From ea7b1ba9fa1aca2f5b31ae3a00b26df363028c74 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Fri, 3 Nov 2017 09:56:41 +0100
Subject: [PATCH] segmentation tweaks
---
.../collections/integer/impl/segmentation.ts | 28 ++++++++-----------
.../collections/integer/segmentation.ts | 3 +-
src/mol-data/structure/query/generators.ts | 4 +--
src/perf-tests/structure.ts | 4 +--
4 files changed, 17 insertions(+), 22 deletions(-)
diff --git a/src/mol-base/collections/integer/impl/segmentation.ts b/src/mol-base/collections/integer/impl/segmentation.ts
index 567eee22d..357252a63 100644
--- a/src/mol-base/collections/integer/impl/segmentation.ts
+++ b/src/mol-base/collections/integer/impl/segmentation.ts
@@ -48,7 +48,6 @@ export class SegmentIterator implements Iterator<Segs.Segment> {
private segmentMax = 0;
private setRange = Interval.Empty;
private value: Segs.Segment = { index: 0, start: 0, end: 0 };
- private last: number = 0;
hasNext: boolean = false;
@@ -65,18 +64,13 @@ export class SegmentIterator implements Iterator<Segs.Segment> {
return this.value;
}
- private getSegmentIndex(value: number) {
- if (value >= this.last) return -1;
- return SortedArray.findPredecessorIndex(this.segments, value + 1) - 1;
- }
-
private updateValue() {
const segmentEnd = this.segments[this.segmentMin + 1];
+ // TODO: add optimized version for interval and array?
const setEnd = OrderedSet.findPredecessorIndexInInterval(this.set, segmentEnd, this.setRange);
this.value.start = Interval.start(this.setRange);
this.value.end = setEnd;
- const rEnd = Interval.end(this.setRange);
- this.setRange = Interval.ofBounds(setEnd, rEnd);
+ this.setRange = Interval.ofBounds(setEnd, Interval.end(this.setRange));
return setEnd > this.value.start;
}
@@ -87,16 +81,18 @@ export class SegmentIterator implements Iterator<Segs.Segment> {
return;
}
- const min = OrderedSet.getAt(this.set, sMin);
- const max = OrderedSet.getAt(this.set, sMax);
- this.segmentMin = this.getSegmentIndex(min);
- this.segmentMax = this.getSegmentIndex(max);
+ this.segmentMin = this.segmentMap[OrderedSet.getAt(this.set, sMin)];
+ this.segmentMax = this.segmentMap[OrderedSet.getAt(this.set, sMax)];
- this.hasNext = this.segmentMax >= this.segmentMin && Interval.size(this.setRange) > 0;
+ this.hasNext = this.segmentMax >= this.segmentMin;
+ }
+
+ setSegment(segment: Segs.Segment) {
+ this.setRange = Interval.ofBounds(segment.start, segment.end);
+ this.updateSegmentRange();
}
- constructor(private segments: SortedArray, private set: OrderedSet, inputRange: Interval) {
- this.last = SortedArray.max(segments);
+ constructor(private segments: SortedArray, private segmentMap: Int32Array, private set: OrderedSet, inputRange: Interval) {
this.setRange = inputRange;
this.updateSegmentRange();
}
@@ -104,5 +100,5 @@ export class SegmentIterator implements Iterator<Segs.Segment> {
export function segments(segs: Segmentation, set: OrderedSet, segment?: Segs.Segment) {
const int = typeof segment !== 'undefined' ? Interval.ofBounds(segment.start, segment.end) : Interval.ofBounds(0, OrderedSet.size(set));
- return new SegmentIterator(segs.segments, set, int);
+ return new SegmentIterator(segs.segments, segs.segmentMap, set, int);
}
\ No newline at end of file
diff --git a/src/mol-base/collections/integer/segmentation.ts b/src/mol-base/collections/integer/segmentation.ts
index b986fe401..3416c530b 100644
--- a/src/mol-base/collections/integer/segmentation.ts
+++ b/src/mol-base/collections/integer/segmentation.ts
@@ -4,7 +4,6 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Iterator from '../iterator'
import Interval from './interval'
import OrderedSet from './ordered-set'
import * as Impl from './impl/segmentation'
@@ -20,7 +19,7 @@ namespace Segmentation {
export const projectValue: (segs: Segmentation, set: OrderedSet, value: number) => Interval = Impl.projectValue as any;
// Segment iterator that mutates a single segment object to mark all the segments.
- export const transientSegments: (segs: Segmentation, set: OrderedSet, segment?: Segment) => Iterator<Segment> = Impl.segments as any;
+ export const transientSegments: (segs: Segmentation, set: OrderedSet, segment?: Segment) => Impl.SegmentIterator = Impl.segments as any;
}
interface Segmentation {
diff --git a/src/mol-data/structure/query/generators.ts b/src/mol-data/structure/query/generators.ts
index eb6cb5403..9a30d0a3d 100644
--- a/src/mol-data/structure/query/generators.ts
+++ b/src/mol-data/structure/query/generators.ts
@@ -74,14 +74,14 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A
builder.beginUnit();
const chainsIt = Segmentation.transientSegments(unit.hierarchy.chainSegments, set);
- const residues = unit.hierarchy.residueSegments;
+ const residuesIt = Segmentation.transientSegments(unit.hierarchy.residueSegments, set);
while (chainsIt.hasNext) {
const chainSegment = chainsIt.move();
l.atom = OrderedSet.getAt(set, chainSegment.start);
// test entity and chain
if (!entityTest(l) || !chainTest(l)) continue;
- const residuesIt = Segmentation.transientSegments(residues, set, chainSegment);
+ residuesIt.setSegment(chainSegment);
while (residuesIt.hasNext) {
const residueSegment = residuesIt.move();
l.atom = OrderedSet.getAt(set, residueSegment.start);
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index 2ed618f65..a1d996834 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -235,8 +235,8 @@ export namespace PropertyAccess {
// }
export async function run() {
- //const { structures, models } = await readCIF('./examples/1cbs_full.bcif');
- const { structures, models } = await readCIF('e:/test/quick/1jj2_full.bcif');
+ const { structures, models } = await readCIF('./examples/1cbs_full.bcif');
+ //const { structures, models } = await readCIF('e:/test/quick/3j3q_full.bcif');
//const { structures, models } = await readCIF('e:/test/quick/3j3q_updated.cif');
console.log('parsed');
--
GitLab