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+/**
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+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
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+ *
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+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
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+ */
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+
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+import { StructureProperties, StructureElement, Link, Model } from 'mol-model/structure';
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+import { ColorScale, Color } from 'mol-util/color';
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+import { Location } from 'mol-model/location';
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+import { ColorTheme, LocationColor } from '../color';
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+import { ParamDefinition as PD } from 'mol-util/param-definition'
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+import { ThemeDataContext } from 'mol-theme/theme';
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+import { ColorListOptions, ColorListName } from 'mol-util/color/scale';
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+import { Table, Column } from 'mol-data/db';
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+import { mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif';
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+
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+const DefaultColor = Color(0xCCCCCC)
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+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'
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+
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+export const EntitySourceColorThemeParams = {
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+ list: PD.ColorScale<ColorListName>('RedYellowBlue', ColorListOptions),
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+}
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+export type EntitySourceColorThemeParams = typeof EntitySourceColorThemeParams
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+export function getEntitySourceColorThemeParams(ctx: ThemeDataContext) {
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+ return EntitySourceColorThemeParams // TODO return copy
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+}
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+
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+function modelEntityKey(modelIndex: number, entityId: string) {
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+ return `${modelIndex}|${entityId}`
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+}
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+
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+type EntitySrc = Table<{
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+ entity_id: mmCIF_Schema['entity_src_gen']['entity_id'],
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+ pdbx_src_id: mmCIF_Schema['entity_src_gen']['pdbx_src_id'],
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+ pdbx_beg_seq_num: mmCIF_Schema['entity_src_gen']['pdbx_beg_seq_num'],
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+ pdbx_end_seq_num: mmCIF_Schema['entity_src_gen']['pdbx_end_seq_num'],
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+}>
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+type GeneSrcGene = Column<mmCIF_Schema['entity_src_gen']['pdbx_gene_src_gene']['T']>
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+
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+function srcKey(modelIndex: number, entityId: string, srcId: number, gene: string) {
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+ return `${modelIndex}|${entityId}|${gene ? gene : srcId}`
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+}
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+
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+function addSrc(seqToSrcByModelEntity: Map<string, Int16Array>, srcKeySerialMap: Map<string, number>, modelIndex: number, model: Model, entity_src: EntitySrc, gene_src_gene?: GeneSrcGene) {
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+ const { entity_id, pdbx_src_id, pdbx_beg_seq_num, pdbx_end_seq_num } = entity_src
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+ for (let j = 0, jl = entity_src._rowCount; j < jl; ++j) {
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+ const entityId = entity_id.value(j)
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+ const mK = modelEntityKey(modelIndex, entityId)
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+ let seqToSrc: Int16Array
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+ if (!seqToSrcByModelEntity.has(mK)) {
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+ const entityIndex = model.entities.getEntityIndex(entityId)
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+ const seq = model.sequence.sequences[entityIndex].sequence
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+ seqToSrc = new Int16Array(seq.sequence.length)
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+ seqToSrcByModelEntity.set(mK, seqToSrc)
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+ } else {
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+ seqToSrc = seqToSrcByModelEntity.get(mK)!
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+ }
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+ const sK = srcKey(modelIndex, entityId, pdbx_src_id.value(j), gene_src_gene ? gene_src_gene.value(j).join(',') : '')
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+
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+ // may not be given (= 0) indicating src is for the whole seq
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+ const beg = pdbx_beg_seq_num.valueKind(j) === Column.ValueKind.Present ? pdbx_beg_seq_num.value(j) : 1
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+ const end = pdbx_end_seq_num.valueKind(j) === Column.ValueKind.Present ? pdbx_end_seq_num.value(j) : seqToSrc.length
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+
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+ let srcIndex: number // serial no starting from 1
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+ if (srcKeySerialMap.has(sK)) {
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+ srcIndex = srcKeySerialMap.get(sK)!
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+ } else {
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+ srcIndex = srcKeySerialMap.size + 1
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+ srcKeySerialMap.set(sK, srcIndex)
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+ }
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+ // set src index
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+ for (let i = beg, il = end; i <= il; ++i) {
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+ seqToSrc[i - 1] = srcIndex
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+ }
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+ }
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+}
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+
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+export function EntitySourceColorTheme(ctx: ThemeDataContext, props: PD.Values<EntitySourceColorThemeParams>): ColorTheme<EntitySourceColorThemeParams> {
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+ let color: LocationColor
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+ const scale = ColorScale.create({ listOrName: props.list, minLabel: 'Start', maxLabel: 'End' })
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+ const { structure } = ctx
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+
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+ if (structure) {
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+ const l = StructureElement.create()
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+ const { models } = structure
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+ const seqToSrcByModelEntity = new Map<string, Int16Array>()
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+ const srcKeySerialMap = new Map<string, number>() // serial no starting from 1
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+
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+ for (let i = 0, il = models.length; i <il; ++i) {
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+ const m = models[i]
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+ if (m.sourceData.kind !== 'mmCIF') continue
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+ const { entity_src_gen, entity_src_nat, pdbx_entity_src_syn } = m.sourceData.data
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+ addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, entity_src_gen, entity_src_gen.pdbx_gene_src_gene)
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+ addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, entity_src_nat)
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+ addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, pdbx_entity_src_syn)
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+ }
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+ scale.setDomain(1, srcKeySerialMap.size)
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+ const scaleColor = scale.color
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+
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+ const getSrcColor = (location: StructureElement) => {
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+ const modelIndex = structure.models.indexOf(location.unit.model)
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+ const entityId = StructureProperties.entity.id(location)
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+ const mK = modelEntityKey(modelIndex, entityId)
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+ const seqToSrc = seqToSrcByModelEntity.get(mK)
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+ if (seqToSrc) {
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+ // minus 1 to convert seqId to array index
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+ return scaleColor(seqToSrc[StructureProperties.residue.label_seq_id(location) - 1])
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+ } else {
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+ return DefaultColor
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+ }
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+ }
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+
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+ color = (location: Location): Color => {
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+ if (StructureElement.isLocation(location)) {
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+ return getSrcColor(location)
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+ } else if (Link.isLocation(location)) {
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+ l.unit = location.aUnit
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+ l.element = location.aUnit.elements[location.aIndex]
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+ return getSrcColor(l)
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+ }
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+ return DefaultColor
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+ }
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+ } else {
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+ color = () => DefaultColor
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+ }
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+
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+ return {
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+ factory: EntitySourceColorTheme,
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+ granularity: 'group',
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+ color,
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+ props,
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+ description: Description,
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+ legend: scale ? scale.legend : undefined
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+ }
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+}
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+
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+export const EntitySourceColorThemeProvider: ColorTheme.Provider<EntitySourceColorThemeParams> = {
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+ label: 'Entity Source',
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+ factory: EntitySourceColorTheme,
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+ getParams: getEntitySourceColorThemeParams,
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+ defaultValues: PD.getDefaultValues(EntitySourceColorThemeParams),
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+ isApplicable: (ctx: ThemeDataContext) => !!ctx.structure
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+}
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Alexander Rose