@jbrowse/plugin-linear-comparative-view 2.17.0 → 3.0.0

package/esm/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.js

@@ -1,9 +1,8 @@
-import React, { useState } from 'react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
 import { Dialog } from '@jbrowse/core/ui';
-import { getSession } from '@jbrowse/core/util';
 import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, TextField, } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
-// locals
 import { navToSynteny } from './util';
 const useStyles = makeStyles()({
     padding: {
@@ -11,41 +10,41 @@ const useStyles = makeStyles()({
         border: '1px solid #ccc',
     },
 });
-export default function LaunchSyntenyViewDialog({ model, feature, trackId, handleClose, }) {
+export default function LaunchSyntenyViewDialog({ session, view, feature, trackId, handleClose, }) {
     const { classes } = useStyles();
     const inverted = feature.get('strand') === -1;
+    const hasCIGAR = !!feature.get('CIGAR');
     const [horizontallyFlip, setHorizontallyFlip] = useState(inverted);
     const [windowSize, setWindowSize] = useState('1000');
-    return (React.createElement(Dialog, { open: true, title: "Launch synteny view", onClose: handleClose },
-        React.createElement(DialogContent, null,
-            inverted ? (React.createElement(FormControlLabel, { className: classes.padding, control: React.createElement(Checkbox, { checked: horizontallyFlip, onChange: event => {
-                        setHorizontallyFlip(event.target.checked);
-                    } }), label: "Note: The feature is inverted in orientation on the target\n            sequence. This will result in the lower panel having genomic\n            coordinates decreasing left to right. Horizontally flip?" })) : null,
-            React.createElement(TextField, { label: "Add window size in bp", value: windowSize, onChange: event => {
-                    setWindowSize(event.target.value);
-                } })),
-        React.createElement(DialogActions, null,
-            React.createElement(Button, { variant: "contained", onClick: () => {
-                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                    ;
-                    (async () => {
-                        try {
-                            await navToSynteny({
-                                feature,
-                                windowSize: +windowSize,
-                                horizontallyFlip,
-                                trackId,
-                                model,
-                            });
-                        }
-                        catch (e) {
-                            console.error(e);
-                            getSession(model).notifyError(`${e}`, e);
-                        }
-                    })();
-                    handleClose();
-                } }, "Submit"),
-            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
-                    handleClose();
-                } }, "Cancel"))));
+    const [useRegionOfInterest, setUseRegionOfInterest] = useState(true);
+    return (_jsxs(Dialog, { open: true, title: "Launch synteny view", onClose: handleClose, children: [_jsxs(DialogContent, { children: [view && hasCIGAR ? (_jsx(FormControlLabel, { className: classes.padding, control: _jsx(Checkbox, { checked: useRegionOfInterest, onChange: event => {
+                                setUseRegionOfInterest(event.target.checked);
+                            } }), label: "Use CIGAR string to navigate the current visible to the target" })) : null, inverted ? (_jsx(FormControlLabel, { className: classes.padding, control: _jsx(Checkbox, { checked: horizontallyFlip, onChange: event => {
+                                setHorizontallyFlip(event.target.checked);
+                            } }), label: "Note: The feature is inverted in orientation on the target\n            sequence. This will result in the lower panel having genomic\n            coordinates decreasing left to right. Horizontally flip?" })) : null, _jsx(TextField, { label: "Add window size in bp", value: windowSize, onChange: event => {
+                            setWindowSize(event.target.value);
+                        } })] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", onClick: () => {
+                            ;
+                            (async () => {
+                                try {
+                                    await navToSynteny({
+                                        feature,
+                                        windowSize: +windowSize,
+                                        horizontallyFlip,
+                                        trackId,
+                                        session,
+                                        region: useRegionOfInterest
+                                            ? view === null || view === void 0 ? void 0 : view.dynamicBlocks.contentBlocks[0]
+                                            : undefined,
+                                    });
+                                }
+                                catch (e) {
+                                    console.error(e);
+                                    session.notifyError(`${e}`, e);
+                                }
+                            })();
+                            handleClose();
+                        }, children: "Submit" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
+                            handleClose();
+                        }, children: "Cancel" })] })] }));
 }

package/esm/LGVSyntenyDisplay/components/util.d.ts

@@ -1,11 +1,14 @@
-import { Feature } from '@jbrowse/core/util';
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export declare function navToSynteny({ feature, windowSize: ws, model, trackId, view, horizontallyFlip, }: {
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
+export interface SimpleRegion {
+    refName: string;
+    start: number;
+    end: number;
+}
+export declare function navToSynteny({ feature, windowSize: ws, session, trackId, region, horizontallyFlip, }: {
     windowSize: number;
     trackId: string;
     horizontallyFlip: boolean;
     feature: Feature;
-    view?: LinearGenomeViewModel;
-    model: IAnyStateTreeNode;
+    session: AbstractSessionModel;
+    region?: SimpleRegion;
 }): Promise<void>;

package/esm/LGVSyntenyDisplay/components/util.js

@@ -1,9 +1,5 @@
-import { getSession } from '@jbrowse/core/util';
 import { MismatchParser } from '@jbrowse/plugin-alignments';
 const { parseCigar } = MismatchParser;
-function f(n) {
-    return Math.floor(n);
-}
 function findPosInCigar(cigar, startX) {
     let featX = 0;
     let mateX = 0;
@@ -27,9 +23,7 @@ function findPosInCigar(cigar, startX) {
     }
     return [featX, mateX];
 }
-export async function navToSynteny({ feature, windowSize: ws, model, trackId, view, horizontallyFlip, }) {
-    const session = getSession(model);
-    const reg = view === null || view === void 0 ? void 0 : view.dynamicBlocks.contentBlocks[0];
+export async function navToSynteny({ feature, windowSize: ws, session, trackId, region, horizontallyFlip, }) {
     const cigar = feature.get('CIGAR');
     const strand = feature.get('strand');
     const featRef = feature.get('refName');
@@ -45,13 +39,12 @@ export async function navToSynteny({ feature, windowSize: ws, model, trackId, vi
     let rMateEnd;
     let rFeatStart;
     let rFeatEnd;
-    if (reg && cigar) {
-        const regStart = reg.start;
-        const regEnd = reg.end;
+    if (region && cigar) {
+        const regStart = region.start;
+        const regEnd = region.end;
         const p = parseCigar(cigar);
         const [fStartX, mStartX] = findPosInCigar(p, regStart - featStart);
         const [fEndX, mEndX] = findPosInCigar(p, regEnd - featStart);
-        // avoid multiply by 0 with strand undefined
         const flipper = strand === -1 ? -1 : 1;
         rFeatStart = featStart + fStartX;
         rFeatEnd = featStart + fEndX;
@@ -89,10 +82,10 @@ export async function navToSynteny({ feature, windowSize: ws, model, trackId, vi
             },
         ],
     });
-    const l1 = `${featRef}:${f(rFeatStart - ws)}-${f(rFeatEnd + ws)}`;
+    const l1 = `${featRef}:${Math.floor(rFeatStart - ws)}-${Math.floor(rFeatEnd + ws)}`;
     const m1 = Math.min(rMateStart, rMateEnd);
     const m2 = Math.max(rMateStart, rMateEnd);
-    const l2 = `${mateRef}:${f(m1 - ws)}-${f(m2 + ws)}${horizontallyFlip ? '[rev]' : ''}`;
+    const l2 = `${mateRef}:${Math.floor(m1 - ws)}-${Math.floor(m2 + ws)}${horizontallyFlip ? '[rev]' : ''}`;
     await Promise.all([
         view2.views[0].navToLocString(l1, featAsm),
         view2.views[1].navToLocString(l2, mateAsm),

package/esm/LGVSyntenyDisplay/configSchemaF.d.ts

@@ -1,10 +1,10 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #config LGVSyntenyDisplay
- * extends config
- * - [LinearPileupDisplay](../linearpileupdisplay)
- */
-declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+import type PluginManager from '@jbrowse/core/PluginManager';
+declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    mouseover: {
+        type: string;
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     defaultRendering: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;
@@ -18,11 +18,20 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
         description: string;
         defaultValue: number;
     };
-    colorScheme: {
+    colorBy: {
         type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
         description: string;
-        defaultValue: string;
+        defaultValue: {
+            type: string;
+        };
+    };
+    filterBy: {
+        type: string;
+        description: string;
+        defaultValue: {
+            flagInclude: number;
+            flagExclude: number;
+        };
     };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     renderer: import("mobx-state-tree").IAnyModelType;

package/esm/LGVSyntenyDisplay/configSchemaF.js

@@ -1,15 +1,18 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { linearPileupDisplayConfigSchemaFactory } from '@jbrowse/plugin-alignments';
-/**
- * #config LGVSyntenyDisplay
- * extends config
- * - [LinearPileupDisplay](../linearpileupdisplay)
- */
 function configSchemaF(pluginManager) {
-    return ConfigurationSchema('LGVSyntenyDisplay', {}, {
-        /**
-         * #baseConfiguration
-         */
+    pluginManager.jexl.addFunction('lgvSyntenyTooltip', (f) => {
+        const m = f.get('mate');
+        return [f.get('name') || f.get('id'), (m === null || m === void 0 ? void 0 : m.name) || (m === null || m === void 0 ? void 0 : m.id)]
+            .filter(f => !!f)
+            .join('<br/>');
+    });
+    return ConfigurationSchema('LGVSyntenyDisplay', {
+        mouseover: {
+            type: 'string',
+            defaultValue: 'jexl:lgvSyntenyTooltip(feature)',
+        },
+    }, {
         baseConfiguration: linearPileupDisplayConfigSchemaFactory(pluginManager),
         explicitlyTyped: true,
     });

package/esm/LGVSyntenyDisplay/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function LGVSyntenyDisplayF(pluginManager: PluginManager): void;

package/esm/LGVSyntenyDisplay/index.js

@@ -1,7 +1,7 @@
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
+import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
 import configSchemaF from './configSchemaF';
 import stateModelF from './model';
-import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
 export default function LGVSyntenyDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaF(pluginManager);

package/esm/LGVSyntenyDisplay/model.d.ts

@@ -1,24 +1,9 @@
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import { Feature } from '@jbrowse/core/util';
-/**
- * #stateModel LGVSyntenyDisplay
- * displays location of "synteny" feature in a plain LGV, allowing linking out
- * to external synteny views
- *
- * extends
- * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
- */
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
 declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
-    rpcDriverName: import("mobx-state-tree" /**
-     * #stateModel LGVSyntenyDisplay
-     * displays location of "synteny" feature in a plain LGV, allowing linking out
-     * to external synteny views
-     *
-     * extends
-     * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
-     */).IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 } & {
@@ -27,23 +12,12 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
 } & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IModelType<{
-            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" /**
-             * #property
-             */).IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, Feature> | undefined;
@@ -61,21 +35,15 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement;
-            features: Map<string, Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -114,17 +82,12 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     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>>;
-    colorBy: import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined>;
-    filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").FilterBy, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy>, [undefined]>;
+    colorBySetting: import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined>;
+    filterBySetting: import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined>;
     jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
 } & {
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"LGVSyntenyDisplay">;
-    /**
-     * #property
-     */
     configuration: AnyConfigurationSchemaType;
 }, {
     rendererTypeName: string;
@@ -215,14 +178,15 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | Feature;
 } & {
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
-    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -249,14 +213,18 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
     afterAttach(): void;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
     featureUnderMouseVolatile: undefined | Feature;
     tagsReady: boolean;
+} & {
+    readonly colorBy: any;
+    readonly filterBy: any;
 } & {
     readonly autorunReady: boolean;
+    readonly hideSmallIndels: boolean | undefined;
 } & {
     setTagsReady(flag: boolean): void;
     setMaxHeight(n?: number): void;
@@ -270,6 +238,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     setConfig(conf: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
     setFilterBy(filter: import("@jbrowse/plugin-alignments/src/shared/types").FilterBy): void;
     setJexlFilters(filters: string[]): void;
+    setHideSmallIndels(arg: boolean): void;
 } & {
     readonly rendererConfig: {
         [x: string]: any;
@@ -303,39 +272,38 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     })[];
     readonly DisplayBlurb: ({ model, }: {
         model: {
-            sortedBy?: {
-                pos: number;
-                refName: number;
-                type: string;
-                tag?: string;
-            };
+            sortedBy?: import("@jbrowse/plugin-alignments/src/shared/types").SortedBy;
         };
-    }) => import("react").JSX.Element | null;
+    }) => import("react/jsx-runtime").JSX.Element | null;
     renderPropsPre(): any;
     colorSchemeSubMenuItems(): {
         label: string;
         onClick: () => void;
     }[];
     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;
+        priority: number;
+        type: string;
+        checked: boolean | undefined;
+        onClick: () => void;
+        icon?: undefined;
+    } | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
         onClick: () => void;
+        priority?: undefined;
+        type?: undefined;
+        checked?: undefined;
     })[];
 } & {
     renderProps(): any;
 } & {
     afterAttach(): void;
 } & {
-    /**
-     * #method
-     */
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
 } & {
-    /**
-     * #method
-     */
     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: {
@@ -344,10 +312,95 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         }[];
     })[];
 } & {
-    /**
-     * #action
-     */
     selectFeature(feature: Feature): void;
     afterCreate(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, {
+    type: string;
+} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+} & {
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+        key: import("mobx-state-tree").ISimpleType<string>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
+        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
+        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    }, {
+        stopToken: string | undefined;
+        filled: boolean;
+        reactElement: React.ReactElement | undefined;
+        features: Map<string, Feature> | undefined;
+        layout: any;
+        status: string;
+        error: unknown;
+        message: string | undefined;
+        maxHeightReached: boolean;
+        ReactComponent: ({ model, }: {
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: React.ReactNode;
+                filled?: boolean;
+                status?: string;
+                reactElement?: React.ReactElement;
+            };
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
+        renderProps: any;
+    } & {
+        doReload(): void;
+        afterAttach(): void;
+        setStatus(message: string): void;
+        setLoading(newStopToken: string): void;
+        setMessage(messageText: string): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
+        setError(error: unknown): void;
+        reload(): void;
+        beforeDestroy(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        maxFeatureScreenDensity: {
+            type: string;
+            description: string;
+            defaultValue: number;
+        };
+        fetchSizeLimit: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        height: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
+} & {
+    configuration: AnyConfigurationSchemaType;
+    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>>;
+    colorBySetting: import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined>;
+    filterBySetting: import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined>;
+    jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export default stateModelFactory;

package/esm/LGVSyntenyDisplay/model.js

@@ -1,35 +1,18 @@
 import { lazy } from 'react';
-import { ConfigurationReference, getConf, } from '@jbrowse/core/configuration';
+import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
 import { getContainingTrack, getContainingView, getSession, isSessionModelWithWidgets, } from '@jbrowse/core/util';
 import { SharedLinearPileupDisplayMixin } from '@jbrowse/plugin-alignments';
 import { types } from 'mobx-state-tree';
 const LaunchSyntenyViewDialog = lazy(() => import('./components/LaunchSyntenyViewDialog'));
-/**
- * #stateModel LGVSyntenyDisplay
- * displays location of "synteny" feature in a plain LGV, allowing linking out
- * to external synteny views
- *
- * extends
- * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
- */
 function stateModelFactory(schema) {
     return types
         .compose('LGVSyntenyDisplay', SharedLinearPileupDisplayMixin(schema), types.model({
-        /**
-         * #property
-         */
         type: types.literal('LGVSyntenyDisplay'),
-        /**
-         * #property
-         */
         configuration: ConfigurationReference(schema),
     }))
         .views(self => {
         const superContextMenuItems = self.contextMenuItems;
         return {
-            /**
-             * #method
-             */
             contextMenuItems() {
                 const feature = self.contextMenuFeature;
                 return [
@@ -42,9 +25,10 @@ function stateModelFactory(schema) {
                                     getSession(self).queueDialog(handleClose => [
                                         LaunchSyntenyViewDialog,
                                         {
-                                            model: self,
+                                            view: getContainingView(self),
                                             trackId: getConf(getContainingTrack(self), 'trackId'),
                                             handleClose,
+                                            session: getSession(self),
                                             feature,
                                         },
                                     ]);
@@ -59,9 +43,6 @@ function stateModelFactory(schema) {
         .views(self => {
         const { trackMenuItems: superTrackMenuItems, colorSchemeSubMenuItems: superColorSchemeSubMenuItems, } = self;
         return {
-            /**
-             * #method
-             */
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
@@ -74,9 +55,6 @@ function stateModelFactory(schema) {
         };
     })
         .actions(self => ({
-        /**
-         * #action
-         */
         selectFeature(feature) {
             const session = getSession(self);
             if (isSessionModelWithWidgets(session)) {
@@ -96,12 +74,7 @@ function stateModelFactory(schema) {
             session.setSelection(feature);
         },
         afterCreate() {
-            // use color by stand to help indicate inversions better on first load,
-            // otherwise use selected orientation
-            if (self.colorBy) {
-                self.setColorScheme({ ...self.colorBy });
-            }
-            else {
+            if (!self.colorBySetting && self.colorBy.type === 'normal') {
                 self.setColorScheme({ type: 'strand' });
             }
         },

package/esm/LaunchLinearSyntenyView.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function LaunchLinearSyntenyView(pluginManager: PluginManager): void;

package/esm/LaunchLinearSyntenyView.js

@@ -4,9 +4,7 @@ function makeMultiDimArray(str) {
     return Array.isArray(str[0]) ? str : [str];
 }
 export default function LaunchLinearSyntenyView(pluginManager) {
-    pluginManager.addToExtensionPoint('LaunchView-LinearSyntenyView', 
-    // @ts-expect-error
-    async ({ session, views, tracks = [], }) => {
+    pluginManager.addToExtensionPoint('LaunchView-LinearSyntenyView', async ({ session, views, tracks = [], }) => {
         try {
             const { assemblyManager } = session;
             const model = session.addView('LinearSyntenyView', {});