@jbrowse/plugin-linear-comparative-view 2.6.1

package/dist/LGVSyntenyDisplay/model.d.ts

@@ -0,0 +1,380 @@
+/// <reference types="react" />
+import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import { Feature } from '@jbrowse/core/util';
+/**
+ * #stateModel LGVSyntenyDisplay
+ * extends `LinearPileupDisplay`, displays location of "synteny" feature in a
+ * plain LGV, allowing linking out to external synteny views
+ */
+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").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").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").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>;
+        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;
+        filled: boolean;
+        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        features: Map<string, Feature> | undefined;
+        layout: any;
+        status: string;
+        error: unknown;
+        message: string | undefined;
+        maxHeightReached: boolean;
+        ReactComponent: ({ model, }: {
+            model: any;
+        }) => any;
+        renderProps: any;
+    } & {
+        doReload(): void;
+        afterAttach(): void;
+        setStatus(message: string): void;
+        setLoading(abortController: AbortController): void;
+        setMessage(messageText: string): void;
+        setRendered(props: {
+            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            features: Map<string, Feature>;
+            layout: any;
+            maxHeightReached: boolean;
+            renderProps: any;
+        } | 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[];
+        };
+    }, 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>>;
+        extra: import("mobx-state-tree").IType<any, any, any>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
+        flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+        flagExclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+        readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            tag: import("mobx-state-tree").ISimpleType<string>;
+            value: import("mobx-state-tree").ISimpleType<string>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+} & {
+    /**
+     * #property
+     */
+    type: import("mobx-state-tree").ISimpleType<"LGVSyntenyDisplay">;
+    /**
+     * #property
+     */
+    configuration: AnyConfigurationSchemaType;
+}, {
+    rendererTypeName: string;
+    error: unknown;
+    message: string | undefined;
+} & {
+    readonly RenderingComponent: import("react").FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        } & import("mobx-state-tree").IStateTreeNode<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").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        onHorizontalScroll?: Function | undefined;
+        blockState?: Record<string, any> | undefined;
+    }>;
+    readonly DisplayBlurb: import("react").FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        } & import("mobx-state-tree").IStateTreeNode<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").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }> | null;
+    readonly adapterConfig: any;
+    readonly parentTrack: any;
+    renderProps(): any;
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+    regionCannotBeRendered(): null;
+} & {
+    setMessage(arg?: string | undefined): void;
+    setError(error?: unknown): void;
+    setRpcDriverName(rpcDriverName: string): void;
+    reload(): void;
+} & {
+    scrollTop: number;
+} & {
+    readonly height: number;
+} & {
+    setScrollTop(scrollTop: number): void;
+    setHeight(displayHeight: number): number;
+    resizeHeight(distance: number): number;
+} & {
+    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
+    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+    currStatsBpPerPx: number;
+} & {
+    readonly currentBytesRequested: number;
+    readonly currentFeatureScreenDensity: number;
+    readonly maxFeatureScreenDensity: any;
+    readonly featureDensityStatsReady: boolean;
+    readonly maxAllowableBytes: number;
+} & {
+    afterAttach(): void;
+} & {
+    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;
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    clearFeatureDensityStats(): void;
+} & {
+    readonly regionTooLarge: boolean;
+    readonly regionTooLargeReason: string;
+} & {
+    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+} & {
+    featureIdUnderMouse: string | undefined;
+    contextMenuFeature: Feature | undefined;
+} & {
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
+    readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
+} & {
+    readonly renderDelay: number;
+    readonly TooltipComponent: import("react").FC<any>;
+    readonly selectedFeatureId: string | undefined;
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+} & {
+    readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
+    readonly featureUnderMouse: Feature | undefined;
+    getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
+    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
+    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+} & {
+    addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
+    deleteBlock(key: string): void;
+    selectFeature(feature: Feature): void;
+    clearFeatureSelection(): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
+    setContextMenuFeature(feature?: Feature | undefined): void;
+} & {
+    reload(): Promise<void>;
+} & {
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    renderProps(): any;
+} & {
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    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;
+    }): 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;
+} & {
+    readonly rendererConfig: {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
+} & {
+    readonly maxHeight: any;
+    readonly featureHeightSetting: any;
+    readonly mismatchAlphaSetting: any;
+    readonly featureUnderMouse: Feature | undefined;
+    readonly renderReady: boolean;
+} & {
+    readonly rendererTypeName: string;
+    contextMenuItems(): ({
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+    } | {
+        label: string;
+        icon: typeof import("@jbrowse/core/ui/Icons").ContentCopy;
+        onClick: () => void;
+    })[];
+    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 | {
+        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;
+    } | {
+        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;
+    })[];
+} & {
+    afterAttach(): void;
+} & {
+    contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+} & {
+    afterCreate(): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export default stateModelFactory;

package/dist/LGVSyntenyDisplay/model.js

@@ -0,0 +1,154 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mobx_1 = require("mobx");
+const { parseCigar } = plugin_alignments_1.MismatchParser;
+function findPosInCigar(cigar, startX) {
+    let featX = 0;
+    let mateX = 0;
+    for (let i = 0; i < cigar.length; i++) {
+        const len = +cigar[i];
+        const op = cigar[i + 1];
+        const min = Math.min(len, startX - featX);
+        if (featX >= startX) {
+            break;
+        }
+        else if (op === 'I') {
+            mateX += len;
+        }
+        else if (op === 'D') {
+            featX += min;
+        }
+        else if (op === 'M') {
+            mateX += min;
+            featX += min;
+        }
+    }
+    return [featX, mateX];
+}
+async function navToSynteny(feature, self) {
+    const session = (0, util_1.getSession)(self);
+    const track = (0, util_1.getContainingTrack)(self);
+    const view = (0, util_1.getContainingView)(self);
+    const reg = view.dynamicBlocks.contentBlocks[0];
+    const cigar = feature.get('CIGAR');
+    const strand = feature.get('strand');
+    const regStart = reg.start;
+    const regEnd = reg.end;
+    const featStart = feature.get('start');
+    const featEnd = feature.get('end');
+    const mate = feature.get('mate');
+    const mateStart = mate.start;
+    const mateEnd = mate.end;
+    const mateAsm = mate.assemblyName;
+    const mateRef = mate.refName;
+    const featAsm = reg.assemblyName;
+    const featRef = reg.refName;
+    let rMateStart;
+    let rMateEnd;
+    let rFeatStart;
+    let rFeatEnd;
+    if (cigar) {
+        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;
+        rMateStart = (strand === -1 ? mateEnd : mateStart) + mStartX * flipper;
+        rMateEnd = (strand === -1 ? mateEnd : mateStart) + mEndX * flipper;
+    }
+    else {
+        rFeatStart = featStart;
+        rFeatEnd = featEnd;
+        rMateStart = mateStart;
+        rMateEnd = mateEnd;
+    }
+    const trackId = track.configuration.trackId;
+    const view2 = session.addView('LinearSyntenyView', {
+        type: 'LinearSyntenyView',
+        views: [
+            {
+                id: `${Math.random()}`,
+                type: 'LinearGenomeView',
+                hideHeader: true,
+            },
+            {
+                id: `${Math.random()}`,
+                type: 'LinearGenomeView',
+                hideHeader: true,
+            },
+        ],
+        tracks: [
+            {
+                configuration: trackId,
+                type: 'SyntenyTrack',
+                displays: [
+                    {
+                        type: 'LinearSyntenyDisplay',
+                        configuration: `${trackId}-LinearSyntenyDisplay`,
+                    },
+                ],
+            },
+        ],
+    });
+    const f = (n) => Math.floor(n);
+    const l1 = `${featRef}:${f(rFeatStart)}-${f(rFeatEnd)}`;
+    const m1 = Math.min(rMateStart, rMateEnd);
+    const m2 = Math.max(rMateStart, rMateEnd);
+    const l2 = `${mateRef}:${f(m1)}-${f(m2)}${strand === -1 ? '[rev]' : ''}`;
+    await (0, mobx_1.when)(() => view2.width !== undefined);
+    await Promise.all([
+        view2.views[0].navToLocString(l1, featAsm),
+        view2.views[1].navToLocString(l2, mateAsm),
+    ]);
+}
+/**
+ * #stateModel LGVSyntenyDisplay
+ * extends `LinearPileupDisplay`, displays location of "synteny" feature in a
+ * plain LGV, allowing linking out to external synteny views
+ */
+function stateModelFactory(schema) {
+    return mobx_state_tree_1.types
+        .compose('LGVSyntenyDisplay', (0, plugin_alignments_1.linearPileupDisplayStateModelFactory)(schema), mobx_state_tree_1.types.model({
+        /**
+         * #property
+         */
+        type: mobx_state_tree_1.types.literal('LGVSyntenyDisplay'),
+        /**
+         * #property
+         */
+        configuration: (0, configuration_1.ConfigurationReference)(schema),
+    }))
+        .views(self => {
+        const superContextMenuItems = self.contextMenuItems;
+        return {
+            contextMenuItems() {
+                const feature = self.contextMenuFeature;
+                return [
+                    ...superContextMenuItems(),
+                    ...(feature
+                        ? [
+                            {
+                                label: 'Open synteny view for this position',
+                                onClick: () => navToSynteny(feature, self),
+                            },
+                        ]
+                        : []),
+                ];
+            },
+        };
+    })
+        .actions(self => ({
+        afterCreate() {
+            // use color by strand to help indicate inversions better
+            self.setColorScheme({ type: 'strand' });
+        },
+    }));
+}
+exports.default = stateModelFactory;
+//# sourceMappingURL=model.js.map

package/dist/LGVSyntenyDisplay/model.js.map

@@ -0,0 +1 @@
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package/dist/LaunchLinearSyntenyView.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function LaunchLinearSyntenyView(pluginManager: PluginManager): void;

package/dist/LaunchLinearSyntenyView.js

@@ -0,0 +1,58 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const mobx_1 = require("mobx");
+function LaunchLinearSyntenyView(pluginManager) {
+    pluginManager.addToExtensionPoint('LaunchView-LinearSyntenyView', 
+    // @ts-expect-error
+    async ({ session, views, tracks = [], }) => {
+        try {
+            const { assemblyManager } = session;
+            const model = session.addView('LinearSyntenyView', {});
+            await (0, mobx_1.when)(() => !!model.width);
+            model.setViews(await Promise.all(views.map(async (view) => {
+                const asm = await assemblyManager.waitForAssembly(view.assembly);
+                if (!asm) {
+                    throw new Error(`Assembly ${view.assembly} failed to load`);
+                }
+                return {
+                    type: 'LinearGenomeView',
+                    bpPerPx: 1,
+                    offsetPx: 0,
+                    hideHeader: true,
+                    displayedRegions: asm.regions,
+                };
+            })));
+            await Promise.all(model.views.map(view => (0, mobx_1.when)(() => view.initialized)));
+            const idsNotFound = [];
+            await Promise.all(views.map(async (data, idx) => {
+                const view = model.views[idx];
+                const { loc, tracks = [] } = data;
+                await view.navToLocString(loc);
+                tracks.forEach(track => tryTrack(view, track, idsNotFound));
+            }));
+            tracks.forEach(track => tryTrack(model, track, idsNotFound));
+            if (idsNotFound.length) {
+                throw new Error(`Could not resolve identifiers: ${idsNotFound.join(',')}`);
+            }
+        }
+        catch (e) {
+            session.notify(`${e}`, 'error');
+            throw e;
+        }
+    });
+}
+exports.default = LaunchLinearSyntenyView;
+function tryTrack(model, trackId, idsNotFound) {
+    try {
+        model.showTrack(trackId);
+    }
+    catch (e) {
+        if (`${e}`.match('Could not resolve identifier')) {
+            idsNotFound.push(trackId);
+        }
+        else {
+            throw e;
+        }
+    }
+}
+//# sourceMappingURL=LaunchLinearSyntenyView.js.map

package/dist/LaunchLinearSyntenyView.js.map

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package/dist/LinearComparativeDisplay/configSchemaF.d.ts

@@ -0,0 +1,5 @@
+/**
+ * #config LinearComparativeDisplay
+ */
+declare function configSchemaFactory(pluginManager: any): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
+export default configSchemaFactory;

package/dist/LinearComparativeDisplay/configSchemaF.js

@@ -0,0 +1,18 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+/* eslint-disable @typescript-eslint/no-explicit-any */
+const configuration_1 = require("@jbrowse/core/configuration");
+/**
+ * #config LinearComparativeDisplay
+ */
+function configSchemaFactory(pluginManager) {
+    return (0, configuration_1.ConfigurationSchema)('LinearComparativeDisplay', {}, {
+        explicitlyTyped: true,
+        /**
+         * #identifier
+         */
+        explicitIdentifier: 'displayId',
+    });
+}
+exports.default = configSchemaFactory;
+//# sourceMappingURL=configSchemaF.js.map

package/dist/LinearComparativeDisplay/configSchemaF.js.map

@@ -0,0 +1 @@
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package/dist/LinearComparativeDisplay/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;