From 6fd5e1908bb7f5024a49b3cad2748d4c746b4c32 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 5 Sep 2017 10:55:22 -0700
Subject: [PATCH] gro, faster atom line handling
---
src/reader/gro.ts | 19 +++++++++++--------
src/utils/tokens.ts | 5 +++++
2 files changed, 16 insertions(+), 8 deletions(-)
diff --git a/src/reader/gro.ts b/src/reader/gro.ts
index 966da0c95..3bf31ce03 100644
--- a/src/reader/gro.ts
+++ b/src/reader/gro.ts
@@ -193,25 +193,28 @@ function handleAtoms (state: GroState, block: GroBlock) {
const columnCount = columns.length
const tokens = Tokens.create(state.numberOfAtoms * 2 * columnCount)
+ let start: number
+ let end: number
+ let valueStart: number
+ let valueEnd: number = state.position
+
for (let i = 0; i < state.numberOfAtoms; ++i) {
state.currentTokenStart = state.position
- eatLine(state)
- // console.log('atom line', state.data.substring(state.currentTokenStart, state.currentTokenEnd))
-
- let start: number
- let end = state.currentTokenStart
+ end = state.currentTokenStart
for (let j = 0; j < columnCount; ++j) {
start = end
end = start + fieldSizes[j]
// trim
- let valueStart = start
- let valueEnd = end
+ valueStart = start
+ valueEnd = end
while (valueStart < valueEnd && state.data.charCodeAt(valueStart) === 32) ++valueStart;
while (valueEnd > valueStart && state.data.charCodeAt(valueEnd - 1) === 32) --valueEnd;
- Tokens.add(tokens, valueStart, valueEnd)
+ Tokens.addUnchecked(tokens, valueStart, valueEnd)
}
+ state.position = valueEnd
+ eatLine(state)
}
block.addTable(new TextTable(state.data, name, columns, tokens));
diff --git a/src/utils/tokens.ts b/src/utils/tokens.ts
index 93af43bb6..32e1a207d 100644
--- a/src/utils/tokens.ts
+++ b/src/utils/tokens.ts
@@ -25,6 +25,11 @@ export namespace Tokens {
tokens.indices[tokens.count++] = end;
}
+ export function addUnchecked(tokens: Tokens, start: number, end: number) {
+ tokens.indices[tokens.count++] = start;
+ tokens.indices[tokens.count++] = end;
+ }
+
export function create(size: number): Tokens {
return {
indicesLenMinus2: (size - 2) | 0,
--
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