jbrowse-plugin-gwas 2.0.6 → 2.1.0

package/dist/LinearManhattanDisplay/AddFiltersDialog.d.ts

@@ -0,0 +1,10 @@
+import React from 'react';
+declare const AddFiltersDialog: ({ model, handleClose, }: {
+    model: {
+        jexlFilters?: string[];
+        activeFilters: string[];
+        setJexlFilters: (arg?: string[]) => void;
+    };
+    handleClose: () => void;
+}) => React.JSX.Element;
+export default AddFiltersDialog;

package/dist/LinearManhattanDisplay/AddFiltersDialog.js

@@ -0,0 +1,79 @@
+import React from 'react';
+import { useEffect, useState } from 'react';
+import { Dialog } from '@jbrowse/core/ui';
+import { stringToJexlExpression } from '@jbrowse/core/util/jexlStrings';
+import { Button, DialogActions, DialogContent, TextField } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()({
+    dialogContent: {
+        width: '80em',
+    },
+    textAreaFont: {
+        fontFamily: 'Courier New',
+    },
+    error: {
+        color: 'red',
+        fontSize: '0.8em',
+    },
+});
+function checkJexl(code) {
+    stringToJexlExpression(code);
+}
+const AddFiltersDialog = observer(function ({ model, handleClose, }) {
+    const { classes } = useStyles();
+    const { activeFilters } = model;
+    const [data, setData] = useState(activeFilters.join('\n'));
+    const [error, setError] = useState();
+    useEffect(() => {
+        try {
+            data
+                .split('\n')
+                .map(line => line.trim())
+                .filter(line => !!line)
+                .map(line => {
+                checkJexl(line.trim());
+            });
+            setError(undefined);
+        }
+        catch (e) {
+            console.error(e);
+            setError(e);
+        }
+    }, [data]);
+    return (React.createElement(Dialog, { maxWidth: "xl", open: true, onClose: handleClose, title: "Add track filters" },
+        React.createElement(DialogContent, null,
+            React.createElement("div", null,
+                "Add filters, in jexl format, one per line, starting with the string jexl:. Examples:",
+                ' ',
+                React.createElement("ul", null,
+                    React.createElement("li", null,
+                        React.createElement("code", null, "jexl:get(feature,'name')=='BRCA1'"),
+                        " - show only feature where the name attribute is BRCA1"),
+                    React.createElement("li", null,
+                        React.createElement("code", null, "jexl:get(feature,'type')=='gene'"),
+                        " - show only gene type features in a GFF that has many other feature types"),
+                    React.createElement("li", null,
+                        React.createElement("code", null, "jexl:get(feature,'score') > 400"),
+                        " - show only features that have a score greater than 400"))),
+            error ? React.createElement("p", { className: classes.error }, `${error}`) : null,
+            React.createElement(TextField, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, className: classes.dialogContent, fullWidth: true, value: data, onChange: event => {
+                    setData(event.target.value);
+                }, slotProps: {
+                    input: {
+                        classes: {
+                            input: classes.textAreaFont,
+                        },
+                    },
+                } })),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, disabled: !!error, onClick: () => {
+                    model.setJexlFilters(data.split('\n'));
+                    handleClose();
+                } }, "Submit"),
+            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
+                    handleClose();
+                } }, "Cancel"))));
+});
+export default AddFiltersDialog;
+//# sourceMappingURL=AddFiltersDialog.js.map

package/dist/LinearManhattanDisplay/AddFiltersDialog.js.map

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

@@ -1,6 +1,9 @@
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
 import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { MenuItem } from '@jbrowse/core/ui';
 import type { Feature } from '@jbrowse/core/util';
-export declare function stateModelFactory(pluginManager: PluginManager, configSchema: any): import("mobx-state-tree").IModelType<{
+export declare function stateModelFactory(pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -12,7 +15,9 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
 } & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util" /**
+         * #property
+         */).Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -30,7 +35,12 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
             model: {
                 error?: unknown;
                 reload: () => void;
-                message: React.ReactNode;
+                message: React.ReactNode /**
+                 * #action
+                 * this overrides the BaseLinearDisplayModel to avoid popping up a
+                 * feature detail display, but still sets the feature selection on the
+                 * model so listeners can detect a click
+                 */;
                 filled?: boolean;
                 status?: string;
                 reactElement?: React.ReactElement;
@@ -93,11 +103,19 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
         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]>;
-    configuration: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    configuration: AnyConfigurationSchemaType;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearManhattanDisplay">;
+    /**
+     * #property
+     */
+    configuration: AnyConfigurationSchemaType;
+    /**
+     * #property
+     */
+    jexlFilters: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -271,9 +289,9 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
                 [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
     readonly autoscaleType: any;
 } & {
     readonly domain: number[] | undefined;
@@ -396,6 +414,10 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
     readonly rendererTypeName: string;
     readonly needsScalebar: boolean;
     readonly regionTooLarge: boolean;
+    /**
+     * #getter
+     */
+    readonly activeFilters: any;
 } & {
     /**
      * #action
@@ -404,5 +426,31 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
      * model so listeners can detect a click
      */
     selectFeature(feature: Feature): void;
+    /**
+     * #action
+     */
+    setJexlFilters(f?: string[]): void;
+} & {
+    /**
+     * #method
+     */
+    renderProps(): {
+        config: {
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                    [x: string]: any;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+            } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
+        filters: SerializableFilterChain;
+    };
+    /**
+     * #method
+     */
+    trackMenuItems(): MenuItem[];
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type LinearManhattanDisplayModel = ReturnType<typeof stateModelFactory>;

package/dist/LinearManhattanDisplay/stateModelFactory.js

@@ -1,14 +1,27 @@
+import { lazy } from 'react';
+import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
 import { getContainingTrack, getContainingView, getSession, isSelectionContainer, isSessionModelWithWidgets, } from '@jbrowse/core/util';
+import { cast, types } from 'mobx-state-tree';
 import TooltipComponent from './TooltipComponent';
+// lazies
+const AddFiltersDialog = lazy(() => import('./AddFiltersDialog'));
 export function stateModelFactory(pluginManager, configSchema) {
-    const { types } = pluginManager.lib['mobx-state-tree'];
     const WigglePlugin = pluginManager.getPlugin('WigglePlugin');
     const { linearWiggleDisplayModelFactory } = WigglePlugin.exports;
-    return types.compose('LinearManhattanDisplay', linearWiggleDisplayModelFactory(pluginManager, configSchema), types
-        .model({
+    return types
+        .compose('LinearManhattanDisplay', linearWiggleDisplayModelFactory(pluginManager, configSchema), types.model({
         type: types.literal('LinearManhattanDisplay'),
-    })
-        .views(() => ({
+        /**
+         * #property
+         */
+        configuration: ConfigurationReference(configSchema),
+        /**
+         * #property
+         */
+        jexlFilters: types.maybe(types.array(types.string)),
+    }))
+        .views(self => ({
         get TooltipComponent() {
             return TooltipComponent;
         },
@@ -21,6 +34,15 @@ export function stateModelFactory(pluginManager, configSchema) {
         get regionTooLarge() {
             return false;
         },
+        /**
+         * #getter
+         */
+        get activeFilters() {
+            var _a;
+            // config jexlFilters are deferred evaluated so they are prepended with
+            // jexl at runtime rather than being stored with jexl in the config
+            return ((_a = self.jexlFilters) !== null && _a !== void 0 ? _a : getConf(self, 'jexlFilters').map((r) => `jexl:${r}`));
+        },
     }))
         .actions(self => ({
         /**
@@ -43,6 +65,50 @@ export function stateModelFactory(pluginManager, configSchema) {
                 session.setSelection(feature);
             }
         },
-    })));
+        /**
+         * #action
+         */
+        setJexlFilters(f) {
+            self.jexlFilters = cast(f);
+        },
+    }))
+        .views(self => {
+        const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
+        return {
+            /**
+             * #method
+             */
+            renderProps() {
+                const superProps = superRenderProps();
+                return {
+                    ...superProps,
+                    config: self.rendererConfig,
+                    filters: new SerializableFilterChain({
+                        filters: self.activeFilters,
+                    }),
+                };
+            },
+            /**
+             * #method
+             */
+            trackMenuItems() {
+                return [
+                    ...superTrackMenuItems(),
+                    {
+                        label: 'Edit filters',
+                        onClick: () => {
+                            getSession(self).queueDialog(handleClose => [
+                                AddFiltersDialog,
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
+                            ]);
+                        },
+                    },
+                ];
+            },
+        };
+    });
 }
 //# sourceMappingURL=stateModelFactory.js.map

package/dist/LinearManhattanDisplay/stateModelFactory.js.map

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