@rcsb/rcsb-saguaro-app 5.1.5 → 6.0.0-development.2

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/SequenceTrackTitleFactory.js

@@ -0,0 +1,67 @@
+import { __awaiter } from "tslib";
+import { SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import resource from "../../../../RcsbServerConfig/web.resources.json";
+import { RcsbAnnotationConstants } from "../../../../RcsbAnnotationConfig/RcsbAnnotationConstants";
+import { TrackUtils } from "../TrackFactoryImpl/Helper/TrackUtils";
+import { Assertions } from "../../../../RcsbUtils/Helpers/Assertions";
+var assertDefined = Assertions.assertDefined;
+import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
+export class SequenceTrackTitleFactory {
+    constructor(entityInstanceTranslator) {
+        this.entityInstanceTranslator = undefined;
+        this.entityInstanceTranslator = entityInstanceTranslator;
+    }
+    getTrackTitle(alignmentQueryContext) {
+        var _a, _b, _c;
+        return __awaiter(this, void 0, void 0, function* () {
+            let rowTitle;
+            if (!alignmentQueryContext.excludeFirstRowLink && alignmentQueryContext.from === SequenceReference.Uniprot) {
+                rowTitle = {
+                    visibleTex: (_a = alignmentQueryContext.queryId) !== null && _a !== void 0 ? _a : "",
+                    url: resource.rcsb_uniprot.url + alignmentQueryContext.queryId,
+                    style: {
+                        fontWeight: "bold",
+                        color: RcsbAnnotationConstants.provenanceColorCode.rcsbLink
+                    }
+                };
+            }
+            else if (!alignmentQueryContext.excludeFirstRowLink && alignmentQueryContext.from === SequenceReference.PdbInstance && this.entityInstanceTranslator != null) {
+                rowTitle = {
+                    visibleTex: alignmentQueryContext.queryId ? this.buildInstanceId(alignmentQueryContext.queryId) : "",
+                    style: {
+                        fontWeight: "bold",
+                    }
+                };
+            }
+            else {
+                rowTitle = {
+                    visibleTex: (_b = alignmentQueryContext.queryId) !== null && _b !== void 0 ? _b : ((_c = alignmentQueryContext.groupId) !== null && _c !== void 0 ? _c : ""),
+                    style: {
+                        fontWeight: "bold",
+                    }
+                };
+            }
+            return rowTitle;
+        });
+    }
+    getTrackTitlePrefix(alignmentQueryContext) {
+        var _a;
+        return __awaiter(this, void 0, void 0, function* () {
+            return (alignmentQueryContext.from && !alignmentQueryContext.from.includes("PDB")) ? alignmentQueryContext.from.replace("_", " ") + " " + TagDelimiter.sequenceTitle : ((_a = alignmentQueryContext.sequencePrefix) !== null && _a !== void 0 ? _a : "");
+        });
+    }
+    getTrackTitleFlagColor(alignmentQueryContext) {
+        var _a;
+        return __awaiter(this, void 0, void 0, function* () {
+            const queryId = (_a = alignmentQueryContext.queryId) !== null && _a !== void 0 ? _a : alignmentQueryContext.groupId;
+            assertDefined(queryId), assertDefined(alignmentQueryContext.from);
+            return TrackUtils.getProvenanceConfigFormTarget(queryId, alignmentQueryContext.from).color;
+        });
+    }
+    buildInstanceId(targetId) {
+        var _a;
+        const labelAsymId = targetId.split(TagDelimiter.instance)[1];
+        const authAsymId = (_a = this.entityInstanceTranslator) === null || _a === void 0 ? void 0 : _a.translateAsymToAuth(labelAsymId);
+        return (labelAsymId === authAsymId || !authAsymId ? labelAsymId : labelAsymId + "[auth " + authAsymId + "]");
+    }
+}

package/{build/dist → lib}/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryInterface.d.ts

@@ -1,4 +1,4 @@
-import { RcsbFvLink } from "@rcsb/rcsb-saguaro";
+import { RcsbFvLink } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
 export interface TrackTitleFactoryInterface<T extends any[]> {
     getTrackTitle(...args: T): Promise<string | RcsbFvLink>;
     getTrackTitlePrefix(...args: T): Promise<string>;

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryInterface.js

@@ -0,0 +1 @@
+export {};

package/{build/dist → lib}/RcsbFvWeb/RcsbFvGroup/GroupPfvTabs.d.ts

@@ -1,4 +1,4 @@
-import * as React from "react";
+import React from "react";
 import { RcsbFvAdditionalConfig } from "../RcsbFvModule/RcsbFvModuleInterface";
 import { SearchQuery } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
 import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";

package/lib/RcsbFvWeb/RcsbFvGroup/GroupPfvTabs.js

@@ -0,0 +1,109 @@
+import { __awaiter } from "tslib";
+import { jsx as _jsx } from "react/jsx-runtime";
+import React from "react";
+import { FieldName, OperationType, Source, } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { searchRequestProperty } from "../../RcsbSeacrh/SearchRequestProperty";
+import { ReturnType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
+import { RcsbTabs } from "../RcsbFvComponents/RcsbTabs";
+import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
+import { SearchQueryTools as SQT } from "../../RcsbSeacrh/SearchQueryTools";
+import { GroupPfvApp as GPA } from "./GroupTabs/GroupPfvApp";
+const ALIGNMENT = "alignment";
+const STRUCTURAL_FEATURES = "structural-features";
+const BINDING_SITES = "binding-sites";
+export class GroupPfvTabs extends React.Component {
+    constructor(props) {
+        super(props);
+        this.featureViewers = new Map();
+        this.filterInstances = undefined;
+        this.filterEntities = undefined;
+        this.entityCount = undefined;
+        this.currentTab = ALIGNMENT;
+    }
+    render() {
+        const additionalComponent = {
+            additionalComponent: this.props.groupProvenanceId === GroupProvenanceId.ProvenanceMatchingUniprotAccession ? _jsx("div", { id: ALIGNMENT + RcsbTabs.SELECT_SUFFIX, style: { height: 38 } }) : undefined
+        };
+        return (_jsx(RcsbTabs, { id: "group-id", tabList: [
+                Object.assign({ key: ALIGNMENT, title: "Sequence Alignments" }, additionalComponent),
+                Object.assign({ key: STRUCTURAL_FEATURES, title: "Structural Features" }, additionalComponent),
+                Object.assign({ key: BINDING_SITES, title: "Binding Sites" }, additionalComponent)
+            ], default: "alignment", onMount: this.onMount.bind(this), onSelect: this.onSelect.bind(this) }));
+    }
+    onMount() {
+        return __awaiter(this, void 0, void 0, function* () {
+            if (this.props.searchQuery && this.props.searchQuery.query) {
+                this.filterEntities = yield searchRequestProperty.requestMembers(Object.assign(Object.assign({}, this.props.searchQuery), { query: SQT.addGroupNodeToSearchQuery(this.props.groupProvenanceId, this.props.groupId, this.props.searchQuery.query), return_type: ReturnType.PolymerEntity }));
+                this.entityCount = this.filterEntities.length;
+                this.filterInstances = yield searchRequestProperty.requestMembers(Object.assign(Object.assign({}, this.props.searchQuery), { query: SQT.addGroupNodeToSearchQuery(this.props.groupProvenanceId, this.props.groupId, this.props.searchQuery.query), return_type: ReturnType.PolymerInstance }));
+                yield this.onSelect(this.currentTab);
+            }
+            else {
+                this.filterInstances = yield searchRequestProperty.requestMembers({ query: SQT.searchGroupQuery(this.props.groupProvenanceId, this.props.groupId), return_type: ReturnType.PolymerInstance });
+                this.entityCount = yield searchRequestProperty.requestCount({ query: SQT.searchGroupQuery(this.props.groupProvenanceId, this.props.groupId), return_type: ReturnType.PolymerEntity });
+                yield this.onSelect(this.currentTab);
+            }
+        });
+    }
+    syncPositionAndHighlight(tabKey) {
+        var _a, _b, _c, _d, _e, _f, _g;
+        if (tabKey !== this.currentTab) {
+            const dom = (_a = this.featureViewers.get(this.currentTab)) === null || _a === void 0 ? void 0 : _a.getFv().getDomain();
+            if (dom)
+                (_b = this.featureViewers.get(tabKey)) === null || _b === void 0 ? void 0 : _b.getFv().setDomain(dom);
+            const sel = (_c = this.featureViewers.get(this.currentTab)) === null || _c === void 0 ? void 0 : _c.getFv().getSelection("select");
+            if (sel && (sel === null || sel === void 0 ? void 0 : sel.length) > 0) {
+                (_d = this.featureViewers.get(tabKey)) === null || _d === void 0 ? void 0 : _d.getFv().clearSelection("select");
+                (_e = this.featureViewers.get(tabKey)) === null || _e === void 0 ? void 0 : _e.getFv().setSelection({
+                    elements: (_f = sel === null || sel === void 0 ? void 0 : sel.map((s) => ({
+                        begin: s.rcsbFvTrackDataElement.begin,
+                        end: s.rcsbFvTrackDataElement.end
+                    }))) !== null && _f !== void 0 ? _f : [],
+                    mode: "select"
+                });
+            }
+            else {
+                (_g = this.featureViewers.get(tabKey)) === null || _g === void 0 ? void 0 : _g.getFv().clearSelection("select");
+            }
+        }
+    }
+    onSelect(tabKey) {
+        return __awaiter(this, void 0, void 0, function* () {
+            if (!this.featureViewers.has(tabKey))
+                yield this.renderPositionalFeatureViewer(tabKey);
+            this.syncPositionAndHighlight(tabKey);
+            this.currentTab = tabKey;
+        });
+    }
+    renderPositionalFeatureViewer(tabKey) {
+        var _a, _b, _c, _d, _e;
+        return __awaiter(this, void 0, void 0, function* () {
+            switch (tabKey) {
+                case ALIGNMENT:
+                    this.featureViewers.set(tabKey, yield GPA.alignment(tabKey.toString(), this.props.groupProvenanceId, this.props.groupId, (_a = this.entityCount) !== null && _a !== void 0 ? _a : 0, Object.assign(Object.assign({ page: { first: 50, after: "0" } }, this.props.additionalConfig), { alignmentFilter: this.filterEntities })));
+                    break;
+                case BINDING_SITES:
+                    this.featureViewers.set(tabKey, yield GPA.bindingSites(tabKey.toString(), this.props.groupProvenanceId, this.props.groupId, (_c = (_b = this.filterInstances) === null || _b === void 0 ? void 0 : _b.length) !== null && _c !== void 0 ? _c : 0, Object.assign(Object.assign({ page: { first: 0, after: "0" } }, this.props.additionalConfig), { alignmentFilter: this.props.searchQuery ? this.filterEntities : undefined, filters: this.props.searchQuery ? [{
+                                source: Source.PdbInstance,
+                                field: FieldName.TargetId,
+                                operation: OperationType.Equals,
+                                values: this.filterInstances
+                            }] : undefined })));
+                    break;
+                case STRUCTURAL_FEATURES:
+                    this.featureViewers.set(tabKey, yield GPA.structure(tabKey.toString(), this.props.groupProvenanceId, this.props.groupId, (_e = (_d = this.filterInstances) === null || _d === void 0 ? void 0 : _d.length) !== null && _e !== void 0 ? _e : 0, Object.assign(Object.assign({ page: { first: 0, after: "0" } }, this.props.additionalConfig), { alignmentFilter: this.props.searchQuery ? this.filterEntities : undefined, filters: this.props.searchQuery ? [{
+                                source: Source.PdbInstance,
+                                field: FieldName.TargetId,
+                                operation: OperationType.Equals,
+                                values: this.filterInstances
+                            }, {
+                                source: Source.PdbEntity,
+                                field: FieldName.TargetId,
+                                operation: OperationType.Equals,
+                                values: this.filterEntities
+                            }] : undefined })));
+                    break;
+            }
+        });
+    }
+}

package/lib/RcsbFvWeb/RcsbFvGroup/GroupTabs/GroupPfvApp.js

@@ -0,0 +1,131 @@
+import { __awaiter } from "tslib";
+import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
+import { RcsbFvUniprotBuilder } from "../../RcsbFvBuilder/RcsbFvUniprotBuilder";
+import { groupExternalTrackBuilder } from "../../../RcsbUtils/TrackGenerators/GroupExternalTrackBuilder";
+import { RcsbFvGroupBuilder } from "../../RcsbFvBuilder/RcsbFvGroupBuilder";
+import { FieldName, GroupReference, OperationType, SequenceReference, Source, Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { alignmentGlobalLigandBindingSite } from "../../../RcsbUtils/TrackGenerators/AlignmentGlobalBindingSite";
+import { RcsbTabs } from "../../RcsbFvComponents/RcsbTabs";
+import { GroupPfvUI } from "../../../RcsbFvUI/GroupPfvUI";
+import { ActionMethods } from "../../../RcsbFvUI/Helper/ActionMethods";
+import { PaginationItemComponent } from "../../../RcsbFvUI/Components/PaginationItemComponent";
+export var GroupPfvApp;
+(function (GroupPfvApp) {
+    function alignment(elementId, groupProvenanceId, groupId, entityCount, additionalConfig) {
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j;
+        return __awaiter(this, void 0, void 0, function* () {
+            switch (groupProvenanceId) {
+                case GroupProvenanceId.ProvenanceMatchingUniprotAccession:
+                    return RcsbFvUniprotBuilder.buildUniprotMultipleEntitySequenceFv(elementId, elementId + RcsbTabs.SELECT_SUFFIX, groupId, {}, additionalConfig);
+                default:
+                    additionalConfig = Object.assign(Object.assign({}, additionalConfig), { externalTrackBuilder: groupExternalTrackBuilder() });
+                    // SequenceReference.PdbEntity && SequenceReference.Uniprot are needed to add row prefixes
+                    const pfvArgs = [
+                        getReferenceFromGroupProvenance(groupProvenanceId),
+                        groupId,
+                        SequenceReference.PdbEntity,
+                        SequenceReference.Uniprot
+                    ];
+                    const pfv = yield RcsbFvGroupBuilder.buildGroupAlignmentFv(elementId, ...pfvArgs, additionalConfig);
+                    const paginationCallback = ActionMethods.paginationCallback();
+                    const uiComp = {
+                        component: PaginationItemComponent,
+                        props: {
+                            count: entityCount,
+                            after: (_b = (_a = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _a === void 0 ? void 0 : _a.after) !== null && _b !== void 0 ? _b : "0",
+                            first: (_d = (_c = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _c === void 0 ? void 0 : _c.first) !== null && _d !== void 0 ? _d : 50,
+                            stateChange: (state, prevState) => {
+                                paginationCallback(elementId, pfv, RcsbFvGroupBuilder.buildGroupAlignmentFv, pfvArgs, Object.assign(Object.assign({}, additionalConfig), { page: {
+                                        first: state.first,
+                                        after: state.after.toString()
+                                    }, excludeLogo: true }));
+                            }
+                        }
+                    };
+                    GroupPfvUI.fvUI(GroupPfvUI.addBootstrapElement(elementId), (_f = (_e = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.externalUiComponents) === null || _e === void 0 ? void 0 : _e.replace) !== null && _f !== void 0 ? _f : (entityCount > ((_h = (_g = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _g === void 0 ? void 0 : _g.first) !== null && _h !== void 0 ? _h : 50) ? [uiComp] : []).concat(((_j = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.externalUiComponents) === null || _j === void 0 ? void 0 : _j.add) ? additionalConfig.externalUiComponents.add : []));
+                    return pfv;
+            }
+        });
+    }
+    GroupPfvApp.alignment = alignment;
+    function structure(elementId, groupProvenanceId, groupId, nTargets, additionalConfig) {
+        var _a;
+        return __awaiter(this, void 0, void 0, function* () {
+            additionalConfig = Object.assign(Object.assign({}, additionalConfig), { filters: [...((_a = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.filters) !== null && _a !== void 0 ? _a : []), {
+                        field: FieldName.Type,
+                        values: [Type.HelixP, Type.Sheet, Type.Cath, Type.Scop],
+                        operation: OperationType.Equals,
+                        source: Source.PdbInstance
+                    }, {
+                        field: FieldName.Type,
+                        values: [Type.Pfam],
+                        operation: OperationType.Equals,
+                        source: Source.PdbEntity
+                    }], sources: [Source.PdbInstance, Source.PdbEntity], annotationProcessing: annotationPositionFrequencyProcessing(nTargets), externalTrackBuilder: groupExternalTrackBuilder() });
+            // SequenceReference.PdbEntity && SequenceReference.Uniprot are needed to add row prefixes
+            const pfvArgs = [
+                getReferenceFromGroupProvenance(groupProvenanceId),
+                groupId,
+                SequenceReference.PdbEntity,
+                SequenceReference.Uniprot
+            ];
+            return yield RcsbFvGroupBuilder.buildGroupAnnotationFv(elementId, ...pfvArgs, additionalConfig);
+        });
+    }
+    GroupPfvApp.structure = structure;
+    function bindingSites(elementId, groupProvenanceId, groupId, nTargets, additionalConfig) {
+        var _a;
+        return __awaiter(this, void 0, void 0, function* () {
+            additionalConfig = Object.assign(Object.assign({}, additionalConfig), { filters: [...((_a = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.filters) !== null && _a !== void 0 ? _a : []), {
+                        field: FieldName.Type,
+                        values: [Type.BindingSite],
+                        operation: OperationType.Equals,
+                        source: Source.PdbInstance
+                    }], sources: [Source.PdbInstance], annotationProcessing: annotationPositionFrequencyProcessing(nTargets), externalTrackBuilder: alignmentGlobalLigandBindingSite() });
+            // SequenceReference.PdbEntity && SequenceReference.Uniprot are needed to add row prefixes
+            const pfvArgs = [
+                getReferenceFromGroupProvenance(groupProvenanceId),
+                groupId,
+                SequenceReference.PdbEntity,
+                SequenceReference.Uniprot
+            ];
+            return yield RcsbFvGroupBuilder.buildGroupAnnotationFv(elementId, ...pfvArgs, additionalConfig);
+        });
+    }
+    GroupPfvApp.bindingSites = bindingSites;
+})(GroupPfvApp || (GroupPfvApp = {}));
+function annotationPositionFrequencyProcessing(nTargets) {
+    const targets = new Map();
+    return {
+        getAnnotationValue: (feature) => {
+            var _a, _b, _c, _d;
+            if (!targets.has(feature.type)) {
+                if (feature.d.value)
+                    targets.set(feature.type, feature.d.value);
+                return (_b = (_a = feature.p.values) === null || _a === void 0 ? void 0 : _a[0]) !== null && _b !== void 0 ? _b : 0;
+            }
+            else {
+                return (_d = (_c = feature.p.values) === null || _c === void 0 ? void 0 : _c[0]) !== null && _d !== void 0 ? _d : 0;
+            }
+        },
+        computeAnnotationValue: (annotationTracks) => {
+            annotationTracks.forEach((at, type) => {
+                const N = (type.includes(Type.Cath) || type.includes(Type.Scop) || type.includes(Type.BindingSite) || type.includes(Type.Pfam)) ? targets.get(type) : nTargets;
+                at.forEach((ann, positionKey) => {
+                    if (ann.source != Source.PdbInterface)
+                        ann.value = Math.ceil(1000 * ann.value / (N !== null && N !== void 0 ? N : 1)) / 1000;
+                });
+            });
+        }
+    };
+}
+export function getReferenceFromGroupProvenance(groupProvenanceId) {
+    switch (groupProvenanceId) {
+        case GroupProvenanceId.ProvenanceMatchingDepositGroupId:
+            throw `Undefined reference for provenance ${groupProvenanceId}`;
+        case GroupProvenanceId.ProvenanceSequenceIdentity:
+            return GroupReference.SequenceIdentity;
+        case GroupProvenanceId.ProvenanceMatchingUniprotAccession:
+            return GroupReference.MatchingUniprotAccession;
+    }
+}

package/lib/RcsbFvWeb/RcsbFvGroup/RcsbFvGroupTabsBuilder.js

@@ -0,0 +1,12 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import { GroupPfvTabs } from "./GroupPfvTabs";
+import { createRoot } from "react-dom/client";
+import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
+var assertDefined = Assertions.assertDefined;
+export class RcsbFvGroupTabsBuilder {
+    static buildGroupTabs(elementId, groupProvenanceId, groupId, query, additionalConfig) {
+        const element = document.getElementById(elementId);
+        assertDefined(element);
+        createRoot(element).render(_jsx(GroupPfvTabs, { groupProvenanceId: groupProvenanceId, groupId: groupId, searchQuery: query, additionalConfig: additionalConfig }));
+    }
+}

package/{build/dist → lib}/RcsbFvWeb/RcsbFvModule/RcsbFvAbstractModule.d.ts

@@ -1,4 +1,5 @@
-import { RcsbFv, RcsbFvBoardConfigInterface, RcsbFvRowConfigInterface } from '@rcsb/rcsb-saguaro';
+import { RcsbFv } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFv";
+import { RcsbFvBoardConfigInterface, RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
 import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { AlignmentCollectorInterface } from "../../RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface";
 import { AnnotationRequestContext, AnnotationCollectorInterface } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvAbstractModule.js

@@ -0,0 +1,143 @@
+import { __awaiter } from "tslib";
+import { AnnotationCollector } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollector";
+import { ComponentsManager } from "../RcsbFvComponents/ComponentsManager";
+import { SingletonMap } from "../../RcsbUtils/Helpers/SingletonMap";
+import { AlignmentCollector } from "../../RcsbCollectTools/AlignmentCollector/AlignmentCollector";
+import { AlignmentTrackFactory } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory";
+import { SequenceTrackFactory } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/SequenceTrackFactory";
+import { AlignmentBlockFactory } from "../RcsbFvFactories/RcsbFvBlockFactory/AlignmentBlockFactory";
+import { AnnotationsBlockFactory } from "../RcsbFvFactories/RcsbFvBlockFactory/AnnotationsBlockFactory";
+import { AnnotationsTrackFactory } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AnnotationsTrackFactory";
+import * as acm from "../../RcsbAnnotationConfig/RcsbAnnotationConfig.ac.json";
+import { AnnotationBlockManager } from "../RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationBlockManager";
+import { RcsbAnnotationConfig } from "../../RcsbAnnotationConfig/RcsbAnnotationConfig";
+import { AnnotationTrackManagerFactory } from "../RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationTrackManager";
+export class RcsbFvAbstractModule {
+    constructor(elementId, rcsbFv) {
+        this.boardConfigData = {
+            length: 0
+        };
+        this.rowConfigData = new Array();
+        this.alignmentCollector = new AlignmentCollector();
+        this.annotationCollector = new AnnotationCollector();
+        this.alignmentTracks = [];
+        this.annotationTracks = [];
+        this.activeDisplayFlag = false;
+        this.rcsbFv = rcsbFv;
+        this.elementId = elementId;
+        ComponentsManager.buildLoaderSpinner(elementId);
+    }
+    setPolymerEntityInstanceTranslator(polymerEntityInstance) {
+        this.polymerEntityInstance = polymerEntityInstance;
+    }
+    getPolymerEntityInstanceTranslator() {
+        return this.polymerEntityInstance;
+    }
+    display() {
+        return __awaiter(this, void 0, void 0, function* () {
+            console.info(`Starting display ${this.elementId}`);
+            yield this.rcsbFv.updateBoardConfig({
+                boardConfigData: yield this.getBoardConfig(),
+                rowConfigData: []
+            });
+            ComponentsManager.unmountLoaderSpinner(this.elementId);
+            console.info(`Rendering tracks ${this.elementId}`);
+            this.rcsbFvRowUpdatePromise = this.rcsbFv.updateBoardConfig({
+                rowConfigData: yield this.getRowsConfig()
+            });
+            this.activeDisplayFlag = true;
+            return void 0;
+        });
+    }
+    activeDisplay() {
+        return this.activeDisplayFlag;
+    }
+    getFv() {
+        return this.rcsbFv;
+    }
+    getTargets() {
+        return __awaiter(this, void 0, void 0, function* () {
+            return yield this.alignmentCollector.getTargets();
+        });
+    }
+    getAlignmentResponse() {
+        return __awaiter(this, void 0, void 0, function* () {
+            return yield this.alignmentCollector.getAlignment();
+        });
+    }
+    getFeatures() {
+        return __awaiter(this, void 0, void 0, function* () {
+            //return (await this.annotationCollector.getAnnotationFeatures()).map(af=>af.features).flat();
+            return yield this.annotationCollector.getFeatures();
+        });
+    }
+    getAnnotationConfigData() {
+        return __awaiter(this, void 0, void 0, function* () {
+            return this.annotationTracks;
+        });
+    }
+    build(buildConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            SingletonMap.update(this.elementId, this);
+            this.buildConfig = buildConfig;
+            yield this.protectedBuild();
+            yield this.buildExternalTracks();
+            this.concatAlignmentAndAnnotationTracks();
+            yield this.display();
+            return void 0;
+        });
+    }
+    wait() {
+        return this.rcsbFvRowUpdatePromise;
+    }
+    buildAlignmentTracks(alignmentRequestContext, alignmentResponse, trackFactories) {
+        var _a, _b, _c, _d;
+        return __awaiter(this, void 0, void 0, function* () {
+            const sequenceTrackFactory = (_a = trackFactories === null || trackFactories === void 0 ? void 0 : trackFactories.sequenceTrackFactory) !== null && _a !== void 0 ? _a : new SequenceTrackFactory(this.getPolymerEntityInstanceTranslator());
+            if (alignmentResponse.query_sequence)
+                this.referenceTrack = yield sequenceTrackFactory.getTrack(alignmentRequestContext, alignmentResponse.query_sequence);
+            const alignmentBlockFactory = new AlignmentBlockFactory((_b = trackFactories === null || trackFactories === void 0 ? void 0 : trackFactories.alignmentTrackFactory) !== null && _b !== void 0 ? _b : new AlignmentTrackFactory(this.getPolymerEntityInstanceTranslator()), (_d = (_c = this.buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.trackConfigModifier) === null || _d === void 0 ? void 0 : _d.alignment);
+            this.alignmentTracks = yield alignmentBlockFactory.getBlock(alignmentRequestContext, alignmentResponse);
+        });
+    }
+    buildAnnotationsTrack(annotationsRequestContext, annotationsFeatures, annotationConfigMap) {
+        var _a, _b;
+        return __awaiter(this, void 0, void 0, function* () {
+            const defaultAnnotationConfigMap = annotationConfigMap !== null && annotationConfigMap !== void 0 ? annotationConfigMap : acm;
+            const annotationsBlockFactory = new AnnotationsBlockFactory(new AnnotationBlockManager(new AnnotationTrackManagerFactory(), new RcsbAnnotationConfig(defaultAnnotationConfigMap), this.getPolymerEntityInstanceTranslator()), new AnnotationsTrackFactory(), (_b = (_a = this.buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.trackConfigModifier) === null || _b === void 0 ? void 0 : _b.annotations);
+            this.annotationTracks = yield annotationsBlockFactory.getBlock(annotationsRequestContext, annotationsFeatures);
+        });
+    }
+    getBoardConfig() {
+        return __awaiter(this, void 0, void 0, function* () {
+            return this.boardConfigData;
+        });
+    }
+    getRowsConfig() {
+        return __awaiter(this, void 0, void 0, function* () {
+            return this.rowConfigData;
+        });
+    }
+    buildExternalTracks() {
+        var _a, _b;
+        return __awaiter(this, void 0, void 0, function* () {
+            const externalTrackBuilder = (_a = this.buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.externalTrackBuilder;
+            const rcsbContext = (_b = this.buildConfig.additionalConfig) === null || _b === void 0 ? void 0 : _b.rcsbContext;
+            if (!externalTrackBuilder)
+                return;
+            if (typeof externalTrackBuilder.processAlignmentAndFeatures === "function")
+                yield externalTrackBuilder.processAlignmentAndFeatures({
+                    annotations: yield this.annotationCollector.getAnnotationFeatures(),
+                    alignments: yield this.alignmentCollector.getAlignment(),
+                    rcsbContext: rcsbContext
+                });
+            if (typeof externalTrackBuilder.addTo === "function")
+                yield externalTrackBuilder.addTo({
+                    alignmentTracks: this.alignmentTracks,
+                    annotationTracks: this.annotationTracks,
+                    rcsbContext: rcsbContext
+                });
+            return void 0;
+        });
+    }
+}