@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

package/lib/RcsbFvExamples/GroupHistogram.d.ts

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

package/lib/RcsbFvExamples/GroupHistogram.js

@@ -1,28 +0,0 @@
-import { buildGroup } from "../RcsbGroupWeb/RcsbGroupBuilder";
-import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
-import { CATH_FACET, DISEASE_FACET, GO_COMPONENT_FACET, GO_FUNCTION_FACET, GO_PROCESS_FACET, INTERPRO_FACET, PHENOTYPE_FACET, RELEASE_DATE_FACET, RESOLUTION_FACET, TAXONOMY_COUNT_FACET } from "../RcsbSeacrh/FacetStore/SingleFacets";
-const groupId = "P01112";
-// buildGroupContent("select", GroupProvenanceId.ProvenanceSequenceIdentity, groupId);
-// buildGroupMembers("carousel", GroupProvenanceId.ProvenanceSequenceIdentity, groupId, 1, 1)
-buildGroup("pfv", GroupProvenanceId.ProvenanceSequenceIdentity, groupId, undefined, [
-    TAXONOMY_COUNT_FACET.attributeName,
-    DISEASE_FACET.attributeName,
-    INTERPRO_FACET.attributeName,
-    PHENOTYPE_FACET.attributeName
-]).then((m) => {
-});
-// buildGroup("pfv_2", GroupProvenanceId.ProvenanceSequenceIdentity, groupId, undefined, ["RESOLUTION_FACET","EXPERIMENTAL_METHOD_FACET"]).then((m)=>{
-// });
-buildGroup("pfv_3", GroupProvenanceId.ProvenanceSequenceIdentity, groupId, undefined, [
-    CATH_FACET.attributeName,
-    RESOLUTION_FACET.attributeName,
-    RELEASE_DATE_FACET.attributeName
-]).then((m) => {
-});
-buildGroup("pfv_2", GroupProvenanceId.ProvenanceSequenceIdentity, groupId, undefined, [
-    GO_PROCESS_FACET.attributeName,
-    GO_COMPONENT_FACET.attributeName,
-    GO_FUNCTION_FACET.attributeName,
-    PHENOTYPE_FACET.attributeName
-]).then((m) => {
-});

package/lib/RcsbFvExamples/InstanceFv.d.ts

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

package/lib/RcsbFvExamples/InstanceFv.js

@@ -1,20 +0,0 @@
-import { buildInstanceFv } from "../RcsbFvWeb/RcsbFvBuilder";
-buildInstanceFv("pfv", "2UZI.C").then((module) => {
-    module.getFv().then(() => {
-        module.getFv().addTrack({
-            trackId: "blockTrack",
-            trackHeight: 20,
-            trackColor: "#F9F9F9",
-            displayType: "block" /* RcsbFvDisplayTypes.BLOCK */,
-            displayColor: "#FF0000",
-            rowTitle: "MY TRACK",
-            titleFlagColor: "#00FF00",
-            trackData: [
-                {
-                    begin: 10,
-                    end: 400
-                }
-            ]
-        });
-    });
-});

package/lib/RcsbFvExamples/InstanceSequenceFv.d.ts

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

package/lib/RcsbFvExamples/InstanceSequenceFv.js

@@ -1,67 +0,0 @@
-import { Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { buildInstanceSequenceFv } from "../RcsbFvWeb/RcsbFvBuilder";
-buildInstanceSequenceFv("pfv", "select", "8PDU", {
-    module: "interface",
-    onChangeCallback: (r) => {
-        console.log(r);
-    },
-    defaultValue: "A"
-}, {
-    externalTrackBuilder: externalTrackBuilder()
-}).then((module) => {
-    console.log(module);
-});
-function externalTrackBuilder() {
-    let myComputedTrack = {
-        trackId: "blockTrack",
-        trackHeight: 20,
-        trackColor: "#F9F9F9",
-        titleFlagColor: "#48a1b3",
-        displayType: "block" /* RcsbFvDisplayTypes.BLOCK */,
-        displayColor: "#56e0f5",
-        rowTitle: "COMPUTED",
-        trackData: [{
-                begin: 10,
-                end: 100
-            }]
-    };
-    return {
-        processAlignmentAndFeatures(data) {
-            return new Promise(resolve => {
-                var _a;
-                myComputedTrack.trackData = [];
-                (_a = data.annotations) === null || _a === void 0 ? void 0 : _a.forEach(a => {
-                    var _a;
-                    (_a = a.features) === null || _a === void 0 ? void 0 : _a.forEach(f => {
-                        var _a, _b;
-                        if (f != null && f.type === Type.RegionOfInterest) {
-                            if (f.feature_positions)
-                                (_a = myComputedTrack.trackData) === null || _a === void 0 ? void 0 : _a.push(...(_b = f.feature_positions) === null || _b === void 0 ? void 0 : _b.map(p => {
-                                    var _a, _b;
-                                    return ({
-                                        begin: (_a = p === null || p === void 0 ? void 0 : p.beg_seq_id) !== null && _a !== void 0 ? _a : 0,
-                                        end: (_b = p === null || p === void 0 ? void 0 : p.end_seq_id) !== null && _b !== void 0 ? _b : undefined
-                                    });
-                                }));
-                        }
-                    });
-                });
-                resolve(void 0);
-            });
-        },
-        addTo(tracks) {
-            return new Promise(resolve => {
-                var _a, _b;
-                if (((_a = tracks.rcsbContext) === null || _a === void 0 ? void 0 : _a.asymId) === "A" && (myComputedTrack === null || myComputedTrack === void 0 ? void 0 : myComputedTrack.trackData) && myComputedTrack.trackData.length > 0) {
-                    (_b = tracks.annotationTracks) === null || _b === void 0 ? void 0 : _b.push(myComputedTrack);
-                }
-                resolve(void 0);
-            });
-        },
-        filterFeatures(data) {
-            return new Promise(resolve => {
-                resolve(data.annotations);
-            });
-        }
-    };
-}

package/lib/RcsbFvExamples/ResidueDistribution.d.ts

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

package/lib/RcsbFvExamples/ResidueDistribution.js

@@ -1,5 +0,0 @@
-import { buildResidueDistribution } from "../RcsbGroupWeb/RcsbGroupBuilder";
-buildResidueDistribution("pfv", "entry", "MA_MABAKCEPC0005", ["MA_QA_METRIC_LOCAL_TYPE_PLDDT", "MA_QA_METRIC_LOCAL_TYPE_OTHER"], {
-    paddingLeft: 100,
-    constWidth: 250
-});

package/lib/RcsbFvExamples/SequenceIdentityGroupAlignmentFv.d.ts

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

package/lib/RcsbFvExamples/SequenceIdentityGroupAlignmentFv.js

@@ -1,60 +0,0 @@
-import { jsx as _jsx } from "react/jsx-runtime";
-import React from "react";
-import { buildSequenceIdentityAlignmentFv } from "../RcsbFvWeb/RcsbFvBuilder";
-import { DataContainer } from "../RcsbUtils/Helpers/DataContainer";
-const fvContainer = new DataContainer();
-class UiComponent extends React.Component {
-    render() {
-        return (_jsx("div", { onClick: () => {
-                var _a;
-                (_a = this.props.fvContainer.get()) === null || _a === void 0 ? void 0 : _a.getFv().setSelection({ elements: { begin: 10, end: 50 }, mode: "select" });
-            }, children: this.props.text }));
-    }
-}
-buildSequenceIdentityAlignmentFv("pfv", "5_30", undefined, {
-    boardConfig: {
-        selectionChangeCallback: (selection) => {
-            console.log(selection);
-        }
-    },
-    page: {
-        first: 200,
-        after: "0"
-    },
-    externalTrackBuilder: {
-        filterAlignments: (data) => {
-            console.log("filterAlignments!!!!!!!!");
-            return new Promise(resolve => resolve(data.alignments));
-        }
-    },
-    trackConfigModifier: {
-        alignment: (alignmentContext, targetAlignment) => {
-            return new Promise(resolve => {
-                resolve({
-                    metadata: {
-                        targetId: targetAlignment.target_id
-                    }
-                });
-            });
-        }
-    },
-    beforeChangeCallback: (module) => {
-        console.log("This happens before change");
-    },
-    onChangeCallback: () => {
-        console.log("This happens after change");
-    },
-    externalUiComponents: {
-        replace: [{
-                component: UiComponent,
-                props: {
-                    text: "Bring Top",
-                    fvContainer,
-                    b: ""
-                }
-            }]
-    },
-}).then(pfv => {
-    fvContainer.set(pfv);
-    console.log(pfv, "rendered");
-});

package/lib/RcsbFvExamples/SequenceIdentityGroupFv.d.ts

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

package/lib/RcsbFvExamples/SequenceIdentityGroupFv.js

@@ -1,41 +0,0 @@
-import { buildGroupFv } from "../RcsbFvWeb/RcsbFvBuilder";
-import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
-// rcsbRequestCtxManager.initializeBorregoClient({api:"https://clustrelax-dev.rcsb.org/graphql"});
-const query = {
-    "query": {
-        "type": "group",
-        "logical_operator": "and",
-        "nodes": [
-            {
-                "type": "terminal",
-                "service": "text",
-                "parameters": {
-                    "attribute": "rcsb_entry_info.structure_determination_methodology",
-                    "negation": false,
-                    "operator": "exact_match",
-                    "value": "experimental"
-                }
-            },
-            {
-                "type": "terminal",
-                "service": "text",
-                "parameters": {
-                    "attribute": "rcsb_polymer_entity_group_membership.group_id",
-                    "negation": false,
-                    "operator": "exact_match",
-                    "value": "1_30"
-                }
-            }
-        ]
-    },
-    "request_options": {
-        "return_all_hits": true,
-        "results_content_type": [
-            "computational",
-            "experimental"
-        ]
-    },
-    "return_type": "polymer_entity"
-};
-buildGroupFv("pfv", GroupProvenanceId.ProvenanceSequenceIdentity, "1_30", query);
-//buildGroupFv("pfv",GroupProvenanceId.ProvenanceSequenceIdentity, "P12694");

package/lib/RcsbFvExamples/SingleEntitySummaryFv.d.ts

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

package/lib/RcsbFvExamples/SingleEntitySummaryFv.js

@@ -1,2 +0,0 @@
-import { buildSingleEntitySummaryFv } from "../RcsbFvWeb/RcsbFvBuilder";
-buildSingleEntitySummaryFv("pfv", "2UZI_3").then(m => console.log(m));

package/lib/RcsbFvExamples/TestCollectors.d.ts

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

package/lib/RcsbFvExamples/TestCollectors.js

@@ -1,112 +0,0 @@
-import { __awaiter } from "tslib";
-import { rcsbRequestCtxManager } from "../RcsbRequest/RcsbRequestContextManager";
-const idSetA = [
-    "7LBE",
-    "7T4R",
-    "7T4Q",
-    "7T4S",
-    "7LBF",
-    "7LBG",
-    "5VOC",
-    "6MYY",
-    "5W23",
-    "6MWN",
-    "8GNH",
-    "6XJQ",
-    "6BPE",
-    "6XJZ",
-    "8DP3",
-    "6WER",
-    "6BPC",
-    "7MX8",
-    "6MZJ",
-    "7SEG",
-    "3SOB",
-    "6UDA",
-    "6WEQ",
-    "7LO8",
-    "6XJY",
-    "6WW5",
-    "5CWS",
-    "7LO7",
-    "6BPB",
-    "8J7E",
-    "4K2U",
-    "7X94",
-    "7X8W",
-    "6J6Y",
-    "7D5Z",
-    "5YFI",
-    "6WMW",
-    "7WUH",
-    "6DWA",
-    "7UL7",
-    "5YWY",
-    "6DWC",
-    "7WUE",
-    "5YHL",
-    "1PKQ",
-    "6BPA",
-    "8FSJ",
-    "7UE9",
-    "3BQU",
-    "6W5D"
-];
-const idSetB = [
-    "7T76",
-    "AF_AFF1R2L7F1",
-    "2C1O",
-    "AF_AFB9A064F1",
-    "3BKC",
-    "3BKJ",
-    "3BKM",
-    "7X93",
-    "7ARN",
-    "7LBE",
-    "7T4R",
-    "7X96",
-    "4IOF",
-    "7X8Y",
-    "4M1C",
-    "7X90",
-    "7Y6N",
-    "5WOB",
-    "7T4Q",
-    "7T4S",
-    "7LBF",
-    "7LBG",
-    "7X92",
-    "7SJO",
-    "7MPG",
-    "7TYV",
-    "6DW2",
-    "7Y6L",
-    "5J13",
-    "7VYR",
-    "7YTN",
-    "5F3J",
-    "7X8Z",
-    "5NJD",
-    "5N2K",
-    "7XQ8",
-    "8IB1",
-    "5MVZ",
-    "6DEZ",
-    "6DF0",
-    "6DF2",
-    "6DF1",
-    "8BS8",
-    "8CIF",
-    "7SN1",
-    "5W24",
-    "7SN2",
-    "5VOB",
-    "7SN3"
-];
-function test() {
-    return __awaiter(this, void 0, void 0, function* () {
-        yield Promise.all([rcsbRequestCtxManager.getEntryProperties(idSetA), rcsbRequestCtxManager.getEntryProperties(idSetB)]);
-        console.log("Done!");
-    });
-}
-test();

package/lib/RcsbFvExamples/UniprotAlignmentFv.d.ts

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

package/lib/RcsbFvExamples/UniprotAlignmentFv.js

@@ -1,2 +0,0 @@
-import { buildUniprotAlignmentFv } from "../RcsbFvWeb/RcsbFvBuilder";
-buildUniprotAlignmentFv("pfv", "P12694");

package/lib/RcsbFvExamples/UniprotEntityInstanceFv.d.ts

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

package/lib/RcsbFvExamples/UniprotEntityInstanceFv.js

@@ -1,42 +0,0 @@
-import { buildUniprotEntityInstanceFv } from "../RcsbFvWeb/RcsbFvBuilder";
-buildUniprotEntityInstanceFv("pfv", "P01112", "2UZI_3", "2UZI.C", { boardConfig: {
-        trackWidth: 600,
-        elementClickCallback: (d) => {
-            const div = document.getElementById("myDiv");
-            if (!div)
-                return;
-            const e = d;
-            if (e == null) {
-                div.innerHTML = "";
-                return;
-            }
-            if (e && e.begin != undefined)
-                div.innerHTML = e.begin.toString();
-            else
-                div.innerHTML = "";
-            if (e.end != undefined)
-                div.innerHTML += " - " + e.end;
-            if (e.name != null)
-                div.innerHTML = e.name + " : " + div.innerHTML;
-            else if (e.type != null)
-                div.innerHTML = e.type + " : " + div.innerHTML;
-        }
-    } }).then((module) => {
-    module.getFv().then(() => {
-        module.getFv().addTrack({
-            trackId: "blockTrack",
-            trackHeight: 20,
-            trackColor: "#F9F9F9",
-            displayType: "block" /* RcsbFvDisplayTypes.BLOCK */,
-            displayColor: "#FF0000",
-            rowTitle: "MY TRACK",
-            titleFlagColor: "#00FF00",
-            trackData: [
-                {
-                    begin: 10,
-                    end: 400
-                }
-            ]
-        });
-    });
-});

package/lib/RcsbFvExamples/UniprotFv.d.ts

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

package/lib/RcsbFvExamples/UniprotFv.js

@@ -1,10 +0,0 @@
-import { buildMultipleAlignmentSequenceFv } from "../RcsbFvWeb/RcsbFvBuilder";
-buildMultipleAlignmentSequenceFv("pfv", "select", "P01112", {}, {
-    boardConfig: {
-        selectionChangeCallback: (s) => {
-            console.log(">", s);
-        }
-    }
-}).then(() => {
-    console.log("render done");
-});

package/lib/RcsbFvExamples/UniprotGroupFv.d.ts

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

package/lib/RcsbFvExamples/UniprotGroupFv.js

@@ -1,70 +0,0 @@
-import { buildGroupFv } from "../RcsbFvWeb/RcsbFvBuilder";
-import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
-const query = {
-    "query": {
-        "type": "group",
-        "nodes": [
-            {
-                "type": "group",
-                "nodes": [
-                    {
-                        "type": "terminal",
-                        "service": "text",
-                        "parameters": {
-                            "attribute": "rcsb_polymer_entity_group_membership.group_id",
-                            "negation": false,
-                            "operator": "exact_match",
-                            "value": "P04585"
-                        }
-                    },
-                    {
-                        "type": "terminal",
-                        "service": "text",
-                        "parameters": {
-                            "attribute": "rcsb_entry_container_identifiers.entry_id",
-                            "operator": "in",
-                            "negation": false,
-                            "value": [
-                                "2WHH"
-                            ]
-                        }
-                    }
-                ],
-                "logical_operator": "and"
-            },
-            {
-                "type": "terminal",
-                "service": "text",
-                "parameters": {
-                    "attribute": "rcsb_polymer_entity_group_membership.group_id",
-                    "negation": false,
-                    "operator": "exact_match",
-                    "value": "P04585"
-                }
-            }
-        ],
-        "logical_operator": "and",
-        "label": "text"
-    },
-    "return_type": "polymer_entity",
-    "request_options": {
-        "paginate": {
-            "start": 0,
-            "rows": 25
-        },
-        "scoring_strategy": "combined",
-        "sort": [
-            {
-                "sort_by": "score",
-                "direction": "desc"
-            }
-        ],
-        "results_content_type": [
-            "computational",
-            "experimental"
-        ]
-    }
-};
-//buildGroupFv("pfv",GroupProvenanceId.ProvenanceMatchingUniprotAccession, "Q8WZ42");
-buildGroupFv("pfv", GroupProvenanceId.ProvenanceMatchingUniprotAccession, "P69905", query);
-//buildGroupFv("pfv",GroupProvenanceId.ProvenanceSequenceIdentity, "1_30");

package/lib/RcsbFvExamples/utils/events.d.ts

@@ -1,2 +0,0 @@
-export declare function getJsonFromUrl(): any;
-export declare function onLoad(f: () => void): void;

package/lib/RcsbFvExamples/utils/events.js

@@ -1,15 +0,0 @@
-export function getJsonFromUrl() {
-    const url = location.search;
-    var query = url.substring(1);
-    var result = {};
-    query.split("&").forEach(function (part) {
-        var item = part.split("=");
-        result[item[0]] = decodeURIComponent(item[1]);
-    });
-    return result;
-}
-export function onLoad(f) {
-    document.addEventListener("DOMContentLoaded", function (event) {
-        f();
-    });
-}

package/lib/RcsbFvUI/AbstractMenuItemComponent.d.ts

@@ -1,11 +0,0 @@
-import React from "react";
-export type MenuItemComponentType<P extends {
-    stateChange(state: S, prevState: S): void;
-}, S extends {}, SS extends S = S> = typeof AbstractMenuItemComponent<P, S, SS>;
-export declare abstract class AbstractMenuItemComponent<P extends {
-    stateChange(state: S, prevState: S): void;
-}, S extends {}, SS extends S = S> extends React.Component<P, S & SS> {
-    componentDidUpdate(prevProps: Readonly<P & {
-        stateChange(newState: S, oldState: S): void;
-    }>, prevState: Readonly<S & SS>, snapshot?: any): void;
-}

package/lib/RcsbFvUI/AbstractMenuItemComponent.js

@@ -1,6 +0,0 @@
-import React from "react";
-export class AbstractMenuItemComponent extends React.Component {
-    componentDidUpdate(prevProps, prevState, snapshot) {
-        this.props.stateChange(this.state, prevState);
-    }
-}

package/lib/RcsbFvUI/Components/FilterItemComponent.d.ts

@@ -1,16 +0,0 @@
-import { AbstractMenuItemComponent } from "../AbstractMenuItemComponent";
-interface FilterItemProps {
-    elements: string[];
-    stateChange: (state: FilterPartialState, prevState: FilterPartialState) => void;
-}
-interface FilterPartialState {
-    filteredElements: string[];
-}
-interface FilterItemState extends FilterPartialState {
-    collapseIn: boolean;
-}
-export declare class FilterItemComponent extends AbstractMenuItemComponent<FilterItemProps, FilterPartialState, FilterItemState> {
-    readonly state: FilterItemState;
-    render(): JSX.Element;
-}
-export {};

package/lib/RcsbFvUI/Components/FilterItemComponent.js

@@ -1,16 +0,0 @@
-import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
-import { Collapse } from "react-bootstrap";
-import { AbstractMenuItemComponent } from "../AbstractMenuItemComponent";
-import { ItemComponent } from "./ItemComponent";
-export class FilterItemComponent extends AbstractMenuItemComponent {
-    constructor() {
-        super(...arguments);
-        this.state = {
-            filteredElements: [],
-            collapseIn: false,
-        };
-    }
-    render() {
-        return (_jsxs(_Fragment, { children: [_jsx(ItemComponent, { onClick: () => this.setState({ collapseIn: !this.state.collapseIn }), children: "FILTER" }), _jsx(Collapse, { in: this.state.collapseIn, children: _jsx("div", { className: "position-absolute" }) })] }));
-    }
-}

package/lib/RcsbFvUI/Components/ItemComponent.d.ts

@@ -1,4 +0,0 @@
-import React from "react";
-export declare class ItemComponent extends React.Component<React.HTMLAttributes<any>> {
-    render(): import("react/jsx-runtime").JSX.Element;
-}

package/lib/RcsbFvUI/Components/ItemComponent.js

@@ -1,7 +0,0 @@
-import { jsx as _jsx } from "react/jsx-runtime";
-import React from "react";
-export class ItemComponent extends React.Component {
-    render() {
-        return (_jsx("div", Object.assign({ role: "button" }, this.props, { className: `user-select-none d-inline-block text-white text-center bg-primary bg-gradient rounded bg-opacity-75${this.props.className ? " " + this.props.className : ''}`, style: Object.assign(Object.assign({}, this.props.style), { width: 130, marginRight: 3, MozUserSelect: "none", WebkitUserSelect: "none", msUserSelect: "none" }) })));
-    }
-}

package/lib/RcsbFvUI/Components/PaginationItemComponent.d.ts

@@ -1,22 +0,0 @@
-import { AbstractMenuItemComponent } from "../AbstractMenuItemComponent";
-export interface PaginationItemState {
-    after: number;
-    first: number;
-}
-export interface PaginationItemProps {
-    count: number;
-    after: string;
-    first: number;
-    stateChange(state: PaginationItemState, prevState: PaginationItemState): void;
-}
-export declare class PaginationItemComponent extends AbstractMenuItemComponent<PaginationItemProps, PaginationItemState> {
-    readonly state: PaginationItemState;
-    render(): JSX.Element;
-    componentDidUpdate(prevProps: Readonly<PaginationItemProps & {
-        stateChange(newState: PaginationItemState, oldState: PaginationItemState): void;
-    }>, prevState: Readonly<PaginationItemState>, snapshot?: any): void;
-    private next;
-    private role;
-    private textColor;
-    private switchAction;
-}