From 98bb9575b6a9563501e57683a3f44eea8cfbd95c Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sat, 22 Jun 2019 07:45:04 -0700
Subject: [PATCH] simplified polymer sequence wrapper
---
src/mol-plugin/ui/sequence/polymer.ts | 29 +++++++--------------------
1 file changed, 7 insertions(+), 22 deletions(-)
diff --git a/src/mol-plugin/ui/sequence/polymer.ts b/src/mol-plugin/ui/sequence/polymer.ts
index 7ccd38272..6a63b0bdf 100644
--- a/src/mol-plugin/ui/sequence/polymer.ts
+++ b/src/mol-plugin/ui/sequence/polymer.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { StructureSelection, StructureQuery, Structure, Queries, StructureProperties as SP, StructureElement, Unit } from '../../../mol-model/structure';
+import { StructureSelection, StructureQuery, Structure, Queries, StructureProperties as SP, StructureElement, Unit, ElementIndex } from '../../../mol-model/structure';
import { SequenceWrapper } from './util';
import { OrderedSet, Interval, SortedArray } from '../../../mol-data/int';
import { Loci } from '../../../mol-model/loci';
@@ -15,7 +15,6 @@ import { ColorNames } from '../../../mol-util/color/tables';
export type StructureUnit = { structure: Structure, unit: Unit }
export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
- private readonly location: StructureElement
private readonly sequence: Sequence
private readonly missing: MissingResidues
private readonly observed: OrderedSet // sequences indices
@@ -41,24 +40,12 @@ export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
if (StructureElement.isLoci(loci)) {
if (!Structure.areParentsEqual(loci.structure, structure)) return false
- const { location } = this
for (const e of loci.elements) {
- let rIprev = -1
- location.unit = e.unit
-
- const { index: residueIndex } = e.unit.model.atomicHierarchy.residueAtomSegments
-
- OrderedSet.forEach(e.indices, v => {
- location.element = e.unit.elements[v]
- const rI = residueIndex[location.element]
- // avoid checking for the same residue multiple times
- if (rI !== rIprev) {
- if (SP.unit.id(location) !== unit.id) return
-
- if (apply(getSeqIndices(location))) changed = true
- rIprev = rI
- }
- })
+ if (e.unit.id === unit.id) {
+ OrderedSet.forEach(e.indices, v => {
+ if (apply(getSeqIndices(e.unit, e.unit.elements[v]))) changed = true
+ })
+ }
}
} else if (Structure.isLoci(loci)) {
if (!Structure.areParentsEqual(loci.structure, structure)) return false
@@ -82,7 +69,6 @@ export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
super(data, markerArray, sequence.sequence.length)
this.sequence = sequence
- this.location = StructureElement.create()
this.missing = data.unit.model.properties.missingResidues
this.modelNum = data.unit.model.modelNum
@@ -114,8 +100,7 @@ function createResidueQuery(unitId: number, label_seq_id: number) {
});
}
-function getSeqIndices(location: StructureElement): Interval {
- const { unit, element } = location
+function getSeqIndices(unit: Unit, element: ElementIndex): Interval {
const { model } = unit
switch (unit.kind) {
case Unit.Kind.Atomic:
--
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