npm - @jbrowse/plugin-variants - Versions diffs - 4.1.1 → 4.1.4 - Mend

@jbrowse/plugin-variants 4.1.1 → 4.1.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (57) hide show

package/esm/shared/MultiVariantBaseModel.d.ts CHANGED Viewed

@@ -39,6 +39,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                 statusMessage?: string;
                 reactElement?: React.ReactElement;
                 isRenderingPending?: boolean;
+                displayHeight?: number;
             };
         }) => import("react/jsx-runtime").JSX.Element;
         renderProps: any;
@@ -57,10 +58,11 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
         beforeDestroy(): void;
     } & {
         readonly statusMessage: any;
+        readonly displayHeight: number | undefined;
     } & {
         afterAttach(): void;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         maxFeatureScreenDensity: {
             type: string;
             description: string;
@@ -87,7 +89,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
             description: string;
             defaultValue: never[];
         };
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
     showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
     showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
 } & {
@@ -108,6 +110,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
     clusterTree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     lineZoneHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    subtreeFilter: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -396,6 +399,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                         statusMessage?: string;
                         reactElement?: React.ReactElement;
                         isRenderingPending?: boolean;
+                        displayHeight?: number;
                     };
                 }) => import("react/jsx-runtime").JSX.Element;
                 renderProps: any;
@@ -414,6 +418,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                 beforeDestroy(): void;
             } & {
                 readonly statusMessage: any;
+                readonly displayHeight: number | undefined;
             } & {
                 afterAttach(): void;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -440,6 +445,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                         statusMessage?: string;
                         reactElement?: React.ReactElement;
                         isRenderingPending?: boolean;
+                        displayHeight?: number;
                     };
                 }) => import("react/jsx-runtime").JSX.Element;
                 renderProps: any;
@@ -458,6 +464,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                 beforeDestroy(): void;
             } & {
                 readonly statusMessage: any;
+                readonly displayHeight: number | undefined;
             } & {
                 afterAttach(): void;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
@@ -471,7 +478,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                         [x: string]: any;
                     } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                 maxFeatureScreenDensity: {
                     type: string;
                     description: string;
@@ -498,7 +505,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                     description: string;
                     defaultValue: never[];
                 };
-            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>>;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>>;
             showLegend: boolean | undefined;
             showTooltips: boolean | undefined;
         } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -788,6 +795,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                         statusMessage?: string;
                         reactElement?: React.ReactElement;
                         isRenderingPending?: boolean;
+                        displayHeight?: number;
                     };
                 }) => import("react/jsx-runtime").JSX.Element;
                 renderProps: any;
@@ -806,10 +814,11 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                 beforeDestroy(): void;
             } & {
                 readonly statusMessage: any;
+                readonly displayHeight: number | undefined;
             } & {
                 afterAttach(): void;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-            configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+            configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                 maxFeatureScreenDensity: {
                     type: string;
                     description: string;
@@ -836,7 +845,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                     description: string;
                     defaultValue: never[];
                 };
-            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
             showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
             showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
         }, {
@@ -1146,6 +1155,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
     setMafFilter(arg: number): void;
     setShowSidebarLabels(arg: boolean): void;
     setShowTree(arg: boolean): void;
+    setSubtreeFilter(names?: string[]): void;
     setPhasedMode(arg: string): void;
     setAutoHeight(auto: boolean): void;
     setHasPhased(arg: boolean): void;
@@ -1191,6 +1201,13 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
             disabled: boolean;
             onClick: () => void;
             helpText?: undefined;
+        } | {
+            label: string;
+            onClick: () => void;
+            type?: undefined;
+            checked?: undefined;
+            disabled?: undefined;
+            helpText?: undefined;
         } | {
             label: string;
             helpText: string;
@@ -1310,6 +1327,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                         statusMessage?: string;
                         reactElement?: React.ReactElement;
                         isRenderingPending?: boolean;
+                        displayHeight?: number;
                     };
                 }) => import("react/jsx-runtime").JSX.Element;
                 renderProps: any;
@@ -1328,6 +1346,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                 beforeDestroy(): void;
             } & {
                 readonly statusMessage: any;
+                readonly displayHeight: number | undefined;
             } & {
                 afterAttach(): void;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -1354,6 +1373,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                         statusMessage?: string;
                         reactElement?: React.ReactElement;
                         isRenderingPending?: boolean;
+                        displayHeight?: number;
                     };
                 }) => import("react/jsx-runtime").JSX.Element;
                 renderProps: any;
@@ -1372,6 +1392,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                 beforeDestroy(): void;
             } & {
                 readonly statusMessage: any;
+                readonly displayHeight: number | undefined;
             } & {
                 afterAttach(): void;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
@@ -1385,7 +1406,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                         [x: string]: any;
                     } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                 maxFeatureScreenDensity: {
                     type: string;
                     description: string;
@@ -1412,7 +1433,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                     description: string;
                     defaultValue: never[];
                 };
-            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">> & AnyConfigurationSchemaType> & {
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">> & AnyConfigurationSchemaType> & {
                 setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
                     [x: string]: any;
                 } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
@@ -1431,6 +1452,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
             clusterTree: string | undefined;
             treeAreaWidth: number;
             lineZoneHeight: number;
+            subtreeFilter: (import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").ISimpleType<string>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>>) | undefined;
         } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
@@ -1719,6 +1741,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                                 statusMessage?: string;
                                 reactElement?: React.ReactElement;
                                 isRenderingPending?: boolean;
+                                displayHeight?: number;
                             };
                         }) => import("react/jsx-runtime").JSX.Element;
                         renderProps: any;
@@ -1737,6 +1760,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                         beforeDestroy(): void;
                     } & {
                         readonly statusMessage: any;
+                        readonly displayHeight: number | undefined;
                     } & {
                         afterAttach(): void;
                     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -1763,6 +1787,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                                 statusMessage?: string;
                                 reactElement?: React.ReactElement;
                                 isRenderingPending?: boolean;
+                                displayHeight?: number;
                             };
                         }) => import("react/jsx-runtime").JSX.Element;
                         renderProps: any;
@@ -1781,6 +1806,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                         beforeDestroy(): void;
                     } & {
                         readonly statusMessage: any;
+                        readonly displayHeight: number | undefined;
                     } & {
                         afterAttach(): void;
                     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
@@ -1794,7 +1820,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                                 [x: string]: any;
                             } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
                         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-                    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+                    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                         maxFeatureScreenDensity: {
                             type: string;
                             description: string;
@@ -1821,7 +1847,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                             description: string;
                             defaultValue: never[];
                         };
-                    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>>;
+                    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>>;
                     showLegend: boolean | undefined;
                     showTooltips: boolean | undefined;
                 } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -2111,6 +2137,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                                 statusMessage?: string;
                                 reactElement?: React.ReactElement;
                                 isRenderingPending?: boolean;
+                                displayHeight?: number;
                             };
                         }) => import("react/jsx-runtime").JSX.Element;
                         renderProps: any;
@@ -2129,10 +2156,11 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                         beforeDestroy(): void;
                     } & {
                         readonly statusMessage: any;
+                        readonly displayHeight: number | undefined;
                     } & {
                         afterAttach(): void;
                     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-                    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+                    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                         maxFeatureScreenDensity: {
                             type: string;
                             description: string;
@@ -2159,7 +2187,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                             description: string;
                             defaultValue: never[];
                         };
-                    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+                    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
                     showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
                     showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
                 }, {
@@ -2469,6 +2497,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
             setMafFilter(arg: number): void;
             setShowSidebarLabels(arg: boolean): void;
             setShowTree(arg: boolean): void;
+            setSubtreeFilter(names?: string[]): void;
             setPhasedMode(arg: string): void;
             setAutoHeight(auto: boolean): void;
             setHasPhased(arg: boolean): void;
@@ -2514,6 +2543,13 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                     disabled: boolean;
                     onClick: () => void;
                     helpText?: undefined;
+                } | {
+                    label: string;
+                    onClick: () => void;
+                    type?: undefined;
+                    checked?: undefined;
+                    disabled?: undefined;
+                    helpText?: undefined;
                 } | {
                     label: string;
                     helpText: string;
@@ -2633,6 +2669,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                         statusMessage?: string;
                         reactElement?: React.ReactElement;
                         isRenderingPending?: boolean;
+                        displayHeight?: number;
                     };
                 }) => import("react/jsx-runtime").JSX.Element;
                 renderProps: any;
@@ -2651,10 +2688,11 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                 beforeDestroy(): void;
             } & {
                 readonly statusMessage: any;
+                readonly displayHeight: number | undefined;
             } & {
                 afterAttach(): void;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-            configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+            configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                 maxFeatureScreenDensity: {
                     type: string;
                     description: string;
@@ -2681,7 +2719,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                     description: string;
                     defaultValue: never[];
                 };
-            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
             showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
             showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
         } & {
@@ -2702,6 +2740,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
             clusterTree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
             treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
             lineZoneHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+            subtreeFilter: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>;
         }, {
             rendererTypeName: string;
             error: unknown;
@@ -2990,6 +3029,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                                 statusMessage?: string;
                                 reactElement?: React.ReactElement;
                                 isRenderingPending?: boolean;
+                                displayHeight?: number;
                             };
                         }) => import("react/jsx-runtime").JSX.Element;
                         renderProps: any;
@@ -3008,6 +3048,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                         beforeDestroy(): void;
                     } & {
                         readonly statusMessage: any;
+                        readonly displayHeight: number | undefined;
                     } & {
                         afterAttach(): void;
                     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -3034,6 +3075,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                                 statusMessage?: string;
                                 reactElement?: React.ReactElement;
                                 isRenderingPending?: boolean;
+                                displayHeight?: number;
                             };
                         }) => import("react/jsx-runtime").JSX.Element;
                         renderProps: any;
@@ -3052,6 +3094,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                         beforeDestroy(): void;
                     } & {
                         readonly statusMessage: any;
+                        readonly displayHeight: number | undefined;
                     } & {
                         afterAttach(): void;
                     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
@@ -3065,7 +3108,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                                 [x: string]: any;
                             } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
                         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-                    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+                    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                         maxFeatureScreenDensity: {
                             type: string;
                             description: string;
@@ -3092,7 +3135,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                             description: string;
                             defaultValue: never[];
                         };
-                    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>>;
+                    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>>;
                     showLegend: boolean | undefined;
                     showTooltips: boolean | undefined;
                 } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -3382,6 +3425,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                                 statusMessage?: string;
                                 reactElement?: React.ReactElement;
                                 isRenderingPending?: boolean;
+                                displayHeight?: number;
                             };
                         }) => import("react/jsx-runtime").JSX.Element;
                         renderProps: any;
@@ -3400,10 +3444,11 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                         beforeDestroy(): void;
                     } & {
                         readonly statusMessage: any;
+                        readonly displayHeight: number | undefined;
                     } & {
                         afterAttach(): void;
                     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-                    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+                    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                         maxFeatureScreenDensity: {
                             type: string;
                             description: string;
@@ -3430,7 +3475,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                             description: string;
                             defaultValue: never[];
                         };
-                    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+                    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
                     showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
                     showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
                 }, {
@@ -3740,6 +3785,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
             setMafFilter(arg: number): void;
             setShowSidebarLabels(arg: boolean): void;
             setShowTree(arg: boolean): void;
+            setSubtreeFilter(names?: string[]): void;
             setPhasedMode(arg: string): void;
             setAutoHeight(auto: boolean): void;
             setHasPhased(arg: boolean): void;
@@ -3785,6 +3831,13 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                     disabled: boolean;
                     onClick: () => void;
                     helpText?: undefined;
+                } | {
+                    label: string;
+                    onClick: () => void;
+                    type?: undefined;
+                    checked?: undefined;
+                    disabled?: undefined;
+                    helpText?: undefined;
                 } | {
                     label: string;
                     helpText: string;
@@ -3910,6 +3963,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                 statusMessage?: string;
                 reactElement?: React.ReactElement;
                 isRenderingPending?: boolean;
+                displayHeight?: number;
             };
         }) => import("react/jsx-runtime").JSX.Element;
         renderProps: any;
@@ -3928,10 +3982,11 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
         beforeDestroy(): void;
     } & {
         readonly statusMessage: any;
+        readonly displayHeight: number | undefined;
     } & {
         afterAttach(): void;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         maxFeatureScreenDensity: {
             type: string;
             description: string;
@@ -3958,7 +4013,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
             description: string;
             defaultValue: never[];
         };
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
     showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
     showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
 } & {
@@ -3979,6 +4034,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
     clusterTree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     lineZoneHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    subtreeFilter: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>;
 }>>;
 export type MultiVariantBaseStateModel = ReturnType<typeof MultiVariantBaseModelF>;
 export type MultiVariantBaseModel = Instance<MultiVariantBaseStateModel>;

package/esm/shared/MultiVariantBaseModel.js CHANGED Viewed

@@ -40,6 +40,7 @@ export default function MultiVariantBaseModelF(configSchema) {
         clusterTree: types.maybe(types.string),
         treeAreaWidth: types.optional(types.number, 80),
         lineZoneHeight: types.optional(types.number, 0),
+        subtreeFilter: types.maybe(types.array(types.string)),
     }))
         .volatile(() => ({
         sourcesLoadingStopToken: undefined,
@@ -131,6 +132,9 @@ export default function MultiVariantBaseModelF(configSchema) {
         setShowTree(arg) {
             self.showTreeSetting = arg;
         },
+        setSubtreeFilter(names) {
+            self.subtreeFilter = names ? cast(names) : undefined;
+        },
         setPhasedMode(arg) {
             const currentMode = self.renderingModeSetting ?? getConf(self, 'renderingMode');
             if (currentMode !== arg) {
@@ -189,7 +193,7 @@ export default function MultiVariantBaseModelF(configSchema) {
                 : undefined;
         },
         get sources() {
-            return self.sourcesVolatile
+            let result = self.sourcesVolatile
                 ? getSources({
                     sources: self.sourcesVolatile,
                     layout: self.layout.length ? self.layout : undefined,
@@ -197,6 +201,11 @@ export default function MultiVariantBaseModelF(configSchema) {
                     sampleInfo: self.sampleInfo,
                 })
                 : undefined;
+            if (result && self.subtreeFilter?.length) {
+                const filterSet = new Set(self.subtreeFilter);
+                result = result.filter(s => filterSet.has(s.baseName ?? s.name));
+            }
+            return result;
         },
         get root() {
             const newick = self.clusterTree;
@@ -204,9 +213,39 @@ export default function MultiVariantBaseModelF(configSchema) {
                 return undefined;
             }
             const tree = fromNewick(newick);
-            return hierarchy(tree, (d) => d.children)
+            let root = hierarchy(tree, (d) => d.children)
                 .sum((d) => (d.children ? 0 : 1))
                 .sort((a, b) => ascending(a.data.height || 1, b.data.height || 1));
+            if (self.subtreeFilter?.length) {
+                const filterSet = new Set(self.subtreeFilter);
+                const getLeafNames = (node) => {
+                    if (!node.children?.length) {
+                        return [node.data.name];
+                    }
+                    return node.children.flatMap(child => getLeafNames(child));
+                };
+                const findSubtree = (node) => {
+                    const leafNames = getLeafNames(node);
+                    if (leafNames.length === filterSet.size &&
+                        leafNames.every(name => filterSet.has(name))) {
+                        return node;
+                    }
+                    if (node.children) {
+                        for (const child of node.children) {
+                            const found = findSubtree(child);
+                            if (found) {
+                                return found;
+                            }
+                        }
+                    }
+                    return undefined;
+                };
+                const subtree = findSubtree(root);
+                if (subtree) {
+                    root = subtree;
+                }
+            }
+            return root;
         },
     }))
         .views(self => {
@@ -275,6 +314,16 @@ export default function MultiVariantBaseModelF(configSchema) {
                                     self.setShowTree(!self.showTree);
                                 },
                             },
+                            ...(self.subtreeFilter?.length
+                                ? [
+                                    {
+                                        label: 'Clear subtree filter',
+                                        onClick: () => {
+                                            self.setSubtreeFilter(undefined);
+                                        },
+                                    },
+                                ]
+                                : []),
                             {
                                 label: 'Show reference alleles',
                                 helpText: 'When this setting is off, the background is colored solid grey and only ALT alleles are colored on top of it. This makes it easier to see potentially overlapping structural variants',
@@ -525,7 +574,7 @@ export default function MultiVariantBaseModelF(configSchema) {
         if (!snap) {
             return snap;
         }
-        const { layout, minorAlleleFrequencyFilterSetting, showSidebarLabelsSetting, showTreeSetting, renderingModeSetting, rowHeightMode, lengthCutoffFilter, jexlFilters, referenceDrawingModeSetting, clusterTree, treeAreaWidth, lineZoneHeight, ...rest } = snap;
+        const { layout, minorAlleleFrequencyFilterSetting, showSidebarLabelsSetting, showTreeSetting, renderingModeSetting, rowHeightMode, lengthCutoffFilter, jexlFilters, referenceDrawingModeSetting, clusterTree, treeAreaWidth, lineZoneHeight, subtreeFilter, ...rest } = snap;
         return {
             ...rest,
             ...(layout.length ? { layout } : {}),
@@ -548,6 +597,7 @@ export default function MultiVariantBaseModelF(configSchema) {
             ...(clusterTree !== undefined ? { clusterTree } : {}),
             ...(treeAreaWidth !== 80 ? { treeAreaWidth } : {}),
             ...(lineZoneHeight ? { lineZoneHeight } : {}),
+            ...(subtreeFilter?.length ? { subtreeFilter } : {}),
         };
     });
 }

package/esm/shared/SharedVariantConfigSchema.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
-export default function sharedVariantConfigFactory(): import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+export default function sharedVariantConfigFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     showReferenceAlleles: {
         type: string;
         defaultValue: boolean;
@@ -24,7 +24,7 @@ export default function sharedVariantConfigFactory(): import("node_modules/@jbro
         type: string;
         defaultValue: string;
     };
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     maxFeatureScreenDensity: {
         type: string;
         description: string;
@@ -51,4 +51,4 @@ export default function sharedVariantConfigFactory(): import("node_modules/@jbro
         description: string;
         defaultValue: never[];
     };
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

package/esm/shared/components/RectBg.js CHANGED Viewed

@@ -1,8 +1,10 @@
 import { jsx as _jsx } from "react/jsx-runtime";
 import { getFillProps } from '@jbrowse/core/util';
 import { alpha, useTheme } from '@mui/material';
+import { SIDEBAR_BACKGROUND_OPACITY } from "../constants.js";
 const RectBg = ({ x, y, width, height, color, }) => {
     const theme = useTheme();
-    return (_jsx("rect", { pointerEvents: "auto", x: x, y: y, width: width, height: height, ...getFillProps(color || alpha(theme.palette.background.paper, 0.8)) }));
+    return (_jsx("rect", { pointerEvents: "auto", x: x, y: y, width: width, height: height, ...getFillProps(color ||
+            alpha(theme.palette.background.paper, SIDEBAR_BACKGROUND_OPACITY)) }));
 };
 export default RectBg;