npm - molstar - Versions diffs - 2.3.3 → 2.3.8 - Mend

molstar 2.3.3 → 2.3.8

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.

Files changed (1829) hide show

package/lib/commonjs/mol-plugin-ui/structure/source.js CHANGED Viewed

@@ -32,23 +32,23 @@ var StructureSourceControls = /** @class */ (function (_super) {
                 case 'model': {
                     var model = (_a = ref.cell.obj) === null || _a === void 0 ? void 0 : _a.data;
                     if (model && structure_1.Model.TrajectoryInfo.get(model).size > 1) {
-                        label = ((_b = ref.cell.obj) === null || _b === void 0 ? void 0 : _b.data.entryId) + " | Model " + (structure_1.Model.TrajectoryInfo.get(model).index + 1) + " of " + structure_1.Model.TrajectoryInfo.get(model).size;
+                        label = "".concat((_b = ref.cell.obj) === null || _b === void 0 ? void 0 : _b.data.entryId, " | Model ").concat(structure_1.Model.TrajectoryInfo.get(model).index + 1, " of ").concat(structure_1.Model.TrajectoryInfo.get(model).size);
                     }
-                    label = ((_c = ref.cell.obj) === null || _c === void 0 ? void 0 : _c.data.entryId) + " | " + ((_d = ref.cell.obj) === null || _d === void 0 ? void 0 : _d.label);
+                    label = "".concat((_c = ref.cell.obj) === null || _c === void 0 ? void 0 : _c.data.entryId, " | ").concat((_d = ref.cell.obj) === null || _d === void 0 ? void 0 : _d.label);
                     break;
                 }
                 case 'structure': {
                     var model = (_e = ref.cell.obj) === null || _e === void 0 ? void 0 : _e.data.models[0];
                     if (model && structure_1.Model.TrajectoryInfo.get(model).size > 1) {
-                        label = model.entryId + " | " + ((_f = ref.cell.obj) === null || _f === void 0 ? void 0 : _f.label) + " (Model " + (structure_1.Model.TrajectoryInfo.get(model).index + 1) + " of " + structure_1.Model.TrajectoryInfo.get(model).size + ")";
+                        label = "".concat(model.entryId, " | ").concat((_f = ref.cell.obj) === null || _f === void 0 ? void 0 : _f.label, " (Model ").concat(structure_1.Model.TrajectoryInfo.get(model).index + 1, " of ").concat(structure_1.Model.TrajectoryInfo.get(model).size, ")");
                         break;
                     }
                     else if (model) {
-                        label = model.entryId + " | " + ((_g = ref.cell.obj) === null || _g === void 0 ? void 0 : _g.label);
+                        label = "".concat(model.entryId, " | ").concat((_g = ref.cell.obj) === null || _g === void 0 ? void 0 : _g.label);
                         break;
                     }
                     else {
-                        label = "" + ((_h = ref.cell.obj) === null || _h === void 0 ? void 0 : _h.label);
+                        label = "".concat((_h = ref.cell.obj) === null || _h === void 0 ? void 0 : _h.label);
                         break;
                     }
                 }
@@ -72,7 +72,7 @@ var StructureSourceControls = /** @class */ (function (_super) {
             if (m.structures.length === 1) {
                 var selected = _this.plugin.managers.structure.hierarchy.seletionSet;
                 var ref = m.structures[0];
-                return { label: ((_a = m.cell.obj) === null || _a === void 0 ? void 0 : _a.label) + " | " + ((_b = ref.cell.obj) === null || _b === void 0 ? void 0 : _b.label), selected: selected.has(ref.cell.transform.ref), value: [m, ref] };
+                return { label: "".concat((_a = m.cell.obj) === null || _a === void 0 ? void 0 : _a.label, " | ").concat((_b = ref.cell.obj) === null || _b === void 0 ? void 0 : _b.label), selected: selected.has(ref.cell.transform.ref), value: [m, ref] };
             }
             return (0, tslib_1.__spreadArray)([action_menu_1.ActionMenu.Header((_c = m.cell.obj) === null || _c === void 0 ? void 0 : _c.label)], m.structures.map(_this.item), true);
         };
@@ -172,7 +172,7 @@ var StructureSourceControls = /** @class */ (function (_super) {
                 if (((_b = (_a = s.model) === null || _a === void 0 ? void 0 : _a.trajectory) === null || _b === void 0 ? void 0 : _b.models) && s.model.trajectory.models.length === 1)
                     return (_c = s.cell.obj) === null || _c === void 0 ? void 0 : _c.data.label;
                 if (s.model)
-                    return ((_d = s.model.cell.obj) === null || _d === void 0 ? void 0 : _d.label) + " | " + ((_e = s.cell.obj) === null || _e === void 0 ? void 0 : _e.data.label);
+                    return "".concat((_d = s.model.cell.obj) === null || _d === void 0 ? void 0 : _d.label, " | ").concat((_e = s.cell.obj) === null || _e === void 0 ? void 0 : _e.data.label);
                 return (_f = s.cell.obj) === null || _f === void 0 ? void 0 : _f.data.label;
             }
             if (structures.length > 1) {
@@ -186,17 +186,17 @@ var StructureSourceControls = /** @class */ (function (_super) {
                         break;
                     }
                 }
-                return sameTraj && t ? ((_j = t.cell.obj) === null || _j === void 0 ? void 0 : _j.label) + " | " + structures.length + " structures" : structures.length + " structures";
+                return sameTraj && t ? "".concat((_j = t.cell.obj) === null || _j === void 0 ? void 0 : _j.label, " | ").concat(structures.length, " structures") : "".concat(structures.length, " structures");
             }
             if (models.length > 0) {
                 var t = models[0].trajectory;
                 if (models.length === 1) {
                     var model = (_k = models[0].cell.obj) === null || _k === void 0 ? void 0 : _k.data;
                     if (model && structure_1.Model.TrajectoryInfo.get(model).size > 1) {
-                        return ((_l = t === null || t === void 0 ? void 0 : t.cell.obj) === null || _l === void 0 ? void 0 : _l.label) + " | Model " + (structure_1.Model.TrajectoryInfo.get(model).index + 1) + " of " + structure_1.Model.TrajectoryInfo.get(model).size;
+                        return "".concat((_l = t === null || t === void 0 ? void 0 : t.cell.obj) === null || _l === void 0 ? void 0 : _l.label, " | Model ").concat(structure_1.Model.TrajectoryInfo.get(model).index + 1, " of ").concat(structure_1.Model.TrajectoryInfo.get(model).size);
                     }
                     else {
-                        return ((_m = t === null || t === void 0 ? void 0 : t.cell.obj) === null || _m === void 0 ? void 0 : _m.label) + " | Model";
+                        return "".concat((_m = t === null || t === void 0 ? void 0 : t.cell.obj) === null || _m === void 0 ? void 0 : _m.label, " | Model");
                     }
                 }
                 var sameTraj = true;
@@ -207,10 +207,10 @@ var StructureSourceControls = /** @class */ (function (_super) {
                         break;
                     }
                 }
-                return sameTraj ? ((_o = t === null || t === void 0 ? void 0 : t.cell.obj) === null || _o === void 0 ? void 0 : _o.label) + " | " + models.length + " models" : models.length + " models";
+                return sameTraj ? "".concat((_o = t === null || t === void 0 ? void 0 : t.cell.obj) === null || _o === void 0 ? void 0 : _o.label, " | ").concat(models.length, " models") : "".concat(models.length, " models");
             }
             if (trajectories.length > 0) {
-                return trajectories.length === 1 ? ((_p = trajectories[0].cell.obj) === null || _p === void 0 ? void 0 : _p.label) + " trajectory" : trajectories.length + " trajectories";
+                return trajectories.length === 1 ? "".concat((_p = trajectories[0].cell.obj) === null || _p === void 0 ? void 0 : _p.label, " trajectory") : "".concat(trajectories.length, " trajectories");
             }
             if (trajectories.length === 0 && models.length === 0 && structures.length === 0) {
                 return 'Nothing Loaded';

package/lib/commonjs/mol-plugin-ui/structure/source.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/commonjs/mol-plugin-ui/structure/superposition.js CHANGED Viewed

@@ -96,7 +96,7 @@ var SuperpositionControls = /** @class */ (function (_super) {
                         _b.sent();
                         labelA = (0, string_1.stripTags)(eA.label);
                         labelB = (0, string_1.stripTags)(eB.label);
-                        this.plugin.log.info("Superposed [" + labelA + "] and [" + labelB + "] with RMSD " + rmsd.toFixed(2) + ".");
+                        this.plugin.log.info("Superposed [".concat(labelA, "] and [").concat(labelB, "] with RMSD ").concat(rmsd.toFixed(2), "."));
                         _b.label = 3;
                     case 3:
                         ++i;
@@ -131,7 +131,7 @@ var SuperpositionControls = /** @class */ (function (_super) {
                         labelA = (0, string_1.stripTags)(eA.label);
                         labelB = (0, string_1.stripTags)(eB.label);
                         count = entries[i].atoms.length;
-                        this.plugin.log.info("Superposed " + count + " " + (count === 1 ? 'atom' : 'atoms') + " of [" + labelA + "] and [" + labelB + "] with RMSD " + rmsd.toFixed(2) + ".");
+                        this.plugin.log.info("Superposed ".concat(count, " ").concat(count === 1 ? 'atom' : 'atoms', " of [").concat(labelA, "] and [").concat(labelB, "] with RMSD ").concat(rmsd.toFixed(2), "."));
                         _b.label = 3;
                     case 3:
                         ++i;
@@ -163,7 +163,7 @@ var SuperpositionControls = /** @class */ (function (_super) {
                         return [3 /*break*/, 1];
                     case 4:
                         rmsd /= transforms.length - 1;
-                        this.plugin.log.info("Superposed " + input.length + " structures with avg. RMSD " + rmsd.toFixed(2) + ".");
+                        this.plugin.log.info("Superposed ".concat(input.length, " structures with avg. RMSD ").concat(rmsd.toFixed(2), "."));
                         return [4 /*yield*/, new Promise(function (res) { return requestAnimationFrame(res); })];
                     case 5:
                         _a.sent();
@@ -269,7 +269,7 @@ var SuperpositionControls = /** @class */ (function (_super) {
                 var stats = structure_1.StructureElement.Stats.ofLoci(selection);
                 var counts = (0, label_1.structureElementStatsLabel)(stats, { countsOnly: true });
                 var chain = (0, label_1.elementLabel)(l, { reverse: true, granularity: 'chain' }).split('|');
-                var label = counts + " | " + chain[0] + " | " + chain[chain.length - 1];
+                var label = "".concat(counts, " | ").concat(chain[0], " | ").concat(chain[chain.length - 1]);
                 entries.push({ loci: selection, label: label, cell: cell });
             });
             return entries;

package/lib/commonjs/mol-plugin-ui/structure/superposition.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/commonjs/mol-plugin-ui/structure/volume.js CHANGED Viewed

@@ -197,7 +197,7 @@ var VolumeSourceControls = /** @class */ (function (_super) {
         get: function () {
             var _a;
             if (this.state.loadingLabel)
-                return "Loading " + this.state.loadingLabel + "...";
+                return "Loading ".concat(this.state.loadingLabel, "...");
             var selected = this.plugin.managers.volume.hierarchy.selection;
             if (!selected)
                 return 'Nothing Selected';
@@ -317,7 +317,7 @@ var VolumeRepresentationControls = /** @class */ (function (_super) {
     VolumeRepresentationControls.prototype.render = function () {
         var _a, _b, _c;
         var repr = this.props.representation.cell;
-        return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-flex-row' }, { children: [(0, jsx_runtime_1.jsxs)(common_1.Button, (0, tslib_1.__assign)({ noOverflow: true, className: 'msp-control-button-label', title: ((_a = repr.obj) === null || _a === void 0 ? void 0 : _a.label) + ". Click to focus.", onClick: this.focus, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlign: 'left' } }, { children: [(_b = repr.obj) === null || _b === void 0 ? void 0 : _b.label, (0, jsx_runtime_1.jsx)("small", (0, tslib_1.__assign)({ className: 'msp-25-lower-contrast-text', style: { float: 'right' } }, { children: (_c = repr.obj) === null || _c === void 0 ? void 0 : _c.description }), void 0)] }), void 0), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: repr.state.isHidden ? icons_1.VisibilityOffOutlinedSvg : icons_1.VisibilityOutlinedSvg, toggleState: false, onClick: this.toggleVisible, title: (repr.state.isHidden ? 'Show' : 'Hide') + " component", small: true, className: 'msp-form-control', flex: true }, void 0), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.DeleteOutlinedSvg, onClick: this.remove, title: 'Remove', small: true }, void 0), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.MoreHorizSvg, onClick: this.toggleUpdate, title: 'Actions', toggleState: this.state.action === 'update' }, void 0)] }), void 0), this.state.action === 'update' && !!repr.parent && (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ style: { marginBottom: '6px' }, className: 'msp-accent-offset' }, { children: (0, jsx_runtime_1.jsx)(update_transform_1.UpdateTransformControl, { state: repr.parent, transform: repr.transform, customHeader: 'none', noMargin: true }, void 0) }), void 0)] }, void 0);
+        return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-flex-row' }, { children: [(0, jsx_runtime_1.jsxs)(common_1.Button, (0, tslib_1.__assign)({ noOverflow: true, className: 'msp-control-button-label', title: "".concat((_a = repr.obj) === null || _a === void 0 ? void 0 : _a.label, ". Click to focus."), onClick: this.focus, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlign: 'left' } }, { children: [(_b = repr.obj) === null || _b === void 0 ? void 0 : _b.label, (0, jsx_runtime_1.jsx)("small", (0, tslib_1.__assign)({ className: 'msp-25-lower-contrast-text', style: { float: 'right' } }, { children: (_c = repr.obj) === null || _c === void 0 ? void 0 : _c.description }), void 0)] }), void 0), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: repr.state.isHidden ? icons_1.VisibilityOffOutlinedSvg : icons_1.VisibilityOutlinedSvg, toggleState: false, onClick: this.toggleVisible, title: "".concat(repr.state.isHidden ? 'Show' : 'Hide', " component"), small: true, className: 'msp-form-control', flex: true }, void 0), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.DeleteOutlinedSvg, onClick: this.remove, title: 'Remove', small: true }, void 0), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.MoreHorizSvg, onClick: this.toggleUpdate, title: 'Actions', toggleState: this.state.action === 'update' }, void 0)] }), void 0), this.state.action === 'update' && !!repr.parent && (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ style: { marginBottom: '6px' }, className: 'msp-accent-offset' }, { children: (0, jsx_runtime_1.jsx)(update_transform_1.UpdateTransformControl, { state: repr.parent, transform: repr.transform, customHeader: 'none', noMargin: true }, void 0) }), void 0)] }, void 0);
     };
     return VolumeRepresentationControls;
 }(base_1.PurePluginUIComponent));

package/lib/commonjs/mol-plugin-ui/structure/volume.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/commonjs/mol-repr/representation.d.ts CHANGED Viewed

@@ -58,6 +58,7 @@ export declare namespace RepresentationProvider {
     function getDetaultParams<R extends RepresentationProvider<D, any, any>, D>(r: R, ctx: ThemeRegistryContext, data: D): PD.Values<any>;
 }
 export declare type AnyRepresentationProvider = RepresentationProvider<any, {}, Representation.State>;
+export declare const EmptyRepresentationProvider: RepresentationProvider;
 export declare class RepresentationRegistry<D, S extends Representation.State> {
     private _list;
     private _map;

package/lib/commonjs/mol-repr/representation.js CHANGED Viewed

@@ -5,9 +5,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Representation = exports.RepresentationRegistry = exports.RepresentationProvider = void 0;
+exports.Representation = exports.RepresentationRegistry = exports.EmptyRepresentationProvider = exports.RepresentationProvider = void 0;
 var tslib_1 = require("tslib");
 var param_definition_1 = require("../mol-util/param-definition");
+var color_1 = require("../mol-theme/color");
+var size_1 = require("../mol-theme/size");
 var theme_1 = require("../mol-theme/theme");
 var rxjs_1 = require("rxjs");
 var mol_task_1 = require("../mol-task");
@@ -27,12 +29,16 @@ var RepresentationProvider;
     }
     RepresentationProvider.getDetaultParams = getDetaultParams;
 })(RepresentationProvider = exports.RepresentationProvider || (exports.RepresentationProvider = {}));
-var EmptyRepresentationProvider = {
+exports.EmptyRepresentationProvider = {
+    name: '',
     label: '',
     description: '',
     factory: function () { return Representation.Empty; },
     getParams: function () { return ({}); },
-    defaultValues: {}
+    defaultValues: {},
+    defaultColorTheme: color_1.ColorTheme.EmptyProvider,
+    defaultSizeTheme: size_1.SizeTheme.EmptyProvider,
+    isApplicable: function () { return true; }
 };
 function getTypes(list) {
     return list.map(function (e) { return [e.name, e.provider.label]; });
@@ -56,7 +62,7 @@ var RepresentationRegistry = /** @class */ (function () {
     ;
     RepresentationRegistry.prototype.add = function (provider) {
         if (this._map.has(provider.name)) {
-            throw new Error(provider.name + " already registered.");
+            throw new Error("".concat(provider.name, " already registered."));
         }
         this._list.push({ name: provider.name, provider: provider });
         this._map.set(provider.name, provider);
@@ -64,7 +70,7 @@ var RepresentationRegistry = /** @class */ (function () {
     };
     RepresentationRegistry.prototype.getName = function (provider) {
         if (!this._name.has(provider))
-            throw new Error("'" + provider.label + "' is not a registered represenatation provider.");
+            throw new Error("'".concat(provider.label, "' is not a registered represenatation provider."));
         return this._name.get(provider);
     };
     RepresentationRegistry.prototype.remove = function (provider) {
@@ -77,7 +83,7 @@ var RepresentationRegistry = /** @class */ (function () {
         }
     };
     RepresentationRegistry.prototype.get = function (name) {
-        return this._map.get(name) || EmptyRepresentationProvider;
+        return this._map.get(name) || exports.EmptyRepresentationProvider;
     };
     Object.defineProperty(RepresentationRegistry.prototype, "list", {
         get: function () {
@@ -202,7 +208,7 @@ var Representation;
                 var qualityProps = (0, util_1.getQualityProps)(Object.assign({}, currentProps, props), currentData);
                 Object.assign(currentProps, props, qualityProps);
                 var visuals = currentProps.visuals;
-                return mol_task_1.Task.create("Creating or updating '" + label + "' representation", function (runtime) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+                return mol_task_1.Task.create("Creating or updating '".concat(label, "' representation"), function (runtime) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
                     var i, il;
                     return (0, tslib_1.__generator)(this, function (_a) {
                         switch (_a.label) {
@@ -285,7 +291,7 @@ var Representation;
                 if (props === void 0) { props = {}; }
                 var qualityProps = (0, util_1.getQualityProps)(Object.assign({}, currentProps, props));
                 Object.assign(currentProps, props, qualityProps);
-                return mol_task_1.Task.create("Updating '" + label + "' representation", function (runtime) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+                return mol_task_1.Task.create("Updating '".concat(label, "' representation"), function (runtime) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
                     return (0, tslib_1.__generator)(this, function (_a) {
                         // TODO
                         updated.next(version++);

package/lib/commonjs/mol-repr/representation.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/commonjs/mol-repr/shape/loci/angle.d.ts CHANGED Viewed

@@ -34,7 +34,7 @@ export declare const AngleParams: {
     fontVariant: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontVariant>;
     fontWeight: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontWeight>;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     ignoreLight: PD.BooleanParam;
     sectorOpacity: PD.Numeric;
     color: PD.Color;

package/lib/commonjs/mol-repr/shape/loci/angle.js CHANGED Viewed

@@ -84,7 +84,7 @@ function getCircle(state, segmentLength) {
 }
 var tmpState = getAngleState();
 function getAngleName(data) {
-    return data.triples.length === 1 ? "Angle " + (0, label_1.angleLabel)(data.triples[0], { measureOnly: true }) : data.triples.length + " Angles";
+    return data.triples.length === 1 ? "Angle ".concat((0, label_1.angleLabel)(data.triples[0], { measureOnly: true })) : "".concat(data.triples.length, " Angles");
 }
 //
 function buildVectorsLines(data, props, lines) {
@@ -156,7 +156,7 @@ function buildText(data, props, text) {
         linear_algebra_1.Vec3.setMagnitude(tmpVec, tmpVec, tmpState.radius);
         linear_algebra_1.Vec3.add(tmpVec, tmpState.sphereB.center, tmpVec);
         var angle = (0, misc_1.radToDeg)(tmpState.angle).toFixed(2);
-        var label = props.customText || angle + "\u00B0";
+        var label = props.customText || "".concat(angle, "\u00B0");
         var radius = Math.max(2, tmpState.sphereA.radius, tmpState.sphereB.radius, tmpState.sphereC.radius);
         var scale = radius / 2;
         builder.add(label, tmpVec[0], tmpVec[1], tmpVec[2], 0.1, scale, i);

package/lib/commonjs/mol-repr/shape/loci/angle.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/lib/commonjs/mol-repr/shape/loci/common.d.ts CHANGED Viewed

@@ -34,6 +34,6 @@ export declare const LociLabelTextParams: {
     fontVariant: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontVariant>;
     fontWeight: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontWeight>;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type LociLabelTextParams = typeof LociLabelTextParams;