DICT') || aString.includes('ESSENTIAL')
+ || aString.includes('WATER') || aString.includes('DIRECT')) {
return true;
}
return false;
@@ -101,7 +101,7 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
let hasStatus_bit = false;
// skip empty lines and '@<TRIPOS>ATOM'
- while(getTokenString(tokenizer) != '@<TRIPOS>ATOM'){
+ while (getTokenString(tokenizer) !== '@<TRIPOS>ATOM') {
markLine(tokenizer);
}
@@ -113,17 +113,17 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
// optional columns are in order "integer string float string".
// Use this to find out which column is missing or empty
- for(let i = 6; i < firstLineLength; i++){
- if(!isNaN(Number(firstLineArray[i]))){
- if(firstLineArray[i].indexOf('.') == -1){
+ for (let i = 6; i < firstLineLength; i++) {
+ if (!isNaN(Number(firstLineArray[i]))) {
+ if (firstLineArray[i].indexOf('.') === -1) {
hasSubst_id = true;
- }else{
+ } else {
hasCharge = true;
}
- }else if(isNaN(Number(firstLineArray[i]))){
- if(!isStatus_bit(firstLineArray[i])){
+ } else if (isNaN(Number(firstLineArray[i]))) {
+ if (!isStatus_bit(firstLineArray[i])) {
hasSubst_name = true;
- }else{
+ } else {
hasStatus_bit = true;
}
}
@@ -131,7 +131,7 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
// required columns
const atom_idTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
- const atom_nameTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);;
+ const atom_nameTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
const xTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
const yTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
const zTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
@@ -160,28 +160,28 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
const undefStr = Column.Undefined(molecule.num_atoms, Column.Schema.str);
let numOfColumn = 6;
- if(hasSubst_id){numOfColumn++}
- if(hasSubst_name){numOfColumn++}
- if(hasCharge){numOfColumn++}
- if(hasStatus_bit){numOfColumn++}
+ if (hasSubst_id) { numOfColumn++ }
+ if (hasSubst_name) { numOfColumn++ }
+ if (hasCharge) { numOfColumn++ }
+ if (hasStatus_bit) { numOfColumn++ }
tokenizer.position = initialTokenizerPosition;
tokenizer.lineNumber = initialTokenizerLineNumber;
const { length } = tokenizer;
let linesAlreadyRead = 0;
- await state.chunker.process(chunkSize => {
+ await chunkedSubtask(state.runtimeCtx, 100000, void 0, chunkSize => {
const linesToRead = Math.min(molecule.num_atoms - linesAlreadyRead, chunkSize);
- for(let i = 0; i < linesToRead; i++){
+ for (let i = 0; i < linesToRead; i++) {
let subst_idWritten = false;
let subst_nameWritten = false;
let chargeWritten = false;
let status_bitWritten = false;
- for(let j = 0; j < numOfColumn; j++){
+ for (let j = 0; j < numOfColumn; j++) {
skipWhitespace(tokenizer);
tokenizer.tokenStart = tokenizer.position;
eatValue(tokenizer);
- switch(j){
+ switch (j) {
case 0:
TokenBuilder.addUnchecked(atom_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
@@ -201,16 +201,16 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
TokenBuilder.addUnchecked(atom_typeTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
default:
- if(hasSubst_id === true && subst_idWritten === false){
+ if (hasSubst_id === true && subst_idWritten === false) {
TokenBuilder.addUnchecked(subst_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
subst_idWritten = true;
- }else if(hasSubst_name === true && subst_nameWritten === false){
+ } else if (hasSubst_name === true && subst_nameWritten === false) {
TokenBuilder.addUnchecked(subst_nameTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
subst_nameWritten = true;
- }else if(hasCharge === true && chargeWritten === false){
+ } else if (hasCharge === true && chargeWritten === false) {
TokenBuilder.addUnchecked(chargeTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
chargeWritten = true;
- }else if(hasStatus_bit === true && status_bitWritten === false){
+ } else if (hasStatus_bit === true && status_bitWritten === false) {
TokenBuilder.addUnchecked(status_bitTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
status_bitWritten = true;
}
@@ -219,7 +219,7 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
}
linesAlreadyRead += linesToRead;
return linesToRead;
- }, update => update({ message: 'Parsing...', current: tokenizer.position, max: length }));
+ }, ctx => ctx.update({ message: 'Parsing...', current: tokenizer.position, max: length }));
const ret = {
count: molecule.num_atoms,
@@ -243,7 +243,7 @@ async function handleBonds(state: State): Promise<Schema.Bonds> {
const { tokenizer, molecule } = state;
let hasStatus_bit = false;
- while(getTokenString(tokenizer) !== '@<TRIPOS>BOND'){
+ while (getTokenString(tokenizer) !== '@<TRIPOS>BOND') {
markLine(tokenizer);
}
@@ -252,7 +252,7 @@ async function handleBonds(state: State): Promise<Schema.Bonds> {
const firstLine = readLine(tokenizer);
const firstLineArray = firstLine.trim().split(/\s+/g)
const firstLineLength = firstLineArray.length;
- if(firstLineLength === 5){
+ if (firstLineLength === 5) {
hasStatus_bit = true;
}
@@ -273,21 +273,21 @@ async function handleBonds(state: State): Promise<Schema.Bonds> {
const undefStr = Column.Undefined(molecule.num_bonds, Column.Schema.str);
let numberOfColumn = 4;
- if(hasStatus_bit){numberOfColumn++}
+ if (hasStatus_bit) { numberOfColumn++ }
tokenizer.position = initialTokenizerPosition;
tokenizer.lineNumber = initialTokenizerLineNumber;
const { length } = tokenizer;
let linesAlreadyRead = 0;
- await state.chunker.process(chunkSize => {
+ await chunkedSubtask(state.runtimeCtx, 100000, void 0, chunkSize => {
const linesToRead = Math.min(molecule.num_bonds - linesAlreadyRead, chunkSize);
- for(let i = 0; i < linesToRead; i++){
- for(let j = 0; j < numberOfColumn; j++){
+ for (let i = 0; i < linesToRead; i++) {
+ for (let j = 0; j < numberOfColumn; j++) {
skipWhitespace(tokenizer);
tokenizer.tokenStart = tokenizer.position;
eatValue(tokenizer);
- switch(j){
+ switch (j) {
case 0:
TokenBuilder.addUnchecked(bond_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
@@ -308,7 +308,7 @@ async function handleBonds(state: State): Promise<Schema.Bonds> {
}
linesAlreadyRead += linesToRead;
return linesToRead;
- }, update => update({ message: 'Parsing...', current: tokenizer.position, max: length }));
+ }, ctx => ctx.update({ message: 'Parsing...', current: tokenizer.position, max: length }));
const ret = {
count: molecule.num_bonds,
@@ -324,7 +324,7 @@ async function handleBonds(state: State): Promise<Schema.Bonds> {
return ret;
}
-async function parseInternal(data: string, ctx: Computation.Context): Promise<Result<Schema.File>> {
+async function parseInternal(data: string, ctx: RuntimeContext): Promise<Result<Schema.File>> {
const tokenizer = Tokenizer(data);
ctx.update({ message: 'Parsing...', current: 0, max: data.length });
@@ -342,7 +342,7 @@ async function parseInternal(data: string, ctx: Computation.Context): Promise<Re
}
export function parse(data: string) {
- return Computation.create<Result<Schema.File>>(async ctx => {
+ return Task.create<Result<Schema.File>>('Parse MOL2', async ctx => {
return await parseInternal(data, ctx);
});
}