@jbrowse/plugin-alignments 2.6.1 → 2.6.2

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -131,4 +131,3 @@ exports.default = (0, mobx_react_1.observer)(function AlignmentFeatureDetails(pr
         SA ? react_1.default.createElement(AlignmentsFeatureSuppAligns_1.default, { model: model, tag: SA }) : null,
         feat.flags !== undefined ? (react_1.default.createElement(AlignmentsFeatureFlags_1.default, { feature: feat, ...props })) : null));
 });
-//# sourceMappingURL=AlignmentsFeatureDetail.js.map

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js

@@ -42,4 +42,3 @@ function AlignmentFlags(props) {
         }))));
 }
 exports.default = AlignmentFlags;
-//# sourceMappingURL=AlignmentsFeatureFlags.js.map

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.js

@@ -34,4 +34,3 @@ function SupplementaryAlignments(props) {
         }))));
 }
 exports.default = SupplementaryAlignments;
-//# sourceMappingURL=AlignmentsFeatureSuppAligns.js.map

package/dist/AlignmentsFeatureDetail/index.js

@@ -51,4 +51,3 @@ function register(pluginManager) {
     }));
 }
 exports.default = register;
-//# sourceMappingURL=index.js.map

package/dist/AlignmentsFeatureDetail/util.js

@@ -24,4 +24,3 @@ async function navToLoc(locString, model) {
     }
 }
 exports.navToLoc = navToLoc;
-//# sourceMappingURL=util.js.map

package/dist/AlignmentsTrack/configSchemaF.js

@@ -16,4 +16,3 @@ function configSchemaFactory(pluginManager) {
     });
 }
 exports.default = configSchemaFactory;
-//# sourceMappingURL=configSchemaF.js.map

package/dist/AlignmentsTrack/index.js

@@ -24,4 +24,3 @@ function register(pm) {
     });
 }
 exports.default = register;
-//# sourceMappingURL=index.js.map

package/dist/BamAdapter/BamAdapter.js

@@ -177,4 +177,3 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
 }
 exports.default = BamAdapter;
-//# sourceMappingURL=BamAdapter.js.map

package/dist/BamAdapter/BamSlightlyLazyFeature.js

@@ -101,4 +101,3 @@ class BamSlightlyLazyFeature {
     }
 }
 exports.default = BamSlightlyLazyFeature;
-//# sourceMappingURL=BamSlightlyLazyFeature.js.map

package/dist/BamAdapter/configSchema.js

@@ -55,4 +55,3 @@ const configSchema = (0, configuration_1.ConfigurationSchema)('BamAdapter', {
     },
 }, { explicitlyTyped: true });
 exports.default = configSchema;
-//# sourceMappingURL=configSchema.js.map

package/dist/BamAdapter/index.js

@@ -38,4 +38,3 @@ exports.default = (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/dist/CramAdapter/CramAdapter.js

@@ -228,4 +228,3 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
 }
 exports.default = CramAdapter;
-//# sourceMappingURL=CramAdapter.js.map

package/dist/CramAdapter/CramSlightlyLazyFeature.js

@@ -138,4 +138,3 @@ class CramSlightlyLazyFeature {
     }
 }
 exports.default = CramSlightlyLazyFeature;
-//# sourceMappingURL=CramSlightlyLazyFeature.js.map

package/dist/CramAdapter/CramTestAdapters.js

@@ -77,4 +77,3 @@ class SequenceAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     freeResources( /* { region } */) { }
 }
 exports.SequenceAdapter = SequenceAdapter;
-//# sourceMappingURL=CramTestAdapters.js.map

package/dist/CramAdapter/configSchema.js

@@ -47,4 +47,3 @@ const configSchema = (0, configuration_1.ConfigurationSchema)('CramAdapter', {
     },
 }, { explicitlyTyped: true });
 exports.default = configSchema;
-//# sourceMappingURL=configSchema.js.map

package/dist/CramAdapter/index.js

@@ -39,4 +39,3 @@ exports.default = (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/dist/CramAdapter/util.js

@@ -238,4 +238,3 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
     return cigar;
 }
 exports.readFeaturesToCIGAR = readFeaturesToCIGAR;
-//# sourceMappingURL=util.js.map

package/dist/GuessAlignmentsTypes/index.js

@@ -53,4 +53,3 @@ exports.default = (pluginManager) => {
         };
     });
 };
-//# sourceMappingURL=index.js.map

package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js

@@ -25,4 +25,3 @@ class HtsgetBamAdapter extends BamAdapter_1.default {
     }
 }
 exports.default = HtsgetBamAdapter;
-//# sourceMappingURL=HtsgetBamAdapter.js.map

package/dist/HtsgetBamAdapter/configSchema.js

@@ -33,4 +33,3 @@ const HtsgetBamAdapter = (0, configuration_1.ConfigurationSchema)('HtsgetBamAdap
     },
 }, { explicitlyTyped: true });
 exports.default = HtsgetBamAdapter;
-//# sourceMappingURL=configSchema.js.map

package/dist/HtsgetBamAdapter/index.js

@@ -41,4 +41,3 @@ exports.default = (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts

@@ -2,6 +2,6 @@ import React from 'react';
 import { AlignmentsDisplayModel } from '../models/model';
 declare function AlignmentsDisplay({ model }: {
     model: AlignmentsDisplayModel;
-}): React.JSX.Element;
+}): React.JSX.Element | null;
 declare const _default: typeof AlignmentsDisplay;
 export default _default;

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js

@@ -16,9 +16,13 @@ const useStyles = (0, mui_1.makeStyles)()({
     },
 });
 function AlignmentsDisplay({ model }) {
+    var _a;
     const { PileupDisplay, SNPCoverageDisplay } = model;
     const { classes } = useStyles();
-    const top = SNPCoverageDisplay.height;
+    if (!SNPCoverageDisplay) {
+        return null;
+    }
+    const top = (_a = SNPCoverageDisplay.height) !== null && _a !== void 0 ? _a : 100;
     return (react_1.default.createElement("div", { "data-testid": `display-${(0, configuration_1.getConf)(model, 'displayId')}`, style: { position: 'relative' } },
         react_1.default.createElement("div", { "data-testid": "Blockset-snpcoverage" },
             react_1.default.createElement(SNPCoverageDisplay.RenderingComponent, { model: SNPCoverageDisplay })),
@@ -33,4 +37,3 @@ function AlignmentsDisplay({ model }) {
             react_1.default.createElement(PileupDisplay.RenderingComponent, { model: PileupDisplay }))));
 }
 exports.default = (0, mobx_react_1.observer)(AlignmentsDisplay);
-//# sourceMappingURL=AlignmentsDisplay.js.map

package/dist/LinearAlignmentsDisplay/index.js

@@ -23,4 +23,3 @@ function default_1(pluginManager) {
     });
 }
 exports.default = default_1;
-//# sourceMappingURL=index.js.map

package/dist/LinearAlignmentsDisplay/models/configSchema.js

@@ -34,4 +34,3 @@ function configModelFactory(pm) {
     });
 }
 exports.default = configModelFactory;
-//# sourceMappingURL=configSchema.js.map

package/dist/LinearAlignmentsDisplay/models/model.js

@@ -145,7 +145,8 @@ function stateModelFactory(pluginManager, configSchema) {
          * #method
          */
         searchFeatureByID(id) {
-            return self.PileupDisplay.searchFeatureByID(id);
+            var _a, _b;
+            return (_b = (_a = self.PileupDisplay).searchFeatureByID) === null || _b === void 0 ? void 0 : _b.call(_a, id);
         },
         /**
          * #getter
@@ -275,6 +276,9 @@ function stateModelFactory(pluginManager, configSchema) {
              * #method
              */
             trackMenuItems() {
+                if (!self.PileupDisplay) {
+                    return [];
+                }
                 const extra = getLowerPanelDisplays(pluginManager).map(d => ({
                     type: 'radio',
                     label: d.displayName,
@@ -312,4 +316,3 @@ function stateModelFactory(pluginManager, configSchema) {
     });
 }
 exports.default = stateModelFactory;
-//# sourceMappingURL=model.js.map

package/dist/LinearPileupDisplay/components/ColorByModifications.js

@@ -38,4 +38,3 @@ function ColorByTagDlg(props) {
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
 }
 exports.default = (0, mobx_react_1.observer)(ColorByTagDlg);
-//# sourceMappingURL=ColorByModifications.js.map

package/dist/LinearPileupDisplay/components/ColorByTag.js

@@ -46,4 +46,3 @@ function ColorByTagDlg(props) {
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: handleClose }, "Cancel")))));
 }
 exports.default = (0, mobx_react_1.observer)(ColorByTagDlg);
-//# sourceMappingURL=ColorByTag.js.map

package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js

@@ -15,4 +15,3 @@ exports.default = (0, mobx_react_1.observer)(function LinearPileupDisplayBlurb(p
             ? `Sorted by ${(_a = sortedBy.tag) !== null && _a !== void 0 ? _a : sortedBy.type} at ${sortedBy.refName}:${sortedBy.pos}`
             : null))) : null;
 });
-//# sourceMappingURL=LinearPileupDisplayBlurb.js.map

package/dist/LinearPileupDisplay/components/ModificationsTable.js

@@ -26,4 +26,3 @@ function ModificationTable({ modifications, }) {
                 } })))))));
 }
 exports.default = ModificationTable;
-//# sourceMappingURL=ModificationsTable.js.map

package/dist/LinearPileupDisplay/components/SetFeatureHeight.js

@@ -47,4 +47,3 @@ function SetFeatureHeightDlg(props) {
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
 }
 exports.default = (0, mobx_react_1.observer)(SetFeatureHeightDlg);
-//# sourceMappingURL=SetFeatureHeight.js.map

package/dist/LinearPileupDisplay/components/SetMaxHeight.js

@@ -50,4 +50,3 @@ function SetMaxHeightDlg(props) {
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
 }
 exports.default = (0, mobx_react_1.observer)(SetMaxHeightDlg);
-//# sourceMappingURL=SetMaxHeight.js.map

package/dist/LinearPileupDisplay/components/SortByTag.js

@@ -47,4 +47,3 @@ function SortByTagDlg(props) {
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
 }
 exports.default = (0, mobx_react_1.observer)(SortByTagDlg);
-//# sourceMappingURL=SortByTag.js.map

package/dist/LinearPileupDisplay/configSchema.js

@@ -57,4 +57,3 @@ function configSchemaF(pluginManager) {
     });
 }
 exports.default = configSchemaF;
-//# sourceMappingURL=configSchema.js.map

package/dist/LinearPileupDisplay/index.js

@@ -28,4 +28,3 @@ var model_2 = require("./model");
 Object.defineProperty(exports, "linearPileupDisplayStateModelFactory", { enumerable: true, get: function () { return __importDefault(model_2).default; } });
 var configSchema_2 = require("./configSchema");
 Object.defineProperty(exports, "linearPileupDisplayConfigSchemaFactory", { enumerable: true, get: function () { return __importDefault(configSchema_2).default; } });
-//# sourceMappingURL=index.js.map

package/dist/LinearPileupDisplay/model.d.ts

@@ -45,19 +45,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined; /**
-         * #property
-         */
+        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         features: Map<string, Feature> | undefined;
         layout: any;
-        status: string; /**
-         * #property
-         */
+        status: string;
         error: unknown;
         message: string | undefined;
-        maxHeightReached: boolean; /**
-         * #property
-         */
+        maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
             model: any;
         }) => any;
@@ -65,7 +59,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     } & {
         doReload(): void;
         afterAttach(): void;
-        setStatus(message: string): void;
+        setStatus(message: string): void; /**
+         * #property
+         */
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
@@ -134,9 +130,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }, {
     rendererTypeName: string;
-    error: unknown; /**
-     * #action
-     */
+    error: unknown;
     message: string | undefined;
 } & {
     readonly RenderingComponent: import("react").FC<{
@@ -157,9 +151,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        /**
-         * #action
-         */
         onHorizontalScroll?: Function | undefined;
         blockState?: Record<string, any> | undefined;
     }>;
@@ -169,9 +160,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             type: string;
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string; /**
-             * #action
-             */
+            rendererTypeName: string;
             error: unknown;
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -185,7 +174,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
-    readonly parentTrack: any;
+    readonly parentTrack: any; /**
+     * #property
+     */
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
@@ -204,10 +195,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     setScrollTop(scrollTop: number): void;
     setHeight(displayHeight: number): number;
-    resizeHeight(distance: number): number; /**
-     * #action
-     * uses copy-to-clipboard and generates notification
-     */
+    resizeHeight(distance: number): number;
 } & {
     featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
     featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
@@ -247,7 +235,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
-    getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
+    getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined; /**
+     * #action
+     */
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
 } & {
@@ -524,7 +514,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     } & {
         doReload(): void;
         afterAttach(): void;
-        setStatus(message: string): void;
+        setStatus(message: string): void; /**
+         * #property
+         */
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {

package/dist/LinearPileupDisplay/model.js

@@ -593,8 +593,8 @@ function stateModelFactory(configSchema) {
                                 onClick: () => self.setColorScheme({ type: 'insertSize' }),
                             },
                             {
-                                label: 'Stranded paired-end',
-                                onClick: () => self.setColorScheme({ type: 'reverseTemplate' }),
+                                label: 'First-of-pair strand',
+                                onClick: () => self.setColorScheme({ type: 'stranded' }),
                             },
                             {
                                 label: 'Color by tag...',
@@ -765,4 +765,3 @@ function stateModelFactory(configSchema) {
     }));
 }
 exports.default = stateModelFactory;
-//# sourceMappingURL=model.js.map

package/dist/LinearReadArcsDisplay/components/ReactComponent.js

@@ -46,4 +46,3 @@ exports.default = (0, mobx_react_1.observer)(function ({ model, }) {
     return (react_1.default.createElement(BaseDisplayComponent_1.default, { model: model },
         react_1.default.createElement(Arcs, { model: model })));
 });
-//# sourceMappingURL=ReactComponent.js.map

package/dist/LinearReadArcsDisplay/configSchema.js

@@ -57,4 +57,3 @@ function configSchemaF(pluginManager) {
     });
 }
 exports.default = configSchemaF;
-//# sourceMappingURL=configSchema.js.map

package/dist/LinearReadArcsDisplay/drawFeats.js

@@ -159,4 +159,3 @@ function drawFeats(self, ctx, width, height) {
     }
 }
 exports.drawFeats = drawFeats;
-//# sourceMappingURL=drawFeats.js.map

package/dist/LinearReadArcsDisplay/index.js

@@ -24,4 +24,3 @@ function register(pluginManager) {
     });
 }
 exports.default = register;
-//# sourceMappingURL=index.js.map

package/dist/LinearReadArcsDisplay/model.js

@@ -328,4 +328,3 @@ function stateModelFactory(configSchema) {
     }));
 }
 exports.default = stateModelFactory;
-//# sourceMappingURL=model.js.map

package/dist/LinearReadArcsDisplay/util.js

@@ -10,4 +10,3 @@ function hasPairedReads(features) {
     return false;
 }
 exports.hasPairedReads = hasPairedReads;
-//# sourceMappingURL=util.js.map

package/dist/LinearReadCloudDisplay/components/ReactComponent.js

@@ -44,4 +44,3 @@ exports.default = (0, mobx_react_1.observer)(function ({ model, }) {
     return (react_1.default.createElement(BaseDisplayComponent_1.default, { model: model },
         react_1.default.createElement(Cloud, { model: model })));
 });
-//# sourceMappingURL=ReactComponent.js.map

package/dist/LinearReadCloudDisplay/configSchema.d.ts

@@ -33,14 +33,14 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
     maxFeatureScreenDensity: {
         type: string;
         description: string;
-        defaultValue: number;
+        defaultValue: number; /**
+         * #slot
+         */
     };
     fetchSizeLimit: {
         type: string;
         defaultValue: number;
-        description: string; /**
-         * #slot
-         */
+        description: string;
     };
     height: {
         type: string;

package/dist/LinearReadCloudDisplay/configSchema.js

@@ -48,4 +48,3 @@ function configSchemaF(pluginManager) {
     });
 }
 exports.default = configSchemaF;
-//# sourceMappingURL=configSchema.js.map

package/dist/LinearReadCloudDisplay/drawFeats.js

@@ -26,4 +26,3 @@ function drawFeats(self, ctx) {
     }
 }
 exports.drawFeats = drawFeats;
-//# sourceMappingURL=drawFeats.js.map

package/dist/LinearReadCloudDisplay/drawLongReadChains.js

@@ -66,4 +66,3 @@ function drawLongReadChains({ ctx, self, chainData, view, asm, }) {
     }
 }
 exports.drawLongReadChains = drawLongReadChains;
-//# sourceMappingURL=drawLongReadChains.js.map

package/dist/LinearReadCloudDisplay/drawPairChains.js

@@ -97,4 +97,3 @@ function getPairedColor({ type, v0, v1, stats, }) {
     return undefined;
 }
 exports.getPairedColor = getPairedColor;
-//# sourceMappingURL=drawPairChains.js.map

package/dist/LinearReadCloudDisplay/index.js

@@ -24,4 +24,3 @@ function register(pluginManager) {
     });
 }
 exports.default = register;
-//# sourceMappingURL=index.js.map

package/dist/LinearReadCloudDisplay/model.d.ts

@@ -128,9 +128,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     setCurrStatsBpPerPx(n: number): void;
     setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
     getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
-    setFeatureDensityStatsP(arg: any): void; /**
-     * #property
-     */
+    setFeatureDensityStatsP(arg: any): void;
     setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
     clearFeatureDensityStats(): void;
 } & {

package/dist/LinearReadCloudDisplay/model.js

@@ -224,4 +224,3 @@ function stateModelFactory(configSchema) {
     }));
 }
 exports.default = stateModelFactory;
-//# sourceMappingURL=model.js.map

package/dist/LinearReadCloudDisplay/util.js

@@ -32,4 +32,3 @@ function strokeRectCtx(x, y, width, height, ctx, strokeColor) {
     ctx.strokeRect(x, y, width, height);
 }
 exports.strokeRectCtx = strokeRectCtx;
-//# sourceMappingURL=util.js.map

package/dist/LinearSNPCoverageDisplay/components/Tooltip.js

@@ -58,4 +58,3 @@ const SNPCoverageTooltip = (0, mobx_react_1.observer)((props) => {
     return feat && feat.get('type') === 'skip' ? null : (react_1.default.createElement(plugin_wiggle_1.Tooltip, { TooltipContents: TooltipContents, ...props }));
 });
 exports.default = SNPCoverageTooltip;
-//# sourceMappingURL=Tooltip.js.map

package/dist/LinearSNPCoverageDisplay/index.js

@@ -22,4 +22,3 @@ function register(pluginManager) {
     });
 }
 exports.default = register;
-//# sourceMappingURL=index.js.map

package/dist/LinearSNPCoverageDisplay/models/configSchema.d.ts

@@ -62,6 +62,9 @@ export default function SNPCoverageConfigFactory(pluginManager: PluginManager):
         defaultValue: number;
     };
     fetchSizeLimit: {
+        /**
+         * #slot
+         */
         type: string;
         defaultValue: number;
         description: string;

package/dist/LinearSNPCoverageDisplay/models/configSchema.js

@@ -73,4 +73,3 @@ function SNPCoverageConfigFactory(pluginManager) {
     });
 }
 exports.default = SNPCoverageConfigFactory;
-//# sourceMappingURL=configSchema.js.map

package/dist/LinearSNPCoverageDisplay/models/model.d.ts

@@ -21,7 +21,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
             end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>; /**
+             * #property
+             */
         } & {
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         }, {
@@ -41,8 +43,13 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
+            /**
+             * #property
+             */
             model: any;
-        }) => any;
+        }) => any; /**
+         * #property
+         */
         renderProps: any;
     } & {
         doReload(): void;
@@ -51,9 +58,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>; /**
-             * #getter
-             */
+            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -67,9 +72,6 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         maxFeatureScreenDensity: {
             type: string;
             description: string;
-            /**
-             * #getter
-             */
             defaultValue: number;
         };
         fetchSizeLimit: {
@@ -96,11 +98,19 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     minSize: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    summaryScoreMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
+     * #property
+     */
+    summaryScoreMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
+     * #property
+     */
     rendererTypeNameState: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    scale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    autoscale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    scale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
+     * #property
+     */
+    autoscale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
+     * #property
+     */
     displayCrossHatches: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     constraints: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         max: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
@@ -190,7 +200,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
-    readonly adapterConfig: any;
+    readonly adapterConfig: any; /**
+     * #getter
+     */
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
@@ -357,7 +369,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     reload(): Promise<void>;
 } & {
     readonly TooltipComponent: import("react").FC<{}>;
-    readonly rendererTypeName: string;
+    readonly rendererTypeName: string; /**
+     * #property
+     */
 } & {
     readonly ticks: {
         range: number[];
@@ -401,7 +415,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         subMenu: {
             label: string;
             type: string;
-            checked: boolean;
+            checked: boolean; /**
+             * #getter
+             */
             onClick: () => void;
         }[];
         type?: undefined;