@jbrowse/plugin-alignments 2.17.0 → 3.0.0

package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.d.ts

@@ -1,12 +1,7 @@
-import React from 'react';
+import type { SortedBy } from '../../shared/types';
 declare const LinearPileupDisplayBlurb: ({ model, }: {
     model: {
-        sortedBy?: {
-            pos: number;
-            refName: number;
-            type: string;
-            tag?: string;
-        };
+        sortedBy?: SortedBy;
     };
-}) => React.JSX.Element | null;
+}) => import("react/jsx-runtime").JSX.Element | null;
 export default LinearPileupDisplayBlurb;

package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js

@@ -1,10 +1,9 @@
-import React from 'react';
-import { observer } from 'mobx-react';
+import { jsx as _jsx } from "react/jsx-runtime";
 import { Typography } from '@mui/material';
+import { observer } from 'mobx-react';
 const LinearPileupDisplayBlurb = observer(function ({ model, }) {
     var _a;
     const { sortedBy } = model;
-    return sortedBy ? (React.createElement("div", { "data-testid": `blurb-${sortedBy}` },
-        React.createElement(Typography, { color: "secondary", variant: "caption" }, `Sorted by ${(_a = sortedBy.tag) !== null && _a !== void 0 ? _a : sortedBy.type} at ${sortedBy.refName}:${sortedBy.pos}`))) : null;
+    return sortedBy ? (_jsx("div", { "data-testid": `blurb-${sortedBy}`, children: _jsx(Typography, { color: "secondary", variant: "caption", children: `Sorted by ${(_a = sortedBy.tag) !== null && _a !== void 0 ? _a : sortedBy.type} at ${sortedBy.refName}:${sortedBy.pos}` }) })) : null;
 });
 export default LinearPileupDisplayBlurb;

package/esm/LinearPileupDisplay/components/SetFeatureHeightDialog.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 declare const SetFeatureHeightDialog: (props: {
     model: {
         setFeatureHeight: (arg?: number) => void;
@@ -7,5 +6,5 @@ declare const SetFeatureHeightDialog: (props: {
         noSpacing?: boolean;
     };
     handleClose: () => void;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default SetFeatureHeightDialog;

package/esm/LinearPileupDisplay/components/SetFeatureHeightDialog.js

@@ -1,30 +1,24 @@
-import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, TextField, Typography, } from '@mui/material';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
 import { Dialog } from '@jbrowse/core/ui';
+import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, TextField, Typography, } from '@mui/material';
+import { observer } from 'mobx-react';
 const SetFeatureHeightDialog = observer(function (props) {
     const { model, handleClose } = props;
     const { featureHeightSetting, noSpacing: noSpacingSetting } = model;
     const [height, setHeight] = useState(`${featureHeightSetting}`);
     const [noSpacing, setNoSpacing] = useState(noSpacingSetting);
     const ok = height !== '' && !Number.isNaN(+height);
-    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Set feature height" },
-        React.createElement(DialogContent, null,
-            React.createElement(Typography, null, "Adjust the feature height and whether there is any spacing between features. Setting feature height to 1 and removing spacing makes the display very compact."),
-            React.createElement(TextField, { value: height, helperText: "Feature height", onChange: event => {
-                    setHeight(event.target.value);
-                } }),
-            React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: !!noSpacing, onChange: () => {
-                        setNoSpacing(val => !val);
-                    } }), label: "Remove spacing between features in y-direction?" }),
-            React.createElement(DialogActions, null,
-                React.createElement(Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, disabled: !ok, onClick: () => {
-                        model.setFeatureHeight(height !== '' && !Number.isNaN(+height) ? +height : undefined);
-                        model.setNoSpacing(noSpacing);
-                        handleClose();
-                    } }, "Submit"),
-                React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
-                        handleClose();
-                    } }, "Cancel")))));
+    return (_jsx(Dialog, { open: true, onClose: handleClose, title: "Set feature height", children: _jsxs(DialogContent, { children: [_jsx(Typography, { children: "Adjust the feature height and whether there is any spacing between features. Setting feature height to 1 and removing spacing makes the display very compact." }), _jsx(TextField, { value: height, helperText: "Feature height", onChange: event => {
+                        setHeight(event.target.value);
+                    } }), _jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: !!noSpacing, onChange: () => {
+                            setNoSpacing(val => !val);
+                        } }), label: "Remove spacing between features in y-direction?" }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, disabled: !ok, onClick: () => {
+                                model.setFeatureHeight(height !== '' && !Number.isNaN(+height) ? +height : undefined);
+                                model.setNoSpacing(noSpacing);
+                                handleClose();
+                            }, children: "Submit" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
+                                handleClose();
+                            }, children: "Cancel" })] })] }) }));
 });
 export default SetFeatureHeightDialog;

package/esm/LinearPileupDisplay/components/SetMaxHeightDialog.d.ts

@@ -1,9 +1,8 @@
-import React from 'react';
 declare const SetMaxHeightDialog: (props: {
     model: {
         maxHeight?: number;
         setMaxHeight: (arg?: number) => void;
     };
     handleClose: () => void;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default SetMaxHeightDialog;

package/esm/LinearPileupDisplay/components/SetMaxHeightDialog.js

@@ -1,7 +1,8 @@
-import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
 import { Dialog } from '@jbrowse/core/ui';
+import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
+import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()({
     root: {
@@ -13,19 +14,13 @@ const SetMaxHeightDialog = observer(function (props) {
     const { classes } = useStyles();
     const { maxHeight = '' } = model;
     const [max, setMax] = useState(`${maxHeight}`);
-    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Set max height" },
-        React.createElement(DialogContent, { className: classes.root },
-            React.createElement(Typography, null, "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\""),
-            React.createElement(TextField, { value: max, autoFocus: true, onChange: event => {
-                    setMax(event.target.value);
-                }, placeholder: "Enter max height for layout" }),
-            React.createElement(DialogActions, null,
-                React.createElement(Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: () => {
-                        model.setMaxHeight(max !== '' && !Number.isNaN(+max) ? +max : undefined);
-                        handleClose();
-                    } }, "Submit"),
-                React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
-                        handleClose();
-                    } }, "Cancel")))));
+    return (_jsx(Dialog, { open: true, onClose: handleClose, title: "Set max height", children: _jsxs(DialogContent, { className: classes.root, children: [_jsx(Typography, { children: "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\"" }), _jsx(TextField, { value: max, autoFocus: true, onChange: event => {
+                        setMax(event.target.value);
+                    }, placeholder: "Enter max height for layout" }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: () => {
+                                model.setMaxHeight(max !== '' && !Number.isNaN(+max) ? +max : undefined);
+                                handleClose();
+                            }, children: "Submit" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
+                                handleClose();
+                            }, children: "Cancel" })] })] }) }));
 });
 export default SetMaxHeightDialog;

package/esm/LinearPileupDisplay/components/SortByTagDialog.d.ts

@@ -1,8 +1,7 @@
-import React from 'react';
 declare const SortByTagDialog: (props: {
     model: {
         setSortedBy: (arg: string, arg2: string) => void;
     };
     handleClose: () => void;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default SortByTagDialog;

package/esm/LinearPileupDisplay/components/SortByTagDialog.js

@@ -1,30 +1,24 @@
-import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
 import { Dialog } from '@jbrowse/core/ui';
+import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
+import { observer } from 'mobx-react';
 const SortByTagDialog = observer(function (props) {
     const { model, handleClose } = props;
     const [tag, setTag] = useState('');
     const validTag = /^[A-Za-z][A-Za-z0-9]$/.exec(tag);
-    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Sort by tag" },
-        React.createElement(DialogContent, null,
-            React.createElement(Typography, null, "Set the tag to sort by"),
-            React.createElement(Typography, { color: "textSecondary" }, "Examples: HP for haplotype, RG for read group, etc."),
-            React.createElement(TextField, { value: tag, onChange: event => {
-                    setTag(event.target.value);
-                }, placeholder: "Enter tag name", error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', autoComplete: "off", "data-testid": "sort-tag-name", slotProps: {
-                    htmlInput: {
-                        maxLength: 2,
-                        'data-testid': 'sort-tag-name-input',
-                    },
-                } }),
-            React.createElement(DialogActions, null,
-                React.createElement(Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: () => {
-                        model.setSortedBy('tag', tag);
-                        handleClose();
-                    } }, "Submit"),
-                React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
-                        handleClose();
-                    } }, "Cancel")))));
+    return (_jsx(Dialog, { open: true, onClose: handleClose, title: "Sort by tag", children: _jsxs(DialogContent, { children: [_jsx(Typography, { children: "Set the tag to sort by" }), _jsx(Typography, { color: "textSecondary", children: "Examples: HP for haplotype, RG for read group, etc." }), _jsx(TextField, { value: tag, onChange: event => {
+                        setTag(event.target.value);
+                    }, placeholder: "Enter tag name", error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', autoComplete: "off", "data-testid": "sort-tag-name", slotProps: {
+                        htmlInput: {
+                            maxLength: 2,
+                            'data-testid': 'sort-tag-name-input',
+                        },
+                    } }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: () => {
+                                model.setSortedBy('tag', tag);
+                                handleClose();
+                            }, children: "Submit" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
+                                handleClose();
+                            }, children: "Cancel" })] })] }) }));
 });
 export default SortByTagDialog;

package/esm/LinearPileupDisplay/configSchema.d.ts

@@ -1,35 +1,32 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     defaultRendering: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         PileupRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    /**
-     * #slot
-     */
     maxFeatureScreenDensity: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
-    colorScheme: {
+    colorBy: {
         type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
         description: string;
-        defaultValue: string;
+        defaultValue: {
+            type: string;
+        };
+    };
+    filterBy: {
+        type: string;
+        description: string;
+        defaultValue: {
+            flagInclude: number;
+            flagExclude: number;
+        };
     };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     renderer: import("mobx-state-tree").IAnyModelType;

package/esm/LinearPileupDisplay/configSchema.js

@@ -1,54 +1,36 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view';
 import { types } from 'mobx-state-tree';
-/**
- * #config LinearPileupDisplay
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+import { defaultFilterFlags } from '../shared/util';
+function x() { }
 function configSchemaF(pluginManager) {
     return ConfigurationSchema('LinearPileupDisplay', {
-        /**
-         * #slot
-         */
         defaultRendering: {
             type: 'stringEnum',
             model: types.enumeration('Rendering', ['pileup']),
             defaultValue: 'pileup',
         },
-        /**
-         * #slot
-         */
         renderers: ConfigurationSchema('RenderersConfiguration', {
             PileupRenderer: pluginManager.getRendererType('PileupRenderer').configSchema,
         }),
-        /**
-         * #slot
-         */
         maxFeatureScreenDensity: {
             type: 'number',
             description: 'maximum features per pixel that is displayed in the view',
             defaultValue: 5,
         },
-        /**
-         * #slot
-         */
-        colorScheme: {
-            type: 'stringEnum',
-            model: types.enumeration('colorScheme', [
-                'strand',
-                'normal',
-                'insertSize',
-                'insertSizeAndOrientation',
-                'mappingQuality',
-                'tag',
-            ]),
+        colorBy: {
+            type: 'frozen',
             description: 'color scheme to use',
-            defaultValue: 'normal',
+            defaultValue: {
+                type: 'normal',
+            },
+        },
+        filterBy: {
+            type: 'frozen',
+            description: 'default filters to use',
+            defaultValue: defaultFilterFlags,
         },
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager),
         explicitlyTyped: true,
     });

package/esm/LinearPileupDisplay/index.d.ts

@@ -1,4 +1,4 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function register(pluginManager: PluginManager): void;
 export { default as linearPileupDisplayStateModelFactory } from './model';
 export { default as linearPileupDisplayConfigSchemaFactory } from './configSchema';

package/esm/LinearPileupDisplay/index.js

@@ -1,7 +1,7 @@
-import configSchemaFactory from './configSchema';
-import modelFactory from './model';
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
 import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
+import configSchemaFactory from './configSchema';
+import modelFactory from './model';
 export default function register(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaFactory(pluginManager);