@jbrowse/plugin-wiggle 1.7.11 → 2.0.0

package/dist/configSchema.js

@@ -1,75 +1,48 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _default = (0, _configuration.ConfigurationSchema)('WiggleRenderer', {
-  color: {
-    type: 'color',
-    description: 'the color of track, overrides posColor and negColor',
-    defaultValue: '#f0f'
-  },
-  posColor: {
-    type: 'color',
-    description: 'the color to use when the score is positive',
-    defaultValue: 'blue'
-  },
-  negColor: {
-    type: 'color',
-    description: 'the color to use when the score is negative',
-    defaultValue: 'red'
-  },
-  highlightColor: {
-    type: 'color',
-    description: 'the color of highlights over the wiggle track',
-    defaultValue: 'rgba(255,255,0,0.5)'
-  },
-  clipColor: {
-    type: 'color',
-    description: 'the color of the clipping marker',
-    defaultValue: 'red'
-  },
-  renderType: {
-    type: 'stringEnum',
-    model: _mobxStateTree.types.enumeration('Rendering type', ['xyplot', 'density', 'line']),
-    description: 'The type of rendering for wiggle data to use',
-    defaultValue: 'xyplot'
-  },
-  filled: {
-    type: 'boolean',
-    description: 'fill in histogram',
-    defaultValue: true
-  },
-  bicolorPivot: {
-    type: 'stringEnum',
-    model: _mobxStateTree.types.enumeration('Scale type', ['numeric', 'mean', 'z_score', 'none']),
-    description: 'type of bicolor pivot',
-    defaultValue: 'numeric'
-  },
-  bicolorPivotValue: {
-    type: 'number',
-    defaultValue: 0,
-    description: 'value to use for bicolor pivot'
-  },
-  summaryScoreMode: {
-    type: 'stringEnum',
-    model: _mobxStateTree.types.enumeration('Score type', ['max', 'min', 'avg', 'whiskers']),
-    description: 'choose whether to use max/min/average or whiskers which combines all three into the same rendering',
-    defaultValue: 'whiskers'
-  },
-  displayCrossHatches: {
-    type: 'boolean',
-    description: 'choose to draw cross hatches (sideways lines)',
-    defaultValue: false
-  }
-}, {
-  explicitlyTyped: true
-});
-
-exports.default = _default;
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+var mobx_state_tree_1 = require("mobx-state-tree");
+exports.default = (0, configuration_1.ConfigurationSchema)('WiggleRenderer', {
+    color: {
+        type: 'color',
+        description: 'the color of track, overrides posColor and negColor',
+        defaultValue: '#f0f',
+    },
+    posColor: {
+        type: 'color',
+        description: 'the color to use when the score is positive',
+        defaultValue: 'blue',
+    },
+    negColor: {
+        type: 'color',
+        description: 'the color to use when the score is negative',
+        defaultValue: 'red',
+    },
+    highlightColor: {
+        type: 'color',
+        description: 'the color of highlights over the wiggle track',
+        defaultValue: 'rgba(255,255,0,0.5)',
+    },
+    clipColor: {
+        type: 'color',
+        description: 'the color of the clipping marker',
+        defaultValue: 'red',
+    },
+    bicolorPivot: {
+        type: 'stringEnum',
+        model: mobx_state_tree_1.types.enumeration('Scale type', [
+            'numeric',
+            'mean',
+            'z_score',
+            'none',
+        ]),
+        description: 'type of bicolor pivot',
+        defaultValue: 'numeric',
+    },
+    bicolorPivotValue: {
+        type: 'number',
+        defaultValue: 0,
+        description: 'value to use for bicolor pivot',
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/dist/configSchema.js.map

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

@@ -11,13 +11,12 @@ export default class WigglePlugin extends Plugin {
     install(pluginManager: PluginManager): void;
     exports: {
         LinearWiggleDisplayReactComponent: (props: {
-            model: import("mobx-state-tree").ModelInstanceTypeProps<{
-                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>>;
-            } & {
-                height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-                blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+            model: {
+                id: string;
+                type: "LinearWiggleDisplay";
+                rpcDriverName: string | undefined;
+                height: number;
+                blockState: import("mobx-state-tree").IMSTMap<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>;
@@ -62,37 +61,83 @@ export default class WigglePlugin extends Plugin {
                     setError(error: unknown): void;
                     reload(): void;
                     beforeDestroy(): void;
-                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-                userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-                userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-            } & {
-                type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
-                configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
-                selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-                resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-                fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-                color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-                posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-                negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-                summaryScoreMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-                rendererTypeNameState: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-                scale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-                autoscale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-                displayCrossHatches: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-                constraints: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<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, import("@jbrowse/core/util").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, import("@jbrowse/core/util").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>>>;
+                userBpPerPxLimit: number | undefined;
+                userByteSizeLimit: number | undefined;
+                configuration: any;
+                selectedRendering: string;
+                resolution: number;
+                fill: boolean | undefined;
+                color: string | undefined;
+                posColor: string | undefined;
+                negColor: string | undefined;
+                summaryScoreMode: string | undefined;
+                rendererTypeNameState: string | undefined;
+                scale: string | undefined;
+                autoscale: string | undefined;
+                displayCrossHatches: boolean | undefined;
+                constraints: {
+                    max: number | undefined;
+                    min: number | undefined;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
                     max: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
                     min: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-                }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-            }> & {
+                }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                 rendererTypeName: string;
                 error: unknown;
             } & {
                 readonly RenderingComponent: import("react").FC<{
-                    model: import("mobx-state-tree").ModelInstanceTypeProps<{
-                        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>>;
-                    }> & {
+                    model: {
+                        id: string;
+                        type: string;
+                        rpcDriverName: string | undefined;
+                    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                         rendererTypeName: string;
                         error: unknown;
                     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -107,11 +152,11 @@ export default class WigglePlugin extends Plugin {
                     blockState?: Record<string, any> | undefined;
                 }>;
                 readonly DisplayBlurb: import("react").FC<{
-                    model: import("mobx-state-tree").ModelInstanceTypeProps<{
-                        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>>;
-                    }> & {
+                    model: {
+                        id: string;
+                        type: string;
+                        rpcDriverName: string | undefined;
+                    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                         rendererTypeName: string;
                         error: unknown;
                     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -197,7 +242,9 @@ export default class WigglePlugin extends Plugin {
                 trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
                 contextMenuItems(): {
                     label: string;
-                    icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
+                    icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+                        muiName: string;
+                    };
                     onClick: () => void;
                 }[];
                 renderProps(): any;
@@ -359,11 +406,11 @@ export default class WigglePlugin extends Plugin {
                 error: unknown;
             } & {
                 readonly RenderingComponent: import("react").FC<{
-                    model: import("mobx-state-tree").ModelInstanceTypeProps<{
-                        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>>;
-                    }> & {
+                    model: {
+                        id: string;
+                        type: string;
+                        rpcDriverName: string | undefined;
+                    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                         rendererTypeName: string;
                         error: unknown;
                     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -378,11 +425,11 @@ export default class WigglePlugin extends Plugin {
                     blockState?: Record<string, any> | undefined;
                 }>;
                 readonly DisplayBlurb: import("react").FC<{
-                    model: import("mobx-state-tree").ModelInstanceTypeProps<{
-                        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>>;
-                    }> & {
+                    model: {
+                        id: string;
+                        type: string;
+                        rpcDriverName: string | undefined;
+                    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                         rendererTypeName: string;
                         error: unknown;
                     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -468,7 +515,9 @@ export default class WigglePlugin extends Plugin {
                 trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
                 contextMenuItems(): {
                     label: string;
-                    icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
+                    icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+                        muiName: string;
+                    };
                     onClick: () => void;
                 }[];
                 renderProps(): any;
@@ -554,10 +603,10 @@ export default class WigglePlugin extends Plugin {
                     overrideHeight: number;
                 }): Promise<JSX.Element>;
             }, import("mobx-state-tree")._NotCustomized, {
-                id: string;
                 type: string;
-                rpcDriverName: string | undefined;
                 height: number;
+                id: string;
+                rpcDriverName: string | undefined;
                 userBpPerPxLimit: number | undefined;
                 userByteSizeLimit: number | undefined;
             } & import("mobx-state-tree")._NotCustomized>>;
@@ -654,11 +703,11 @@ export default class WigglePlugin extends Plugin {
             error: unknown;
         } & {
             readonly RenderingComponent: import("react").FC<{
-                model: import("mobx-state-tree").ModelInstanceTypeProps<{
-                    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>>;
-                }> & {
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                     rendererTypeName: string;
                     error: unknown;
                 } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -673,11 +722,11 @@ export default class WigglePlugin extends Plugin {
                 blockState?: Record<string, any> | undefined;
             }>;
             readonly DisplayBlurb: import("react").FC<{
-                model: import("mobx-state-tree").ModelInstanceTypeProps<{
-                    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>>;
-                }> & {
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                     rendererTypeName: string;
                     error: unknown;
                 } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -763,7 +812,9 @@ export default class WigglePlugin extends Plugin {
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
             contextMenuItems(): {
                 label: string;
-                icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
+                icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+                    muiName: string;
+                };
                 onClick: () => void;
             }[];
             renderProps(): any;
@@ -849,10 +900,10 @@ export default class WigglePlugin extends Plugin {
                 overrideHeight: number;
             }): Promise<JSX.Element>;
         }, import("mobx-state-tree")._NotCustomized, {
-            id: string;
             type: string;
-            rpcDriverName: string | undefined;
             height: number;
+            id: string;
+            rpcDriverName: string | undefined;
             userBpPerPxLimit: number | undefined;
             userByteSizeLimit: number | undefined;
         } & import("mobx-state-tree")._NotCustomized>;