From a69f1337d7314aaaa74ebafcefca10b9b22c0683 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 20 Aug 2019 12:51:27 -0700
Subject: [PATCH] color refactoring
---
.../rcsb/themes/assembly-symmetry-cluster.ts | 2 +-
src/mol-theme/color/chain-id.ts | 69 +++++++++-------
src/mol-theme/color/element-index.ts | 11 +--
src/mol-theme/color/entity-source.ts | 52 +++++++-----
src/mol-theme/color/model-index.ts | 6 +-
src/mol-theme/color/polymer-id.ts | 80 ++++++++++++-------
src/mol-theme/color/polymer-index.ts | 4 +-
src/mol-theme/color/unit-index.ts | 6 +-
.../util.ts => mol-util/color/palette.ts} | 17 ++--
9 files changed, 148 insertions(+), 99 deletions(-)
rename src/{mol-theme/color/util.ts => mol-util/color/palette.ts} (84%)
diff --git a/src/mol-model-props/rcsb/themes/assembly-symmetry-cluster.ts b/src/mol-model-props/rcsb/themes/assembly-symmetry-cluster.ts
index d435ee69a..4f4388110 100644
--- a/src/mol-model-props/rcsb/themes/assembly-symmetry-cluster.ts
+++ b/src/mol-model-props/rcsb/themes/assembly-symmetry-cluster.ts
@@ -14,7 +14,7 @@ import { Unit, StructureElement, StructureProperties } from '../../../mol-model/
import { Location } from '../../../mol-model/location';
import { ScaleLegend } from '../../../mol-util/color/scale';
import { getSymmetrySelectParam } from '../util';
-import { getPalette, getPaletteParams } from '../../../mol-theme/color/util';
+import { getPalette, getPaletteParams } from '../../../mol-util/color/palette';
import { TableLegend } from '../../../mol-util/color/lists';
const DefaultColor = Color(0xCCCCCC)
diff --git a/src/mol-theme/color/chain-id.ts b/src/mol-theme/color/chain-id.ts
index 089dd2d78..2c5c945ed 100644
--- a/src/mol-theme/color/chain-id.ts
+++ b/src/mol-theme/color/chain-id.ts
@@ -4,26 +4,33 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit, StructureProperties, StructureElement, Link } from '../../mol-model/structure';
+import { Unit, StructureProperties, StructureElement, Link, Structure } from '../../mol-model/structure';
import { Color } from '../../mol-util/color';
import { Location } from '../../mol-model/location';
import { ColorTheme, LocationColor } from '../color';
import { ParamDefinition as PD } from '../../mol-util/param-definition'
import { ThemeDataContext } from '../../mol-theme/theme';
import { ScaleLegend } from '../../mol-util/color/scale';
-import { Column } from '../../mol-data/db';
-import { getPaletteParams, getPalette } from './util';
+import { getPaletteParams, getPalette } from '../../mol-util/color/palette';
import { TableLegend } from '../../mol-util/color/lists';
+import { Segmentation } from '../../mol-data/int';
-const DefaultColor = Color(0xCCCCCC)
+const DefaultColor = Color(0xFAFAFA)
const Description = 'Gives every chain a color based on its `asym_id` value.'
export const ChainIdColorThemeParams = {
- ...getPaletteParams({ scaleList: 'red-yellow-blue' }),
+ ...getPaletteParams({ type: 'set', setList: 'set-3' }),
}
export type ChainIdColorThemeParams = typeof ChainIdColorThemeParams
export function getChainIdColorThemeParams(ctx: ThemeDataContext) {
- return ChainIdColorThemeParams // TODO return copy
+ const params = PD.clone(ChainIdColorThemeParams)
+ if (ctx.structure) {
+ if (getAsymIdSerialMap(ctx.structure.root).size > 12) {
+ params.palette.defaultValue.name = 'scale'
+ params.palette.defaultValue.params = { list: 'red-yellow-blue' }
+ }
+ }
+ return params
}
function getAsymId(unit: Unit): StructureElement.Property<string> {
@@ -36,15 +43,32 @@ function getAsymId(unit: Unit): StructureElement.Property<string> {
}
}
-function addAsymIds(map: Map<string, number>, data: Column<string>) {
- let j = map.size
- for (let o = 0, ol = data.rowCount; o < ol; ++o) {
- const k = data.value(o)
- if (!map.has(k)) {
- map.set(k, j)
- j += 1
+function getAsymIdSerialMap(structure: Structure) {
+ const map = new Map<string, number>()
+ for (let i = 0, il = structure.unitSymmetryGroups.length; i < il; ++i) {
+ const unit = structure.unitSymmetryGroups[i].units[0]
+ const { model } = unit
+ if (Unit.isAtomic(unit)) {
+ const { chainAtomSegments, chains } = model.atomicHierarchy
+ const chainIt = Segmentation.transientSegments(chainAtomSegments, unit.elements)
+ while (chainIt.hasNext) {
+ const { index: chainIndex } = chainIt.move()
+ const asymId = chains.label_asym_id.value(chainIndex)
+ if (!map.has(asymId)) map.set(asymId, map.size)
+ }
+ } else if (Unit.isCoarse(unit)) {
+ const { chainElementSegments, asym_id } = Unit.isSpheres(unit)
+ ? model.coarseHierarchy.spheres
+ : model.coarseHierarchy.gaussians
+ const chainIt = Segmentation.transientSegments(chainElementSegments, unit.elements)
+ while (chainIt.hasNext) {
+ const { index: chainIndex } = chainIt.move()
+ const asymId = asym_id.value(chainIndex)
+ if (!map.has(asymId)) map.set(asymId, map.size)
+ }
}
}
+ return map
}
export function ChainIdColorTheme(ctx: ThemeDataContext, props: PD.Values<ChainIdColorThemeParams>): ColorTheme<ChainIdColorThemeParams> {
@@ -52,33 +76,24 @@ export function ChainIdColorTheme(ctx: ThemeDataContext, props: PD.Values<ChainI
let legend: ScaleLegend | TableLegend | undefined
if (ctx.structure) {
- // TODO same asym ids in different models should get different color
const l = StructureElement.create()
- const { models } = ctx.structure
- const asymIdSerialMap = new Map<string, number>()
- for (let i = 0, il = models.length; i <il; ++i) {
- const m = models[i]
- addAsymIds(asymIdSerialMap, m.atomicHierarchy.chains.label_asym_id)
- if (m.coarseHierarchy.isDefined) {
- addAsymIds(asymIdSerialMap, m.coarseHierarchy.spheres.asym_id)
- addAsymIds(asymIdSerialMap, m.coarseHierarchy.gaussians.asym_id)
- }
- }
+ const asymIdSerialMap = getAsymIdSerialMap(ctx.structure.root)
const palette = getPalette(asymIdSerialMap.size, props)
legend = palette.legend
color = (location: Location): Color => {
+ let serial: number | undefined = undefined
if (StructureElement.isLocation(location)) {
const asym_id = getAsymId(location.unit)
- return palette.color(asymIdSerialMap.get(asym_id(location)) || 0)
+ serial = asymIdSerialMap.get(asym_id(location))
} else if (Link.isLocation(location)) {
const asym_id = getAsymId(location.aUnit)
l.unit = location.aUnit
l.element = location.aUnit.elements[location.aIndex]
- return palette.color(asymIdSerialMap.get(asym_id(l)) || 0)
+ serial = asymIdSerialMap.get(asym_id(l))
}
- return DefaultColor
+ return serial === undefined ? DefaultColor : palette.color(serial)
}
} else {
color = () => DefaultColor
diff --git a/src/mol-theme/color/element-index.ts b/src/mol-theme/color/element-index.ts
index 8e5fa08ef..c3ad6db92 100644
--- a/src/mol-theme/color/element-index.ts
+++ b/src/mol-theme/color/element-index.ts
@@ -11,7 +11,7 @@ import { OrderedSet } from '../../mol-data/int';
import { ColorTheme, LocationColor } from '../color';
import { ParamDefinition as PD } from '../../mol-util/param-definition'
import { ThemeDataContext } from '../../mol-theme/theme';
-import { getPaletteParams, getPalette } from './util';
+import { getPaletteParams, getPalette } from '../../mol-util/color/palette';
import { TableLegend } from '../../mol-util/color/lists';
import { ScaleLegend } from '../../mol-util/color/scale';
@@ -19,7 +19,7 @@ const DefaultColor = Color(0xCCCCCC)
const Description = 'Gives every element (atom or coarse sphere/gaussian) a unique color based on the position (index) of the element in the list of elements in the structure.'
export const ElementIndexColorThemeParams = {
- ...getPaletteParams({ scaleList: 'red-yellow-blue' }),
+ ...getPaletteParams({ type: 'scale', scaleList: 'red-yellow-blue' }),
}
export type ElementIndexColorThemeParams = typeof ElementIndexColorThemeParams
export function getElementIndexColorThemeParams(ctx: ThemeDataContext) {
@@ -31,7 +31,7 @@ export function ElementIndexColorTheme(ctx: ThemeDataContext, props: PD.Values<E
let legend: ScaleLegend | TableLegend | undefined
if (ctx.structure) {
- const { units } = ctx.structure
+ const { units } = ctx.structure.root
const unitCount = units.length
const cummulativeElementCount = new Map<number, number>()
const unitIdIndex = new Map<number, number>()
@@ -49,11 +49,12 @@ export function ElementIndexColorTheme(ctx: ThemeDataContext, props: PD.Values<E
color = (location: Location): Color => {
if (StructureElement.isLocation(location)) {
const unitIndex = unitIdIndex.get(location.unit.id)!
- const unitElementIndex = OrderedSet.findPredecessorIndex(location.unit.elements, location.element)
+ const unitElementIndex = OrderedSet.findPredecessorIndex(units[unitIndex].elements, location.element)
return palette.color(cummulativeElementCount.get(unitIndex)! + unitElementIndex)
} else if (Link.isLocation(location)) {
const unitIndex = unitIdIndex.get(location.aUnit.id)!
- return palette.color(cummulativeElementCount.get(unitIndex)! + location.aIndex)
+ const unitElementIndex = OrderedSet.findPredecessorIndex(units[unitIndex].elements, location.aUnit.elements[location.aIndex])
+ return palette.color(cummulativeElementCount.get(unitIndex)! + unitElementIndex)
}
return DefaultColor
}
diff --git a/src/mol-theme/color/entity-source.ts b/src/mol-theme/color/entity-source.ts
index e3be5eb8e..e86948bc6 100644
--- a/src/mol-theme/color/entity-source.ts
+++ b/src/mol-theme/color/entity-source.ts
@@ -13,18 +13,25 @@ import { ThemeDataContext } from '../../mol-theme/theme';
import { ScaleLegend } from '../../mol-util/color/scale';
import { Table, Column } from '../../mol-data/db';
import { mmCIF_Schema } from '../../mol-io/reader/cif/schema/mmcif';
-import { getPaletteParams, getPalette } from './util';
+import { getPaletteParams, getPalette } from '../../mol-util/color/palette';
import { TableLegend } from '../../mol-util/color/lists';
-const DefaultColor = Color(0xCCCCCC)
-const Description = 'Gives ranges of a polymer chain a color based on the entity source it originates from. Genes get the same color per entity'
+const DefaultColor = Color(0xFAFAFA)
+const Description = 'Gives ranges of a polymer chain a color based on the entity source it originates from. Genes get the same color per entity.'
export const EntitySourceColorThemeParams = {
- ...getPaletteParams({ scaleList: 'red-yellow-blue' }),
+ ...getPaletteParams({ type: 'set', setList: 'set-3' }),
}
export type EntitySourceColorThemeParams = typeof EntitySourceColorThemeParams
export function getEntitySourceColorThemeParams(ctx: ThemeDataContext) {
- return EntitySourceColorThemeParams // TODO return copy
+ const params = PD.clone(EntitySourceColorThemeParams)
+ if (ctx.structure) {
+ if (getMaps(ctx.structure.root.models).srcKeySerialMap.size > 12) {
+ params.palette.defaultValue.name = 'scale'
+ params.palette.defaultValue.params = { list: 'red-yellow-blue' }
+ }
+ }
+ return params
}
function modelEntityKey(modelIndex: number, entityId: string) {
@@ -77,31 +84,36 @@ function addSrc(seqToSrcByModelEntity: Map<string, Int16Array>, srcKeySerialMap:
}
}
+function getMaps(models: ReadonlyArray<Model>) {
+ const seqToSrcByModelEntity = new Map<string, Int16Array>()
+ const srcKeySerialMap = new Map<string, number>() // serial no starting from 1
+
+ for (let i = 0, il = models.length; i <il; ++i) {
+ const m = models[i]
+ if (m.sourceData.kind !== 'mmCIF') continue
+ const { entity_src_gen, entity_src_nat, pdbx_entity_src_syn } = m.sourceData.data
+ addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, entity_src_gen, entity_src_gen.pdbx_gene_src_gene)
+ addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, entity_src_nat)
+ addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, pdbx_entity_src_syn)
+ }
+
+ return { seqToSrcByModelEntity, srcKeySerialMap }
+}
+
export function EntitySourceColorTheme(ctx: ThemeDataContext, props: PD.Values<EntitySourceColorThemeParams>): ColorTheme<EntitySourceColorThemeParams> {
let color: LocationColor
let legend: ScaleLegend | TableLegend | undefined
- const { structure } = ctx
- if (structure) {
+ if (ctx.structure) {
const l = StructureElement.create()
- const { models } = structure
- const seqToSrcByModelEntity = new Map<string, Int16Array>()
- const srcKeySerialMap = new Map<string, number>() // serial no starting from 1
-
- for (let i = 0, il = models.length; i <il; ++i) {
- const m = models[i]
- if (m.sourceData.kind !== 'mmCIF') continue
- const { entity_src_gen, entity_src_nat, pdbx_entity_src_syn } = m.sourceData.data
- addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, entity_src_gen, entity_src_gen.pdbx_gene_src_gene)
- addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, entity_src_nat)
- addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, pdbx_entity_src_syn)
- }
+ const { models } = ctx.structure.root
+ const { seqToSrcByModelEntity, srcKeySerialMap } = getMaps(models)
const palette = getPalette(srcKeySerialMap.size + 1, props)
legend = palette.legend
const getSrcColor = (location: StructureElement) => {
- const modelIndex = structure.models.indexOf(location.unit.model)
+ const modelIndex = models.indexOf(location.unit.model)
const entityId = StructureProperties.entity.id(location)
const mK = modelEntityKey(modelIndex, entityId)
const seqToSrc = seqToSrcByModelEntity.get(mK)
diff --git a/src/mol-theme/color/model-index.ts b/src/mol-theme/color/model-index.ts
index f7857456f..d518b8c4b 100644
--- a/src/mol-theme/color/model-index.ts
+++ b/src/mol-theme/color/model-index.ts
@@ -11,14 +11,14 @@ import { ColorTheme, LocationColor } from '../color';
import { ParamDefinition as PD } from '../../mol-util/param-definition'
import { ThemeDataContext } from '../../mol-theme/theme';
import { ScaleLegend } from '../../mol-util/color/scale';
-import { getPaletteParams, getPalette } from './util';
+import { getPaletteParams, getPalette } from '../../mol-util/color/palette';
import { TableLegend } from '../../mol-util/color/lists';
const DefaultColor = Color(0xCCCCCC)
const Description = 'Gives every model a unique color based on the position (index) of the model in the list of models in the structure.'
export const ModelIndexColorThemeParams = {
- ...getPaletteParams({ scaleList: 'red-yellow-blue' }),
+ ...getPaletteParams({ type: 'scale', scaleList: 'red-yellow-blue' }),
}
export type ModelIndexColorThemeParams = typeof ModelIndexColorThemeParams
export function getModelIndexColorThemeParams(ctx: ThemeDataContext) {
@@ -30,7 +30,7 @@ export function ModelIndexColorTheme(ctx: ThemeDataContext, props: PD.Values<Mod
let legend: ScaleLegend | TableLegend | undefined
if (ctx.structure) {
- const { models } = ctx.structure
+ const { models } = ctx.structure.root
const palette = getPalette(models.length, props)
legend = palette.legend
const modelColor = new Map<string, Color>()
diff --git a/src/mol-theme/color/polymer-id.ts b/src/mol-theme/color/polymer-id.ts
index 068015844..65d0b8296 100644
--- a/src/mol-theme/color/polymer-id.ts
+++ b/src/mol-theme/color/polymer-id.ts
@@ -4,28 +4,34 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit, StructureProperties, StructureElement, Link } from '../../mol-model/structure';
+import { Unit, StructureProperties, StructureElement, Link, Structure } from '../../mol-model/structure';
import { Color } from '../../mol-util/color';
import { Location } from '../../mol-model/location';
import { ColorTheme, LocationColor } from '../color';
import { ParamDefinition as PD } from '../../mol-util/param-definition'
import { ThemeDataContext } from '../../mol-theme/theme';
-import { Column } from '../../mol-data/db';
-import { Entities } from '../../mol-model/structure/model/properties/common';
-import { getPalette, getPaletteParams } from './util';
+import { getPalette, getPaletteParams } from '../../mol-util/color/palette';
import { ScaleLegend } from '../../mol-util/color/scale';
import { TableLegend } from '../../mol-util/color/lists';
+import { Segmentation } from '../../mol-data/int';
-const DefaultColor = Color(0xCCCCCC)
+const DefaultColor = Color(0xFAFAFA)
const Description = 'Gives every polymer chain a color based on its `asym_id` value.'
export const PolymerIdColorThemeParams = {
- ...getPaletteParams({ scaleList: 'red-yellow-blue' }),
+ ...getPaletteParams({ type: 'set', setList: 'set-3' }),
}
export type PolymerIdColorThemeParams = typeof PolymerIdColorThemeParams
export function getPolymerIdColorThemeParams(ctx: ThemeDataContext) {
- return PolymerIdColorThemeParams // TODO return copy
+ const params = PD.clone(PolymerIdColorThemeParams)
+ if (ctx.structure) {
+ if (getPolymerAsymIdSerialMap(ctx.structure.root).size > 12) {
+ params.palette.defaultValue.name = 'scale'
+ params.palette.defaultValue.params = { list: 'red-yellow-blue' }
+ }
+ }
+ return params
}
function getAsymId(unit: Unit): StructureElement.Property<string> {
@@ -38,19 +44,40 @@ function getAsymId(unit: Unit): StructureElement.Property<string> {
}
}
-function addPolymerAsymIds(map: Map<string, number>, asymId: Column<string>, entityId: Column<string>, entities: Entities) {
- let j = map.size
- for (let o = 0, ol = asymId.rowCount; o < ol; ++o) {
- const e = entityId.value(o)
- const eI = entities.getEntityIndex(e)
- if (entities.data.type.value(eI) === 'polymer') {
- const k = asymId.value(o)
- if (!map.has(k)) {
- map.set(k, j)
- j += 1
+function getPolymerAsymIdSerialMap(structure: Structure) {
+ const map = new Map<string, number>()
+ for (let i = 0, il = structure.unitSymmetryGroups.length; i < il; ++i) {
+ const unit = structure.unitSymmetryGroups[i].units[0]
+ const { model } = unit
+ if (Unit.isAtomic(unit)) {
+ const { chainAtomSegments, chains } = model.atomicHierarchy
+ const chainIt = Segmentation.transientSegments(chainAtomSegments, unit.elements)
+ while (chainIt.hasNext) {
+ const { index: chainIndex } = chainIt.move()
+ const entityId = chains.label_entity_id.value(chainIndex)
+ const eI = model.entities.getEntityIndex(entityId)
+ if (model.entities.data.type.value(eI) === 'polymer') {
+ const asymId = chains.label_asym_id.value(chainIndex)
+ if (!map.has(asymId)) map.set(asymId, map.size)
+ }
+ }
+ } else if (Unit.isCoarse(unit)) {
+ const { chainElementSegments, asym_id, entity_id } = Unit.isSpheres(unit)
+ ? model.coarseHierarchy.spheres
+ : model.coarseHierarchy.gaussians
+ const chainIt = Segmentation.transientSegments(chainElementSegments, unit.elements)
+ while (chainIt.hasNext) {
+ const { index: chainIndex } = chainIt.move()
+ const entityId = entity_id.value(chainIndex)
+ const eI = model.entities.getEntityIndex(entityId)
+ if (model.entities.data.type.value(eI) === 'polymer') {
+ const asymId = asym_id.value(chainIndex)
+ if (!map.has(asymId)) map.set(asymId, map.size)
+ }
}
}
}
+ return map
}
export function PolymerIdColorTheme(ctx: ThemeDataContext, props: PD.Values<PolymerIdColorThemeParams>): ColorTheme<PolymerIdColorThemeParams> {
@@ -58,33 +85,24 @@ export function PolymerIdColorTheme(ctx: ThemeDataContext, props: PD.Values<Poly
let legend: ScaleLegend | TableLegend | undefined
if (ctx.structure) {
- // TODO same asym ids in different models should get different color
const l = StructureElement.create()
- const { models } = ctx.structure
- const polymerAsymIdSerialMap = new Map<string, number>()
- for (let i = 0, il = models.length; i <il; ++i) {
- const m = models[i]
- addPolymerAsymIds(polymerAsymIdSerialMap, m.atomicHierarchy.chains.label_asym_id, m.atomicHierarchy.chains.label_entity_id, m.entities)
- if (m.coarseHierarchy.isDefined) {
- addPolymerAsymIds(polymerAsymIdSerialMap, m.coarseHierarchy.spheres.asym_id, m.coarseHierarchy.spheres.entity_id, m.entities)
- addPolymerAsymIds(polymerAsymIdSerialMap, m.coarseHierarchy.gaussians.asym_id, m.coarseHierarchy.spheres.entity_id, m.entities)
- }
- }
+ const polymerAsymIdSerialMap = getPolymerAsymIdSerialMap(ctx.structure.root)
const palette = getPalette(polymerAsymIdSerialMap.size, props)
legend = palette.legend
color = (location: Location): Color => {
+ let serial: number | undefined = undefined
if (StructureElement.isLocation(location)) {
const asym_id = getAsymId(location.unit)
- return palette.color(polymerAsymIdSerialMap.get(asym_id(location)) || 0)
+ serial = polymerAsymIdSerialMap.get(asym_id(location))
} else if (Link.isLocation(location)) {
const asym_id = getAsymId(location.aUnit)
l.unit = location.aUnit
l.element = location.aUnit.elements[location.aIndex]
- return palette.color(polymerAsymIdSerialMap.get(asym_id(l)) || 0)
+ serial = polymerAsymIdSerialMap.get(asym_id(l))
}
- return DefaultColor
+ return serial === undefined ? DefaultColor : palette.color(serial)
}
} else {
color = () => DefaultColor
diff --git a/src/mol-theme/color/polymer-index.ts b/src/mol-theme/color/polymer-index.ts
index 513095041..88f5bb938 100644
--- a/src/mol-theme/color/polymer-index.ts
+++ b/src/mol-theme/color/polymer-index.ts
@@ -12,7 +12,7 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition'
import { ThemeDataContext } from '../../mol-theme/theme';
import { ScaleLegend } from '../../mol-util/color/scale';
import { TableLegend } from '../../mol-util/color/lists';
-import { getPaletteParams, getPalette } from './util';
+import { getPaletteParams, getPalette } from '../../mol-util/color/palette';
const DefaultColor = Color(0xCCCCCC)
const Description = 'Gives every polymer a unique color based on the position (index) of the polymer in the list of polymers in the structure.'
@@ -31,7 +31,7 @@ export function PolymerIndexColorTheme(ctx: ThemeDataContext, props: PD.Values<P
let legend: ScaleLegend | TableLegend | undefined
if (ctx.structure) {
- const { units } = ctx.structure
+ const { units } = ctx.structure.root
let polymerCount = 0
for (let i = 0, il = units.length; i <il; ++i) {
if (units[i].polymerElements.length > 0) ++polymerCount
diff --git a/src/mol-theme/color/unit-index.ts b/src/mol-theme/color/unit-index.ts
index 9876f424d..b645541a9 100644
--- a/src/mol-theme/color/unit-index.ts
+++ b/src/mol-theme/color/unit-index.ts
@@ -11,14 +11,14 @@ import { ColorTheme, LocationColor } from '../color';
import { ParamDefinition as PD } from '../../mol-util/param-definition'
import { ThemeDataContext } from '../../mol-theme/theme';
import { ScaleLegend } from '../../mol-util/color/scale';
-import { getPaletteParams, getPalette } from './util';
+import { getPaletteParams, getPalette } from '../../mol-util/color/palette';
import { TableLegend } from '../../mol-util/color/lists';
const DefaultColor = Color(0xCCCCCC)
const Description = 'Gives every unit (single chain or collection of single elements) a unique color based on the position (index) of the unit in the list of units in the structure.'
export const UnitIndexColorThemeParams = {
- ...getPaletteParams({ scaleList: 'red-yellow-blue' }),
+ ...getPaletteParams({ type: 'scale', scaleList: 'red-yellow-blue' }),
}
export type UnitIndexColorThemeParams = typeof UnitIndexColorThemeParams
export function getUnitIndexColorThemeParams(ctx: ThemeDataContext) {
@@ -30,7 +30,7 @@ export function UnitIndexColorTheme(ctx: ThemeDataContext, props: PD.Values<Unit
let legend: ScaleLegend | TableLegend | undefined
if (ctx.structure) {
- const { units } = ctx.structure
+ const { units } = ctx.structure.root
const palette = getPalette(units.length, props)
legend = palette.legend
const unitIdColor = new Map<number, Color>()
diff --git a/src/mol-theme/color/util.ts b/src/mol-util/color/palette.ts
similarity index 84%
rename from src/mol-theme/color/util.ts
rename to src/mol-util/color/palette.ts
index 7925c82f8..e0791f8f9 100644
--- a/src/mol-theme/color/util.ts
+++ b/src/mol-util/color/palette.ts
@@ -4,22 +4,25 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { ParamDefinition as PD } from '../../mol-util/param-definition'
-import { DistinctColorsParams, distinctColors } from '../../mol-util/color/distinct';
-import { ScaleLegend, ColorScale } from '../../mol-util/color/scale';
-import { Color } from '../../mol-util/color';
-import { TableLegend, ColorListName, ColorListOptionsScale, ColorListOptionsSet, getColorListFromName } from '../../mol-util/color/lists';
+import { ParamDefinition as PD } from '../param-definition'
+import { DistinctColorsParams, distinctColors } from './distinct';
+import { ScaleLegend, ColorScale } from './scale';
+import { Color } from '.';
+import { TableLegend, ColorListName, ColorListOptionsScale, ColorListOptionsSet, getColorListFromName } from './lists';
+
+type PaletteType = 'generate' | 'scale' | 'set'
const DefaultGetPaletteProps = {
+ type: 'generate' as PaletteType,
scaleList: 'red-yellow-blue' as ColorListName,
setList: 'set-1' as ColorListName
}
type GetPaletteProps = typeof DefaultGetPaletteProps
export function getPaletteParams(props: Partial<GetPaletteProps> = {}) {
- const p = { ...DefaultGetPaletteProps, props }
+ const p = { ...DefaultGetPaletteProps, ...props }
return {
- palette: PD.MappedStatic('generate', {
+ palette: PD.MappedStatic(p.type, {
scale: PD.Group({
list: PD.ColorList<ColorListName>(p.scaleList, ColorListOptionsScale),
}, { isFlat: true }),
--
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