From ed1ae71f71806721438d241cc0a8800bca2b4f7e Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sun, 18 Aug 2019 13:01:31 -0700
Subject: [PATCH] optimized repr loci iteration, marking and
extendToWholeChains
---
src/mol-model/structure/structure/element.ts | 13 +++++--
.../structure/units-representation.ts | 2 ++
.../structure/visual/util/nucleotide.ts | 36 ++++++++++++-------
src/mol-repr/structure/visual/util/polymer.ts | 32 ++++++++++-------
4 files changed, 54 insertions(+), 29 deletions(-)
diff --git a/src/mol-model/structure/structure/element.ts b/src/mol-model/structure/structure/element.ts
index eb0cb0577..ca472c660 100644
--- a/src/mol-model/structure/structure/element.ts
+++ b/src/mol-model/structure/structure/element.ts
@@ -282,7 +282,7 @@ namespace StructureElement {
const elements: Loci['elements'][0][] = [];
for (const lociElement of loci.elements) {
- const newIndices: UnitIndex[] = [];
+ const _newIndices: UnitIndex[] = [];
const unitElements = lociElement.unit.elements;
const { index: chainIndex, offsets: chainOffsets } = getChainSegments(lociElement.unit)
@@ -298,11 +298,18 @@ namespace StructureElement {
for (let j = chainOffsets[cI], _j = chainOffsets[cI + 1]; j < _j; j++) {
const idx = OrderedSet.indexOf(unitElements, j);
- if (idx >= 0) newIndices[newIndices.length] = idx as UnitIndex;
+ if (idx >= 0) _newIndices[_newIndices.length] = idx as UnitIndex;
}
}
- elements[elements.length] = { unit: lociElement.unit, indices: SortedArray.ofSortedArray(newIndices) };
+ let newIndices: OrderedSet<UnitIndex>
+ if (_newIndices.length > 12 && _newIndices[_newIndices.length - 1] - _newIndices[0] === _newIndices.length - 1) {
+ newIndices = Interval.ofRange(_newIndices[0], _newIndices[_newIndices.length - 1])
+ } else {
+ newIndices = SortedArray.ofSortedArray(_newIndices)
+ }
+
+ elements[elements.length] = { unit: lociElement.unit, indices: newIndices };
}
return Loci(loci.structure, elements);
diff --git a/src/mol-repr/structure/units-representation.ts b/src/mol-repr/structure/units-representation.ts
index cbc6eb000..63e206604 100644
--- a/src/mol-repr/structure/units-representation.ts
+++ b/src/mol-repr/structure/units-representation.ts
@@ -169,8 +169,10 @@ export function UnitsRepresentation<P extends UnitsParams>(label: string, ctx: R
if (!Structure.areParentsEquivalent(loci.structure, _structure)) return false
if (StructureElement.isLoci(loci)) {
loci = StructureElement.Loci.remap(loci, _structure)
+ if (loci.elements.length === 0) return false
} else if (Link.isLoci(loci)) {
loci = Link.remapLoci(loci, _structure)
+ if (loci.links.length === 0) return false
}
visuals.forEach(({ visual }) => {
changed = visual.mark(loci, action) || changed
diff --git a/src/mol-repr/structure/visual/util/nucleotide.ts b/src/mol-repr/structure/visual/util/nucleotide.ts
index e3d968dea..9d9787fb6 100644
--- a/src/mol-repr/structure/visual/util/nucleotide.ts
+++ b/src/mol-repr/structure/visual/util/nucleotide.ts
@@ -41,6 +41,10 @@ export function getNucleotideElementLoci(pickingId: PickingId, structureGroup: S
return EmptyLoci
}
+/**
+ * Mark a nucleotide element (e.g. part of a cartoon block)
+ * - mark only when all its residue's elements are in a loci
+ */
export function eachNucleotideElement(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
let changed = false
if (!StructureElement.isLoci(loci)) return false
@@ -56,19 +60,25 @@ export function eachNucleotideElement(loci: Loci, structureGroup: StructureGroup
const unitIdx = group.unitIndexMap.get(e.unit.id)
const eUnit = e.unit
if (unitIdx !== undefined && Unit.isAtomic(eUnit)) {
- // TODO optimized implementation for intervals
- OrderedSet.forEach(e.indices, v => {
- const rI = index[elements[v]]
- const unitIndexMin = OrderedSet.findPredecessorIndex(elements, offsets[rI])
- const unitIndexMax = OrderedSet.findPredecessorIndex(elements, offsets[rI + 1] - 1)
- const unitIndexInterval = Interval.ofRange(unitIndexMin, unitIndexMax)
- if (!OrderedSet.isSubset(e.indices, unitIndexInterval)) return
- const eI = traceElementIndex[rI]
- const idx = OrderedSet.indexOf(eUnit.nucleotideElements, eI)
- if (idx !== -1) {
- if (apply(Interval.ofSingleton(unitIdx * groupCount + idx))) changed = true
- }
- })
+ // TODO optimized implementation for intervals covering only part of the unit
+ if (Interval.is(e.indices) && Interval.start(e.indices) === 0 && Interval.end(e.indices) === e.unit.elements.length) {
+ const start = unitIdx * groupCount;
+ const end = unitIdx * groupCount + groupCount;
+ if (apply(Interval.ofBounds(start, end))) changed = true
+ } else {
+ OrderedSet.forEach(e.indices, v => {
+ const rI = index[elements[v]]
+ const unitIndexMin = OrderedSet.findPredecessorIndex(elements, offsets[rI])
+ const unitIndexMax = OrderedSet.findPredecessorIndex(elements, offsets[rI + 1] - 1)
+ const unitIndexInterval = Interval.ofRange(unitIndexMin, unitIndexMax)
+ if (!OrderedSet.isSubset(e.indices, unitIndexInterval)) return
+ const eI = traceElementIndex[rI]
+ const idx = OrderedSet.indexOf(eUnit.nucleotideElements, eI)
+ if (idx !== -1) {
+ if (apply(Interval.ofSingleton(unitIdx * groupCount + idx))) changed = true
+ }
+ })
+ }
}
}
return changed
diff --git a/src/mol-repr/structure/visual/util/polymer.ts b/src/mol-repr/structure/visual/util/polymer.ts
index 401626df0..33f99c023 100644
--- a/src/mol-repr/structure/visual/util/polymer.ts
+++ b/src/mol-repr/structure/visual/util/polymer.ts
@@ -104,19 +104,25 @@ export function eachPolymerElement(loci: Loci, structureGroup: StructureGroup, a
const unitIdx = group.unitIndexMap.get(e.unit.id)
if (unitIdx !== undefined) {
if (Unit.isAtomic(e.unit)) {
- // TODO optimized implementation for intervals
- OrderedSet.forEach(e.indices, v => {
- const rI = index[elements[v]]
- const unitIndexMin = OrderedSet.findPredecessorIndex(elements, offsets[rI])
- const unitIndexMax = OrderedSet.findPredecessorIndex(elements, offsets[rI + 1] - 1)
- const unitIndexInterval = Interval.ofRange(unitIndexMin, unitIndexMax)
- if (!OrderedSet.isSubset(e.indices, unitIndexInterval)) return
- const eI = traceElementIndex[rI]
- const idx = OrderedSet.indexOf(e.unit.polymerElements, eI)
- if (idx !== -1) {
- if (apply(Interval.ofSingleton(unitIdx * groupCount + idx))) changed = true
- }
- })
+ // TODO optimized implementation for intervals covering only part of the unit
+ if (Interval.is(e.indices) && Interval.start(e.indices) === 0 && Interval.end(e.indices) === e.unit.elements.length) {
+ const start = unitIdx * groupCount;
+ const end = unitIdx * groupCount + groupCount;
+ if (apply(Interval.ofBounds(start, end))) changed = true
+ } else {
+ OrderedSet.forEach(e.indices, v => {
+ const rI = index[elements[v]]
+ const unitIndexMin = OrderedSet.findPredecessorIndex(elements, offsets[rI])
+ const unitIndexMax = OrderedSet.findPredecessorIndex(elements, offsets[rI + 1] - 1)
+ const unitIndexInterval = Interval.ofRange(unitIndexMin, unitIndexMax)
+ if (!OrderedSet.isSubset(e.indices, unitIndexInterval)) return
+ const eI = traceElementIndex[rI]
+ const idx = OrderedSet.indexOf(e.unit.polymerElements, eI)
+ if (idx !== -1) {
+ if (apply(Interval.ofSingleton(unitIdx * groupCount + idx))) changed = true
+ }
+ })
+ }
} else {
if (Interval.is(e.indices)) {
const start = unitIdx * groupCount + Interval.start(e.indices);
--
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