From a4157fdd284f549ba85babb6ed8fb131dd3d25f4 Mon Sep 17 00:00:00 2001
From: Zepei Xu <xuzepei19950617@gmail.com>
Date: Wed, 3 Jan 2018 16:46:59 -0800
Subject: [PATCH] fixed switch statements, and the code now should be
cancelable.
---
src/mol-io/reader/mol2/parser.ts | 134 +++++++++++++++++++------------
1 file changed, 82 insertions(+), 52 deletions(-)
diff --git a/src/mol-io/reader/mol2/parser.ts b/src/mol-io/reader/mol2/parser.ts
index c1dabdd13..4d3f20992 100644
--- a/src/mol-io/reader/mol2/parser.ts
+++ b/src/mol-io/reader/mol2/parser.ts
@@ -104,7 +104,7 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
}
const initialTokenizerPosition = tokenizer.position;
- const initialTOkenizerLineNumber = tokenizer.lineNumber;
+ const initialTokenizerLineNumber = tokenizer.lineNumber;
const firstLine = Tokenizer.readLine(tokenizer);
const firstLineArray = firstLine.trim().split(/\s+/g)
const firstLineLength = firstLineArray.length;
@@ -164,46 +164,64 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
if(hasStatus_bit){numOfColumn++}
tokenizer.position = initialTokenizerPosition;
- tokenizer.lineNumber = initialTOkenizerLineNumber;
+ tokenizer.lineNumber = initialTokenizerLineNumber;
+
+
- for(let i = 0; i < molecule.num_atoms; i++){
+
+ const { length } = tokenizer;
+ let linesAlreadyRead = 0;
+ await state.chunker.process(chunkSize => {
+ const linesToRead = Math.min(molecule.num_atoms - linesAlreadyRead, chunkSize);
+ 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++){
- Tokenizer.skipWhitespace(tokenizer);
- Tokenizer.eatValue(tokenizer);
- switch(j){
- case 0:
- TokenBuilder.addUnchecked(atom_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
- case 1:
- TokenBuilder.addUnchecked(atom_nameTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
- case 2:
- TokenBuilder.addUnchecked(xTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
- case 3:
- TokenBuilder.addUnchecked(yTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
- case 4:
- TokenBuilder.addUnchecked(zTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
- case 5:
- TokenBuilder.addUnchecked(atom_typeTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
- default:
- 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){
- TokenBuilder.addUnchecked(subst_nameTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
- subst_nameWritten = true;
- }else if(hasCharge == true && chargeWritten == false){
- TokenBuilder.addUnchecked(chargeTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
- chargeWritten = true;
- }else if(hasStatus_bit == true && status_bitWritten == false){
- TokenBuilder.addUnchecked(status_bitTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
- status_bitWritten = true;
- }
+ for(let j = 0; j < numOfColumn; j++){
+ Tokenizer.skipWhitespace(tokenizer);
+ Tokenizer.eatValue(tokenizer);
+ switch(j){
+ case 0:
+ TokenBuilder.addUnchecked(atom_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+ break;
+ case 1:
+ TokenBuilder.addUnchecked(atom_nameTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+ break;
+ case 2:
+ TokenBuilder.addUnchecked(xTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+ break;
+ case 3:
+ TokenBuilder.addUnchecked(yTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+ break;
+ case 4:
+ TokenBuilder.addUnchecked(zTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+ break;
+ case 5:
+ TokenBuilder.addUnchecked(atom_typeTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+ break;
+ default:
+ 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){
+ TokenBuilder.addUnchecked(subst_nameTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+ subst_nameWritten = true;
+ }else if(hasCharge == true && chargeWritten == false){
+ TokenBuilder.addUnchecked(chargeTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+ chargeWritten = true;
+ }else if(hasStatus_bit == true && status_bitWritten == false){
+ TokenBuilder.addUnchecked(status_bitTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+ status_bitWritten = true;
+ }
+ }
}
}
- }
+ linesAlreadyRead += linesToRead;
+ return linesToRead;
+ }, update => update({ message: 'Parsing...', current: tokenizer.position, max: length }));
+
+
const ret = {
count: molecule.num_atoms,
@@ -224,8 +242,6 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
}
-
-
async function handleBonds(state: State): Promise<Schema.Bonds> {
const { tokenizer, molecule } = state;
let hasStatus_bit = false;
@@ -265,24 +281,38 @@ async function handleBonds(state: State): Promise<Schema.Bonds> {
tokenizer.position = initialTokenizerPosition;
tokenizer.lineNumber = initialTokenizerLineNumber;
- for(let i = 0; i < molecule.num_bonds; i++){
- for(let j = 0; j < numberOfColumn; j++){
- Tokenizer.skipWhitespace(tokenizer);
- Tokenizer.eatValue(tokenizer);
- switch(j){
- case 0:
- TokenBuilder.addUnchecked(bond_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
- case 1:
- TokenBuilder.addUnchecked(origin_bond_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
- case 2:
- TokenBuilder.addUnchecked(target_bond_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
- case 3:
- TokenBuilder.addUnchecked(bondTypeTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
- default:
- TokenBuilder.addUnchecked(status_bitTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+ const { length } = tokenizer;
+ let linesAlreadyRead = 0;
+ await state.chunker.process(chunkSize => {
+ const linesToRead = Math.min(molecule.num_bonds - linesAlreadyRead, chunkSize);
+ for(let i = 0; i < linesToRead; i++){
+ for(let j = 0; j < numberOfColumn; j++){
+ Tokenizer.skipWhitespace(tokenizer);
+ Tokenizer.eatValue(tokenizer);
+ switch(j){
+ case 0:
+ TokenBuilder.addUnchecked(bond_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+ break;
+ case 1:
+ TokenBuilder.addUnchecked(origin_bond_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+ break;
+ case 2:
+ TokenBuilder.addUnchecked(target_bond_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+ break;
+ case 3:
+ TokenBuilder.addUnchecked(bondTypeTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+ break;
+ default:
+ TokenBuilder.addUnchecked(status_bitTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+ break;
+ }
}
}
- }
+ linesAlreadyRead += linesToRead;
+ return linesToRead;
+ }, update => update({ message: 'Parsing...', current: tokenizer.position, max: length }));
+
+
const ret = {
count: molecule.num_bonds,
--
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