@jbrowse/plugin-linear-genome-view 2.11.1 → 2.12.0

package/dist/index.d.ts

@@ -143,6 +143,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         defaultValue: string;
                         contextVariable: string[];
                     };
+                    jexlFilters: {
+                        type: string;
+                        description: string;
+                        defaultValue: never[];
+                    };
                 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>>;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                 rendererTypeName: string;
@@ -258,6 +263,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
                 deleteBlock(key: string): void;
                 selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+                navToFeature(feature: import("@jbrowse/core/util").Feature): void;
                 clearFeatureSelection(): void;
                 setFeatureIdUnderMouse(feature?: string | undefined): void;
                 setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
@@ -355,6 +361,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         defaultValue: string;
                         contextVariable: string[];
                     };
+                    jexlFilters: {
+                        type: string;
+                        description: string;
+                        defaultValue: never[];
+                    };
                 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
             }, {
                 rendererTypeName: string;
@@ -470,6 +481,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
                 deleteBlock(key: string): void;
                 selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+                navToFeature(feature: import("@jbrowse/core/util").Feature): void;
                 clearFeatureSelection(): void;
                 setFeatureIdUnderMouse(feature?: string | undefined): void;
                 setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
@@ -567,6 +579,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         defaultValue: string;
                         contextVariable: string[];
                     };
+                    jexlFilters: {
+                        type: string;
+                        description: string;
+                        defaultValue: never[];
+                    };
                 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
             }>>, {
                 type: string;
@@ -664,6 +681,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     defaultValue: string;
                     contextVariable: string[];
                 };
+                jexlFilters: {
+                    type: string;
+                    description: string;
+                    defaultValue: never[];
+                };
             }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
         }, {
             rendererTypeName: string;
@@ -779,6 +801,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
             deleteBlock(key: string): void;
             selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+            navToFeature(feature: import("@jbrowse/core/util").Feature): void;
             clearFeatureSelection(): void;
             setFeatureIdUnderMouse(feature?: string | undefined): void;
             setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
@@ -876,6 +899,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     defaultValue: string;
                     contextVariable: string[];
                 };
+                jexlFilters: {
+                    type: string;
+                    description: string;
+                    defaultValue: never[];
+                };
             }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
         }>>, {
             type: string;
@@ -908,6 +936,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 defaultValue: string;
                 contextVariable: string[];
             };
+            jexlFilters: {
+                type: string;
+                description: string;
+                defaultValue: never[];
+            };
         }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
         SearchBox: ({ model, showHelp, }: {
             showHelp?: boolean | undefined;
@@ -918,25 +951,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 type: string;
                 offsetPx: number;
                 bpPerPx: number;
-                displayedRegions: import("mobx-state-tree").IMSTArray<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>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<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>>>;
+                displayedRegions: import("@jbrowse/core/util").Region[] & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>>;
                 tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
                 hideHeader: boolean;
                 hideHeaderOverview: boolean;
@@ -1039,6 +1054,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
                     start: number;
                     end: number;
+                    type: string;
                     regionNumber?: number | undefined;
                     reversed?: boolean | undefined;
                     refName: string;
@@ -1232,7 +1248,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     offset: number;
                     start: number;
                     end: number;
-                    reversed: boolean;
+                    reversed?: boolean | undefined;
                 };
                 readonly centerLineInfo: {
                     coord: number;
@@ -1243,7 +1259,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     offset: number;
                     start: number;
                     end: number;
-                    reversed: boolean;
+                    reversed?: boolean | undefined;
                 } | undefined;
             } & {
                 afterCreate(): void;
@@ -1256,16 +1272,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 type: import("mobx-state-tree").IType<string | undefined, string, string>;
                 offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
                 bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-                displayedRegions: import("mobx-state-tree").IArrayType<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>>;
+                displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
                 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>;
@@ -1368,6 +1375,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
                     start: number;
                     end: number;
+                    type: string;
                     regionNumber?: number | undefined;
                     reversed?: boolean | undefined;
                     refName: string;
@@ -1561,7 +1569,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     offset: number;
                     start: number;
                     end: number;
-                    reversed: boolean;
+                    reversed?: boolean | undefined;
                 };
                 readonly centerLineInfo: {
                     coord: number;
@@ -1572,7 +1580,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     offset: number;
                     start: number;
                     end: number;
-                    reversed: boolean;
+                    reversed?: boolean | undefined;
                 } | undefined;
             } & {
                 afterCreate(): void;
@@ -1585,16 +1593,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 type: import("mobx-state-tree").IType<string | undefined, string, string>;
                 offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
                 bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-                displayedRegions: import("mobx-state-tree").IArrayType<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>>;
+                displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
                 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>;
@@ -1616,25 +1615,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 type: string;
                 offsetPx: number;
                 bpPerPx: number;
-                displayedRegions: import("mobx-state-tree").IMSTArray<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>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<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>>>;
+                displayedRegions: import("@jbrowse/core/util").Region[] & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>>;
                 tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
                 hideHeader: boolean;
                 hideHeaderOverview: boolean;
@@ -1737,6 +1718,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
                     start: number;
                     end: number;
+                    type: string;
                     regionNumber?: number | undefined;
                     reversed?: boolean | undefined;
                     refName: string;
@@ -1930,7 +1912,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     offset: number;
                     start: number;
                     end: number;
-                    reversed: boolean;
+                    reversed?: boolean | undefined;
                 };
                 readonly centerLineInfo: {
                     coord: number;
@@ -1941,7 +1923,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     offset: number;
                     start: number;
                     end: number;
-                    reversed: boolean;
+                    reversed?: boolean | undefined;
                 } | undefined;
             } & {
                 afterCreate(): void;
@@ -1954,16 +1936,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 type: import("mobx-state-tree").IType<string | undefined, string, string>;
                 offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
                 bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-                displayedRegions: import("mobx-state-tree").IArrayType<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>>;
+                displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
                 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>;
@@ -2066,6 +2039,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
                     start: number;
                     end: number;
+                    type: string;
                     regionNumber?: number | undefined;
                     reversed?: boolean | undefined;
                     refName: string;
@@ -2259,7 +2233,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     offset: number;
                     start: number;
                     end: number;
-                    reversed: boolean;
+                    reversed?: boolean | undefined;
                 };
                 readonly centerLineInfo: {
                     coord: number;
@@ -2270,7 +2244,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     offset: number;
                     start: number;
                     end: number;
-                    reversed: boolean;
+                    reversed?: boolean | undefined;
                 } | undefined;
             } & {
                 afterCreate(): void;
@@ -2283,16 +2257,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 type: import("mobx-state-tree").IType<string | undefined, string, string>;
                 offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
                 bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-                displayedRegions: import("mobx-state-tree").IArrayType<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>>;
+                displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
                 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>;
@@ -2314,25 +2279,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 type: string;
                 offsetPx: number;
                 bpPerPx: number;
-                displayedRegions: import("mobx-state-tree").IMSTArray<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>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<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>>>;
+                displayedRegions: import("@jbrowse/core/util").Region[] & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>>;
                 tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
                 hideHeader: boolean;
                 hideHeaderOverview: boolean;
@@ -2435,6 +2382,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
                     start: number;
                     end: number;
+                    type: string;
                     regionNumber?: number | undefined;
                     reversed?: boolean | undefined;
                     refName: string;
@@ -2628,7 +2576,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     offset: number;
                     start: number;
                     end: number;
-                    reversed: boolean;
+                    reversed?: boolean | undefined;
                 };
                 readonly centerLineInfo: {
                     coord: number;
@@ -2639,7 +2587,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     offset: number;
                     start: number;
                     end: number;
-                    reversed: boolean;
+                    reversed?: boolean | undefined;
                 } | undefined;
             } & {
                 afterCreate(): void;
@@ -2652,16 +2600,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 type: import("mobx-state-tree").IType<string | undefined, string, string>;
                 offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
                 bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-                displayedRegions: import("mobx-state-tree").IArrayType<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>>;
+                displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
                 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>;
@@ -2764,6 +2703,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
                     start: number;
                     end: number;
+                    type: string;
                     regionNumber?: number | undefined;
                     reversed?: boolean | undefined;
                     refName: string;
@@ -2957,7 +2897,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     offset: number;
                     start: number;
                     end: number;
-                    reversed: boolean;
+                    reversed?: boolean | undefined;
                 };
                 readonly centerLineInfo: {
                     coord: number;
@@ -2968,7 +2908,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     offset: number;
                     start: number;
                     end: number;
-                    reversed: boolean;
+                    reversed?: boolean | undefined;
                 } | undefined;
             } & {
                 afterCreate(): void;
@@ -2981,16 +2921,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 type: import("mobx-state-tree").IType<string | undefined, string, string>;
                 offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
                 bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-                displayedRegions: import("mobx-state-tree").IArrayType<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>>;
+                displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
                 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>;

package/esm/BaseLinearDisplay/components/LinearBlocks.js

@@ -2,7 +2,6 @@ import React from 'react';
 import { makeStyles } from 'tss-react/mui';
 import { getContainingView } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
-import { ContentBlock, ElidedBlock, InterRegionPaddingBlock, } from '@jbrowse/core/util/blockTypes';
 import { ContentBlock as ContentBlockComponent, ElidedBlock as ElidedBlockComponent, InterRegionPaddingBlock as InterRegionPaddingBlockComponent, } from './Block';
 const useStyles = makeStyles()({
     linearBlocks: {
@@ -29,9 +28,10 @@ const RenderedBlocks = observer(function ({ model, }) {
     const { classes } = useStyles();
     const { blockDefinitions, blockState } = model;
     return (React.createElement(React.Fragment, null, blockDefinitions.map(block => {
-        if (block instanceof ContentBlock) {
+        const key = `${model.id}-${block.key}`;
+        if (block.type === 'ContentBlock') {
             const state = blockState.get(block.key);
-            return (React.createElement(ContentBlockComponent, { block: block, key: `${model.id}-${block.key}` },
+            return (React.createElement(ContentBlockComponent, { block: block, key: key },
                 (state === null || state === void 0 ? void 0 : state.ReactComponent) ? (React.createElement(state.ReactComponent, { model: state })) : null,
                 (state === null || state === void 0 ? void 0 : state.maxHeightReached) ? (React.createElement("div", { className: classes.heightOverflowed, style: {
                         top: state.layout.getTotalHeight() - 16,
@@ -39,11 +39,11 @@ const RenderedBlocks = observer(function ({ model, }) {
                         height: 16,
                     } }, "Max height reached")) : null));
         }
-        if (block instanceof ElidedBlock) {
-            return (React.createElement(ElidedBlockComponent, { key: `${model.id}-${block.key}`, width: block.widthPx }));
+        else if (block.type === 'ElidedBlock') {
+            return React.createElement(ElidedBlockComponent, { key: key, width: block.widthPx });
         }
-        if (block instanceof InterRegionPaddingBlock) {
-            return (React.createElement(InterRegionPaddingBlockComponent, { key: block.key, width: block.widthPx, style: { background: 'none' }, boundary: block.variant === 'boundary' }));
+        else if (block.type === 'InterRegionPaddingBlock') {
+            return (React.createElement(InterRegionPaddingBlockComponent, { key: key, width: block.widthPx, style: { background: 'none' }, boundary: block.variant === 'boundary' }));
         }
         throw new Error(`invalid block type ${JSON.stringify(block)}`);
     })));

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts

@@ -110,6 +110,11 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 }, {
     rendererTypeName: string;
@@ -200,7 +205,9 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
-    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
+    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features"; /**
+     * #action
+     */
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): React.JSX.Element | null;
 } & {
     featureIdUnderMouse: string | undefined;
@@ -273,6 +280,10 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
      * #action
      */
     selectFeature(feature: Feature): void;
+    /**
+     * #action
+     */
+    navToFeature(feature: Feature): void;
     /**
      * #action
      */
@@ -401,6 +412,11 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 }>>, {
     type: string;

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js

@@ -7,6 +7,7 @@ import { autorun } from 'mobx';
 import { addDisposer, isAlive, types } from 'mobx-state-tree';
 // icons
 import MenuOpenIcon from '@mui/icons-material/MenuOpen';
+import CenterFocusStrongIcon from '@mui/icons-material/CenterFocusStrong';
 import { Tooltip } from '../components/BaseLinearDisplay';
 import BlockState from './serverSideRenderedBlock';
 import configSchema from './configSchema';
@@ -182,6 +183,17 @@ function stateModelFactory() {
                 session.setSelection(feature);
             }
         },
+        /**
+         * #action
+         */
+        navToFeature(feature) {
+            const view = getContainingView(self);
+            view.navTo({
+                refName: feature.get('refName'),
+                start: feature.get('start'),
+                end: feature.get('end'),
+            });
+        },
         /**
          * #action
          */
@@ -239,6 +251,15 @@ function stateModelFactory() {
                                 }
                             },
                         },
+                        {
+                            label: 'Zoom to feature',
+                            icon: CenterFocusStrongIcon,
+                            onClick: () => {
+                                if (self.contextMenuFeature) {
+                                    self.navToFeature(self.contextMenuFeature);
+                                }
+                            },
+                        },
                     ]
                     : []),
             ];

package/esm/BaseLinearDisplay/models/configSchema.d.ts

@@ -32,5 +32,15 @@ declare const baseLinearDisplayConfigSchema: import("@jbrowse/core/configuration
         defaultValue: string;
         contextVariable: string[];
     };
+    /**
+     * #slot
+     * config jexlFilters are deferred evaluated so they are prepended with
+     * jexl at runtime rather than being stored with jexl in the config
+     */
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 export default baseLinearDisplayConfigSchema;

package/esm/BaseLinearDisplay/models/configSchema.js

@@ -2,9 +2,11 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration';
 /**
  * #config BaseLinearDisplay
  * #category display
- * `BaseLinearDisplay` is a "base" config that is extended by classes like
- * `LinearBasicDisplay` (used for feature tracks, etc) and `LinearBareDisplay`
- * (more stripped down than even the basic display, not commonly used)
+ *
+ * `BaseLinearDisplay` is a "base" config that is extended by other configs including
+ * - `LinearBasicDisplay` (used for feature tracks, etc)
+ * - `LinearBareDisplay` (more stripped down than even the basic display, not
+ *   commonly used)
  */
 function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 const baseLinearDisplayConfigSchema = ConfigurationSchema('BaseLinearDisplay', {
@@ -41,6 +43,16 @@ const baseLinearDisplayConfigSchema = ConfigurationSchema('BaseLinearDisplay', {
         defaultValue: `jexl:get(feature,'name')`,
         contextVariable: ['feature'],
     },
+    /**
+     * #slot
+     * config jexlFilters are deferred evaluated so they are prepended with
+     * jexl at runtime rather than being stored with jexl in the config
+     */
+    jexlFilters: {
+        type: 'stringArray',
+        description: 'default set of jexl filters to apply to a track. note: these do not use the jexl prefix because they have a deferred evaluation system',
+        defaultValue: [],
+    },
 }, {
     /**
      * #identifier

package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js

@@ -96,6 +96,7 @@ const blockState = types
             renderInProgress = undefined;
         },
         setError(error) {
+            console.error(error);
             if (renderInProgress && !renderInProgress.signal.aborted) {
                 renderInProgress.abort();
             }

package/esm/LinearBareDisplay/configSchema.d.ts

@@ -30,5 +30,10 @@ declare function configSchemaFactory(pluginManager: PluginManager): import("@jbr
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;
 export { configSchemaFactory };