@jbrowse/plugin-wiggle 3.6.5 → 4.0.0

package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialogBulkEditPanel.js

@@ -0,0 +1,81 @@
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+import { useState } from 'react';
+import { ErrorMessage } from '@jbrowse/core/ui';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
+import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
+const useStyles = makeStyles()({
+    textAreaFont: {
+        fontFamily: 'Courier New',
+    },
+});
+export default function SetColorDialogBulkEditPanel({ onClose, currLayout, }) {
+    const { classes } = useStyles();
+    const [val, setVal] = useState('');
+    const [error, setError] = useState();
+    return (_jsxs(_Fragment, { children: [_jsxs(DialogContent, { children: [_jsx(Typography, { children: "Paste CSV or TSV. If a header column is present. First line is a header. If a column called \"name\" is present, it uses that to connect to IDs in the table, otherwise it uses the first column no." }), error ? _jsx(ErrorMessage, { error: error }) : null, _jsx(TextField, { variant: "outlined", multiline: true, minRows: 5, placeholder: 'name,population\nHG00098,GBR\nHG00101,GBR\nHG00459,CHS\n...', maxRows: 10, fullWidth: true, value: val, onChange: event => {
+                            setVal(event.target.value);
+                        }, slotProps: {
+                            input: {
+                                classes: {
+                                    input: classes.textAreaFont,
+                                },
+                            },
+                        } })] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
+                            const lines = val
+                                .split('\n')
+                                .map(f => f.trim())
+                                .filter(f => !!f);
+                            const fields = lines[0].split(/[,\t]/gm);
+                            if (fields.includes('name')) {
+                                setError('');
+                                const oldLayout = Object.fromEntries(currLayout.map(record => [record.name, record]));
+                                const newData = Object.fromEntries(lines.slice(1).map(line => {
+                                    const cols = line.split(/[,\t]/gm);
+                                    const newRecord = Object.fromEntries(cols.map((col, idx) => [fields[idx], col]));
+                                    return [
+                                        newRecord.name,
+                                        {
+                                            ...newRecord,
+                                            ...oldLayout[newRecord.name],
+                                        },
+                                    ];
+                                }));
+                                onClose(currLayout.map(record => ({
+                                    ...record,
+                                    ...newData[record.name],
+                                })));
+                            }
+                            else {
+                                setError(new Error('No "name" column found on line 1'));
+                            }
+                        }, children: "Update rows" }), _jsx(Button, { variant: "contained", color: "primary", onClick: () => {
+                            const lines = val
+                                .split('\n')
+                                .map(f => f.trim())
+                                .filter(f => !!f);
+                            const fields = lines[0].split(/[,\t]/gm);
+                            if (fields.includes('name')) {
+                                setError('');
+                                const oldLayout = Object.fromEntries(currLayout.map(record => [record.name, record]));
+                                const newData = Object.fromEntries(lines.slice(1).map(line => {
+                                    const cols = line.split(/[,\t]/gm);
+                                    const newRecord = Object.fromEntries(cols.map((col, idx) => [fields[idx], col]));
+                                    return [
+                                        newRecord.name,
+                                        {
+                                            ...newRecord,
+                                            ...oldLayout[newRecord.name],
+                                        },
+                                    ];
+                                }));
+                                onClose(currLayout.map(record => ({
+                                    ...newData[record.name],
+                                })));
+                            }
+                            else {
+                                setError(new Error('No "name" column found on line 1'));
+                            }
+                        }, children: "Replace rows" }), _jsx(Button, { variant: "contained", color: "inherit", onClick: () => {
+                            onClose();
+                        }, children: "Cancel" })] })] }));
+}

package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialogHelpfulTips.d.ts

@@ -0,0 +1 @@
+export default function SetColorDialogHelpfulTips(): import("react/jsx-runtime").JSX.Element;

package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialogHelpfulTips.js

@@ -0,0 +1,4 @@
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+export default function SetColorDialogHelpfulTips() {
+    return (_jsxs(_Fragment, { children: ["Helpful tips", _jsxs("ul", { children: [_jsx("li", { children: "You can select rows in the table with the checkboxes" }), _jsx("li", { children: "Multi-select is enabled with shift-click and control-click" }), _jsx("li", { children: "The \"Move selected items up/down\" can re-arrange subtracks" }), _jsx("li", { children: "Sorting the data grid itself can also re-arrange subtracks" }), _jsx("li", { children: "Changes are applied when you hit Submit" }), _jsx("li", { children: "You can click and drag the dialog box to move it on the screen" }), _jsx("li", { children: "Columns in the table can be hidden using a vertical '...' menu on the right side of each column" })] })] }));
+}

package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialogRowPalettizer.d.ts

@@ -0,0 +1,10 @@
+export default function SetColorDialogRowPalettizer({ setCurrLayout, currLayout, }: {
+    currLayout: {
+        name: string;
+        [key: string]: unknown;
+    }[];
+    setCurrLayout: (arg: {
+        name: string;
+        [key: string]: unknown;
+    }[]) => void;
+}): import("react/jsx-runtime").JSX.Element | null;

package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialogRowPalettizer.js

@@ -0,0 +1,39 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { set1 } from '@jbrowse/core/ui/colors';
+import { randomColor } from '@jbrowse/core/util/color';
+import { Button } from '@mui/material';
+export default function SetColorDialogRowPalettizer({ setCurrLayout, currLayout, }) {
+    if (!currLayout.length || !currLayout[0]) {
+        return null;
+    }
+    const fields = Object.keys(currLayout[0]).filter(f => f !== 'name' &&
+        f !== 'color' &&
+        f !== 'source' &&
+        f !== 'label' &&
+        f !== 'id' &&
+        f !== 'HP');
+    return (_jsxs("div", { children: ["Create color palette based on...", fields.map(r => (_jsx(Button, { variant: "contained", color: "inherit", onClick: () => {
+                    const map = new Map();
+                    for (const row of currLayout) {
+                        const val = map.get(row[r]);
+                        if (!val) {
+                            map.set(row[r], 1);
+                        }
+                        else {
+                            map.set(row[r], val + 1);
+                        }
+                    }
+                    const ret = Object.fromEntries([...map.entries()]
+                        .sort((a, b) => a[1] - b[1])
+                        .map((r, idx) => [r[0], set1[idx] || randomColor(r[0])]));
+                    setCurrLayout(currLayout.map(row => ({
+                        ...row,
+                        color: ret[row[r]],
+                    })));
+                }, children: r }, r))), _jsx(Button, { onClick: () => {
+                    setCurrLayout(currLayout.map(row => ({
+                        ...row,
+                        color: undefined,
+                    })));
+                }, children: "Clear colors" })] }));
+}

package/esm/MultiLinearWiggleDisplay/components/util.d.ts

@@ -1,13 +1,9 @@
-import type { WiggleDisplayModel } from '../model';
+import type { WiggleDisplayModel } from '../model.ts';
 import type { GridRowId } from '@mui/x-data-grid';
-export declare function moveUp(arr: {
+export declare function moveUp<T extends {
     name: string;
-}[], sel: GridRowId[], by?: number): {
+}>(arr: T[], sel: GridRowId[], by?: number): T[];
+export declare function moveDown<T extends {
     name: string;
-}[];
-export declare function moveDown(arr: {
-    name: string;
-}[], sel: GridRowId[], by?: number): {
-    name: string;
-}[];
+}>(arr: T[], sel: GridRowId[], by?: number): T[];
 export declare function getOffset(model: WiggleDisplayModel): number;

package/esm/MultiLinearWiggleDisplay/configSchema.d.ts

@@ -1,26 +1,26 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+export default function WiggleConfigFactory(pluginManager: PluginManager): import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
     defaultRendering: {
         type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
+        model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         defaultValue: string;
     };
-    renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    renderers: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
         MultiXYPlotRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
         MultiDensityRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
         MultiRowXYPlotRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
         MultiLineRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
         MultiRowLineRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
     height: {
         type: string;
         defaultValue: number;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
     autoscale: {
         type: string;
         defaultValue: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
+        model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         description: string;
     };
     minimalTicks: {
@@ -45,7 +45,7 @@ export default function WiggleConfigFactory(pluginManager: PluginManager): impor
     };
     scaleType: {
         type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
+        model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         description: string;
         defaultValue: string;
     };
@@ -54,7 +54,7 @@ export default function WiggleConfigFactory(pluginManager: PluginManager): impor
         description: string;
         defaultValue: boolean;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
     maxFeatureScreenDensity: {
         type: string;
         description: string;
@@ -81,4 +81,4 @@ export default function WiggleConfigFactory(pluginManager: PluginManager): impor
         description: string;
         defaultValue: never[];
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;

package/esm/MultiLinearWiggleDisplay/configSchema.js

@@ -1,6 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { types } from 'mobx-state-tree';
-import sharedWiggleConfigFactory from '../shared/SharedWiggleConfigSchema';
+import { types } from '@jbrowse/mobx-state-tree';
+import sharedWiggleConfigFactory from "../shared/SharedWiggleConfigSchema.js";
 function x() { }
 export default function WiggleConfigFactory(pluginManager) {
     const MultiXYPlotRendererConfigSchema = pluginManager.getRendererType('MultiXYPlotRenderer').configSchema;

package/esm/MultiLinearWiggleDisplay/index.js

@@ -1,7 +1,7 @@
 import { lazy } from 'react';
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
-import configSchemaFactory from './configSchema';
-import modelFactory from './model';
+import configSchemaFactory from "./configSchema.js";
+import modelFactory from "./model.js";
 export default function MultiLinearWiggleDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaFactory(pluginManager);
@@ -12,7 +12,7 @@ export default function MultiLinearWiggleDisplayF(pluginManager) {
             stateModel: modelFactory(pluginManager, configSchema),
             trackType: 'MultiQuantitativeTrack',
             viewType: 'LinearGenomeView',
-            ReactComponent: lazy(() => import('./components/WiggleDisplayComponent')),
+            ReactComponent: lazy(() => import("./components/WiggleDisplayComponent.js")),
         });
     });
 }