wip PDB parser

src/mol-io/reader/ccp4/parser.ts

@@ -6,7 +6,7 @@
 
 import { Task, RuntimeContext } from 'mol-task';
 import { Ccp4File, Ccp4Header } from './schema'
-import Result from '../result'
+import { ReaderResult as Result } from '../result'
 import { FileHandle } from '../../common/file-handle';
 
 async function parseInternal(file: FileHandle, ctx: RuntimeContext): Promise<Result<Ccp4File>> {

src/mol-io/reader/cif/binary/parser.ts

@@ -7,7 +7,7 @@
 import * as Data from '../data-model'
 import { EncodedCategory, EncodedFile } from '../../../common/binary-cif'
 import Field from './field'
-import Result from '../../result'
+import { ReaderResult as Result } from '../../result'
 import decodeMsgPack from '../../../common/msgpack/decode'
 import { Task } from 'mol-task'
 

src/mol-io/reader/cif/text/parser.ts

@@ -25,7 +25,7 @@
 import * as Data from '../data-model'
 import Field from './field'
 import { Tokens, TokenBuilder } from '../../common/text/tokenizer'
-import Result from '../../result'
+import { ReaderResult as Result } from '../../result'
 import { Task, RuntimeContext, chunkedSubtask } from 'mol-task'
 
 /**

src/mol-io/reader/common/text/tokenizer.ts

@@ -8,7 +8,9 @@
 
 import { chunkedSubtask, RuntimeContext } from 'mol-task'
 
-export interface Tokenizer {
+export { Tokenizer }
+
+interface Tokenizer {
     data: string,
 
     position: number,
@@ -25,7 +27,7 @@ export interface Tokens {
     indices: ArrayLike<number>
 }
 
-export function Tokenizer(data: string): Tokenizer {
+function Tokenizer(data: string): Tokenizer {
     return {
         data,
         position: 0,
@@ -36,7 +38,7 @@ export function Tokenizer(data: string): Tokenizer {
     };
 }
 
-export namespace Tokenizer {
+namespace Tokenizer {
     export function getTokenString(state: Tokenizer) {
         return state.data.substring(state.tokenStart, state.tokenEnd);
     }
@@ -269,6 +271,4 @@ export namespace TokenBuilder {
             indices: new Uint32Array(size)
         }
     }
-}
-
-export default Tokenizer
+}

src/mol-io/reader/csv/parser.ts

@@ -8,7 +8,7 @@
 import { Tokens, TokenBuilder, Tokenizer } from '../common/text/tokenizer'
 import * as Data from './data-model'
 import Field from './field'
-import Result from '../result'
+import { ReaderResult as Result } from '../result'
 import { Task, RuntimeContext, chunkedSubtask, } from 'mol-task'
 
 const enum CsvTokenType {

src/mol-io/reader/dsn6/parser.ts

@@ -6,7 +6,7 @@
 
 import { Task, RuntimeContext } from 'mol-task';
 import { Dsn6File, Dsn6Header } from './schema'
-import Result from '../result'
+import { ReaderResult as Result } from '../result'
 import { FileHandle } from '../../common/file-handle';
 
 function parseBrixHeader(str: string): Dsn6Header {

src/mol-io/reader/gro/parser.ts

@@ -6,10 +6,10 @@
  */
 
 import { Column } from 'mol-data/db'
-import Tokenizer from '../common/text/tokenizer'
+import { Tokenizer } from '../common/text/tokenizer'
 import FixedColumn from '../common/text/column/fixed'
 import * as Schema from './schema'
-import Result from '../result'
+import { ReaderResult as Result } from '../result'
 import { Task, RuntimeContext } from 'mol-task'
 
 interface State {

src/mol-io/reader/mol2/parser.ts

@@ -15,7 +15,7 @@ import { Column } from 'mol-data/db'
 import { TokenBuilder, Tokenizer } from '../common/text/tokenizer'
 import TokenColumn from '../common/text/column/token'
 import * as Schema from './schema'
-import Result from '../result'
+import { ReaderResult as Result } from '../result'
 import { Task, RuntimeContext, chunkedSubtask } from 'mol-task'
 
 const { skipWhitespace, eatValue, markLine, getTokenString, readLine } = Tokenizer;

src/mol-io/reader/obj/parser.ts

@@ -4,7 +4,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import Result from '../result'
+import { ReaderResult as Result } from '../result'
 import { Task, RuntimeContext } from 'mol-task'
 import { Mesh } from 'mol-geo/geometry/mesh/mesh';
 

src/mol-io/reader/pdb/parser.ts

@@ -0,0 +1,14 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { PdbFile } from './schema';
+import { Task } from 'mol-task';
+import { ReaderResult } from '../result';
+import { Tokenizer } from '../common/text/tokenizer';
+
+export function parse(data: string): Task<ReaderResult<PdbFile>> {
+    return Task.create('Parse PDB', async ctx => ReaderResult.success({ lines: await Tokenizer.readAllLinesAsync(data, ctx) }));
+}

src/mol-io/reader/pdb/schema.ts

@@ -0,0 +1,11 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Tokens } from '../common/text/tokenizer';
+
+export interface PdbFile {
+    lines: Tokens
+}

src/mol-io/reader/result.ts

@@ -5,7 +5,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-type ReaderResult<T> = Success<T> | Error
+type ReaderResult<T> = ReaderResult.Success<T> | ReaderResult.Error
 
 namespace ReaderResult {
     export function error<T>(message: string, line = -1): ReaderResult<T> {
@@ -15,28 +15,28 @@ namespace ReaderResult {
     export function success<T>(result: T, warnings: string[] = []): ReaderResult<T> {
         return new Success<T>(result, warnings);
     }
-}
 
-export class Error {
-    isError: true = true;
+    export class Error {
+        isError: true = true;
 
-    toString() {
-        if (this.line >= 0) {
-            return `[Line ${this.line}] ${this.message}`;
+        toString() {
+            if (this.line >= 0) {
+                return `[Line ${this.line}] ${this.message}`;
+            }
+            return this.message;
         }
-        return this.message;
-    }
 
-    constructor(
-        public message: string,
-        public line: number) {
+        constructor(
+            public message: string,
+            public line: number) {
+        }
     }
-}
 
-export class Success<T> {
-    isError: false = false;
+    export class Success<T> {
+        isError: false = false;
 
-    constructor(public result: T, public warnings: string[]) { }
+        constructor(public result: T, public warnings: string[]) { }
+    }
 }
 
-export default ReaderResult
+export { ReaderResult }