diff --git a/src/mol-app/ui/transform/backbone.tsx b/src/mol-app/ui/transform/backbone.tsx
index 3586f32082a2c0a7712bba2000880c4935116528..e93e15b56990fe967e1b19d894fe266d7a840b2f 100644
--- a/src/mol-app/ui/transform/backbone.tsx
+++ b/src/mol-app/ui/transform/backbone.tsx
@@ -15,7 +15,7 @@ import { Toggle } from '../controls/common';
import { BackboneEntity } from 'mol-view/state/entity';
import { BackboneUpdate } from 'mol-view/state/transform'
import { StateContext } from 'mol-view/state/context';
-import { ColorTheme, SizeTheme, ColorThemeNames, ColorThemeName } from 'mol-geo/theme';
+import { ColorThemeProps, SizeTheme, ColorThemeNames, ColorThemeName } from 'mol-geo/theme';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
import { VisualQuality } from 'mol-geo/representation/util';
@@ -26,7 +26,7 @@ interface BackboneState {
flipSided: boolean
flatShaded: boolean
detail: number
- colorTheme: ColorTheme
+ colorTheme: ColorThemeProps
colorValue: Color
sizeTheme: SizeTheme
visible: boolean
@@ -43,7 +43,7 @@ export class Backbone extends View<Controller<any>, BackboneState, { transform:
flipSided: false,
flatShaded: false,
detail: 2,
- colorTheme: { name: 'element-symbol' } as ColorTheme,
+ colorTheme: { name: 'element-symbol' } as ColorThemeProps,
colorValue: 0x000000,
sizeTheme: { name: 'uniform' } as SizeTheme,
visible: true,
diff --git a/src/mol-app/ui/transform/ball-and-stick.tsx b/src/mol-app/ui/transform/ball-and-stick.tsx
index 0b62b3d2a7ca4060b0b51bc7fb85e859716a698e..f94afce448f32faaeedb759a1f054026215e8a82 100644
--- a/src/mol-app/ui/transform/ball-and-stick.tsx
+++ b/src/mol-app/ui/transform/ball-and-stick.tsx
@@ -15,7 +15,7 @@ import { Toggle } from '../controls/common';
import { DistanceRestraintEntity } from 'mol-view/state/entity';
import { DistanceRestraintUpdate } from 'mol-view/state/transform'
import { StateContext } from 'mol-view/state/context';
-import { ColorTheme, SizeTheme, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
+import { ColorThemeProps, SizeTheme, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
import { VisualQuality } from 'mol-geo/representation/util';
@@ -25,7 +25,7 @@ interface BallAndStickState {
doubleSided: boolean
flipSided: boolean
flatShaded: boolean
- colorTheme: ColorTheme
+ colorTheme: ColorThemeProps
colorValue: Color
sizeTheme: SizeTheme
visible: boolean
@@ -46,7 +46,7 @@ export class BallAndStick extends View<Controller<any>, BallAndStickState, { tra
doubleSided: true,
flipSided: false,
flatShaded: false,
- colorTheme: { name: 'element-symbol' } as ColorTheme,
+ colorTheme: { name: 'element-symbol' } as ColorThemeProps,
colorValue: 0x000000,
sizeTheme: { name: 'uniform' } as SizeTheme,
visible: true,
diff --git a/src/mol-app/ui/transform/carbohydrate.tsx b/src/mol-app/ui/transform/carbohydrate.tsx
index d5115bf810d26193bc1af4b29174eab7fb2dff9f..c9a93065cbf968e5d21654a167db551c7e755494 100644
--- a/src/mol-app/ui/transform/carbohydrate.tsx
+++ b/src/mol-app/ui/transform/carbohydrate.tsx
@@ -15,7 +15,7 @@ import { Toggle } from '../controls/common';
import { CarbohydrateEntity } from 'mol-view/state/entity';
import { CarbohydrateUpdate } from 'mol-view/state/transform'
import { StateContext } from 'mol-view/state/context';
-import { ColorTheme, SizeTheme, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
+import { ColorThemeProps, SizeTheme, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
import { VisualQuality } from 'mol-geo/representation/util';
@@ -26,7 +26,7 @@ interface CarbohydrateState {
flipSided: boolean
flatShaded: boolean
detail: number
- colorTheme: ColorTheme
+ colorTheme: ColorThemeProps
colorValue: Color
sizeTheme: SizeTheme
visible: boolean
@@ -47,7 +47,7 @@ export class Carbohydrate extends View<Controller<any>, CarbohydrateState, { tra
flipSided: false,
flatShaded: false,
detail: 2,
- colorTheme: { name: 'element-symbol' } as ColorTheme,
+ colorTheme: { name: 'element-symbol' } as ColorThemeProps,
colorValue: 0x000000,
sizeTheme: { name: 'uniform' } as SizeTheme,
visible: true,
diff --git a/src/mol-app/ui/transform/cartoon.tsx b/src/mol-app/ui/transform/cartoon.tsx
index 41bfcad2625896344aa056349beb1240654f7cc6..f3bb8e6645d36bbfff03a62a04cdc7350f4ca417 100644
--- a/src/mol-app/ui/transform/cartoon.tsx
+++ b/src/mol-app/ui/transform/cartoon.tsx
@@ -15,7 +15,7 @@ import { Toggle } from '../controls/common';
import { CartoonEntity } from 'mol-view/state/entity';
import { CartoonUpdate } from 'mol-view/state/transform'
import { StateContext } from 'mol-view/state/context';
-import { ColorTheme, SizeTheme, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
+import { ColorThemeProps, SizeTheme, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
import { VisualQuality } from 'mol-geo/representation/util';
@@ -26,7 +26,7 @@ interface CartoonState {
flipSided: boolean
flatShaded: boolean
detail: number
- colorTheme: ColorTheme
+ colorTheme: ColorThemeProps
colorValue: Color
sizeTheme: SizeTheme
visible: boolean
@@ -43,7 +43,7 @@ export class Cartoon extends View<Controller<any>, CartoonState, { transform: Ca
flipSided: false,
flatShaded: false,
detail: 2,
- colorTheme: { name: 'element-symbol' } as ColorTheme,
+ colorTheme: { name: 'element-symbol' } as ColorThemeProps,
colorValue: 0x000000,
sizeTheme: { name: 'uniform' } as SizeTheme,
visible: true,
diff --git a/src/mol-app/ui/transform/distance-restraint.tsx b/src/mol-app/ui/transform/distance-restraint.tsx
index d8453d71d2264b146ec668d2a640d2d174c98a42..36a5f3361d03c672cf02151c7164e802ff4d9826 100644
--- a/src/mol-app/ui/transform/distance-restraint.tsx
+++ b/src/mol-app/ui/transform/distance-restraint.tsx
@@ -15,7 +15,7 @@ import { Toggle } from '../controls/common';
import { DistanceRestraintEntity } from 'mol-view/state/entity';
import { DistanceRestraintUpdate } from 'mol-view/state/transform'
import { StateContext } from 'mol-view/state/context';
-import { ColorTheme, SizeTheme, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
+import { ColorThemeProps, SizeTheme, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
import { VisualQuality } from 'mol-geo/representation/util';
@@ -25,7 +25,7 @@ interface DistanceRestraintState {
doubleSided: boolean
flipSided: boolean
flatShaded: boolean
- colorTheme: ColorTheme
+ colorTheme: ColorThemeProps
colorValue: Color
sizeTheme: SizeTheme
visible: boolean
@@ -46,7 +46,7 @@ export class DistanceRestraint extends View<Controller<any>, DistanceRestraintSt
doubleSided: true,
flipSided: false,
flatShaded: false,
- colorTheme: { name: 'element-symbol' } as ColorTheme,
+ colorTheme: { name: 'element-symbol' } as ColorThemeProps,
colorValue: 0x000000,
sizeTheme: { name: 'uniform' } as SizeTheme,
visible: true,
diff --git a/src/mol-app/ui/transform/spacefill.tsx b/src/mol-app/ui/transform/spacefill.tsx
index 05d2ae6aa87acd9d1d7d3c067a36a1e488c426d6..99e750e347e5db416d537bbdba46ac8a4362f230 100644
--- a/src/mol-app/ui/transform/spacefill.tsx
+++ b/src/mol-app/ui/transform/spacefill.tsx
@@ -15,7 +15,7 @@ import { Toggle } from '../controls/common';
import { SpacefillEntity } from 'mol-view/state/entity';
import { SpacefillUpdate } from 'mol-view/state/transform'
import { StateContext } from 'mol-view/state/context';
-import { ColorTheme, SizeTheme, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
+import { ColorThemeProps, SizeTheme, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
import { VisualQuality } from 'mol-geo/representation/util';
@@ -26,7 +26,7 @@ interface SpacefillState {
flipSided: boolean
flatShaded: boolean
detail: number
- colorTheme: ColorTheme
+ colorTheme: ColorThemeProps
colorValue: Color
sizeTheme: SizeTheme
visible: boolean
@@ -43,7 +43,7 @@ export class Spacefill extends View<Controller<any>, SpacefillState, { transform
flipSided: false,
flatShaded: false,
detail: 2,
- colorTheme: { name: 'element-symbol' } as ColorTheme,
+ colorTheme: { name: 'element-symbol' } as ColorThemeProps,
colorValue: 0x000000,
sizeTheme: { name: 'uniform' } as SizeTheme,
visible: true,
diff --git a/src/mol-geo/representation/structure/index.ts b/src/mol-geo/representation/structure/index.ts
index 951d433699b5ce2f47ffe4a46f6a6ab94891f519..4a65056760c5afd04cc3011887db121082038fae 100644
--- a/src/mol-geo/representation/structure/index.ts
+++ b/src/mol-geo/representation/structure/index.ts
@@ -7,14 +7,14 @@
import { Structure } from 'mol-model/structure';
import { Representation, RepresentationProps } from '..';
-import { ColorTheme, SizeTheme } from '../../theme';
+import { ColorThemeProps, SizeTheme } from '../../theme';
import { DefaultBaseProps, DefaultMeshProps } from '../util';
export interface StructureRepresentation<P extends RepresentationProps = {}> extends Representation<Structure, P> { }
export const DefaultStructureProps = {
...DefaultBaseProps,
- colorTheme: { name: 'instance-index' } as ColorTheme,
+ colorTheme: { name: 'unit-index' } as ColorThemeProps,
sizeTheme: { name: 'physical' } as SizeTheme,
}
export type StructureProps = typeof DefaultStructureProps
diff --git a/src/mol-geo/representation/structure/visual/util/common.ts b/src/mol-geo/representation/structure/visual/util/common.ts
index e07b033c5d054c54d3d009e50b9b704af0e2fdc5..3d5dbc7e21bc874bba26f01769d6887e52d9972b 100644
--- a/src/mol-geo/representation/structure/visual/util/common.ts
+++ b/src/mol-geo/representation/structure/visual/util/common.ts
@@ -8,15 +8,14 @@
import { Unit, Structure } from 'mol-model/structure';
import { Mat4 } from 'mol-math/linear-algebra'
-import { createUniformColor, ColorData } from '../../../../util/color-data';
+import { createUniformColor, ColorData, createElementColor, createElementInstanceColor, createInstanceColor } from '../../../../util/color-data';
import { createUniformSize, SizeData } from '../../../../util/size-data';
import { physicalSizeData } from '../../../../theme/structure/size/physical';
import VertexMap from '../../../../shape/vertex-map';
-import { ColorTheme, SizeTheme } from '../../../../theme';
-import { elementIndexColorData, elementSymbolColorData, instanceIndexColorData, chainIdColorData } from '../../../../theme/structure/color';
+import { ColorThemeProps, SizeTheme } from '../../../../theme';
+import { ColorTheme } from '../../../../theme/structure/color';
import { ValueCell, defaults } from 'mol-util';
import { LocationIterator } from './location-iterator';
-import { carbohydrateSymbolColorData } from '../../../../theme/structure/color/carbohydrate-symbol';
import { Mesh } from '../../../../shape/mesh';
import { MeshValues } from 'mol-gl/renderable';
import { getMeshData } from '../../../../util/mesh-data';
@@ -41,20 +40,14 @@ export function createIdentityTransform(transforms?: ValueCell<Float32Array>) {
return transforms ? ValueCell.update(transforms, identityTransform) : ValueCell.create(identityTransform)
}
-export function createColors(locationIt: LocationIterator, props: ColorTheme, colorData?: ColorData) {
- switch (props.name) {
- case 'atom-index':
- return elementIndexColorData(locationIt, colorData)
- case 'carbohydrate-symbol':
- return carbohydrateSymbolColorData(locationIt, props, colorData)
- case 'chain-id':
- return chainIdColorData(locationIt, colorData)
- case 'element-symbol':
- return elementSymbolColorData(locationIt, colorData)
- case 'instance-index':
- return instanceIndexColorData(locationIt, colorData)
- case 'uniform':
- return createUniformColor(locationIt, () => props.value || 0x000000, colorData)
+export function createColors(locationIt: LocationIterator, props: ColorThemeProps, colorData?: ColorData) {
+ const colorTheme = ColorTheme(props)
+ switch (colorTheme.kind) {
+ case 'uniform': return createUniformColor(locationIt, colorTheme.color, colorData)
+ case 'element': return createElementColor(locationIt, colorTheme.color, colorData)
+ case 'elementInstance': return createElementInstanceColor(locationIt, colorTheme.color, colorData)
+ case 'instance': return createInstanceColor(locationIt, colorTheme.color, colorData)
+ case 'attribute': throw new Error('not implemented') // TODO
}
}
diff --git a/src/mol-geo/theme/index.ts b/src/mol-geo/theme/index.ts
index 0e0ed1a9c73405bcc3a52371f0d7d17b346e85ef..19791a5d63f75e84a9d295c8b28f1ecd027eaac1 100644
--- a/src/mol-geo/theme/index.ts
+++ b/src/mol-geo/theme/index.ts
@@ -7,19 +7,19 @@
import { Color } from 'mol-util/color';
import { Structure } from 'mol-model/structure';
-export interface ColorTheme {
- name: 'atom-index' | 'chain-id'| 'instance-index' | 'uniform' | 'carbohydrate-symbol' | 'element-symbol'
+export interface ColorThemeProps {
+ name: 'element-index' | 'chain-id'| 'unit-index' | 'uniform' | 'carbohydrate-symbol' | 'element-symbol'
domain?: [number, number]
value?: Color
structure?: Structure
}
export const ColorThemeInfo = {
- 'atom-index': {},
+ 'element-index': {},
'carbohydrate-symbol': {},
'chain-id': {},
'element-symbol': {},
- 'instance-index': {},
+ 'unit-index': {},
'uniform': {}
}
export type ColorThemeName = keyof typeof ColorThemeInfo
diff --git a/src/mol-geo/theme/structure/color/carbohydrate-symbol.ts b/src/mol-geo/theme/structure/color/carbohydrate-symbol.ts
index 1417b4e39578e8776ac4ea0ab6e36e6fcb14f212..d6487d50ce7ab85fb5d87457501f1192e6412ca7 100644
--- a/src/mol-geo/theme/structure/color/carbohydrate-symbol.ts
+++ b/src/mol-geo/theme/structure/color/carbohydrate-symbol.ts
@@ -6,16 +6,16 @@
import { StructureElement, Link, ElementIndex, Unit } from 'mol-model/structure';
-import { ColorData, createElementColor } from '../../../util/color-data';
-import { Color } from 'mol-util/color';
-import { LocationIterator, LocationValue } from '../../../representation/structure/visual/util/location-iterator';
-import { ColorTheme } from '../..';
+import { ColorThemeProps } from '../..';
import { SaccharideColors } from 'mol-model/structure/structure/carbohydrates/constants';
+import { Location } from 'mol-model/location';
+import { ColorTheme } from '.';
+import { LocationColor } from '../../../util/color-data';
const DefaultColor = 0xCCCCCC;
-export function carbohydrateSymbolColorData(locationIt: LocationIterator, props: ColorTheme, colorData?: ColorData) {
- let colorFn: (locationValue: LocationValue) => Color
+export function CarbohydrateSymbolColorTheme(props: ColorThemeProps): ColorTheme {
+ let colorFn: LocationColor
if (props.structure) {
const { elements, getElementIndex, getAnomericCarbon } = props.structure.carbohydrates
@@ -30,15 +30,14 @@ export function carbohydrateSymbolColorData(locationIt: LocationIterator, props:
return DefaultColor
}
- colorFn = (locationValue: LocationValue) => {
- const { location: l } = locationValue
- if (locationValue.isSecondary) {
+ colorFn = (location: Location, isSecondary: boolean) => {
+ if (isSecondary) {
return SaccharideColors.Secondary
} else {
- if (StructureElement.isLocation(l)) {
- return getColor(l.unit, l.element)
- } else if (Link.isLocation(l)) {
- return getColor(l.aUnit, l.aUnit.elements[l.aIndex])
+ if (StructureElement.isLocation(location)) {
+ return getColor(location.unit, location.element)
+ } else if (Link.isLocation(location)) {
+ return getColor(location.aUnit, location.aUnit.elements[location.aIndex])
}
}
return DefaultColor
@@ -47,5 +46,8 @@ export function carbohydrateSymbolColorData(locationIt: LocationIterator, props:
colorFn = () => DefaultColor
}
- return createElementColor(locationIt, colorFn, colorData)
+ return {
+ kind: 'element',
+ color: colorFn
+ }
}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/color/chain-id.ts b/src/mol-geo/theme/structure/color/chain-id.ts
index c0bc8e83f658e0e53e4d729befceb1cf550bb146..32d347a1d9c26073bebf0c2fa5d26ab856a5f93a 100644
--- a/src/mol-geo/theme/structure/color/chain-id.ts
+++ b/src/mol-geo/theme/structure/color/chain-id.ts
@@ -6,9 +6,10 @@
import { Unit, StructureProperties, StructureElement, Link } from 'mol-model/structure';
-import { ColorData, createElementColor } from '../../../util/color-data';
import { ColorScale, Color } from 'mol-util/color';
-import { LocationIterator, LocationValue } from '../../../representation/structure/visual/util/location-iterator';
+import { Location } from 'mol-model/location';
+import { ColorThemeProps } from '../..';
+import { ColorTheme } from '.';
function getAsymId(unit: Unit): StructureElement.Property<string> {
switch (unit.kind) {
@@ -20,11 +21,10 @@ function getAsymId(unit: Unit): StructureElement.Property<string> {
}
}
-export function chainIdColorData(locationIt: LocationIterator, colorData?: ColorData) {
+export function ChainIdColorTheme(props: ColorThemeProps): ColorTheme {
const l = StructureElement.create()
- function colorFn(locationValue: LocationValue): Color {
- const { location } = locationValue
+ function colorFn(location: Location): Color {
if (StructureElement.isLocation(location)) {
const map = location.unit.model.properties.asymIdSerialMap
const scale = ColorScale.create({ domain: [ 0, map.size - 1 ] })
@@ -41,5 +41,8 @@ export function chainIdColorData(locationIt: LocationIterator, colorData?: Color
return 0
}
- return createElementColor(locationIt, colorFn, colorData)
+ return {
+ kind: 'element',
+ color: colorFn
+ }
}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/color/element-index.ts b/src/mol-geo/theme/structure/color/element-index.ts
index 7cd06ef40a7be1b70c7e1379e43946fa612becc2..388d4ce1c41c8e57749eb496006cf91b6551e362 100644
--- a/src/mol-geo/theme/structure/color/element-index.ts
+++ b/src/mol-geo/theme/structure/color/element-index.ts
@@ -4,18 +4,48 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { ColorScale } from 'mol-util/color';
-import { createElementInstanceColor, ColorData } from '../../../util/color-data';
-import { LocationIterator, LocationValue } from '../../../representation/structure/visual/util/location-iterator';
+import { ColorScale, Color } from 'mol-util/color';
+import { Location } from 'mol-model/location';
+import { ColorThemeProps } from '../..';
+import { StructureElement, Link, Unit } from 'mol-model/structure';
+import { OrderedSet } from 'mol-data/int';
+import { ColorTheme } from '.';
+import { LocationColor } from '../../../util/color-data';
-export function elementIndexColorData(locationIt: LocationIterator, colorData?: ColorData) {
- const { elementCount, instanceCount } = locationIt
+const DefaultColor = 0xCCCCCC;
- const domain = [ 0, instanceCount * elementCount - 1 ]
- const scale = ColorScale.create({ domain })
- return createElementInstanceColor(
- locationIt,
- (value: LocationValue) => scale.color(value.instanceIndex * elementCount + value.elementIndex),
- colorData
- )
+export function ElementIndexColorTheme(props: ColorThemeProps): ColorTheme {
+ let colorFn: LocationColor
+
+ if (props.structure) {
+ const { units } = props.structure
+ const unitCount = units.length
+ const cummulativeElementCount = new Map<number, number>()
+
+ let elementCount = 0
+ for (let i = 0; i < unitCount; ++i) {
+ cummulativeElementCount.set(i, elementCount)
+ elementCount += units[i].elements.length
+ }
+ const scale = ColorScale.create({ domain: [ 0, elementCount ] })
+
+ colorFn = (location: Location): Color => {
+ if (StructureElement.isLocation(location)) {
+ const unitIndex = Unit.findUnitById(location.unit.id, units)
+ const unitElementIndex = OrderedSet.findPredecessorIndex(location.unit.elements, location.element)
+ return scale.color(cummulativeElementCount.get(unitIndex) || 0 + unitElementIndex)
+ } else if (Link.isLocation(location)) {
+ const unitId = Unit.findUnitById(location.aUnit.id, units)
+ return scale.color(cummulativeElementCount.get(unitId) || 0 + location.aIndex)
+ }
+ return 0
+ }
+ } else {
+ colorFn = () => DefaultColor
+ }
+
+ return {
+ kind: 'elementInstance',
+ color: colorFn
+ }
}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/color/element-symbol.ts b/src/mol-geo/theme/structure/color/element-symbol.ts
index 5c99412f67a9faeba1d2f81214e900b413360f04..009aac7238dd3a1103200ec2338cc35f2eef8b90 100644
--- a/src/mol-geo/theme/structure/color/element-symbol.ts
+++ b/src/mol-geo/theme/structure/color/element-symbol.ts
@@ -6,9 +6,10 @@
import { ElementSymbol } from 'mol-model/structure/model/types';
import { Color } from 'mol-util/color';
-import { createElementColor, ColorData } from '../../../util/color-data';
import { StructureElement, Unit, Link } from 'mol-model/structure';
-import { LocationIterator, LocationValue } from '../../../representation/structure/visual/util/location-iterator';
+import { Location } from 'mol-model/location';
+import { ColorThemeProps } from '../..';
+import { ColorTheme } from '.';
// from Jmol http://jmol.sourceforge.net/jscolors/ (or 0xFFFFFF)
export const ElementSymbolColors: { [k: string]: Color } = {
@@ -22,9 +23,8 @@ export function elementSymbolColor(element: ElementSymbol): Color {
return c === void 0 ? DefaultElementSymbolColor : c
}
-export function elementSymbolColorData(locationIt: LocationIterator, colorData?: ColorData) {
- function colorFn(locationValue: LocationValue): Color {
- const { location } = locationValue
+export function ElementSymbolColorTheme(props: ColorThemeProps): ColorTheme {
+ function colorFn(location: Location): Color {
if (StructureElement.isLocation(location)) {
if (Unit.isAtomic(location.unit)) {
const { type_symbol } = location.unit.model.atomicHierarchy.atoms
@@ -39,5 +39,8 @@ export function elementSymbolColorData(locationIt: LocationIterator, colorData?:
return DefaultElementSymbolColor
}
- return createElementColor(locationIt, colorFn, colorData)
+ return {
+ kind: 'element',
+ color: colorFn
+ }
}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/color/index.ts b/src/mol-geo/theme/structure/color/index.ts
index 05e8c32000a48bc98be0563577e957dbeb76b3e3..70da74a020e9bc97bf140770f02775b322d26c2b 100644
--- a/src/mol-geo/theme/structure/color/index.ts
+++ b/src/mol-geo/theme/structure/color/index.ts
@@ -4,14 +4,28 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit } from 'mol-model/structure';
+import { ColorThemeProps } from '../..';
-export interface StructureColorDataProps {
- group: Unit.SymmetryGroup,
- elementCount: number
+import { ElementIndexColorTheme } from './element-index';
+import { CarbohydrateSymbolColorTheme } from './carbohydrate-symbol';
+import { ChainIdColorTheme } from './chain-id';
+import { ElementSymbolColorTheme } from './element-symbol';
+import { UnitIndexColorTheme } from './unit-index';
+import { UniformColorTheme } from './uniform';
+import { ColorType, LocationColor } from '../../../util/color-data';
+
+export interface ColorTheme {
+ kind: ColorType
+ color: LocationColor
}
-export { elementIndexColorData } from './element-index'
-export { chainIdColorData } from './chain-id'
-export { elementSymbolColorData } from './element-symbol'
-export { instanceIndexColorData } from './instance-index'
\ No newline at end of file
+export function ColorTheme(props: ColorThemeProps): ColorTheme {
+ switch (props.name) {
+ case 'element-index': return ElementIndexColorTheme(props)
+ case 'carbohydrate-symbol': return CarbohydrateSymbolColorTheme(props)
+ case 'chain-id': return ChainIdColorTheme(props)
+ case 'element-symbol': return ElementSymbolColorTheme(props)
+ case 'unit-index': return UnitIndexColorTheme(props)
+ case 'uniform': return UniformColorTheme(props)
+ }
+}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/color/instance-index.ts b/src/mol-geo/theme/structure/color/instance-index.ts
deleted file mode 100644
index ca40a1d004ede661b4e5d46a04150cf709e77c35..0000000000000000000000000000000000000000
--- a/src/mol-geo/theme/structure/color/instance-index.ts
+++ /dev/null
@@ -1,21 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { ColorScale } from 'mol-util/color';
-import { createInstanceColor, ColorData } from '../../../util/color-data';
-import { LocationIterator, LocationValue } from '../../../representation/structure/visual/util/location-iterator';
-
-export function instanceIndexColorData(locationIt: LocationIterator, colorData?: ColorData) {
- const { instanceCount } = locationIt
- const domain = [ 0, instanceCount - 1 ]
- const scale = ColorScale.create({ domain })
-
- function colorFn(locationValue: LocationValue) {
- return scale.color(locationValue.instanceIndex)
- }
-
- return createInstanceColor(locationIt, colorFn, colorData)
-}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/color/uniform.ts b/src/mol-geo/theme/structure/color/uniform.ts
new file mode 100644
index 0000000000000000000000000000000000000000..2c1e700cf5adb8308fb36a66aae2830b152b7588
--- /dev/null
+++ b/src/mol-geo/theme/structure/color/uniform.ts
@@ -0,0 +1,19 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ColorThemeProps } from '../..';
+import { ColorTheme } from '.';
+
+const DefaultColor = 0xCCCCCC;
+
+export function UniformColorTheme(props: ColorThemeProps): ColorTheme {
+ const color = props.value || DefaultColor
+
+ return {
+ kind: 'uniform',
+ color: () => color
+ }
+}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/color/unit-index.ts b/src/mol-geo/theme/structure/color/unit-index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..d77021e47faf8a592f249e0635cf9faf5c52f21e
--- /dev/null
+++ b/src/mol-geo/theme/structure/color/unit-index.ts
@@ -0,0 +1,41 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ColorScale, Color } from 'mol-util/color';
+import { Location } from 'mol-model/location';
+import { ColorThemeProps } from '../..';
+import { Unit, StructureElement, Link } from 'mol-model/structure';
+import { ColorTheme } from '.';
+import { LocationColor } from '../../../util/color-data';
+
+const DefaultColor = 0xCCCCCC;
+
+export function UnitIndexColorTheme(props: ColorThemeProps): ColorTheme {
+ let colorFn: LocationColor
+
+ if (props.structure) {
+ const { units } = props.structure
+ const unitCount = units.length
+
+ const scale = ColorScale.create({ domain: [ 0, unitCount ] })
+
+ colorFn = (location: Location): Color => {
+ if (StructureElement.isLocation(location)) {
+ return scale.color(Unit.findUnitById(location.unit.id, units))
+ } else if (Link.isLocation(location)) {
+ return scale.color(Unit.findUnitById(location.aUnit.id, units))
+ }
+ return 0
+ }
+ } else {
+ colorFn = () => DefaultColor
+ }
+
+ return {
+ kind: 'instance',
+ color: colorFn
+ }
+}
\ No newline at end of file
diff --git a/src/mol-geo/util/color-data.ts b/src/mol-geo/util/color-data.ts
index 7b207d8db6338e46595ae033c1e9c17a570401d3..fc21510c4f2dd52bef47a37ac0f97a7e84a73a03 100644
--- a/src/mol-geo/util/color-data.ts
+++ b/src/mol-geo/util/color-data.ts
@@ -8,7 +8,8 @@ import { ValueCell } from 'mol-util';
import { TextureImage, createTextureImage } from 'mol-gl/renderable/util';
import { Color } from 'mol-util/color';
import { Vec2, Vec3 } from 'mol-math/linear-algebra';
-import { LocationIterator, LocationValue, NullLocationValue } from '../representation/structure/visual/util/location-iterator';
+import { LocationIterator } from '../representation/structure/visual/util/location-iterator';
+import { Location, NullLocation } from 'mol-model/location';
export type ColorType = 'uniform' | 'attribute' | 'instance' | 'element' | 'elementInstance'
@@ -20,7 +21,7 @@ export type ColorData = {
dColorType: ValueCell<string>,
}
-export type LocationColor = (locationValue: LocationValue) => Color
+export type LocationColor = (location: Location, isSecondary: boolean) => Color
const emptyColorTexture = { array: new Uint8Array(3), width: 1, height: 1 }
function createEmptyColorTexture() {
@@ -49,7 +50,7 @@ export function createValueColor(value: Color, colorData?: ColorData): ColorData
/** Creates color uniform */
export function createUniformColor(locationIt: LocationIterator, colorFn: LocationColor, colorData?: ColorData): ColorData {
- return createValueColor(colorFn(NullLocationValue), colorData)
+ return createValueColor(colorFn(NullLocation, false), colorData)
}
// export interface AttributeColorProps {
@@ -110,8 +111,8 @@ export function createInstanceColor(locationIt: LocationIterator, colorFn: Locat
const { instanceCount} = locationIt
const colors = colorData && colorData.tColor.ref.value.array.length >= instanceCount * 3 ? colorData.tColor.ref.value : createTextureImage(instanceCount, 3)
while (locationIt.hasNext && !locationIt.isNextNewInstance) {
- const value = locationIt.move()
- Color.toArray(colorFn(value), colors.array, value.index * 3)
+ const v = locationIt.move()
+ Color.toArray(colorFn(v.location, v.isSecondary), colors.array, v.index * 3)
locationIt.skipInstance()
}
return createTextureColor(colors, 'instance', colorData)
@@ -122,9 +123,9 @@ export function createElementColor(locationIt: LocationIterator, colorFn: Locati
const { elementCount } = locationIt
const colors = colorData && colorData.tColor.ref.value.array.length >= elementCount * 3 ? colorData.tColor.ref.value : createTextureImage(elementCount, 3)
while (locationIt.hasNext && !locationIt.isNextNewInstance) {
- const value = locationIt.move()
- // console.log(value)
- Color.toArray(colorFn(value), colors.array, value.elementIndex * 3)
+ const v = locationIt.move()
+ // console.log(v)
+ Color.toArray(colorFn(v.location, v.isSecondary), colors.array, v.elementIndex * 3)
}
return createTextureColor(colors, 'element', colorData)
}
@@ -135,8 +136,8 @@ export function createElementInstanceColor(locationIt: LocationIterator, colorFn
const count = instanceCount * elementCount
const colors = colorData && colorData.tColor.ref.value.array.length >= count * 3 ? colorData.tColor.ref.value : createTextureImage(count, 3)
while (locationIt.hasNext && !locationIt.isNextNewInstance) {
- const value = locationIt.move()
- Color.toArray(colorFn(value), colors.array, value.index * 3)
+ const v = locationIt.move()
+ Color.toArray(colorFn(v.location, v.isSecondary), colors.array, v.index * 3)
}
return createTextureColor(colors, 'elementInstance', colorData)
}
\ No newline at end of file