From db350ddfd32f708c018d5f3e35b2bb3c1da97ee5 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Mon, 30 Aug 2021 22:42:16 -0700
Subject: [PATCH] loci/marking performance improvements
- use Interval for ranges instead of SortedArray
- pre-check if loci overlaps with unit visual
---
CHANGELOG.md | 10 ++++++--
.../structure/structure/element/loci.ts | 23 +++++++++++--------
src/mol-repr/structure/units-visual.ts | 13 ++++++++++-
src/mol-repr/structure/visual/util/element.ts | 3 ++-
src/mol-repr/visual.ts | 1 +
5 files changed, 36 insertions(+), 14 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 72167849c..2117ef1b1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,9 +10,15 @@ Note that since we don't clearly distinguish between a public and private interf
- Add ``Mesh`` processing helper ``.smoothEdges``
- Smooth border of molecular-surface with ``includeParent`` enabled
- Hide ``includeParent`` option from gaussian-surface visuals (not particularly useful)
-- Improved ``StructureElement.Loci.size`` performance (for marking large cellpack models)
- Fix new ``TransformData`` issues (camera/bounding helper not showing up)
-- Improve marking performance (avoid superfluous calls to ``StructureElement.Loci.isWholeStructure``)
+- Improve marking performance
+ - Avoid superfluous calls to ``StructureElement.Loci.isWholeStructure``
+ - Check if loci is superset of visual
+ - Check if loci overlaps with unit visual
+ - Ensure ``Interval`` is used for ranges instead of ``SortedArray``
+ - Inline ``StructureElement.Loci.size`` code
+ - Add uniform marker type
+ - Special case for reversing previous mark
- Add optional marking pass
- Outlines visible and hidden parts of highlighted/selected groups
- Add highlightStrength/selectStrength renderer params
diff --git a/src/mol-model/structure/structure/element/loci.ts b/src/mol-model/structure/structure/element/loci.ts
index cce5eff09..cb68abbdd 100644
--- a/src/mol-model/structure/structure/element/loci.ts
+++ b/src/mol-model/structure/structure/element/loci.ts
@@ -253,6 +253,14 @@ export namespace Loci {
return isSubset;
}
+ function makeIndexSet(newIndices: ArrayLike<UnitIndex>): OrderedSet<UnitIndex> {
+ if (newIndices.length > 3 && SortedArray.isRange(newIndices)) {
+ return Interval.ofRange(newIndices[0], newIndices[newIndices.length - 1]);
+ } else {
+ return SortedArray.ofSortedArray(newIndices);
+ }
+ }
+
export function extendToWholeResidues(loci: Loci, restrictToConformation?: boolean): Loci {
const elements: Loci['elements'][0][] = [];
const residueAltIds = new Set<string>();
@@ -297,7 +305,7 @@ export namespace Loci {
}
}
- elements[elements.length] = { unit: lociElement.unit, indices: SortedArray.ofSortedArray(newIndices) };
+ elements[elements.length] = { unit: lociElement.unit, indices: makeIndexSet(newIndices) };
} else {
// coarse elements are already by-residue
elements[elements.length] = lociElement;
@@ -319,14 +327,6 @@ export namespace Loci {
return element.unit.elements.length === OrderedSet.size(element.indices);
}
- function makeIndexSet(newIndices: number[]): OrderedSet<UnitIndex> {
- if (newIndices.length > 12 && newIndices[newIndices.length - 1] - newIndices[0] === newIndices.length - 1) {
- return Interval.ofRange(newIndices[0], newIndices[newIndices.length - 1]);
- } else {
- return SortedArray.ofSortedArray(newIndices);
- }
- }
-
function collectChains(unit: Unit, chainIndices: Set<ChainIndex>, elements: Loci['elements'][0][]) {
const { index } = getChainSegments(unit);
const xs = unit.elements;
@@ -470,7 +470,10 @@ export namespace Loci {
}
function getUnitIndices(elements: SortedArray<ElementIndex>, indices: SortedArray<ElementIndex>) {
- return OrderedSet.ofSortedArray(SortedArray.indicesOf<ElementIndex, UnitIndex>(elements, indices));
+ if (SortedArray.areEqual(elements, indices) && SortedArray.isRange(elements)) {
+ return Interval.ofLength(elements.length);
+ }
+ return makeIndexSet(SortedArray.indicesOf<ElementIndex, UnitIndex>(elements, indices));
}
export function extendToAllInstances(loci: Loci): Loci {
diff --git a/src/mol-repr/structure/units-visual.ts b/src/mol-repr/structure/units-visual.ts
index 8acaf871b..e4105f9eb 100644
--- a/src/mol-repr/structure/units-visual.ts
+++ b/src/mol-repr/structure/units-visual.ts
@@ -290,7 +290,18 @@ export function UnitsVisual<G extends Geometry, P extends StructureParams & Geom
return renderObject ? getLoci(pickingId, currentStructureGroup, renderObject.id) : EmptyLoci;
},
mark(loci: Loci, action: MarkerAction) {
- return Visual.mark(renderObject, loci, action, lociApply, previousMark);
+ let hasInvariantId = true;
+ if (StructureElement.Loci.is(loci)) {
+ hasInvariantId = false;
+ const { invariantId } = currentStructureGroup.group.units[0];
+ for (const e of loci.elements) {
+ if (e.unit.invariantId === invariantId) {
+ hasInvariantId = true;
+ break;
+ }
+ }
+ }
+ return hasInvariantId ? Visual.mark(renderObject, loci, action, lociApply, previousMark) : false;
},
setVisibility(visible: boolean) {
Visual.setVisibility(renderObject, visible);
diff --git a/src/mol-repr/structure/visual/util/element.ts b/src/mol-repr/structure/visual/util/element.ts
index b9a8ea919..34ca57ffa 100644
--- a/src/mol-repr/structure/visual/util/element.ts
+++ b/src/mol-repr/structure/visual/util/element.ts
@@ -164,8 +164,9 @@ export function eachElement(loci: Loci, structureGroup: StructureGroup, apply: (
const { structure, group } = structureGroup;
if (!Structure.areEquivalent(loci.structure, structure)) return false;
const elementCount = group.elements.length;
+ const { unitIndexMap } = group;
for (const e of loci.elements) {
- const unitIdx = group.unitIndexMap.get(e.unit.id);
+ const unitIdx = unitIndexMap.get(e.unit.id);
if (unitIdx !== undefined) {
const offset = unitIdx * elementCount; // to target unit instance
if (Interval.is(e.indices)) {
diff --git a/src/mol-repr/visual.ts b/src/mol-repr/visual.ts
index 13689cee5..163a47dfa 100644
--- a/src/mol-repr/visual.ts
+++ b/src/mol-repr/visual.ts
@@ -84,6 +84,7 @@ namespace Visual {
intervalSize += Interval.size(interval);
return true;
}, true);
+ if (intervalSize === 0) return false;
if (intervalSize === count) loci = EveryLoci;
}
--
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