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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,9 @@ | ||
| import {buildEntitySummaryFv} from "../RcsbFvWeb/RcsbFvBuilder"; | ||
| import {getJsonFromUrl, onLoad} from "./utils/events"; | ||
|
|
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| buildEntitySummaryFv("pfv", "select", "AF_AFQ8WZ42F1_1").then((module)=>{ | ||
| console.log(module) | ||
| }); | ||
| onLoad(()=>{ | ||
| const args: {entityId:string} = getJsonFromUrl().entityId ? getJsonFromUrl() : {entityId:"3HBX_1"}; | ||
| buildEntitySummaryFv("pfv", "select", args.entityId).then((module)=>{ | ||
| console.log(module) | ||
| }); | ||
| }); |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
|
|
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| export function getJsonFromUrl() { | ||
| const url = location.search; | ||
| var query = url.substring(1); | ||
| var result: any = {}; | ||
| query.split("&").forEach(function(part) { | ||
| var item = part.split("="); | ||
| result[item[0]] = decodeURIComponent(item[1]); | ||
| }); | ||
| return result; | ||
| } | ||
|
|
||
| export function onLoad(f:()=>void){ | ||
| document.addEventListener("DOMContentLoaded", function(event) { | ||
| f(); | ||
| }); | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,141 @@ | ||
| import { | ||
| AnnotationFeatures, | ||
| Feature, | ||
| FeaturePosition, | ||
| Source, | ||
| Type | ||
| } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes"; | ||
| import {PolymerEntityInstanceInterface} from "../../RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector"; | ||
| import {range} from "lodash"; | ||
| import {rcsbRequestCtxManager} from "../../RcsbRequest/RcsbRequestContextManager"; | ||
| import {RcsbFvTooltipInterface} from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvTooltip/RcsbFvTooltipInterface"; | ||
| import {RcsbFvTooltip} from "../../RcsbFvWeb/RcsbFvTooltip/RcsbFvTooltip"; | ||
| import { | ||
| RcsbFvTrackDataAnnotationInterface | ||
| } from "../../RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/RcsbFvTrackDataAnnotationInterface"; | ||
| import {ExternalTrackBuilderInterface} from "../../RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface"; | ||
|
|
||
| export function addUnmodeledTrackBuilder( | ||
| unmodeledTrackBuilder: UnmodeledTrackBuilder, | ||
| externalTrackBuilder?: ExternalTrackBuilderInterface | ||
| ): ExternalTrackBuilderInterface { | ||
| const trackBuilder = async (data: { | ||
| annotations: Array<AnnotationFeatures>; | ||
| rcsbContext?: Partial<PolymerEntityInstanceInterface> | ||
| }): Promise<Array<AnnotationFeatures>> => { | ||
| return [ | ||
| ... await externalTrackBuilder?.filterFeatures?.(data) ?? [], | ||
| ... await unmodeledTrackBuilder.filterFeatures(data) | ||
| ]; | ||
| } | ||
| return { | ||
| ... externalTrackBuilder, | ||
| filterFeatures: async (data) => { | ||
| externalTrackBuilder?.filterFeatures?.(data); | ||
| return trackBuilder({ | ||
| annotations: await externalTrackBuilder?.filterFeatures?.(data) ?? data.annotations, | ||
| rcsbContext: data.rcsbContext | ||
| }); | ||
| } | ||
| } | ||
| } | ||
|
|
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| export class UnmodeledTrackBuilder { | ||
|
|
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| private readonly unmodeledDescription: Map<string,[number,number]> = new Map(); | ||
| public async filterFeatures(data: { | ||
| annotations: Array<AnnotationFeatures>; | ||
| rcsbContext?: Partial<PolymerEntityInstanceInterface>; | ||
| }): Promise<Array<AnnotationFeatures>> { | ||
| if (!data.rcsbContext) | ||
| return data.annotations; | ||
| return [ | ||
| ...await this.buildUnobserved(data.annotations, data.rcsbContext), | ||
| ...filterUnobserved(data.annotations) | ||
| ]; | ||
| } | ||
|
|
||
| public getTooltip(): RcsbFvTooltipInterface{ | ||
| return new UnobservedToolTip(this.unmodeledDescription); | ||
| } | ||
|
|
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| private async buildUnobserved(annotations: Array<AnnotationFeatures>, rcsbContext: Partial<PolymerEntityInstanceInterface>): Promise<Array<AnnotationFeatures>> { | ||
| const nInstances = (await rcsbRequestCtxManager.getEntityProperties(rcsbContext.entityId ?? "none"))[0].instances.length; | ||
| const featurePositions = Array.from(annotations.filter( | ||
| ann => ann.features?.filter( | ||
| f => f?.type == Type.UnobservedResidueXyz | ||
| )?.length ?? 0 > 0 | ||
| ).map( | ||
| ann => ann.features?.filter( | ||
| (f): f is Feature => f?.type == Type.UnobservedResidueXyz | ||
| ) ?? [] | ||
| ).flat().map( | ||
| feature => feature.feature_positions?.filter( | ||
| (p): p is FeaturePosition => typeof p != "undefined" | ||
| ) ?? [] | ||
| ).flat().map( | ||
| p => p.beg_seq_id && p.end_seq_id ? range(p.beg_seq_id,p.end_seq_id+1) : [] | ||
| ).flat().reduce( | ||
| (map,idx) => map.set(idx, (map.get(idx) ?? 0) + 1), | ||
| new Map<number,number> | ||
| ).entries()).map(([idx,unobserved])=>{ | ||
| this.unmodeledDescription.set(`${rcsbContext.entityId}:${idx}`, [unobserved, nInstances]); | ||
| return { | ||
| beg_seq_id: idx, | ||
| values: [Math.round(unobserved / nInstances * 100)/100] | ||
| } | ||
| }); | ||
| return [{ | ||
| source: Source.PdbEntity, | ||
| target_id: rcsbContext.entityId, | ||
| features: [{ | ||
| type: UNMODELED as Type, | ||
| feature_positions: featurePositions | ||
| }] | ||
| }] | ||
| } | ||
|
|
||
| } | ||
|
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| class UnobservedToolTip implements RcsbFvTooltipInterface { | ||
|
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| private readonly regularTooltip: RcsbFvTooltip = new RcsbFvTooltip(); | ||
| private readonly trackDescription: Map<string,[number,number]>; | ||
|
|
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| constructor(trackDescription: Map<string,[number,number]>) { | ||
| this.trackDescription = trackDescription; | ||
| } | ||
|
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| showTooltip(d: RcsbFvTrackDataAnnotationInterface): HTMLElement | undefined { | ||
| return this.regularTooltip.showTooltip(d); | ||
| } | ||
|
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| showTooltipDescription(d: RcsbFvTrackDataAnnotationInterface): HTMLElement | undefined { | ||
| if(d.title == UNMODELED as Type) | ||
| return this.overloadTooltipDescription(d); | ||
| return this.regularTooltip.showTooltipDescription(d); | ||
| } | ||
|
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| overloadTooltipDescription(d: RcsbFvTrackDataAnnotationInterface): HTMLElement | undefined { | ||
| if(!this.trackDescription.has(`${d.sourceId}:${d.begin}`)) | ||
| return undefined; | ||
| const tooltipDescriptionDiv = document.createElement<"div">("div"); | ||
| const [unobserved, total] = this.trackDescription.get(`${d.sourceId}:${d.begin}`) ?? [0,0]; | ||
| tooltipDescriptionDiv.append(`Unmodeled in ${unobserved} of ${total} chains`); | ||
| return tooltipDescriptionDiv; | ||
| } | ||
|
|
||
| } | ||
|
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| function filterUnobserved(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures> { | ||
| return annotations.map(ann=>{ | ||
| return { | ||
| ...ann, | ||
| features: ann.features?.filter( | ||
| f=> f?.type != Type.UnobservedResidueXyz && f?.type != Type.UnobservedAtomXyz | ||
| ) | ||
| } | ||
| }); | ||
| } | ||
|
|
||
| const UNMODELED = "UNMODELED"; |
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