From 5e83c3350acc773666c1c208c5d90e945819e139 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 20 Aug 2019 12:51:16 -0700
Subject: [PATCH] added Structure.root
---
src/mol-model/structure/structure/element.ts | 6 +++---
src/mol-model/structure/structure/structure.ts | 15 ++++++++++-----
src/mol-plugin/state/transforms/representation.ts | 12 +++++-------
src/mol-plugin/ui/sequence/hetero.ts | 4 ++--
src/mol-plugin/ui/sequence/polymer.ts | 4 ++--
src/mol-plugin/util/interactivity.ts | 2 +-
src/mol-plugin/util/structure-overpaint-helper.ts | 3 +--
src/mol-repr/structure/complex-representation.ts | 2 +-
src/mol-repr/structure/complex-visual.ts | 2 +-
src/mol-repr/structure/units-representation.ts | 2 +-
src/mol-repr/structure/units-visual.ts | 2 +-
src/mol-repr/structure/visual/util/polymer.ts | 4 ++--
12 files changed, 30 insertions(+), 28 deletions(-)
diff --git a/src/mol-model/structure/structure/element.ts b/src/mol-model/structure/structure/element.ts
index ca472c660..5e4809a5e 100644
--- a/src/mol-model/structure/structure/element.ts
+++ b/src/mol-model/structure/structure/element.ts
@@ -575,7 +575,7 @@ namespace StructureElement {
elements.push({ groupedUnits, set: e.set, ranges: e.ranges })
})
- return { hash: (loci.structure.parent || loci.structure).hashCode, elements }
+ return { hash: loci.structure.root.hashCode, elements }
}
function getUnitsFromIds(unitIds: ArrayLike<number>, structure: Structure) {
@@ -588,7 +588,7 @@ namespace StructureElement {
}
export function toLoci(query: Query, parent: Structure): Loci {
- if (query.hash !== -1 && query.hash !== (parent.parent || parent).hashCode) {
+ if (query.hash !== -1 && query.hash !== parent.root.hashCode) {
new Error('Query not compatible with given structure')
}
const elements: Loci['elements'][0][] = []
@@ -625,7 +625,7 @@ namespace StructureElement {
}
export function toStructure(query: Query, parent: Structure): Structure {
- if (query.hash !== -1 && query.hash !== (parent.parent || parent).hashCode) {
+ if (query.hash !== -1 && query.hash !== parent.root.hashCode) {
new Error('Query not compatible with given structure')
}
const units: Unit[] = []
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 08bc5c107..1e278d2b9 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -146,7 +146,12 @@ class Structure {
return new Structure.ElementLocationIterator(this);
}
- /** the root/top-most parent or `undefined` in case this is the root */
+ /** The parent or itself in case this is the root */
+ get root() {
+ return this._props.parent || this;
+ }
+
+ /** The root/top-most parent or `undefined` in case this is the root */
get parent() {
return this._props.parent;
}
@@ -629,13 +634,13 @@ namespace Structure {
}
/** Check if the structures or their parents are equivalent */
- export function areParentsEquivalent(a: Structure, b: Structure) {
- return areEquivalent(a.parent || a, b.parent || b)
+ export function areRootsEquivalent(a: Structure, b: Structure) {
+ return areEquivalent(a.root, b.root)
}
/** Check if the structures or their parents are equal */
- export function areParentsEqual(a: Structure, b: Structure) {
- return (a.parent || a) === (b.parent || b)
+ export function areRootsEqual(a: Structure, b: Structure) {
+ return a.root === b.root
}
export class ElementLocationIterator implements Iterator<StructureElement> {
diff --git a/src/mol-plugin/state/transforms/representation.ts b/src/mol-plugin/state/transforms/representation.ts
index 8ec62e7bd..00349cc8d 100644
--- a/src/mol-plugin/state/transforms/representation.ts
+++ b/src/mol-plugin/state/transforms/representation.ts
@@ -302,23 +302,21 @@ const ExplodeStructureRepresentation3D = PluginStateTransform.BuiltIn({
},
apply({ a, params }) {
const structure = a.data.source.data;
- const rootStructure = structure.parent || structure;
- const unitTransforms = new StructureUnitTransforms(rootStructure);
+ const unitTransforms = new StructureUnitTransforms(structure.root);
explodeStructure(structure, unitTransforms, params.t);
return new SO.Molecule.Structure.Representation3DState({
state: { unitTransforms },
- initialState: { unitTransforms: new StructureUnitTransforms(rootStructure) },
- info: rootStructure,
+ initialState: { unitTransforms: new StructureUnitTransforms(structure.root) },
+ info: structure.root,
source: a
}, { label: `Explode T = ${params.t.toFixed(2)}` });
},
update({ a, b, newParams, oldParams }) {
const structure = a.data.source.data;
- const rootStructure = structure.parent || structure;
- if (b.data.info !== rootStructure) return StateTransformer.UpdateResult.Recreate;
+ if (b.data.info !== structure.root) return StateTransformer.UpdateResult.Recreate;
if (oldParams.t === newParams.t) return StateTransformer.UpdateResult.Unchanged;
const unitTransforms = b.data.state.unitTransforms!;
- explodeStructure(rootStructure, unitTransforms, newParams.t);
+ explodeStructure(structure.root, unitTransforms, newParams.t);
b.label = `Explode T = ${newParams.t.toFixed(2)}`;
b.data.source = a;
return StateTransformer.UpdateResult.Updated;
diff --git a/src/mol-plugin/ui/sequence/hetero.ts b/src/mol-plugin/ui/sequence/hetero.ts
index e42017d80..edf2ee50c 100644
--- a/src/mol-plugin/ui/sequence/hetero.ts
+++ b/src/mol-plugin/ui/sequence/hetero.ts
@@ -26,7 +26,7 @@ export class HeteroSequenceWrapper extends SequenceWrapper<StructureUnit> {
let changed = false
const { structure, unit } = this.data
if (StructureElement.isLoci(loci)) {
- if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ if (!Structure.areRootsEquivalent(loci.structure, structure)) return false
loci = StructureElement.Loci.remap(loci, structure)
for (const e of loci.elements) {
@@ -39,7 +39,7 @@ export class HeteroSequenceWrapper extends SequenceWrapper<StructureUnit> {
}
}
} else if (Structure.isLoci(loci)) {
- if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ if (!Structure.areRootsEquivalent(loci.structure, structure)) return false
if (apply(Interval.ofBounds(0, this.length))) changed = true
}
diff --git a/src/mol-plugin/ui/sequence/polymer.ts b/src/mol-plugin/ui/sequence/polymer.ts
index 0e5f1a26d..fa25a3255 100644
--- a/src/mol-plugin/ui/sequence/polymer.ts
+++ b/src/mol-plugin/ui/sequence/polymer.ts
@@ -37,7 +37,7 @@ export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
let changed = false
const { structure, unit } = this.data
if (StructureElement.isLoci(loci)) {
- if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ if (!Structure.areRootsEquivalent(loci.structure, structure)) return false
loci = StructureElement.Loci.remap(loci, structure)
const { offset } = this.sequence
@@ -49,7 +49,7 @@ export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
}
}
} else if (Structure.isLoci(loci)) {
- if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ if (!Structure.areRootsEquivalent(loci.structure, structure)) return false
if (apply(this.observed)) changed = true
}
diff --git a/src/mol-plugin/util/interactivity.ts b/src/mol-plugin/util/interactivity.ts
index 41289157b..31babee35 100644
--- a/src/mol-plugin/util/interactivity.ts
+++ b/src/mol-plugin/util/interactivity.ts
@@ -101,7 +101,7 @@ namespace Interactivity {
}
if (Structure.isLoci(loci)) {
// convert to StructureElement.Loci of root structure
- loci = Structure.toStructureElementLoci(Structure.Loci(loci.structure.parent || loci.structure))
+ loci = Structure.toStructureElementLoci(Structure.Loci(loci.structure.root))
}
if (StructureElement.isLoci(loci) && loci.structure.parent) {
// ensure the root structure is used
diff --git a/src/mol-plugin/util/structure-overpaint-helper.ts b/src/mol-plugin/util/structure-overpaint-helper.ts
index 120ea8ef0..47b3399f8 100644
--- a/src/mol-plugin/util/structure-overpaint-helper.ts
+++ b/src/mol-plugin/util/structure-overpaint-helper.ts
@@ -34,9 +34,8 @@ export class StructureOverpaintHelper {
const overpaint = state.select(StateSelection.Generators.ofTransformer(StateTransforms.Representation.OverpaintStructureRepresentation3D, r.transform.ref).withTag(OverpaintManagerTag));
const structure = r.obj!.data.source.data
- const rootStructure = structure.parent || structure
- callback(update, r, rootStructure, overpaint[0])
+ callback(update, r, structure.root, overpaint[0])
}
await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }));
diff --git a/src/mol-repr/structure/complex-representation.ts b/src/mol-repr/structure/complex-representation.ts
index bdd23b1ae..120e7332d 100644
--- a/src/mol-repr/structure/complex-representation.ts
+++ b/src/mol-repr/structure/complex-representation.ts
@@ -57,7 +57,7 @@ export function ComplexRepresentation<P extends StructureParams>(label: string,
function mark(loci: Loci, action: MarkerAction) {
if (!_structure) return false
if (!StructureElement.isLoci(loci) && !Link.isLoci(loci)) return false
- if (!Structure.areParentsEquivalent(loci.structure, _structure)) return false
+ if (!Structure.areRootsEquivalent(loci.structure, _structure)) return false
if (StructureElement.isLoci(loci)) {
loci = StructureElement.Loci.remap(loci, _structure)
} else if (Link.isLoci(loci)) {
diff --git a/src/mol-repr/structure/complex-visual.ts b/src/mol-repr/structure/complex-visual.ts
index 7770c03f5..7366c99e9 100644
--- a/src/mol-repr/structure/complex-visual.ts
+++ b/src/mol-repr/structure/complex-visual.ts
@@ -165,7 +165,7 @@ export function ComplexVisual<G extends Geometry, P extends ComplexParams & Geom
}
function lociApply(loci: Loci, apply: (interval: Interval) => boolean) {
- if (isEveryLoci(loci) || (Structure.isLoci(loci) && Structure.areParentsEquivalent(loci.structure, currentStructure))) {
+ if (isEveryLoci(loci) || (Structure.isLoci(loci) && Structure.areRootsEquivalent(loci.structure, currentStructure))) {
return apply(Interval.ofBounds(0, locationIt.groupCount * locationIt.instanceCount))
} else {
return eachLocation(loci, currentStructure, apply)
diff --git a/src/mol-repr/structure/units-representation.ts b/src/mol-repr/structure/units-representation.ts
index 63e206604..9bc1adc3e 100644
--- a/src/mol-repr/structure/units-representation.ts
+++ b/src/mol-repr/structure/units-representation.ts
@@ -166,7 +166,7 @@ export function UnitsRepresentation<P extends UnitsParams>(label: string, ctx: R
let changed = false
if (!_structure) return false
if (!StructureElement.isLoci(loci) && !Link.isLoci(loci)) return false
- if (!Structure.areParentsEquivalent(loci.structure, _structure)) return false
+ if (!Structure.areRootsEquivalent(loci.structure, _structure)) return false
if (StructureElement.isLoci(loci)) {
loci = StructureElement.Loci.remap(loci, _structure)
if (loci.elements.length === 0) return false
diff --git a/src/mol-repr/structure/units-visual.ts b/src/mol-repr/structure/units-visual.ts
index b440d393f..b6b38d23d 100644
--- a/src/mol-repr/structure/units-visual.ts
+++ b/src/mol-repr/structure/units-visual.ts
@@ -215,7 +215,7 @@ export function UnitsVisual<G extends Geometry, P extends UnitsParams & Geometry
}
function lociApply(loci: Loci, apply: (interval: Interval) => boolean) {
- if (isEveryLoci(loci) || (Structure.isLoci(loci) && Structure.areParentsEquivalent(loci.structure, currentStructureGroup.structure))) {
+ if (isEveryLoci(loci) || (Structure.isLoci(loci) && Structure.areRootsEquivalent(loci.structure, currentStructureGroup.structure))) {
return apply(Interval.ofBounds(0, locationIt.groupCount * locationIt.instanceCount))
} else {
return eachLocation(loci, currentStructureGroup, apply)
diff --git a/src/mol-repr/structure/visual/util/polymer.ts b/src/mol-repr/structure/visual/util/polymer.ts
index 33f99c023..61f369720 100644
--- a/src/mol-repr/structure/visual/util/polymer.ts
+++ b/src/mol-repr/structure/visual/util/polymer.ts
@@ -162,7 +162,7 @@ export function eachPolymerGapElement(loci: Loci, structureGroup: StructureGroup
let changed = false
if (Link.isLoci(loci)) {
const { structure, group } = structureGroup
- if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ if (!Structure.areRootsEquivalent(loci.structure, structure)) return false
loci = Link.remapLoci(loci, structure)
const groupCount = group.units[0].gapElements.length
for (const b of loci.links) {
@@ -177,7 +177,7 @@ export function eachPolymerGapElement(loci: Loci, structureGroup: StructureGroup
}
} else if (StructureElement.isLoci(loci)) {
const { structure, group } = structureGroup
- if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ if (!Structure.areRootsEquivalent(loci.structure, structure)) return false
loci = StructureElement.Loci.remap(loci, structure)
const groupCount = group.units[0].gapElements.length
for (const e of loci.elements) {
--
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