From f10a135deac9bf1200b85c6c844f9cadc798429a Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sat, 22 Jun 2019 07:24:01 -0700
Subject: [PATCH] sequence view, better handling of missing residues, full
structure loci
---
src/mol-data/int/ordered-set.ts | 1 +
src/mol-data/int/sorted-array.ts | 8 +--
src/mol-plugin/ui/sequence/polymer.ts | 76 ++++++++++++++++-----------
src/mol-plugin/ui/sequence/util.ts | 14 ++---
4 files changed, 56 insertions(+), 43 deletions(-)
diff --git a/src/mol-data/int/ordered-set.ts b/src/mol-data/int/ordered-set.ts
index 7f671e22a..4ec45b17f 100644
--- a/src/mol-data/int/ordered-set.ts
+++ b/src/mol-data/int/ordered-set.ts
@@ -37,6 +37,7 @@ namespace OrderedSet {
export const union: <T extends number = number>(a: OrderedSet<T>, b: OrderedSet<T>) => OrderedSet<T> = Base.union as any;
export const intersect: <T extends number = number>(a: OrderedSet<T>, b: OrderedSet<T>) => OrderedSet<T> = Base.intersect as any;
+ /** Returns elements of `a` that are not in `b`, i.e `a` - `b` */
export const subtract: <T extends number = number>(a: OrderedSet<T>, b: OrderedSet<T>) => OrderedSet<T> = Base.subtract as any;
export const findPredecessorIndex: <T extends number = number>(set: OrderedSet<T>, x: number) => number = Base.findPredecessorIndex as any;
diff --git a/src/mol-data/int/sorted-array.ts b/src/mol-data/int/sorted-array.ts
index bd1c202b0..8858aed3d 100644
--- a/src/mol-data/int/sorted-array.ts
+++ b/src/mol-data/int/sorted-array.ts
@@ -12,9 +12,9 @@ namespace SortedArray {
export const ofUnsortedArray: <T extends number = number>(xs: ArrayLike<number>) => SortedArray<T> = Impl.ofUnsortedArray as any;
export const ofSingleton: <T extends number = number>(v: number) => SortedArray<T> = Impl.ofSingleton as any;
export const ofSortedArray: <T extends number = number>(xs: ArrayLike<number>) => SortedArray<T> = Impl.ofSortedArray as any;
- // create sorted array [min, max] (it DOES contain the max value)
+ /** create sorted array [min, max] (it DOES contain the max value) */
export const ofRange: <T extends number = number>(min: T, max: T) => SortedArray<T> = Impl.ofRange as any;
- // create sorted array [min, max) (it does NOT contain the max value)
+ /** create sorted array [min, max) (it does NOT contain the max value) */
export const ofBounds: <T extends number = number>(min: T, max: T) => SortedArray<T> = (min, max) => Impl.ofRange(min, max - 1) as any;
export const is: <T extends number = number>(v: any) => v is SortedArray<T> = Impl.is as any;
@@ -23,9 +23,9 @@ namespace SortedArray {
export const indexOf: <T extends number = number>(array: SortedArray<T>, x: T) => number = Impl.indexOf as any;
export const indexOfInInterval: <T extends number = number>(array: SortedArray<T>, x: number, bounds: Interval) => number = Impl.indexOfInInterval as any;
- // array[0]
+ /** Returns `array[0]` */
export const start: <T extends number = number>(array: SortedArray<T>) => T = Impl.start as any;
- // array[array.length - 1] + 1
+ /** Returns `array[array.length - 1] + 1` */
export const end: <T extends number = number>(array: SortedArray<T>) => T = Impl.end as any;
export const min: <T extends number = number>(array: SortedArray<T>) => T = Impl.min as any;
export const max: <T extends number = number>(array: SortedArray<T>) => T = Impl.max as any;
diff --git a/src/mol-plugin/ui/sequence/polymer.ts b/src/mol-plugin/ui/sequence/polymer.ts
index 03b1f60d0..7ccd38272 100644
--- a/src/mol-plugin/ui/sequence/polymer.ts
+++ b/src/mol-plugin/ui/sequence/polymer.ts
@@ -6,7 +6,7 @@
import { StructureSelection, StructureQuery, Structure, Queries, StructureProperties as SP, StructureElement, Unit } from '../../../mol-model/structure';
import { SequenceWrapper } from './util';
-import { OrderedSet, Interval } from '../../../mol-data/int';
+import { OrderedSet, Interval, SortedArray } from '../../../mol-data/int';
import { Loci } from '../../../mol-model/loci';
import { Sequence } from '../../../mol-model/sequence';
import { MissingResidues } from '../../../mol-model/structure/model/properties/common';
@@ -18,46 +18,52 @@ export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
private readonly location: StructureElement
private readonly sequence: Sequence
private readonly missing: MissingResidues
+ private readonly observed: OrderedSet // sequences indices
private readonly modelNum: number
private readonly asymId: string
- seqId(i: number) {
- return this.sequence.offset + i + 1
+ seqId(seqIdx: number) {
+ return this.sequence.offset + seqIdx + 1
}
- residueLabel(i: number) {
- return this.sequence.sequence[i]
+ residueLabel(seqIdx: number) {
+ return this.sequence.sequence[seqIdx]
}
- residueColor(i: number) {
- return this.missing.has(this.modelNum, this.asymId, this.seqId(i))
+ residueColor(seqIdx: number) {
+ return this.missing.has(this.modelNum, this.asymId, this.seqId(seqIdx))
? ColorNames.grey
: ColorNames.black
}
- eachResidue(loci: Loci, apply: (interval: Interval) => boolean) {
+ eachResidue(loci: Loci, apply: (set: OrderedSet) => boolean) {
let changed = false
const { structure, unit } = this.data
- if (!StructureElement.isLoci(loci)) return false
- if (!Structure.areParentsEquivalent(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(getSeqIdInterval(location))) changed = true
- rIprev = rI
- }
- })
+ 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
+ }
+ })
+ }
+ } else if (Structure.isLoci(loci)) {
+ if (!Structure.areParentsEqual(loci.structure, structure)) return false
+
+ if (apply(this.observed)) changed = true
}
return changed
}
@@ -70,7 +76,8 @@ export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
constructor(data: StructureUnit) {
const l = StructureElement.create(data.unit, data.unit.elements[0])
const sequence = data.unit.model.sequence.byEntityKey[SP.entity.key(l)].sequence
- const markerArray = new Uint8Array(sequence.sequence.length)
+ const length = sequence.sequence.length
+ const markerArray = new Uint8Array(length)
super(data, markerArray, sequence.sequence.length)
@@ -80,6 +87,12 @@ export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
this.modelNum = data.unit.model.modelNum
this.asymId = SP.chain.label_asym_id(l)
+
+ const missing: number[] = []
+ for (let i = 0; i < length; ++i) {
+ if (this.missing.has(this.modelNum, this.asymId, this.seqId(i))) missing.push(i)
+ }
+ this.observed = OrderedSet.subtract(Interval.ofBounds(0, length), SortedArray.ofSortedArray(missing))
}
}
@@ -101,8 +114,7 @@ function createResidueQuery(unitId: number, label_seq_id: number) {
});
}
-/** Zero-indexed */
-function getSeqIdInterval(location: StructureElement): Interval {
+function getSeqIndices(location: StructureElement): Interval {
const { unit, element } = location
const { model } = unit
switch (unit.kind) {
diff --git a/src/mol-plugin/ui/sequence/util.ts b/src/mol-plugin/ui/sequence/util.ts
index 91813be7a..158b47294 100644
--- a/src/mol-plugin/ui/sequence/util.ts
+++ b/src/mol-plugin/ui/sequence/util.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Interval } from '../../../mol-data/int';
+import { OrderedSet } from '../../../mol-data/int';
import { Loci } from '../../../mol-model/loci';
import { MarkerAction, applyMarkerAction } from '../../../mol-util/marker-action';
import { StructureElement } from '../../../mol-model/structure';
@@ -13,16 +13,16 @@ import { Color } from '../../../mol-util/color';
export { SequenceWrapper }
abstract class SequenceWrapper<D> {
- abstract seqId(i: number): number
- abstract residueLabel(i: number): string
- abstract residueColor(i: number): Color
+ abstract seqId(seqIdx: number): number
+ abstract residueLabel(seqIdx: number): string
+ abstract residueColor(seqIdx: number): Color
- abstract eachResidue(loci: Loci, apply: (interval: Interval) => boolean): boolean
+ abstract eachResidue(loci: Loci, apply: (set: OrderedSet) => boolean): boolean
abstract getLoci(seqId: number): StructureElement.Loci
markResidue(loci: Loci, action: MarkerAction) {
- return this.eachResidue(loci, (i: Interval) => {
- return applyMarkerAction(this.markerArray, i, action)
+ return this.eachResidue(loci, (set: OrderedSet) => {
+ return applyMarkerAction(this.markerArray, set, action)
})
}
--
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