@haniffalab/cherita-react 1.4.1-dev.2025-10-22.61540191 → 1.4.1-dev.2025-10-23.3179e534
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/cjs/components/controls/Controls.js +38 -30
- package/dist/cjs/components/dotplot/Dotplot.js +40 -33
- package/dist/cjs/components/dotplot/DotplotControls.js +103 -83
- package/dist/cjs/components/full-page/FullPage.js +92 -69
- package/dist/cjs/components/full-page/PlotAlert.js +25 -16
- package/dist/cjs/components/full-page/PlotTypeSelector.js +43 -36
- package/dist/cjs/components/heatmap/Heatmap.js +40 -33
- package/dist/cjs/components/heatmap/HeatmapControls.js +6 -3
- package/dist/cjs/components/icons/DotPlotIcon.js +16 -10
- package/dist/cjs/components/icons/HeatmapIcon.js +17 -11
- package/dist/cjs/components/icons/MatrixPlotIcon.1.js +22 -16
- package/dist/cjs/components/icons/MatrixPlotIcon.js +22 -16
- package/dist/cjs/components/icons/ScatterplotIcon.1.js +21 -15
- package/dist/cjs/components/icons/ScatterplotIcon.js +21 -15
- package/dist/cjs/components/icons/ViolinPlotIcon.js +22 -14
- package/dist/cjs/components/matrixplot/Matrixplot.js +40 -33
- package/dist/cjs/components/matrixplot/MatrixplotControls.js +8 -5
- package/dist/cjs/components/obs-list/ObsItem.js +238 -190
- package/dist/cjs/components/obs-list/ObsList.js +106 -87
- package/dist/cjs/components/obs-list/ObsToolbar.js +2 -3
- package/dist/cjs/components/obsm-list/ObsmList.js +47 -32
- package/dist/cjs/components/offcanvas/index.js +61 -31
- package/dist/cjs/components/pseudospatial/Pseudospatial.js +46 -36
- package/dist/cjs/components/pseudospatial/PseudospatialToolbar.js +98 -68
- package/dist/cjs/components/scatterplot/Scatterplot.js +87 -65
- package/dist/cjs/components/scatterplot/ScatterplotControls.js +35 -27
- package/dist/cjs/components/scatterplot/SpatialControls.js +134 -107
- package/dist/cjs/components/scatterplot/Toolbox.js +41 -30
- package/dist/cjs/components/search-bar/SearchBar.js +157 -110
- package/dist/cjs/components/search-bar/SearchInfo.js +73 -47
- package/dist/cjs/components/search-bar/SearchResults.js +93 -71
- package/dist/cjs/components/toolbar/Toolbar.js +43 -34
- package/dist/cjs/components/var-list/VarItem.js +106 -79
- package/dist/cjs/components/var-list/VarList.js +67 -53
- package/dist/cjs/components/var-list/VarListToolbar.js +56 -51
- package/dist/cjs/components/var-list/VarSet.js +115 -97
- package/dist/cjs/components/violin/Violin.js +77 -58
- package/dist/cjs/components/violin/ViolinControls.js +8 -5
- package/dist/cjs/context/DatasetContext.js +20 -13
- package/dist/cjs/context/FilterContext.js +9 -7
- package/dist/cjs/context/SettingsContext.js +11 -9
- package/dist/cjs/context/ZarrDataContext.js +6 -5
- package/dist/cjs/utils/Histogram.js +35 -33
- package/dist/cjs/utils/ImageViewer.js +9 -6
- package/dist/cjs/utils/Legend.js +36 -29
- package/dist/cjs/utils/LoadingIndicators.js +14 -12
- package/dist/cjs/utils/Skeleton.js +10 -10
- package/dist/cjs/utils/StyledTooltip.js +7 -2
- package/dist/cjs/utils/VirtualizedList.js +32 -25
- package/dist/cjs/utils/errors.js +1 -1
- package/dist/css/cherita.css +6 -1
- package/dist/css/cherita.css.map +1 -1
- package/dist/esm/components/controls/Controls.js +38 -30
- package/dist/esm/components/dotplot/Dotplot.js +40 -33
- package/dist/esm/components/dotplot/DotplotControls.js +103 -82
- package/dist/esm/components/full-page/FullPage.js +92 -69
- package/dist/esm/components/full-page/PlotAlert.js +25 -16
- package/dist/esm/components/full-page/PlotTypeSelector.js +43 -36
- package/dist/esm/components/heatmap/Heatmap.js +40 -33
- package/dist/esm/components/heatmap/HeatmapControls.js +6 -2
- package/dist/esm/components/icons/DotPlotIcon.js +16 -10
- package/dist/esm/components/icons/HeatmapIcon.js +17 -11
- package/dist/esm/components/icons/MatrixPlotIcon.1.js +22 -16
- package/dist/esm/components/icons/MatrixPlotIcon.js +22 -16
- package/dist/esm/components/icons/ScatterplotIcon.1.js +21 -15
- package/dist/esm/components/icons/ScatterplotIcon.js +21 -15
- package/dist/esm/components/icons/ViolinPlotIcon.js +22 -14
- package/dist/esm/components/matrixplot/Matrixplot.js +40 -33
- package/dist/esm/components/matrixplot/MatrixplotControls.js +8 -4
- package/dist/esm/components/obs-list/ObsItem.js +237 -186
- package/dist/esm/components/obs-list/ObsList.js +106 -86
- package/dist/esm/components/obs-list/ObsToolbar.js +2 -2
- package/dist/esm/components/obsm-list/ObsmList.js +47 -31
- package/dist/esm/components/offcanvas/index.js +61 -31
- package/dist/esm/components/pseudospatial/Pseudospatial.js +46 -36
- package/dist/esm/components/pseudospatial/PseudospatialToolbar.js +98 -68
- package/dist/esm/components/scatterplot/Scatterplot.js +87 -64
- package/dist/esm/components/scatterplot/ScatterplotControls.js +35 -26
- package/dist/esm/components/scatterplot/SpatialControls.js +134 -106
- package/dist/esm/components/scatterplot/Toolbox.js +41 -29
- package/dist/esm/components/search-bar/SearchBar.js +157 -109
- package/dist/esm/components/search-bar/SearchInfo.js +73 -46
- package/dist/esm/components/search-bar/SearchResults.js +93 -70
- package/dist/esm/components/toolbar/Toolbar.js +43 -33
- package/dist/esm/components/var-list/VarItem.js +106 -78
- package/dist/esm/components/var-list/VarList.js +67 -52
- package/dist/esm/components/var-list/VarListToolbar.js +56 -50
- package/dist/esm/components/var-list/VarSet.js +115 -96
- package/dist/esm/components/violin/Violin.js +77 -58
- package/dist/esm/components/violin/ViolinControls.js +8 -4
- package/dist/esm/context/DatasetContext.js +20 -12
- package/dist/esm/context/FilterContext.js +9 -6
- package/dist/esm/context/SettingsContext.js +11 -8
- package/dist/esm/context/ZarrDataContext.js +6 -4
- package/dist/esm/utils/Histogram.js +35 -33
- package/dist/esm/utils/ImageViewer.js +9 -5
- package/dist/esm/utils/Legend.js +36 -28
- package/dist/esm/utils/LoadingIndicators.js +14 -11
- package/dist/esm/utils/Skeleton.js +10 -9
- package/dist/esm/utils/StyledTooltip.js +7 -2
- package/dist/esm/utils/VirtualizedList.js +32 -24
- package/dist/esm/utils/errors.js +1 -1
- package/package.json +3 -3
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@@ -5,25 +5,31 @@ import { ButtonGroup, Dropdown, Form } from "react-bootstrap";
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import { PSEUDOSPATIAL_CATEGORICAL_MODES as MODES, PSEUDOSPATIAL_PLOT_TYPES as PLOT_TYPES } from "../../constants/constants";
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import { useDataset } from "../../context/DatasetContext";
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import { useSettings, useSettingsDispatch } from "../../context/SettingsContext";
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import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
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function CategoricalMode() {
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const settings = useSettings();
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const dispatch = useSettingsDispatch();
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const modeList = _.map(MODES, (m, key) => /*#__PURE__*/
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key: key,
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const modeList = _.map(MODES, (m, key) => /*#__PURE__*/_jsx(Dropdown.Item, {
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active: settings.pseudospatial.categoricalMode === m,
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onClick: () => {
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dispatch({
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type: "set.pseudospatial.categoricalMode",
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}, key));
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const mode = _.find(MODES, {
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value: settings.pseudospatial.categoricalMode
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return /*#__PURE__*/_jsxs(Dropdown, {
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function MaskSet() {
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var _settings$pseudospati5, _settings$pseudospati6, _maskSets$settings$ps2, _settings$pseudospati7, _settings$pseudospati8, _maskSets$settings$ps3, _settings$pseudospati9;
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const {
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pseudospatial: maskSets
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const maskSetList = _.map(maskSets, (ms, key) => /*#__PURE__*/_jsx(Dropdown.Item, {
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dispatch({
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const handleMaskChange = mask => {
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let newMasks = settings.pseudospatial.maskValues || (maskSets === null || maskSets === void 0 ? void 0 : maskSets[(_settings$pseudospati = settings.pseudospatial) === null || _settings$pseudospati === void 0 ? void 0 : _settings$pseudospati.maskSet]);
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const masksList = _.map(maskSets === null || maskSets === void 0 ? void 0 : maskSets[(_settings$pseudospati5 = settings.pseudospatial) === null || _settings$pseudospati5 === void 0 ? void 0 : _settings$pseudospati5.maskSet], mask => /*#__PURE__*/
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const masksList = _.map(maskSets === null || maskSets === void 0 ? void 0 : maskSets[(_settings$pseudospati5 = settings.pseudospatial) === null || _settings$pseudospati5 === void 0 ? void 0 : _settings$pseudospati5.maskSet], mask => /*#__PURE__*/_jsx(Dropdown.ItemText, {
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const nMasks = settings.pseudospatial.maskValues ? (_settings$pseudospati6 = settings.pseudospatial.maskValues) === null || _settings$pseudospati6 === void 0 ? void 0 : _settings$pseudospati6.length : (maskSets === null || maskSets === void 0 || (_maskSets$settings$ps2 = maskSets[(_settings$pseudospati7 = settings.pseudospatial) === null || _settings$pseudospati7 === void 0 ? void 0 : _settings$pseudospati7.maskSet]) === null || _maskSets$settings$ps2 === void 0 ? void 0 : _maskSets$settings$ps2.length) || "No";
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const toggleAllChecked = !settings.pseudospatial.maskValues || ((_settings$pseudospati8 = settings.pseudospatial.maskValues) === null || _settings$pseudospati8 === void 0 ? void 0 : _settings$pseudospati8.length) === (maskSets === null || maskSets === void 0 || (_maskSets$settings$ps3 = maskSets[(_settings$pseudospati9 = settings.pseudospatial) === null || _settings$pseudospati9 === void 0 ? void 0 : _settings$pseudospati9.maskSet]) === null || _maskSets$settings$ps3 === void 0 ? void 0 : _maskSets$settings$ps3.length);
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return /*#__PURE__*/_jsxs(_Fragment, {
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}), /*#__PURE__*/_jsx(ButtonGroup, {
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children: plotType === PLOT_TYPES.CATEGORICAL && /*#__PURE__*/_jsx(CategoricalMode, {})
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function _defineProperty(e, r, t) { return (r = _toPropertyKey(r)) in e ? Object.defineProperty(e, r, { value: t, enumerable: !0, configurable: !0, writable: !0 }) : e[r] = t, e; }
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function _toPropertyKey(t) { var i = _toPrimitive(t, "string"); return "symbol" == typeof i ? i : i + ""; }
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function _toPrimitive(t, r) { if ("object" != typeof t || !t) return t; var e = t[Symbol.toPrimitive]; if (void 0 !== e) { var i = e.call(t, r || "default"); if ("object" != typeof i) return i; throw new TypeError("@@toPrimitive must return a primitive value."); } return ("string" === r ? String : Number)(t); }
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import { useCallback, useDeferredValue, useEffect, useMemo, useRef, useState } from "react";
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import { ScatterplotLayer } from "@deck.gl/layers";
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import { DeckGL } from "@deck.gl/react";
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import { faTriangleExclamation } from "@fortawesome/free-solid-svg-icons";
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import { EditableGeoJsonLayer } from "@nebula.gl/layers";
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import _ from "lodash";
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import { Alert } from "react-bootstrap";
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import { SpatialControls } from "./SpatialControls";
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import { Toolbox } from "./Toolbox";
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import { COLOR_ENCODINGS, OBS_TYPES, SELECTED_POLYGON_FILLCOLOR, UNSELECTED_POLYGON_FILLCOLOR } from "../../constants/constants";
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import { useDataset } from "../../context/DatasetContext";
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import { useFilteredData } from "../../context/FilterContext";
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import { useSelectedObs } from "../../utils/Resolver";
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import { formatNumerical } from "../../utils/string";
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import { useLabelObsData } from "../../utils/zarrData";
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import { PlotAlert } from "../full-page/PlotAlert";
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import { SpatialControls } from "./SpatialControls";
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import { Toolbox } from "./Toolbox";
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import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
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window.deck.log.level = 1;
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const INITIAL_VIEW_STATE = {
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longitude: 0,
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radius = null,
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setShowObs,
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setShowVars,
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plotType,
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setPlotType,
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} = _ref;
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});
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const [coordsError, setCoordsError] = useState(null);
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const [dataError, setDataError] = useState(null);
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const error = settings.selectedObsm && ((_obsmData$serverError = obsmData.serverError) === null || _obsmData$serverError === void 0 ? void 0 : _obsmData$serverError.length) || dataError || settings.labelObs.length && ((_labelObsData$serverE = labelObsData.serverError) === null || _labelObsData$serverE === void 0 ? void 0 : _labelObsData$serverE.length) || coordsError;
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if (!hasObsm) {
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return /*#__PURE__*/_jsx(PlotAlert, {
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variant: "info",
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heading: "Scatterplot unavailable for this dataset",
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plotType: plotType,
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children: "This dataset does not include any embeddings, so a scatterplot cannot be displayed. Please choose a different plot type to explore the data."
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});
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}
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return /*#__PURE__*/_jsx("div", {
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className: "cherita-container-scatterplot",
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children: /*#__PURE__*/_jsxs("div", {
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className: "cherita-scatterplot",
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children: [obsmData.isPending && /*#__PURE__*/_jsx(LoadingSpinner, {
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disableShrink: true
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}), isPending && /*#__PURE__*/_jsx(LoadingLinear, {}), /*#__PURE__*/_jsx(DeckGL, {
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viewState: viewState,
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onViewStateChange: e => setViewState(e.viewState),
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controller: {
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doubleClickZoom: mode === ViewMode
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},
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layers: layers,
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onClick: onLayerClick,
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getTooltip: getTooltip,
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},
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useDevicePixels: false,
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getCursor: _ref6 => {
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isDragging
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} = _ref6;
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return mode !== ViewMode ? "crosshair" : isDragging ? "grabbing" : "grab";
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},
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ref: deckRef
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}), /*#__PURE__*/_jsx(SpatialControls, {
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mode: mode,
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setMode: setMode,
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features: features,
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setFeatures: setFeatures,
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selectedFeatureIndexes: selectedFeatureIndexes,
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resetBounds: () => setViewState(getBounds()),
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increaseZoom: () => setViewState(v => _objectSpread(_objectSpread({}, v), {}, {
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zoom: v.zoom + 1
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})),
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decreaseZoom: () => setViewState(v => _objectSpread(_objectSpread({}, v), {}, {
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zoom: v.zoom - 1
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})),
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setShowObs: setShowObs,
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setShowVars: setShowVars,
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isFullscreen: isFullscreen
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}), /*#__PURE__*/_jsxs("div", {
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className: "cherita-spatial-footer",
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children: [/*#__PURE__*/_jsxs("div", {
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className: "cherita-toolbox-footer",
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children: [!!error && !isRendering && /*#__PURE__*/_jsxs(Alert, {
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variant: "danger",
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children: [/*#__PURE__*/_jsxs(Alert.Heading, {
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children: [/*#__PURE__*/_jsx(FontAwesomeIcon, {
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icon: faTriangleExclamation
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}), "\xA0Error loading data"]
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}), /*#__PURE__*/_jsx("p", {
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children: error.message
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})]
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}), /*#__PURE__*/_jsx(Toolbox, {
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mode: settings.colorEncoding === COLOR_ENCODINGS.VAR ? (_settings$selectedVar = settings.selectedVar) === null || _settings$selectedVar === void 0 ? void 0 : _settings$selectedVar.name : settings.colorEncoding === COLOR_ENCODINGS.OBS ? selectedObs === null || selectedObs === void 0 ? void 0 : selectedObs.name : null,
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obsLength: parseInt((_data$positions = data.positions) === null || _data$positions === void 0 ? void 0 : _data$positions.length),
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slicedLength: parseInt(slicedLength),
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setHasObsm: setHasObsm
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})]
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}), !error && /*#__PURE__*/_jsx(Legend, {
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isCategorical: isCategorical,
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min: min,
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max: max
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})]
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}
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import { useState, useEffect } from "react";
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import { Box, Slider, Typography } from "@mui/material";
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import { Form } from "react-bootstrap";
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import { COLOR_ENCODINGS, OBS_TYPES } from "../../constants/constants";
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@@ -6,10 +6,11 @@ import { useFilteredData } from "../../context/FilterContext";
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import { useSettings, useSettingsDispatch } from "../../context/SettingsContext";
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import { useSelectedObs } from "../../utils/Resolver";
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import { ColorscaleSelect } from "../controls/Controls";
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import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
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export const ScatterplotControls = () => {
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const settings = useSettings();
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const dispatch = useSettingsDispatch();
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const [sliderValue, setSliderValue] =
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const [sliderValue, setSliderValue] = useState(settings.controls.range || [0, 1]);
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const {
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valueMin,
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valueMax
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useEffect(() => {
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setSliderValue(settings.controls.range);
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}, [settings.controls.range]);
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const rangeSlider = /*#__PURE__*/
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const rangeSlider = /*#__PURE__*/_jsxs(Box, {
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className: "w-100",
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children: [/*#__PURE__*/_jsx(Typography, {
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id: "colorscale-range",
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gutterBottom: true,
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children: "Colorscale range"
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}), /*#__PURE__*/_jsx("div", {
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onChange: updateSlider,
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onChangeCommitted: updateRange,
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valueLabelDisplay: "auto",
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valueLabelFormat: valueLabelFormat,
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children: /*#__PURE__*/_jsxs(Form, {
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children: [/*#__PURE__*/_jsx(ColorscaleSelect, {}), /*#__PURE__*/_jsx(Form.Group, {
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className: "mb-2",
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children: rangeSlider
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