From 1f2631ffd6e1a918de936ebf33458acc23cf1c07 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 5 Mar 2019 10:51:06 -0800
Subject: [PATCH] refactored repr.mark
---
.../representations/assembly-symmetry-axes.ts | 4 +-
src/mol-repr/shape/representation.ts | 50 ++++++++++++-------
src/mol-repr/structure/complex-visual.ts | 6 +--
src/mol-repr/structure/units-visual.ts | 6 +--
.../visual/carbohydrate-link-cylinder.ts | 4 +-
.../visual/carbohydrate-symbol-mesh.ts | 6 +--
.../carbohydrate-terminal-link-cylinder.ts | 6 +--
.../visual/cross-link-restraint-cylinder.ts | 4 +-
.../structure/visual/element-point.ts | 4 +-
.../structure/visual/element-sphere.ts | 6 +--
.../visual/gaussian-density-point.ts | 2 +-
.../visual/gaussian-density-volume.ts | 2 +-
.../structure/visual/gaussian-surface-mesh.ts | 4 +-
.../visual/gaussian-surface-wireframe.ts | 4 +-
.../visual/inter-unit-link-cylinder.ts | 4 +-
.../visual/intra-unit-link-cylinder.ts | 4 +-
.../structure/visual/nucleotide-block-mesh.ts | 4 +-
.../visual/polymer-backbone-cylinder.ts | 4 +-
.../visual/polymer-direction-wedge.ts | 4 +-
.../structure/visual/polymer-gap-cylinder.ts | 4 +-
.../structure/visual/polymer-trace-mesh.ts | 4 +-
src/mol-repr/structure/visual/util/element.ts | 2 +-
.../structure/visual/util/nucleotide.ts | 2 +-
src/mol-repr/structure/visual/util/polymer.ts | 4 +-
24 files changed, 80 insertions(+), 64 deletions(-)
diff --git a/src/mol-model-props/rcsb/representations/assembly-symmetry-axes.ts b/src/mol-model-props/rcsb/representations/assembly-symmetry-axes.ts
index a949d4dfc..09abfebeb 100644
--- a/src/mol-model-props/rcsb/representations/assembly-symmetry-axes.ts
+++ b/src/mol-model-props/rcsb/representations/assembly-symmetry-axes.ts
@@ -65,7 +65,7 @@ export function AssemblySymmetryAxesVisual(): ComplexVisual<AssemblySymmetryAxes
createGeometry: createAssemblySymmetryAxesMesh,
createLocationIterator,
getLoci,
- mark,
+ eachLocation: eachAxisLocation,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<AssemblySymmetryAxesParams>, currentProps: PD.Values<AssemblySymmetryAxesParams>) => {
state.createGeometry = (
newProps.sizeFactor !== currentProps.sizeFactor ||
@@ -93,7 +93,7 @@ function getLoci(pickingId: PickingId, structure: Structure, id: number) {
return EmptyLoci
}
-function mark(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
+function eachAxisLocation(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
let changed = false
if (!isDataLoci(loci) || loci.tag !== 'axes') return false
const assemblySymmetry = AssemblySymmetry.get(structure.models[0])
diff --git a/src/mol-repr/shape/representation.ts b/src/mol-repr/shape/representation.ts
index 7083810e3..7128c985b 100644
--- a/src/mol-repr/shape/representation.ts
+++ b/src/mol-repr/shape/representation.ts
@@ -169,24 +169,19 @@ export function ShapeRepresentation<D, G extends Geometry, P extends Geometry.Pa
mark(loci: Loci, action: MarkerAction) {
if (!_renderObject) return false
const { tMarker } = _renderObject.values
+ const { groupCount, instanceCount } = locationIt
+
+ function apply(interval: Interval) {
+ const start = Interval.start(interval)
+ const end = Interval.end(interval)
+ return applyMarkerAction(tMarker.ref.value.array, start, end, action)
+ }
+
let changed = false
- const { groupCount, count } = locationIt
- if (isEveryLoci(loci)) {
- if (applyMarkerAction(tMarker.ref.value.array, 0, count, action)) changed = true
- } else if (Shape.isLoci(loci)) {
- const { instance, groups } = loci
- for (const g of groups) {
- if (Interval.is(g.ids)) {
- const start = instance * groupCount + Interval.start(g.ids)
- const end = instance * groupCount + Interval.end(g.ids)
- if (applyMarkerAction(tMarker.ref.value.array, start, end, action)) changed = true
- } else {
- for (let i = 0, _i = g.ids.length; i < _i; i++) {
- const idx = instance * groupCount + g.ids[i];
- if (applyMarkerAction(tMarker.ref.value.array, idx, idx + 1, action)) changed = true
- }
- }
- }
+ if (isEveryLoci(loci) || (Shape.isLoci(loci) && loci.shape === _shape)) {
+ changed = apply(Interval.ofBounds(0, groupCount * instanceCount))
+ } else {
+ changed = eachShapeLocation(loci, _shape, apply)
}
if (changed) {
ValueCell.update(tMarker, tMarker.ref.value)
@@ -221,6 +216,27 @@ function createShapeTransform(transforms: Mat4[], transformData?: TransformData)
return createTransform(transformArray, transforms.length, transformData)
}
+function eachShapeLocation(loci: Loci, shape: Shape, apply: (interval: Interval) => boolean) {
+ if (!Shape.isLoci(loci)) return false
+ if (loci.shape !== shape) return false
+ let changed = false
+ const { groupCount } = shape
+ const { instance, groups } = loci
+ for (const g of groups) {
+ if (Interval.is(g.ids)) {
+ const start = instance * groupCount + Interval.start(g.ids)
+ const end = instance * groupCount + Interval.end(g.ids)
+ if (apply(Interval.ofBounds(start, end))) changed = true
+ } else {
+ for (let i = 0, _i = g.ids.length; i < _i; i++) {
+ const idx = instance * groupCount + g.ids[i];
+ if (apply(Interval.ofSingleton(idx))) changed = true
+ }
+ }
+ }
+ return changed
+}
+
export namespace ShapeGroupIterator {
export function fromShape(shape: Shape): LocationIterator {
const instanceCount = shape.transforms.length
diff --git a/src/mol-repr/structure/complex-visual.ts b/src/mol-repr/structure/complex-visual.ts
index 833e2126c..c58d824cd 100644
--- a/src/mol-repr/structure/complex-visual.ts
+++ b/src/mol-repr/structure/complex-visual.ts
@@ -50,7 +50,7 @@ interface ComplexVisualBuilder<P extends ComplexParams, G extends Geometry> {
createGeometry(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<P>, geometry?: G): Promise<G> | G
createLocationIterator(structure: Structure): LocationIterator
getLoci(pickingId: PickingId, structure: Structure, id: number): Loci
- mark(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean): boolean,
+ eachLocation(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean): boolean,
setUpdateState(state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme): void
}
@@ -59,7 +59,7 @@ interface ComplexVisualGeometryBuilder<P extends UnitsParams, G extends Geometry
}
export function ComplexVisual<G extends Geometry, P extends ComplexParams & Geometry.Params<G>>(builder: ComplexVisualGeometryBuilder<P, G>): ComplexVisual<P> {
- const { defaultProps, createGeometry, createLocationIterator, getLoci, mark, setUpdateState } = builder
+ const { defaultProps, createGeometry, createLocationIterator, getLoci, eachLocation, setUpdateState } = builder
const { updateValues, updateBoundingSphere, updateRenderableState } = builder.geometryUtils
const updateState = VisualUpdateState.create()
@@ -187,7 +187,7 @@ export function ComplexVisual<G extends Geometry, P extends ComplexParams & Geom
if (isEveryLoci(loci) || (Structure.isLoci(loci) && loci.structure === currentStructure)) {
changed = apply(Interval.ofBounds(0, groupCount * instanceCount))
} else {
- changed = mark(loci, currentStructure, apply)
+ changed = eachLocation(loci, currentStructure, apply)
}
if (changed) {
ValueCell.update(tMarker, tMarker.ref.value)
diff --git a/src/mol-repr/structure/units-visual.ts b/src/mol-repr/structure/units-visual.ts
index 074597241..b036046bd 100644
--- a/src/mol-repr/structure/units-visual.ts
+++ b/src/mol-repr/structure/units-visual.ts
@@ -49,7 +49,7 @@ interface UnitsVisualBuilder<P extends UnitsParams, G extends Geometry> {
createGeometry(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<P>, geometry?: G): Promise<G> | G
createLocationIterator(group: Unit.SymmetryGroup): LocationIterator
getLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): Loci
- mark(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean): boolean
+ eachLocation(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean): boolean
setUpdateState(state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme): void
}
@@ -58,7 +58,7 @@ interface UnitsVisualGeometryBuilder<P extends UnitsParams, G extends Geometry>
}
export function UnitsVisual<G extends Geometry, P extends UnitsParams & Geometry.Params<G>>(builder: UnitsVisualGeometryBuilder<P, G>): UnitsVisual<P> {
- const { defaultProps, createGeometry, createLocationIterator, getLoci, mark, setUpdateState } = builder
+ const { defaultProps, createGeometry, createLocationIterator, getLoci, eachLocation, setUpdateState } = builder
const { createEmpty: createEmptyGeometry, updateValues, updateBoundingSphere, updateRenderableState } = builder.geometryUtils
const updateState = VisualUpdateState.create()
@@ -233,7 +233,7 @@ export function UnitsVisual<G extends Geometry, P extends UnitsParams & Geometry
if (isEveryLoci(loci) || (Structure.isLoci(loci) && loci.structure === currentStructureGroup.structure)) {
changed = apply(Interval.ofBounds(0, groupCount * instanceCount))
} else {
- changed = mark(loci, currentStructureGroup, apply)
+ changed = eachLocation(loci, currentStructureGroup, apply)
}
if (changed) {
ValueCell.update(tMarker, tMarker.ref.value)
diff --git a/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts b/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
index e9c9cfb4a..431faff76 100644
--- a/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
@@ -61,7 +61,7 @@ export function CarbohydrateLinkVisual(): ComplexVisual<CarbohydrateLinkParams>
createGeometry: createCarbohydrateLinkCylinderMesh,
createLocationIterator: CarbohydrateLinkIterator,
getLoci: getLinkLoci,
- mark: markLink,
+ eachLocation: eachCarbohydrateLink,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<CarbohydrateLinkParams>, currentProps: PD.Values<CarbohydrateLinkParams>) => {
state.createGeometry = (
newProps.linkSizeFactor !== currentProps.linkSizeFactor ||
@@ -116,7 +116,7 @@ function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
return EmptyLoci
}
-function markLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
+function eachCarbohydrateLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
let changed = false
if (Link.isLoci(loci)) {
if (loci.structure !== structure) return false
diff --git a/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts b/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
index e0df24ab3..2650b9405 100644
--- a/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
@@ -154,7 +154,7 @@ export function CarbohydrateSymbolVisual(): ComplexVisual<CarbohydrateSymbolPara
createGeometry: createCarbohydrateSymbolMesh,
createLocationIterator: CarbohydrateElementIterator,
getLoci: getCarbohydrateLoci,
- mark: markCarbohydrate,
+ eachLocation: eachCarbohydrate,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<CarbohydrateSymbolParams>, currentProps: PD.Values<CarbohydrateSymbolParams>) => {
state.createGeometry = (
newProps.sizeFactor !== currentProps.sizeFactor ||
@@ -191,8 +191,8 @@ function getCarbohydrateLoci(pickingId: PickingId, structure: Structure, id: num
return EmptyLoci
}
-/** Mark a carbohydrate (usually a monosaccharide) when all its residue's elements are in a loci. */
-function markCarbohydrate(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
+/** For each carbohydrate (usually a monosaccharide) when all its residue's elements are in a loci. */
+function eachCarbohydrate(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
const { getElementIndex, getAnomericCarbon } = structure.carbohydrates
let changed = false
if (StructureElement.isLoci(loci)) {
diff --git a/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts b/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
index 69368d4ca..ae52c083a 100644
--- a/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
@@ -71,7 +71,7 @@ export function CarbohydrateTerminalLinkVisual(): ComplexVisual<CarbohydrateTerm
createGeometry: createCarbohydrateTerminalLinkCylinderMesh,
createLocationIterator: CarbohydrateTerminalLinkIterator,
getLoci: getTerminalLinkLoci,
- mark: markTerminalLink,
+ eachLocation: eachTerminalLink,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<CarbohydrateTerminalLinkParams>, currentProps: PD.Values<CarbohydrateTerminalLinkParams>) => {
state.createGeometry = (
newProps.linkSizeFactor !== currentProps.linkSizeFactor ||
@@ -128,8 +128,8 @@ function getTerminalLinkLoci(pickingId: PickingId, structure: Structure, id: num
return EmptyLoci
}
-// TODO mark link when both of the link elements are in a StructureElement.Loci
-function markTerminalLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
+// TODO for each link when both of the link elements are in a StructureElement.Loci
+function eachTerminalLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
const { getTerminalLinkIndex } = structure.carbohydrates
let changed = false
diff --git a/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts b/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts
index 5c5c8d388..1eb290b62 100644
--- a/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts
+++ b/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts
@@ -64,7 +64,7 @@ export function CrossLinkRestraintVisual(): ComplexVisual<CrossLinkRestraintPara
createGeometry: createCrossLinkRestraintCylinderMesh,
createLocationIterator: CrossLinkRestraintIterator,
getLoci: getLinkLoci,
- mark: markLink,
+ eachLocation: eachCrossLink,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<CrossLinkRestraintParams>, currentProps: PD.Values<CrossLinkRestraintParams>) => {
state.createGeometry = (
newProps.sizeFactor !== currentProps.sizeFactor ||
@@ -104,7 +104,7 @@ function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
return EmptyLoci
}
-function markLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
+function eachCrossLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
const crossLinks = structure.crossLinkRestraints
let changed = false
diff --git a/src/mol-repr/structure/visual/element-point.ts b/src/mol-repr/structure/visual/element-point.ts
index 73c77715b..64db953cb 100644
--- a/src/mol-repr/structure/visual/element-point.ts
+++ b/src/mol-repr/structure/visual/element-point.ts
@@ -7,7 +7,7 @@
import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual } from '../representation';
import { VisualUpdateState } from '../../util';
-import { getElementLoci, StructureElementIterator, markElement } from './util/element';
+import { getElementLoci, StructureElementIterator, eachElement } from './util/element';
import { Vec3 } from 'mol-math/linear-algebra';
import { UnitsPointsVisual, UnitsPointsParams } from '../units-visual';
import { ParamDefinition as PD } from 'mol-util/param-definition';
@@ -48,7 +48,7 @@ export function ElementPointVisual(): UnitsVisual<ElementPointParams> {
createGeometry: createElementPoint,
createLocationIterator: StructureElementIterator.fromGroup,
getLoci: getElementLoci,
- mark: markElement,
+ eachLocation: eachElement,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<ElementPointParams>, currentProps: PD.Values<ElementPointParams>) => {
}
diff --git a/src/mol-repr/structure/visual/element-sphere.ts b/src/mol-repr/structure/visual/element-sphere.ts
index 4608121fc..afbe90fbb 100644
--- a/src/mol-repr/structure/visual/element-sphere.ts
+++ b/src/mol-repr/structure/visual/element-sphere.ts
@@ -7,7 +7,7 @@
import { UnitsVisual } from '../representation';
import { VisualUpdateState } from '../../util';
-import { createElementSphereMesh, markElement, getElementLoci, StructureElementIterator, createElementSphereImpostor } from './util/element';
+import { createElementSphereMesh, eachElement, getElementLoci, StructureElementIterator, createElementSphereImpostor } from './util/element';
import { UnitsMeshVisual, UnitsMeshParams, UnitsSpheresVisual, UnitsSpheresParams } from '../units-visual';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { WebGLContext } from 'mol-gl/webgl/context';
@@ -30,7 +30,7 @@ export function ElementSphereImpostorVisual(): UnitsVisual<ElementSphereParams>
createGeometry: createElementSphereImpostor,
createLocationIterator: StructureElementIterator.fromGroup,
getLoci: getElementLoci,
- mark: markElement,
+ eachLocation: eachElement,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<ElementSphereParams>, currentProps: PD.Values<ElementSphereParams>) => {
}
@@ -43,7 +43,7 @@ export function ElementSphereMeshVisual(): UnitsVisual<ElementSphereParams> {
createGeometry: createElementSphereMesh,
createLocationIterator: StructureElementIterator.fromGroup,
getLoci: getElementLoci,
- mark: markElement,
+ eachLocation: eachElement,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<ElementSphereParams>, currentProps: PD.Values<ElementSphereParams>) => {
state.createGeometry = (
newProps.sizeFactor !== currentProps.sizeFactor ||
diff --git a/src/mol-repr/structure/visual/gaussian-density-point.ts b/src/mol-repr/structure/visual/gaussian-density-point.ts
index 3e260df8c..beef6aae6 100644
--- a/src/mol-repr/structure/visual/gaussian-density-point.ts
+++ b/src/mol-repr/structure/visual/gaussian-density-point.ts
@@ -61,7 +61,7 @@ export function GaussianDensityPointVisual(): UnitsVisual<GaussianDensityPointPa
createGeometry: createGaussianDensityPoint,
createLocationIterator: StructureElementIterator.fromGroup,
getLoci: () => EmptyLoci,
- mark: () => false,
+ eachLocation: () => false,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<GaussianDensityPointParams>, currentProps: PD.Values<GaussianDensityPointParams>) => {
if (newProps.resolution !== currentProps.resolution) state.createGeometry = true
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
diff --git a/src/mol-repr/structure/visual/gaussian-density-volume.ts b/src/mol-repr/structure/visual/gaussian-density-volume.ts
index 51b8b809e..7aac5a7b9 100644
--- a/src/mol-repr/structure/visual/gaussian-density-volume.ts
+++ b/src/mol-repr/structure/visual/gaussian-density-volume.ts
@@ -40,7 +40,7 @@ export function GaussianDensityVolumeVisual(): ComplexVisual<GaussianDensityVolu
createGeometry: createGaussianDensityVolume,
createLocationIterator: (structure: Structure) => LocationIterator(structure.elementCount, 1, () => NullLocation),
getLoci: () => EmptyLoci, // TODO
- mark: () => false, // TODO
+ eachLocation: () => false, // TODO
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<GaussianDensityVolumeParams>, currentProps: PD.Values<GaussianDensityVolumeParams>) => {
if (newProps.resolution !== currentProps.resolution) state.createGeometry = true
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
diff --git a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
index 9dc645bbc..166252a81 100644
--- a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
@@ -8,7 +8,7 @@ import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual } from '../representation';
import { VisualUpdateState } from '../../util';
import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
-import { StructureElementIterator, getElementLoci, markElement } from './util/element';
+import { StructureElementIterator, getElementLoci, eachElement } from './util/element';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { Mesh } from 'mol-geo/geometry/mesh/mesh';
import { computeMarchingCubesMesh } from 'mol-geo/util/marching-cubes/algorithm';
@@ -46,7 +46,7 @@ export function GaussianSurfaceVisual(): UnitsVisual<GaussianSurfaceParams> {
createGeometry: createGaussianSurfaceMesh,
createLocationIterator: StructureElementIterator.fromGroup,
getLoci: getElementLoci,
- mark: markElement,
+ eachLocation: eachElement,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<GaussianSurfaceParams>, currentProps: PD.Values<GaussianSurfaceParams>) => {
if (newProps.resolution !== currentProps.resolution) state.createGeometry = true
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
diff --git a/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts b/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
index a292ff3e5..5efe3f47b 100644
--- a/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
@@ -8,7 +8,7 @@ import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual } from '../representation';
import { VisualUpdateState } from '../../util';
import { UnitsLinesVisual, UnitsLinesParams } from '../units-visual';
-import { StructureElementIterator, getElementLoci, markElement } from './util/element';
+import { StructureElementIterator, getElementLoci, eachElement } from './util/element';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { Lines } from 'mol-geo/geometry/lines/lines';
import { computeMarchingCubesLines } from 'mol-geo/util/marching-cubes/algorithm';
@@ -45,7 +45,7 @@ export function GaussianWireframeVisual(): UnitsVisual<GaussianWireframeParams>
createGeometry: createGaussianWireframe,
createLocationIterator: StructureElementIterator.fromGroup,
getLoci: getElementLoci,
- mark: markElement,
+ eachLocation: eachElement,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<GaussianWireframeParams>, currentProps: PD.Values<GaussianWireframeParams>) => {
if (newProps.resolution !== currentProps.resolution) state.createGeometry = true
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
diff --git a/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts b/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts
index b16a312d3..7d10b6771 100644
--- a/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts
@@ -64,7 +64,7 @@ export function InterUnitLinkVisual(): ComplexVisual<InterUnitLinkParams> {
createGeometry: createInterUnitLinkCylinderMesh,
createLocationIterator: LinkIterator.fromStructure,
getLoci: getLinkLoci,
- mark: markLink,
+ eachLocation: eachLink,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<InterUnitLinkParams>, currentProps: PD.Values<InterUnitLinkParams>) => {
state.createGeometry = (
newProps.sizeFactor !== currentProps.sizeFactor ||
@@ -95,7 +95,7 @@ function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
return EmptyLoci
}
-function markLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
+function eachLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
let changed = false
if (Link.isLoci(loci)) {
if (loci.structure !== structure) return false
diff --git a/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts b/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts
index fad35df52..d04f8d58f 100644
--- a/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts
@@ -78,7 +78,7 @@ export function IntraUnitLinkVisual(): UnitsVisual<IntraUnitLinkParams> {
createGeometry: createIntraUnitLinkCylinderMesh,
createLocationIterator: LinkIterator.fromGroup,
getLoci: getLinkLoci,
- mark: markLink,
+ eachLocation: eachLink,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<IntraUnitLinkParams>, currentProps: PD.Values<IntraUnitLinkParams>) => {
state.createGeometry = (
newProps.sizeFactor !== currentProps.sizeFactor ||
@@ -112,7 +112,7 @@ function getLinkLoci(pickingId: PickingId, structureGroup: StructureGroup, id: n
return EmptyLoci
}
-function markLink(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
+function eachLink(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
let changed = false
if (Link.isLoci(loci)) {
const { structure, group } = structureGroup
diff --git a/src/mol-repr/structure/visual/nucleotide-block-mesh.ts b/src/mol-repr/structure/visual/nucleotide-block-mesh.ts
index 6e638cf3e..78fa5aa2f 100644
--- a/src/mol-repr/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-repr/structure/visual/nucleotide-block-mesh.ts
@@ -10,7 +10,7 @@ import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { Segmentation } from 'mol-data/int';
import { isNucleic, isPurinBase, isPyrimidineBase } from 'mol-model/structure/model/types';
import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
-import { NucleotideLocationIterator, markNucleotideElement, getNucleotideElementLoci } from './util/nucleotide';
+import { NucleotideLocationIterator, eachNucleotideElement, getNucleotideElementLoci } from './util/nucleotide';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { Box } from 'mol-geo/primitive/box';
import { Mesh } from 'mol-geo/geometry/mesh/mesh';
@@ -134,7 +134,7 @@ export function NucleotideBlockVisual(): UnitsVisual<NucleotideBlockParams> {
createGeometry: createNucleotideBlockMesh,
createLocationIterator: NucleotideLocationIterator.fromGroup,
getLoci: getNucleotideElementLoci,
- mark: markNucleotideElement,
+ eachLocation: eachNucleotideElement,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<NucleotideBlockParams>, currentProps: PD.Values<NucleotideBlockParams>) => {
state.createGeometry = (
newProps.sizeFactor !== currentProps.sizeFactor ||
diff --git a/src/mol-repr/structure/visual/polymer-backbone-cylinder.ts b/src/mol-repr/structure/visual/polymer-backbone-cylinder.ts
index 60e8ba403..858424522 100644
--- a/src/mol-repr/structure/visual/polymer-backbone-cylinder.ts
+++ b/src/mol-repr/structure/visual/polymer-backbone-cylinder.ts
@@ -8,7 +8,7 @@ import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual } from '../representation';
import { VisualUpdateState } from '../../util';
import { PolymerBackboneIterator } from './util/polymer';
-import { getElementLoci, markElement, StructureElementIterator } from './util/element';
+import { getElementLoci, eachElement, StructureElementIterator } from './util/element';
import { Vec3 } from 'mol-math/linear-algebra';
import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
import { OrderedSet } from 'mol-data/int';
@@ -74,7 +74,7 @@ export function PolymerBackboneVisual(): UnitsVisual<PolymerBackboneParams> {
// TODO create a specialized location iterator
createLocationIterator: StructureElementIterator.fromGroup,
getLoci: getElementLoci,
- mark: markElement,
+ eachLocation: eachElement,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerBackboneParams>, currentProps: PD.Values<PolymerBackboneParams>) => {
state.createGeometry = (
newProps.sizeFactor !== currentProps.sizeFactor ||
diff --git a/src/mol-repr/structure/visual/polymer-direction-wedge.ts b/src/mol-repr/structure/visual/polymer-direction-wedge.ts
index d94e90efb..ab3e03754 100644
--- a/src/mol-repr/structure/visual/polymer-direction-wedge.ts
+++ b/src/mol-repr/structure/visual/polymer-direction-wedge.ts
@@ -6,7 +6,7 @@
import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual } from '../representation';
-import { PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment, PolymerLocationIterator, getPolymerElementLoci, markPolymerElement } from './util/polymer';
+import { PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment, PolymerLocationIterator, getPolymerElementLoci, eachPolymerElement } from './util/polymer';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { SecondaryStructureType, isNucleic } from 'mol-model/structure/model/types';
import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
@@ -98,7 +98,7 @@ export function PolymerDirectionVisual(): UnitsVisual<PolymerDirectionParams> {
createGeometry: createPolymerDirectionWedgeMesh,
createLocationIterator: PolymerLocationIterator.fromGroup,
getLoci: getPolymerElementLoci,
- mark: markPolymerElement,
+ eachLocation: eachPolymerElement,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerDirectionParams>, currentProps: PD.Values<PolymerDirectionParams>) => {
state.createGeometry = (
newProps.sizeFactor !== currentProps.sizeFactor
diff --git a/src/mol-repr/structure/visual/polymer-gap-cylinder.ts b/src/mol-repr/structure/visual/polymer-gap-cylinder.ts
index d2ebb496e..dc80fba74 100644
--- a/src/mol-repr/structure/visual/polymer-gap-cylinder.ts
+++ b/src/mol-repr/structure/visual/polymer-gap-cylinder.ts
@@ -7,7 +7,7 @@
import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual } from '../representation';
import { VisualUpdateState } from '../../util';
-import { PolymerGapIterator, PolymerGapLocationIterator, markPolymerGapElement, getPolymerGapElementLoci } from './util/polymer';
+import { PolymerGapIterator, PolymerGapLocationIterator, eachPolymerGapElement, getPolymerGapElementLoci } from './util/polymer';
import { Vec3 } from 'mol-math/linear-algebra';
import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
import { ParamDefinition as PD } from 'mol-util/param-definition';
@@ -91,7 +91,7 @@ export function PolymerGapVisual(): UnitsVisual<PolymerGapParams> {
createGeometry: createPolymerGapCylinderMesh,
createLocationIterator: PolymerGapLocationIterator.fromGroup,
getLoci: getPolymerGapElementLoci,
- mark: markPolymerGapElement,
+ eachLocation: eachPolymerGapElement,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerGapParams>, currentProps: PD.Values<PolymerGapParams>) => {
state.createGeometry = (
newProps.sizeFactor !== currentProps.sizeFactor ||
diff --git a/src/mol-repr/structure/visual/polymer-trace-mesh.ts b/src/mol-repr/structure/visual/polymer-trace-mesh.ts
index c30503dc1..dfbd3b6a3 100644
--- a/src/mol-repr/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-repr/structure/visual/polymer-trace-mesh.ts
@@ -7,7 +7,7 @@
import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual } from '../representation';
import { VisualUpdateState } from '../../util';
-import { PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment, PolymerLocationIterator, getPolymerElementLoci, markPolymerElement, interpolateSizes } from './util/polymer';
+import { PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment, PolymerLocationIterator, getPolymerElementLoci, eachPolymerElement, interpolateSizes } from './util/polymer';
import { SecondaryStructureType, isNucleic } from 'mol-model/structure/model/types';
import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
import { ParamDefinition as PD } from 'mol-util/param-definition';
@@ -110,7 +110,7 @@ export function PolymerTraceVisual(): UnitsVisual<PolymerTraceParams> {
createGeometry: createPolymerTraceMesh,
createLocationIterator: PolymerLocationIterator.fromGroup,
getLoci: getPolymerElementLoci,
- mark: markPolymerElement,
+ eachLocation: eachPolymerElement,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerTraceParams>, currentProps: PD.Values<PolymerTraceParams>) => {
state.createGeometry = (
newProps.sizeFactor !== currentProps.sizeFactor ||
diff --git a/src/mol-repr/structure/visual/util/element.ts b/src/mol-repr/structure/visual/util/element.ts
index baab3d964..37aaff1be 100644
--- a/src/mol-repr/structure/visual/util/element.ts
+++ b/src/mol-repr/structure/visual/util/element.ts
@@ -68,7 +68,7 @@ export function createElementSphereImpostor(ctx: VisualContext, unit: Unit, stru
return builder.getSpheres()
}
-export function markElement(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
+export function eachElement(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
let changed = false
if (!StructureElement.isLoci(loci)) return false
const { structure, group } = structureGroup
diff --git a/src/mol-repr/structure/visual/util/nucleotide.ts b/src/mol-repr/structure/visual/util/nucleotide.ts
index 44ce2c3e8..ff5ada0d5 100644
--- a/src/mol-repr/structure/visual/util/nucleotide.ts
+++ b/src/mol-repr/structure/visual/util/nucleotide.ts
@@ -40,7 +40,7 @@ export function getNucleotideElementLoci(pickingId: PickingId, structureGroup: S
return EmptyLoci
}
-export function markNucleotideElement(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
+export function eachNucleotideElement(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
let changed = false
if (!StructureElement.isLoci(loci)) return false
const { structure, group } = structureGroup
diff --git a/src/mol-repr/structure/visual/util/polymer.ts b/src/mol-repr/structure/visual/util/polymer.ts
index 288bf8527..7dd84c2d9 100644
--- a/src/mol-repr/structure/visual/util/polymer.ts
+++ b/src/mol-repr/structure/visual/util/polymer.ts
@@ -78,7 +78,7 @@ export function getPolymerElementLoci(pickingId: PickingId, structureGroup: Stru
}
/** Mark a polymer element (e.g. part of a cartoon trace) when all its residue's elements are in a loci. */
-export function markPolymerElement(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
+export function eachPolymerElement(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
let changed = false
if (!StructureElement.isLoci(loci)) return false
const { structure, group } = structureGroup
@@ -126,7 +126,7 @@ export function getPolymerGapElementLoci(pickingId: PickingId, structureGroup: S
return EmptyLoci
}
-export function markPolymerGapElement(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
+export function eachPolymerGapElement(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
let changed = false
if (!Link.isLoci(loci)) return false
const { structure, group } = structureGroup
--
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