diff --git a/src/mol-data/int/sorted-ranges.ts b/src/mol-data/int/sorted-ranges.ts
index 967595e0f670ba6840665ca03ebce519fcdde4bb..18b7c6b6470f5c3945e35894b17861c986e353eb 100644
--- a/src/mol-data/int/sorted-ranges.ts
+++ b/src/mol-data/int/sorted-ranges.ts
@@ -38,14 +38,14 @@ namespace SortedRanges {
hasNext: boolean = false;
- updateInterval() {
+ private updateInterval() {
this.interval = Interval.ofRange(this.ranges[this.curIndex], this.ranges[this.curIndex + 1])
}
- updateValue() {
+ private updateValue() {
this.value.index = this.curIndex / 2 as I
this.value.start = OrderedSet.findPredecessorIndex(this.set, this.ranges[this.curIndex])
- this.value.end = OrderedSet.findPredecessorIndex(this.set, this.ranges[this.curIndex + 1]) + 1
+ this.value.end = OrderedSet.findPredecessorIndex(this.set, this.ranges[this.curIndex + 1])
}
move() {
@@ -62,23 +62,22 @@ namespace SortedRanges {
return this.value;
}
- getRangeIndex(value: number) {
+ private getRangeIndex(value: number) {
const index = SortedArray.findPredecessorIndex(this.ranges, value)
return (index % 2 === 1) ? index - 1 : index
}
constructor(private ranges: SortedRanges<T>, private set: OrderedSet<T>) {
- // TODO cleanup, refactor to make it clearer
- const min = SortedArray.findPredecessorIndex(this.ranges, OrderedSet.min(set))
- const max = SortedArray.findPredecessorIndex(this.ranges, OrderedSet.max(set) + 1)
- if (ranges.length && min !== max) {
- this.curIndex = this.getRangeIndex(OrderedSet.min(set))
- this.maxIndex = Math.min(ranges.length - 2, this.getRangeIndex(OrderedSet.max(set)))
- this.curMin = this.ranges[this.curIndex]
+ const min = OrderedSet.min(set)
+ const max = OrderedSet.max(set)
+ const b = ranges.length > 0 && ranges[0] <= max && ranges[ranges.length - 1] >= min
+ if (b) {
+ this.curIndex = this.getRangeIndex(min)
+ this.maxIndex = Math.min(ranges.length - 2, this.getRangeIndex(max) + 2)
+ this.curMin = ranges[this.curIndex]
this.updateInterval()
}
-
- this.hasNext = ranges.length > 0 && min !== max && this.curIndex <= this.maxIndex
+ this.hasNext = b && this.curIndex <= this.maxIndex
}
}
}
diff --git a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
index fc96a75077a5681eeab5165dcc86421fdab6ce9f..b34b22a03c964b1762afbf45f3e7e3eb21eb3f38 100644
--- a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
+++ b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
@@ -5,7 +5,7 @@
*/
import { Unit, StructureElement, ElementIndex, ResidueIndex, Structure } from '../../../../../mol-model/structure';
-import { Segmentation } from '../../../../../mol-data/int';
+import { Segmentation, SortedArray } from '../../../../../mol-data/int';
import { MoleculeType, SecondaryStructureType } from '../../../../../mol-model/structure/model/types';
import Iterator from '../../../../../mol-data/iterator';
import { Vec3 } from '../../../../../mol-math/linear-algebra';
@@ -69,12 +69,14 @@ const tmpVecB = Vec3()
export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement> {
private value: PolymerTraceElement
- private polymerIt: SortedRanges.Iterator<ElementIndex, ResidueIndex>
+ private polymerIt: SortedRanges.Iterator<ElementIndex, number>
private residueIt: Segmentation.SegmentIterator<ResidueIndex>
- private polymerSegment: Segmentation.Segment<ResidueIndex>
+ private polymerSegment: Segmentation.Segment<number>
private cyclicPolymerMap: Map<ResidueIndex, ResidueIndex>
private secondaryStructureType: SecondaryStructure['type']
private secondaryStructureGetIndex: SecondaryStructure['getIndex']
+ private residueSegmentBeg: ResidueIndex
+ private residueSegmentEnd: ResidueIndex
private residueSegmentMin: ResidueIndex
private residueSegmentMax: ResidueIndex
private prevSecStrucType: SecondaryStructureType
@@ -84,6 +86,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
private currCoarseBackbone: boolean
private nextCoarseBackbone: boolean
private state: AtomicPolymerTraceIteratorState = AtomicPolymerTraceIteratorState.nextPolymer
+ private polymerRanges: SortedArray<ElementIndex>
private residueAtomSegments: Segmentation<ElementIndex, ResidueIndex>
private traceElementIndex: ArrayLike<ElementIndex>
private directionFromElementIndex: ArrayLike<ElementIndex | -1>
@@ -114,10 +117,12 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
}
}
- private updateResidueSegmentRange(polymerSegment: Segmentation.Segment<ResidueIndex>) {
+ private updateResidueSegmentRange(polymerSegment: Segmentation.Segment<number>) {
const { index } = this.residueAtomSegments
- this.residueSegmentMin = index[this.unit.elements[polymerSegment.start]]
- this.residueSegmentMax = index[this.unit.elements[polymerSegment.end - 1]]
+ this.residueSegmentBeg = index[this.unit.elements[polymerSegment.start]]
+ this.residueSegmentEnd = index[this.unit.elements[polymerSegment.end - 1]]
+ this.residueSegmentMin = index[this.polymerRanges[polymerSegment.index * 2]]
+ this.residueSegmentMax = index[this.polymerRanges[polymerSegment.index * 2 + 1] - 1]
}
private getResidueIndex(residueIndex: number) {
@@ -181,9 +186,9 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
if (residueIt.hasNext) {
this.state = AtomicPolymerTraceIteratorState.nextResidue
this.currSecStrucType = SecStrucTypeNA
- this.nextSecStrucType = this.getSecStruc(this.residueSegmentMin)
+ this.nextSecStrucType = this.getSecStruc(this.residueSegmentBeg)
this.currCoarseBackbone = false
- this.nextCoarseBackbone = this.directionFromElementIndex[this.residueSegmentMin] === -1 || this.directionToElementIndex[this.residueSegmentMin] === -1
+ this.nextCoarseBackbone = this.directionFromElementIndex[this.residueSegmentBeg] === -1 || this.directionToElementIndex[this.residueSegmentBeg] === -1
break
}
}
@@ -205,8 +210,8 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
value.isCoarseBackbone = this.currCoarseBackbone
value.coarseBackboneFirst = this.prevCoarseBackbone !== this.currCoarseBackbone
value.coarseBackboneLast = this.currCoarseBackbone !== this.nextCoarseBackbone
- value.first = residueIndex === this.residueSegmentMin
- value.last = residueIndex === this.residueSegmentMax
+ value.first = residueIndex === this.residueSegmentBeg
+ value.last = residueIndex === this.residueSegmentEnd
value.moleculeType = this.moleculeType[residueIndex]
value.isCoarseBackbone = this.directionFromElementIndex[residueIndex] === -1 || this.directionToElementIndex[residueIndex] === -1
@@ -272,12 +277,13 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
constructor(private unit: Unit.Atomic, structure: Structure) {
this.atomicConformation = unit.model.atomicConformation
this.residueAtomSegments = unit.model.atomicHierarchy.residueAtomSegments
+ this.polymerRanges = unit.model.atomicHierarchy.polymerRanges
this.traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex as ArrayLike<ElementIndex> // can assume it won't be -1 for polymer residues
this.directionFromElementIndex = unit.model.atomicHierarchy.derived.residue.directionFromElementIndex
this.directionToElementIndex = unit.model.atomicHierarchy.derived.residue.directionToElementIndex
this.moleculeType = unit.model.atomicHierarchy.derived.residue.moleculeType
this.cyclicPolymerMap = unit.model.atomicHierarchy.cyclicPolymerMap
- this.polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements)
+ this.polymerIt = SortedRanges.transientSegments(this.polymerRanges, unit.elements)
this.residueIt = Segmentation.transientSegments(this.residueAtomSegments, unit.elements);
this.value = createPolymerTraceElement(unit)
this.hasNext = this.residueIt.hasNext && this.polymerIt.hasNext