chimeric facet

CHANGELOG.md

@@ -2,6 +2,14 @@
 
 [Semantic Versioning](https://semver.org/)
 
+## [6.0.2] - 2023-11-28
+### Improvement
+- `FacetMemberInterface.facetConfig` interface attribute to encode histogram data transformations and other configuration
+  - `facetTransform` can be used to transform Search API facets into other facets
+  - `bucketClickSearchQuery` can be used to overwrite bucket click events
+  - `mergeDomainMaxValue` has been moved from `FacetMemberInterface.chartConfig`
+- `CHIMERIC_FACET` New facet histogram to display wild type vs chimeric protein group distribution
+
 ## [6.0.1] - 2023-11-27
 ### Improvement
 - `MultipleEntryPropertyCollector` includes polymer entity prd ids

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@rcsb/rcsb-saguaro-app",
-  "version": "6.0.1",
+  "version": "6.0.2",
   "description": "RCSB 1D Saguaro Web App",
   "main": "build/app.js",
   "files": [

src/RcsbFvExamples/GroupHistogram.ts

@@ -1,13 +1,13 @@
 import {buildGroup, buildGroupContent, buildGroupMembers} from "../RcsbGroupWeb/RcsbGroupBuilder";
 import {GroupProvenanceId} from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
 
-const groupId = "1534_30";
+const groupId = "P00720";
 
 buildGroupContent("select", GroupProvenanceId.ProvenanceSequenceIdentity, groupId);
 
 buildGroupMembers("carousel", GroupProvenanceId.ProvenanceSequenceIdentity, groupId, 1, 1)
 
-buildGroup("pfv", GroupProvenanceId.ProvenanceSequenceIdentity, groupId, undefined, ["ENTITY_NAME_FACET", "RELEASE_DATE_FACET", "METHODOLOGY_FACET"]).then((m)=>{
+buildGroup("pfv", GroupProvenanceId.ProvenanceSequenceIdentity, groupId, undefined, ["CHIMERIC_FACET"]).then((m)=>{
 });
 
 buildGroup("pfv_2", GroupProvenanceId.ProvenanceSequenceIdentity, groupId, undefined, ["RESOLUTION_FACET","EXPERIMENTAL_METHOD_FACET"]).then((m)=>{

src/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartEvents.ts

@@ -63,12 +63,17 @@ export namespace GroupChartEvents {
             chart.chartConfig.barClickCallback = async (datum:ChartDataValueInterface<GroupChartMap.ChartObjectIdType>, data: ChartDataColumnInterface[], e?: React.MouseEvent) => {
                 if(datum.id === "excluded")
                     return;
-                let query: SearchQueryType = SQT.searchAttributeQuery(chart.attribute, datum.x, Operator.ExactMatch, Service.Text);
-                if(chart.filters)
-                    chart.filters.forEach(f=>{
-                        query = SQT.addNewNodeToAttributeSearchQuery(f.attribute, f.value, f.operator, query, f.service)
-                    })
-                await clickEvent(e ?? {shiftKey: false}, chart, query, returnType);
+                if(chart.facetConfig?.bucketClickSearchQuery){
+                    const query: SearchQueryType = chart.facetConfig?.bucketClickSearchQuery(datum, data, e);
+                    await clickEvent(e ?? {shiftKey: false}, chart, query, returnType);
+                }else{
+                    let query: SearchQueryType = SQT.searchAttributeQuery(chart.attribute, datum.x, Operator.ExactMatch, Service.Text);
+                    if(chart.filters)
+                        chart.filters.forEach(f=>{
+                            query = SQT.addNewNodeToAttributeSearchQuery(f.attribute, f.value, f.operator, query, f.service)
+                        })
+                    await clickEvent(e ?? {shiftKey: false}, chart, query, returnType);
+                }
             };
     }
 
@@ -77,8 +82,11 @@ export namespace GroupChartEvents {
             chart.chartConfig.barClickCallback = async (datum:ChartDataValueInterface, data: ChartDataColumnInterface[], e?: React.MouseEvent) => {
                 if(datum.id === "excluded")
                     return;
-                if(chart.chartConfig?.mergeDomainMaxValue && parseFloat(datum.x.toString()) >= chart.chartConfig.mergeDomainMaxValue) {
-                    const query: SearchQueryType = SQT.searchAttributeQuery(chart.attribute, chart.chartConfig.mergeDomainMaxValue, Operator.GreaterOrEqual,  Service.Text);
+                if(chart.facetConfig?.bucketClickSearchQuery){
+                    const query: SearchQueryType = chart.facetConfig?.bucketClickSearchQuery(datum, data, e);
+                    await clickEvent(e ?? {shiftKey: false}, chart, query, returnType);
+                } else if(chart.facetConfig?.mergeDomainMaxValue && parseFloat(datum.x.toString()) >= chart.facetConfig.mergeDomainMaxValue) {
+                    const query: SearchQueryType = SQT.searchAttributeQuery(chart.attribute, chart.facetConfig.mergeDomainMaxValue, Operator.GreaterOrEqual,  Service.Text);
                     await clickEvent(e ?? {shiftKey: false}, chart, query, returnType);
                 }else{
                     const range: Range|DateRange = formatRange(chart, datum);

src/RcsbSeacrh/FacetStore/FacetMemberInterface.ts

@@ -1,10 +1,16 @@
 
 import {ChartConfigInterface, ChartType} from "@rcsb/rcsb-charts/lib/RcsbChartComponent/ChartConfigInterface";
 import {
-    AttributeFacetType,
+    AttributeFacetType, BucketDataType,
     FilterFacetType
 } from "@rcsb/rcsb-search-tools/lib/SearchParseTools/SearchFacetInterface";
 import {RcsbSearchAttributeType} from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchMetadata";
+import {SearchQueryType} from "@rcsb/rcsb-search-tools/lib/SearchQueryTools/SearchQueryInterfaces";
+import {
+    ChartDataColumnInterface,
+    ChartDataValueInterface
+} from "@rcsb/rcsb-charts/lib/RcsbChartDataProvider/ChartDataProviderInterface";
+import React from "react";
 
 export type FacetType = AttributeFacetType  | FilterFacetType;
 
@@ -14,7 +20,14 @@ export interface FacetMemberInterface {
     attributeName: string;
     attribute: RcsbSearchAttributeType;
     chartType: ChartType;
-    chartConfig?: ChartConfigInterface & { mergeDomainMaxValue?:number; };
+    chartConfig?: ChartConfigInterface;
+    facetConfig?: FacetConfigInterface;
     facet: FacetType;
     contentType:"date"|"number"|"string";
+}
+
+export interface FacetConfigInterface {
+    mergeDomainMaxValue?: number;
+    facetTransform?: (d: BucketDataType[])=>BucketDataType[];
+    bucketClickSearchQuery?: (datum:ChartDataValueInterface, data: ChartDataColumnInterface[], e?: React.MouseEvent)=>SearchQueryType;
 }

src/RcsbSeacrh/FacetStore/SequenceGroupFacetStore.ts

@@ -20,7 +20,7 @@ import {
     ECOD_FACET,
     ENZYME_CLASS_FACET,
     GO_FUNCTION_FACET, GO_PROCESS_FACET, GO_COMPONENT_FACET,
-    METHODOLOGY_FACET
+    METHODOLOGY_FACET, CHIMERIC_FACET
 } from "./SingleFacets";
 import {cloneDeep} from "lodash";
 
@@ -45,7 +45,8 @@ class SequenceGroupFacetStore implements FacetStoreInterface{
         cloneDeep<FacetMemberInterface>(ENTITY_NAME_FACET),
         cloneDeep<FacetMemberInterface>(GO_FUNCTION_FACET),
         cloneDeep<FacetMemberInterface>(GO_PROCESS_FACET),
-        cloneDeep<FacetMemberInterface>(GO_COMPONENT_FACET)
+        cloneDeep<FacetMemberInterface>(GO_COMPONENT_FACET),
+        cloneDeep<FacetMemberInterface>(CHIMERIC_FACET)
     ];
     private readonly nonPolymerFacet: FacetMemberInterface[] = [
         cloneDeep<FacetMemberInterface>(CHEM_COMP_FACET)

src/RcsbSeacrh/FacetStore/SingleFacets.ts

@@ -1,9 +1,11 @@
 import {RcsbSearchMetadata} from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchMetadata";
-import {AggregationType, Service, Type} from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
+import {AggregationType, Operator, Service, Type} from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
 import {FacetMemberInterface} from "./FacetMemberInterface";
 import {ChartType} from "@rcsb/rcsb-charts/lib/RcsbChartComponent/ChartConfigInterface";
 import {ChartDataValueInterface} from "@rcsb/rcsb-charts/lib/RcsbChartDataProvider/ChartDataProviderInterface";
 import {GroupChartMap} from "../../RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartTools";
+import {BucketDataType} from "@rcsb/rcsb-search-tools/lib/SearchParseTools/SearchFacetInterface";
+import {SearchQueryTools as SQT} from "../SearchQueryTools";
 
 
 export const EXPERIMENTAL_METHOD_FACET: FacetMemberInterface = {
@@ -49,7 +51,6 @@ export const RESOLUTION_FACET: FacetMemberInterface = {
             constHeight: 225
         },
         histogramBinIncrement: 0.5,
-        mergeDomainMaxValue: 5,
         domainMinValue: 0,
         domainMaxValue: 6,
         axisLabel: "Angstroms",
@@ -59,6 +60,9 @@ export const RESOLUTION_FACET: FacetMemberInterface = {
             return `Resolution ${d.x as number - 0.25} - ${d.x as number + 0.25}`;
         }
     },
+    facetConfig: {
+        mergeDomainMaxValue: 5
+    },
     facet: {
         name: "RESOLUTION_FACET",
         aggregation_type: AggregationType.Histogram,
@@ -86,6 +90,68 @@ export const METHODOLOGY_FACET: FacetMemberInterface = {
     }
 };
 
+export const CHIMERIC_FACET: FacetMemberInterface = {
+    id: "chimeric",
+    title: "Protein Sequence Composition",
+    attributeName: "CHIMERIC_FACET",
+    attribute: RcsbSearchMetadata.RcsbPolymerEntity.RcsbSourcePartCount.path,
+    chartType: ChartType.barplot,
+    contentType: "string",
+    facetConfig: {
+        facetTransform: (buckets)=>{
+            const out: BucketDataType[] = [];
+            const  wt = buckets.find(b=>b.label == 1)
+            if(wt)
+                out.push({
+                    label: "Wild Type",
+                    population: wt.population
+                });
+            const synthetic = buckets.find(b=>b.label == 0)
+            if(synthetic)
+                out.push({
+                    label: "Synthetic",
+                    population: synthetic.population
+                });
+            const chimeric = buckets.filter(b=> parseInt(b.label.toString()) > 1);
+            if(chimeric?.length > 0)
+                out.push({
+                    label: "Chimeric",
+                    population: chimeric.reduce((c,p)=>c+p.population,0)
+                });
+            return out;
+        },
+        bucketClickSearchQuery: (datum, data, e) => {
+            if(datum.x == "Wild Type")
+                return SQT.searchAttributeQuery(
+                    CHIMERIC_FACET.attribute,
+                    1,
+                    Operator.Equals,
+                    Service.Text
+                );
+            else if(datum.x == "Synthetic")
+                return SQT.searchAttributeQuery(
+                    CHIMERIC_FACET.attribute,
+                    0,
+                    Operator.Equals,
+                    Service.Text
+                );
+            else
+                return SQT.searchAttributeQuery(
+                    CHIMERIC_FACET.attribute,
+                    1,
+                    Operator.Greater,
+                    Service.Text
+                );
+        }
+    },
+    facet: {
+        name: "CHIMERIC_FACET",
+        aggregation_type: AggregationType.Terms,
+        attribute: RcsbSearchMetadata.RcsbPolymerEntity.RcsbSourcePartCount.path,
+        min_interval_population: 1
+    }
+};
+
 export const RELEASE_DATE_FACET: FacetMemberInterface = {
     id: "release_date",
     title: undefined,
@@ -579,5 +645,6 @@ export const SearchFacets = {
     GO_PROCESS_FACET,
     GO_COMPONENT_FACET,
     LIGAND_OF_INTEREST_FACET,
-    METHODOLOGY_FACET
+    METHODOLOGY_FACET,
+    CHIMERIC_FACET
 };

src/RcsbSeacrh/FacetStore/UniprotGroupFacetStore.ts

@@ -20,7 +20,7 @@ import {
     ECOD_FACET,
     ENZYME_CLASS_FACET,
     GO_FUNCTION_FACET, GO_PROCESS_FACET, GO_COMPONENT_FACET,
-    METHODOLOGY_FACET
+    METHODOLOGY_FACET, CHIMERIC_FACET
 } from "./SingleFacets";
 import {cloneDeep} from "lodash";
 
@@ -45,7 +45,8 @@ class UniprotGroupFacetStore implements FacetStoreInterface{
         cloneDeep<FacetMemberInterface>(ENTITY_NAME_FACET),
         cloneDeep<FacetMemberInterface>(GO_FUNCTION_FACET),
         cloneDeep<FacetMemberInterface>(GO_PROCESS_FACET),
-        cloneDeep<FacetMemberInterface>(GO_COMPONENT_FACET)
+        cloneDeep<FacetMemberInterface>(GO_COMPONENT_FACET),
+        cloneDeep<FacetMemberInterface>(CHIMERIC_FACET)
     ];
     private readonly nonPolymerFacet: FacetMemberInterface[] = [
         cloneDeep<FacetMemberInterface>(CHEM_COMP_FACET)

src/RcsbSeacrh/FacetTools.ts

@@ -7,8 +7,8 @@ import {
 } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
 import {Service} from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
 import {
-    ChartConfigInterface, ChartDisplayConfigInterface,
-    ChartObjectInterface, ChartType,
+    ChartDisplayConfigInterface,
+    ChartObjectInterface,
 } from "@rcsb/rcsb-charts/lib/RcsbChartComponent/ChartConfigInterface";
 import {RcsbSearchAttributeType} from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchMetadata";
 import {
@@ -19,16 +19,10 @@ import {
 import {getBucketsFromFacets} from "@rcsb/rcsb-search-tools/lib/SearchParseTools/SearchFacetTools";
 
 export type SearchFilter = {attribute:RcsbSearchAttributeType;value:AttributeTextQueryParameters['value'];operator:AttributeTextQueryParameters["operator"];service:Service.Text|Service.TextChem};
-export interface RcsbChartInterface<T=any> {
-    chartType: ChartType;
+export interface RcsbChartInterface<T=any> extends Omit<FacetMemberInterface, "id"|"facet">{
     labelList?: string[];
-    attribute: RcsbSearchAttributeType;
-    attributeName: string;
-    chartConfig?: FacetMemberInterface["chartConfig"],
-    title?: string,
     data: ChartObjectInterface<T>[];
     filters?:SearchFilter[];
-    contentType:FacetMemberInterface['contentType'];
 }
 
 export class FacetTools {
@@ -40,15 +34,13 @@ export class FacetTools {
             const facet = FacetTools.getFacetFromName(facetMembers,bucket.name);
             if(!facet)
                 return;
-            const chart: {chartType: ChartType; chartConfig?: ChartConfigInterface; title?: string;} = FacetTools.getFacetChartTypeFromAttribute(facetMembers, bucket.name);
+            const chart= FacetTools.getFacetChartTypeFromAttribute(facetMembers, bucket.name);
             out.push({
-                chartType: chart.chartType,
-                chartConfig: chart.chartConfig,
+                ...chart,
                 labelList: [],
                 attributeName: bucket.name,
                 attribute: facet.attribute,
-                title: chart.title,
-                data: applyChartConfigToData(bucket.data, facet?.chartConfig),
+                data: applyChartConfigToData(bucket.data, facet?.facetConfig),
                 filters: FacetTools.getFacetFiltersFromName(facetMembers, bucket.name),
                 contentType: facet.contentType
             });
@@ -100,11 +92,11 @@ export class FacetTools {
         });
     }
 
-    private static getFacetChartTypeFromAttribute(facetMembers: FacetMemberInterface[], attribute: string): {chartType: ChartType, chartConfig?: ChartConfigInterface, title?: string} {
+    private static getFacetChartTypeFromAttribute(facetMembers: FacetMemberInterface[], attribute: string):FacetMemberInterface {
         const facet: FacetMemberInterface | undefined = facetMembers.find((facet)=>(facet.attributeName === attribute));
         if(!facet)
             throw `Unknown facet attribute ${attribute}`;
-        return {chartType: facet.chartType, chartConfig:facet.chartConfig, title: facet.title};
+        return facet;
     }
 
     private static getFacetFiltersFromName(facetMembers: FacetMemberInterface[], attribute: string): SearchFilter[] {
@@ -133,9 +125,11 @@ export class FacetTools {
     }
 }
 
-function applyChartConfigToData(data: BucketDataType[], chartConfig?: FacetMemberInterface["chartConfig"]): BucketDataType[] {
-    if(chartConfig?.mergeDomainMaxValue)
-        return mergeDomainMaxValue(data, chartConfig.mergeDomainMaxValue)
+function applyChartConfigToData(data: BucketDataType[], facetConfig?: FacetMemberInterface["facetConfig"]): BucketDataType[] {
+    if(facetConfig?.mergeDomainMaxValue)
+        return mergeDomainMaxValue(data, facetConfig.mergeDomainMaxValue)
+    if(facetConfig?.facetTransform)
+        return facetConfig.facetTransform(data)
     return data;
 }