@jbrowse/plugin-linear-comparative-view 2.6.1 → 2.6.3

package/dist/LGVSyntenyDisplay/configSchemaF.d.ts

@@ -6,9 +6,7 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
     defaultRendering: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;
-        defaultValue: string; /**
-         * #baseConfiguration
-         */
+        defaultValue: string;
     };
     renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         PileupRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/dist/LGVSyntenyDisplay/configSchemaF.js

@@ -15,4 +15,3 @@ function configSchemaF(pluginManager) {
     });
 }
 exports.default = configSchemaF;
-//# sourceMappingURL=configSchemaF.js.map

package/dist/LGVSyntenyDisplay/index.js

@@ -21,4 +21,3 @@ exports.default = (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/dist/LGVSyntenyDisplay/model.d.ts

@@ -86,21 +86,11 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
-    type: import("mobx-state-tree").ISimpleType<"LinearPileupDisplay">;
     configuration: AnyConfigurationSchemaType;
-    showSoftClipping: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    mismatchAlpha: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    sortedBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-        type: import("mobx-state-tree").ISimpleType<string>;
-        pos: import("mobx-state-tree").ISimpleType<number>;
-        tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        refName: import("mobx-state-tree").ISimpleType<string>;
-        assemblyName: import("mobx-state-tree").ISimpleType<string>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
         type: import("mobx-state-tree").ISimpleType<string>;
         tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -219,7 +209,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: Feature | undefined;
 } & {
-    readonly blockType: "staticBlocks" | "dynamicBlocks";
+    readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -250,43 +240,30 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     afterAttach(): void;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
-    modificationTagMap: import("mobx").ObservableMap<string, string>;
     featureUnderMouseVolatile: Feature | undefined;
-    currSortBpPerPx: number;
-    modificationsReady: boolean;
-    sortReady: boolean;
     tagsReady: boolean;
 } & {
     readonly autorunReady: boolean;
 } & {
-    setModificationsReady(flag: boolean): void;
     setTagsReady(flag: boolean): void;
-    setSortReady(flag: boolean): void;
-    setCurrSortBpPerPx(n: number): void;
     setMaxHeight(n: number): void;
     setFeatureHeight(n?: number | undefined): void;
     setNoSpacing(flag?: boolean | undefined): void;
     setColorScheme(colorScheme: {
         type: string;
         tag?: string | undefined;
+        extra?: import("@jbrowse/plugin-alignments/src/shared/color").ExtraColorBy | undefined;
     }): void;
-    updateModificationColorMap(uniqueModifications: string[]): void;
     updateColorTagMap(uniqueTag: string[]): void;
     setFeatureUnderMouse(feat?: Feature | undefined): void;
     selectFeature(feature: Feature): void;
-    clearSelected(): void;
     copyFeatureToClipboard(feature: Feature): void;
-    toggleSoftClipping(): void;
-    toggleMismatchAlpha(): void;
     setConfig(conf: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>): void;
-    setSortedBy(type: string, tag?: string | undefined): void;
-    setFilterBy(filter: import("@jbrowse/plugin-alignments/src/LinearPileupDisplay/model").Filter): void;
-} & {
-    reload(): void;
+    setFilterBy(filter: import("@jbrowse/plugin-alignments/src/LinearPileupDisplay/SharedLinearPileupDisplayMixin").Filter): void;
 } & {
     readonly rendererConfig: {
         [x: string]: any;
@@ -296,9 +273,8 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
 } & {
     readonly maxHeight: any;
     readonly featureHeightSetting: any;
-    readonly mismatchAlphaSetting: any;
     readonly featureUnderMouse: Feature | undefined;
-    readonly renderReady: boolean;
+    renderReady(): boolean;
 } & {
     readonly rendererTypeName: string;
     contextMenuItems(): ({
@@ -314,66 +290,31 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     })[];
     readonly DisplayBlurb: (props: import("@jbrowse/plugin-alignments/src/LinearPileupDisplay/components/LinearPileupDisplayBlurb").LinearPileupDisplayBlurbProps) => import("react").JSX.Element | null;
     renderPropsPre(): any;
-    renderProps(): any;
-    trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
+    colorSchemeSubMenuItems(): {
         label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        type: string;
-        checked: boolean;
         onClick: () => void;
-        disabled?: undefined;
-        subMenu?: undefined;
-    } | {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        disabled: boolean;
-        subMenu: {
-            label: string;
-            onClick: () => void;
-        }[];
-        type?: undefined;
-        checked?: undefined;
-        onClick?: undefined;
-    } | {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        subMenu: {
-            label: string;
-            onClick: () => void;
-        }[];
-        type?: undefined;
-        checked?: undefined;
-        onClick?: undefined;
-        disabled?: undefined;
-    } | {
+    }[];
+    trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
         onClick: () => void;
-        type?: undefined;
-        checked?: undefined;
-        disabled?: undefined;
-        subMenu?: undefined;
-    } | {
-        label: string;
-        type: string;
-        checked: any;
-        onClick: () => void;
-        icon?: undefined;
-        disabled?: undefined;
-        subMenu?: undefined;
     })[];
+} & {
+    renderProps(): any;
 } & {
     afterAttach(): void;
 } & {
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+} & {
+    trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
+        label: string;
+        subMenu: {
+            label: string;
+            onClick: () => void;
+        }[];
+    })[];
 } & {
     afterCreate(): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/LGVSyntenyDisplay/model.js

@@ -114,7 +114,7 @@ async function navToSynteny(feature, self) {
  */
 function stateModelFactory(schema) {
     return mobx_state_tree_1.types
-        .compose('LGVSyntenyDisplay', (0, plugin_alignments_1.linearPileupDisplayStateModelFactory)(schema), mobx_state_tree_1.types.model({
+        .compose('LGVSyntenyDisplay', (0, plugin_alignments_1.SharedLinearPileupDisplayMixin)(schema), mobx_state_tree_1.types.model({
         /**
          * #property
          */
@@ -142,13 +142,31 @@ function stateModelFactory(schema) {
                 ];
             },
         };
+    })
+        .views(self => {
+        const { trackMenuItems: superTrackMenuItems, colorSchemeSubMenuItems: superColorSchemeSubMenuItems, } = self;
+        return {
+            trackMenuItems() {
+                return [
+                    ...superTrackMenuItems(),
+                    {
+                        label: 'Color scheme',
+                        subMenu: [...superColorSchemeSubMenuItems()],
+                    },
+                ];
+            },
+        };
     })
         .actions(self => ({
         afterCreate() {
-            // use color by strand to help indicate inversions better
-            self.setColorScheme({ type: 'strand' });
+            // use color by stand to help indicate inversions better on first load, otherwise use selected orientation
+            if (self.colorBy) {
+                self.setColorScheme({ ...self.colorBy });
+            }
+            else {
+                self.setColorScheme({ type: 'strand' });
+            }
         },
     }));
 }
 exports.default = stateModelFactory;
-//# sourceMappingURL=model.js.map

package/dist/LaunchLinearSyntenyView.js

@@ -55,4 +55,3 @@ function tryTrack(model, trackId, idsNotFound) {
         }
     }
 }
-//# sourceMappingURL=LaunchLinearSyntenyView.js.map

package/dist/LinearComparativeDisplay/configSchemaF.js

@@ -15,4 +15,3 @@ function configSchemaFactory(pluginManager) {
     });
 }
 exports.default = configSchemaFactory;
-//# sourceMappingURL=configSchemaF.js.map

package/dist/LinearComparativeDisplay/index.js

@@ -21,4 +21,3 @@ exports.default = (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/dist/LinearComparativeDisplay/stateModelFactory.js

@@ -169,4 +169,3 @@ async function renderBlockEffect(props) {
     };
 }
 exports.default = stateModelFactory;
-//# sourceMappingURL=stateModelFactory.js.map

package/dist/LinearComparativeView/components/Header.js

@@ -35,6 +35,7 @@ const ui_1 = require("@jbrowse/core/ui");
 // icons
 const MoreVert_1 = __importDefault(require("@mui/icons-material/MoreVert"));
 const Icons_1 = require("@jbrowse/core/ui/Icons");
+const CascadingMenuButton_1 = __importDefault(require("@jbrowse/core/ui/CascadingMenuButton"));
 const useStyles = (0, mui_1.makeStyles)()(() => ({
     headerBar: {
         gridArea: '1/1/auto/span 2',
@@ -59,7 +60,16 @@ const useStyles = (0, mui_1.makeStyles)()(() => ({
     },
 }));
 const TrackSelector = (0, mobx_react_1.observer)(({ model }) => {
-    return (react_1.default.createElement(material_1.IconButton, { onClick: model.activateTrackSelector, title: "Open track selector" },
+    return (react_1.default.createElement(CascadingMenuButton_1.default, { menuItems: [
+            {
+                label: 'Synteny track selector',
+                onClick: () => model.activateTrackSelector(),
+            },
+            ...model.views.map((view, idx) => ({
+                label: `View ${idx + 1} track selector`,
+                onClick: () => view.activateTrackSelector(),
+            })),
+        ] },
         react_1.default.createElement(Icons_1.TrackSelector, null)));
 });
 const Header = (0, mobx_react_1.observer)(function ({ model }) {
@@ -86,4 +96,3 @@ const Header = (0, mobx_react_1.observer)(function ({ model }) {
             }, menuItems: model.headerMenuItems(), onClose: () => setMenuAnchorEl(undefined) })) : null));
 });
 exports.default = Header;
-//# sourceMappingURL=Header.js.map

package/dist/LinearComparativeView/components/LinearComparativeView.js

@@ -96,4 +96,3 @@ exports.default = (0, mobx_react_1.observer)(function (props) {
     const middle = model.tracks.some(({ displays }) => displays.some((d) => (0, configuration_1.getConf)(d, 'middle')));
     return middle ? (react_1.default.createElement(MiddleComparativeView, { ...props })) : (react_1.default.createElement(OverlayComparativeView, { ...props }));
 });
-//# sourceMappingURL=LinearComparativeView.js.map

package/dist/LinearComparativeView/components/Rubberband.js

@@ -22,6 +22,9 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __setModuleDefault(result, mod);
     return result;
 };
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const mobx_react_1 = require("mobx-react");
@@ -29,6 +32,7 @@ const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
 const util_1 = require("@jbrowse/core/util");
 const ui_1 = require("@jbrowse/core/ui");
+const VerticalGuide_1 = __importDefault(require("./VerticalGuide"));
 const useStyles = (0, mui_1.makeStyles)()(theme => {
     const { tertiary, primary } = theme.palette;
     const background = tertiary
@@ -59,28 +63,8 @@ const useStyles = (0, mui_1.makeStyles)()(theme => {
             paddingLeft: theme.spacing(1),
             paddingRight: theme.spacing(1),
         },
-        guide: {
-            pointerEvents: 'none',
-            height: '100%',
-            width: 1,
-            position: 'absolute',
-            zIndex: 10,
-        },
-        sm: {
-            fontSize: 10,
-        },
     };
 });
-const VerticalGuide = (0, mobx_react_1.observer)(({ model, coordX }) => {
-    const { classes } = useStyles();
-    return (react_1.default.createElement(material_1.Tooltip, { open: true, placement: "top", title: model.views
-            .map(view => view.pxToBp(coordX))
-            .map(elt => (react_1.default.createElement(material_1.Typography, { className: classes.sm, key: JSON.stringify(elt) }, (0, util_1.stringify)(elt)))), arrow: true },
-        react_1.default.createElement("div", { className: classes.guide, style: {
-                left: coordX,
-                background: 'red',
-            } })));
-});
 function Rubberband({ model, ControlComponent = react_1.default.createElement("div", null), }) {
     const [startX, setStartX] = (0, react_1.useState)();
     const [currentX, setCurrentX] = (0, react_1.useState)();
@@ -182,10 +166,9 @@ function Rubberband({ model, ControlComponent = react_1.default.createElement("d
     }
     if (startX === undefined) {
         return (react_1.default.createElement(react_1.default.Fragment, null,
-            guideX !== undefined ? (react_1.default.createElement(VerticalGuide, { model: model, coordX: guideX })) : null,
-            react_1.default.createElement("div", { "data-testid": "rubberband_controls", className: classes.rubberbandControl, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
+            guideX !== undefined ? (react_1.default.createElement(VerticalGuide_1.default, { model: model, coordX: guideX })) : null,
+            react_1.default.createElement("div", { ref: controlsRef, className: classes.rubberbandControl, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
     }
-    /* Calculating Pixels for Mouse Dragging */
     const right = anchorPosition ? anchorPosition.offsetX : currentX || 0;
     const left = right < startX ? right : startX;
     const width = Math.abs(right - startX);
@@ -195,31 +178,26 @@ function Rubberband({ model, ControlComponent = react_1.default.createElement("d
     const numOfBpSelected = views.map(view => Math.ceil(width * view.bpPerPx));
     return (react_1.default.createElement(react_1.default.Fragment, null,
         rubberbandRef.current ? (react_1.default.createElement(react_1.default.Fragment, null,
-            react_1.default.createElement(material_1.Popover, { className: classes.popover, classes: {
-                    paper: classes.paper,
-                }, open: true, anchorEl: rubberbandRef.current, anchorOrigin: {
+            react_1.default.createElement(material_1.Popover, { className: classes.popover, classes: { paper: classes.paper }, open: true, anchorEl: rubberbandRef.current, anchorOrigin: {
                     vertical: 'top',
                     horizontal: 'left',
                 }, transformOrigin: {
                     vertical: 'bottom',
                     horizontal: 'right',
-                }, keepMounted: true, disableRestoreFocus: true }, leftBpOffset.map(l => (react_1.default.createElement(material_1.Typography, { key: JSON.stringify(l) }, (0, util_1.stringify)(l))))),
-            react_1.default.createElement(material_1.Popover, { className: classes.popover, classes: {
-                    paper: classes.paper,
-                }, open: true, anchorEl: rubberbandRef.current, anchorOrigin: {
+                }, keepMounted: true, disableRestoreFocus: true }, leftBpOffset.map((l, idx) => (react_1.default.createElement(material_1.Typography, { key: [JSON.stringify(l), idx, 'left'].join('-') }, (0, util_1.stringify)(l, true))))),
+            react_1.default.createElement(material_1.Popover, { className: classes.popover, classes: { paper: classes.paper }, open: true, anchorEl: rubberbandRef.current, anchorOrigin: {
                     vertical: 'top',
                     horizontal: 'right',
                 }, transformOrigin: {
                     vertical: 'bottom',
                     horizontal: 'left',
-                }, keepMounted: true, disableRestoreFocus: true }, rightBpOffset.map(l => (react_1.default.createElement(material_1.Typography, { key: JSON.stringify(l) }, (0, util_1.stringify)(l))))))) : null,
+                }, keepMounted: true, disableRestoreFocus: true }, rightBpOffset.map((l, idx) => (react_1.default.createElement(material_1.Typography, { key: [JSON.stringify(l), idx, 'right'].join('-') }, (0, util_1.stringify)(l, true))))))) : null,
         react_1.default.createElement("div", { ref: rubberbandRef, className: classes.rubberband, style: { left, width } },
             react_1.default.createElement(material_1.Typography, { variant: "h6", className: classes.rubberbandText }, numOfBpSelected.map((n, i) => (react_1.default.createElement(material_1.Typography, { key: `${n}_${i}` }, `${n.toLocaleString('en-US')}bp`))))),
-        react_1.default.createElement("div", { "data-testid": "rubberband_controls", className: classes.rubberbandControl, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent),
+        react_1.default.createElement("div", { className: classes.rubberbandControl, ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent),
         anchorPosition ? (react_1.default.createElement(ui_1.Menu, { anchorReference: "anchorPosition", anchorPosition: {
                 left: anchorPosition.clientX,
                 top: anchorPosition.clientY,
             }, onMenuItemClick: handleMenuItemClick, open: open, onClose: handleClose, menuItems: model.rubberBandMenuItems() })) : null));
 }
 exports.default = (0, mobx_react_1.observer)(Rubberband);
-//# sourceMappingURL=Rubberband.js.map

package/dist/LinearComparativeView/components/VerticalGuide.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { LinearComparativeViewModel } from '../model';
+type LCV = LinearComparativeViewModel;
+declare const VerticalGuide: ({ model, coordX, }: {
+    model: LCV;
+    coordX: number;
+}) => React.JSX.Element;
+export default VerticalGuide;

package/dist/LinearComparativeView/components/VerticalGuide.js

@@ -0,0 +1,33 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const util_1 = require("@jbrowse/core/util");
+const mui_1 = require("tss-react/mui");
+const useStyles = (0, mui_1.makeStyles)()({
+    guide: {
+        pointerEvents: 'none',
+        height: '100%',
+        width: 1,
+        position: 'absolute',
+        zIndex: 10,
+    },
+    sm: {
+        fontSize: 10,
+    },
+});
+const VerticalGuide = (0, mobx_react_1.observer)(function ({ model, coordX, }) {
+    const { classes } = useStyles();
+    return (react_1.default.createElement(material_1.Tooltip, { open: true, placement: "top", title: model.views
+            .map(view => view.pxToBp(coordX))
+            .map((elt, idx) => (react_1.default.createElement(material_1.Typography, { className: classes.sm, key: [JSON.stringify(elt), idx].join('-') }, (0, util_1.stringify)(elt, true)))), arrow: true },
+        react_1.default.createElement("div", { className: classes.guide, style: {
+                left: coordX,
+                background: 'red',
+            } })));
+});
+exports.default = VerticalGuide;

package/dist/LinearComparativeView/index.js

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

package/dist/LinearComparativeView/model.d.ts

@@ -32,19 +32,18 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
             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]>; /**
-             * #getter
-             */
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
+            /**
+             * #property
+             */
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         }, {
             setRefName(newRefName: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
         hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>; /**
-         * #getter
-         */
+        hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -72,9 +71,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
         coarseTotalBp: number;
         leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
-        rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined; /**
-         * #action
-         */
+        rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
     } & {
         readonly width: number;
         readonly interRegionPaddingWidth: number;
@@ -89,9 +86,6 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         readonly scaleBarHeight: number;
         readonly headerHeight: number;
         readonly trackHeights: number;
-        /**
-         * #action
-         */
         readonly trackHeightsWithResizeHandles: number;
         readonly height: number;
         readonly totalBp: number;
@@ -120,12 +114,12 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         toggleNoTracksActive(): void;
         toggleShowGridlines(): void;
         scrollTo(offsetPx: number): number;
-        zoomTo(bpPerPx: number, offset?: number | undefined, centerAtOffset?: boolean | undefined): number;
+        zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
         setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
         setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string | undefined): void;
         setNewView(bpPerPx: number, offsetPx: number): void;
         horizontallyFlip(): void;
-        showTrack(trackId: string, initialSnapshot?: {} | undefined, displayInitialSnapshot?: {} | undefined): any;
+        showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
         hideTrack(trackId: string): number;
     } & {
         moveTrack(movingId: string, targetId: string): void;
@@ -156,7 +150,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setDraggingTrackId(idx?: string | undefined): void;
         setScaleFactor(factor: number): void;
         clearView(): void;
-        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions | undefined): Promise<void>;
+        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
     } & {
         slide: (viewWidths: number) => void;
     } & {

package/dist/LinearComparativeView/model.js

@@ -343,4 +343,3 @@ function stateModelFactory(pluginManager) {
     }));
 }
 exports.default = stateModelFactory;
-//# sourceMappingURL=model.js.map

package/dist/LinearReadVsRef/LinearReadVsRef.js

@@ -281,4 +281,3 @@ function ReadVsRefDialog({ track, feature: preFeature, handleClose, }) {
             react_1.default.createElement(material_1.Button, { disabled: !primaryFeature, variant: "contained", color: "primary", onClick: onSubmit }, "Submit"))));
 }
 exports.default = ReadVsRefDialog;
-//# sourceMappingURL=LinearReadVsRef.js.map

package/dist/LinearReadVsRef/index.js

@@ -52,4 +52,3 @@ function default_1(pm) {
     });
 }
 exports.default = default_1;
-//# sourceMappingURL=index.js.map

package/dist/LinearSyntenyDisplay/afterAttach.js

@@ -105,4 +105,3 @@ function doAfterAttach(self) {
     }, { fireImmediately: true }));
 }
 exports.doAfterAttach = doAfterAttach;
-//# sourceMappingURL=afterAttach.js.map

package/dist/LinearSyntenyDisplay/components/Component.js

@@ -84,4 +84,3 @@ const ServerSideRenderedBlockContent = (0, mobx_react_1.observer)(function ({ mo
     return react_1.default.createElement(LinearSyntenyRendering_1.default, { model: model });
 });
 exports.default = ServerSideRenderedBlockContent;
-//# sourceMappingURL=Component.js.map

package/dist/LinearSyntenyDisplay/components/LinearSyntenyRendering.js

@@ -157,4 +157,3 @@ exports.default = (0, mobx_react_1.observer)(function LinearSyntenyRendering({ m
             }, width: width, height: height }),
         model.mouseoverId && tooltip && currX && currY ? (react_1.default.createElement(SyntenyTooltip_1.default, { x: currX, y: currY, title: tooltip })) : null));
 });
-//# sourceMappingURL=LinearSyntenyRendering.js.map

package/dist/LinearSyntenyDisplay/components/SyntenyTooltip.js

@@ -80,4 +80,3 @@ const SyntenyTooltip = (0, mobx_react_1.observer)(function ({ x, y, title, }) {
             react_1.default.createElement(ui_1.SanitizedHTML, { html: title })))) : null;
 });
 exports.default = SyntenyTooltip;
-//# sourceMappingURL=SyntenyTooltip.js.map

package/dist/LinearSyntenyDisplay/components/util.js

@@ -81,4 +81,3 @@ function drawBezierBox(ctx, x1, x2, y1, x3, x4, y2, mid) {
     ctx.fill();
 }
 exports.drawBezierBox = drawBezierBox;
-//# sourceMappingURL=util.js.map

package/dist/LinearSyntenyDisplay/configSchemaF.js

@@ -33,4 +33,3 @@ function configSchemaFactory(pluginManager) {
     });
 }
 exports.default = configSchemaFactory;
-//# sourceMappingURL=configSchemaF.js.map

package/dist/LinearSyntenyDisplay/drawSynteny.js

@@ -232,4 +232,3 @@ function drawMouseoverSynteny(model) {
     }
 }
 exports.drawMouseoverSynteny = drawMouseoverSynteny;
-//# sourceMappingURL=drawSynteny.js.map

package/dist/LinearSyntenyDisplay/index.js

@@ -44,4 +44,3 @@ exports.default = (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/dist/LinearSyntenyDisplay/model.js

@@ -176,4 +176,3 @@ function stateModelFactory(configSchema) {
     }));
 }
 exports.default = stateModelFactory;
-//# sourceMappingURL=model.js.map

package/dist/LinearSyntenyView/components/ExportSvgDialog.js

@@ -83,4 +83,3 @@ function ExportSvgDlg({ model, handleClose, }) {
                 } }, "Submit"))));
 }
 exports.default = ExportSvgDlg;
-//# sourceMappingURL=ExportSvgDialog.js.map

package/dist/LinearSyntenyView/components/Icons.js

@@ -16,4 +16,3 @@ function StraightLines(props) {
         react_1.default.createElement("path", { fill: "currentColor", d: "M22 12L17 22L7.1 6.04L4.24 12H2L7 2L16.9 17.96L19.76 12H22Z" })));
 }
 exports.StraightLines = StraightLines;
-//# sourceMappingURL=Icons.js.map

package/dist/LinearSyntenyView/components/ImportCustomTrack.js

@@ -177,4 +177,3 @@ const OpenTrack = (0, mobx_react_1.observer)(({ sessionTrackData, assembly1, ass
                         react_1.default.createElement(ui_1.FileSelector, { name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: loc => setBed2Location(loc) }))))) : (react_1.default.createElement(ui_1.FileSelector, { name: value ? value + ' location' : '', description: "", location: fileLocation, setLocation: loc => setFileLocation(loc) }))))));
 });
 exports.default = OpenTrack;
-//# sourceMappingURL=ImportCustomTrack.js.map

package/dist/LinearSyntenyView/components/ImportForm.js

@@ -124,4 +124,3 @@ exports.default = (0, mobx_react_1.observer)(function ({ model, }) {
                                 react_1.default.createElement(material_1.Button, { onClick: onOpenClick, variant: "contained", color: "primary" }, "Launch"))))),
                 react_1.default.createElement(TrackSelector, { setShowTrackId: setShowTrackId, assembly2: assembly2, assembly1: assembly1, setSessionTrackData: setSessionTrackData, sessionTrackData: sessionTrackData, model: model })))));
 });
-//# sourceMappingURL=ImportForm.js.map

package/dist/LinearSyntenyView/components/ImportSyntenyTrackSelector.js

@@ -60,4 +60,3 @@ const Selector = (0, mobx_react_1.observer)(({ model, assembly1, assembly2, setS
         filteredTracks.length ? (react_1.default.createElement(material_1.Select, { value: value, onChange: event => setValue(event.target.value) }, filteredTracks.map(track => (react_1.default.createElement(material_1.MenuItem, { key: track.trackId, value: track.trackId }, (0, tracks_1.getTrackName)(track, session)))))) : (react_1.default.createElement(ui_1.ErrorMessage, { error: `No synteny tracks found for ${assembly1},${assembly2}` }))));
 });
 exports.default = Selector;
-//# sourceMappingURL=ImportSyntenyTrackSelector.js.map

package/dist/LinearSyntenyView/components/LinearSyntenyView.js

@@ -35,4 +35,3 @@ const LinearSyntenyView = (0, mobx_react_1.observer)(({ model }) => {
     return !model.initialized ? (react_1.default.createElement(ImportForm, { model: model })) : (react_1.default.createElement(LinearComparativeView_1.default, { model: model }));
 });
 exports.default = LinearSyntenyView;
-//# sourceMappingURL=LinearSyntenyView.js.map

package/dist/LinearSyntenyView/index.js

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