@jbrowse/plugin-alignments 2.17.0 → 3.0.0

package/dist/LinearPileupDisplay/components/GroupByDialog.js

@@ -1,51 +1,25 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
-const mobx_state_tree_1 = require("mobx-state-tree");
 const util_1 = require("@jbrowse/core/util");
-// locals
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const mobx_state_tree_1 = require("mobx-state-tree");
 const getUniqueTags_1 = require("../../shared/getUniqueTags");
-function clone(c) {
-    return JSON.parse(JSON.stringify(c));
-}
+const util_2 = require("../../shared/util");
 const GroupByTagDialog = (0, mobx_react_1.observer)(function (props) {
     const { model, handleClose } = props;
-    const [tag, setTag] = (0, react_1.useState)('');
-    const [tagSet, setTagSet] = (0, react_1.useState)();
+    const [tag, setGroupByTag] = (0, react_1.useState)('');
+    const [tagSet, setGroupByTagSet] = (0, react_1.useState)();
     const [loading, setLoading] = (0, react_1.useState)(false);
     const [error, setError] = (0, react_1.useState)();
-    const [includeUndefined, setIncludeUndefined] = (0, react_1.useState)(true);
     const validTag = /^[A-Za-z][A-Za-z0-9]$/.exec(tag);
     const isInvalid = tag.length === 2 && !validTag;
     const debouncedTag = (0, util_1.useDebounce)(tag, 1000);
+    const [type, setType] = (0, react_1.useState)('');
     (0, react_1.useEffect)(() => {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
         (async () => {
             try {
@@ -58,7 +32,7 @@ const GroupByTagDialog = (0, mobx_react_1.observer)(function (props) {
                         blocks: (0, util_1.getContainingView)(model)
                             .staticBlocks,
                     });
-                    setTagSet(vals);
+                    setGroupByTagSet(vals);
                 }
             }
             catch (e) {
@@ -70,62 +44,102 @@ const GroupByTagDialog = (0, mobx_react_1.observer)(function (props) {
             }
         })();
     }, [model, isInvalid, debouncedTag]);
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Group by tag" },
-        react_1.default.createElement(material_1.DialogContent, null,
-            react_1.default.createElement(material_1.Typography, null, "Set the tag to group by. NOTE: this will make a set of fully functional subtracks with the filter by by default set to the values of the tag that are visible in the current view"),
-            react_1.default.createElement(material_1.Typography, { color: "textSecondary" }, "Examples: HP for haplotype, RG for read group, etc."),
-            react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: includeUndefined, onChange: () => {
-                        setIncludeUndefined(!includeUndefined);
-                    } }), label: "Make a new subtrack for undefined values of tag as well?" }),
-            react_1.default.createElement(material_1.TextField, { value: tag, onChange: event => {
-                    setTag(event.target.value);
-                }, placeholder: "Enter tag name", error: isInvalid, helperText: isInvalid ? 'Not a valid tag' : '', autoComplete: "off", "data-testid": "group-tag-name", slotProps: {
-                    htmlInput: {
-                        maxLength: 2,
-                        'data-testid': 'group-tag-name-input',
-                    },
-                } }),
-            error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : loading ? (react_1.default.createElement(ui_1.LoadingEllipses, { title: "Loading unique tags" })) : tagSet ? (react_1.default.createElement("div", null,
-                react_1.default.createElement("div", null,
-                    "Found unique ",
-                    tag,
-                    " values:"),
-                react_1.default.createElement("div", null, tagSet.join(', ')))) : null),
-        react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", disabled: !tagSet, autoFocus: true, onClick: () => {
-                    const track = (0, util_1.getContainingTrack)(model);
-                    const trackConf = clone((0, mobx_state_tree_1.getSnapshot)(track.configuration));
-                    const session = (0, util_1.getSession)(model);
-                    if (tagSet) {
-                        const ret = [...tagSet];
-                        if (includeUndefined) {
-                            ret.push(undefined);
-                        }
-                        for (const tagValue of ret) {
-                            // @ts-expect-error
-                            const newTrackConf = session.addTrackConf({
-                                ...trackConf,
-                                trackId: `${trackConf.trackId}-${tag}:${tagValue}-${+Date.now()}-sessionTrack`,
-                                name: `${trackConf.name} ${tag}:${tagValue}`,
-                                displays: undefined,
-                            });
+    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Group by", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "NOTE: this will create new session tracks with the \"filter by\" set to the values chosen here rather than affecting the current track state" }), (0, jsx_runtime_1.jsxs)(material_1.TextField, { fullWidth: true, value: type, onChange: event => {
+                            setType(event.target.value);
+                        }, label: "Group by...", select: true, children: [(0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: "strand", children: "Strand" }), (0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: "tag", children: "Tag" })] }), type === 'tag' ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { color: "textSecondary", children: "Examples: HP for haplotype, RG for read group, etc." }), (0, jsx_runtime_1.jsx)(material_1.TextField, { value: tag, onChange: event => {
+                                    setGroupByTag(event.target.value);
+                                }, placeholder: "Enter tag name", error: isInvalid, helperText: isInvalid ? 'Not a valid tag' : '', autoComplete: "off", "data-testid": "group-tag-name", slotProps: {
+                                    htmlInput: {
+                                        maxLength: 2,
+                                        'data-testid': 'group-tag-name-input',
+                                    },
+                                } }), error ? ((0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error })) : loading ? ((0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { title: "Loading unique tags" })) : tagSet ? ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsxs)("div", { children: ["Found unique ", tag, " values:"] }), (0, jsx_runtime_1.jsx)("div", { children: tagSet.join(', ') })] })) : null] })) : null] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", type: "submit", disabled: !tagSet, autoFocus: true, onClick: () => {
+                            const track = (0, util_1.getContainingTrack)(model);
+                            const trackConf = structuredClone((0, mobx_state_tree_1.getSnapshot)(track.configuration));
+                            const session = (0, util_1.getSession)(model);
                             const view = (0, util_1.getContainingView)(model);
-                            const t = view.showTrack(newTrackConf.trackId);
-                            const d = t.displays[0];
-                            d.setFilterBy({
-                                flagInclude: 0,
-                                flagExclude: 1540,
-                                tagFilter: {
-                                    tag,
-                                    value: tagValue,
-                                },
-                            });
-                        }
-                    }
-                    handleClose();
-                } }, "Submit"),
-            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                    handleClose();
-                } }, "Cancel"))));
+                            if (type === 'tag') {
+                                if (tagSet) {
+                                    const ret = [...tagSet, undefined];
+                                    for (const tagValue of ret) {
+                                        const t1 = `${trackConf.trackId}-${tag}:${tagValue}-${+Date.now()}-sessionTrack`;
+                                        session.addTrackConf({
+                                            ...trackConf,
+                                            trackId: t1,
+                                            name: `${trackConf.name} (${tag}:${tagValue})`,
+                                            displays: [
+                                                {
+                                                    displayId: `${t1}-LinearAlignmentsDisplay`,
+                                                    type: 'LinearAlignmentsDisplay',
+                                                    pileupDisplay: {
+                                                        displayId: `${t1}-LinearAlignmentsDisplay-LinearPileupDisplay`,
+                                                        type: 'LinearPileupDisplay',
+                                                        filterBy: {
+                                                            ...util_2.defaultFilterFlags,
+                                                            tagFilter: {
+                                                                tag,
+                                                                value: tagValue,
+                                                            },
+                                                        },
+                                                    },
+                                                },
+                                            ],
+                                        });
+                                        view.showTrack(t1);
+                                    }
+                                }
+                            }
+                            else if (type === 'strand') {
+                                const t1 = `${trackConf.trackId}-${tag}:(-)-${+Date.now()}-sessionTrack`;
+                                const t2 = `${trackConf.trackId}-${tag}:(+)-${+Date.now()}-sessionTrack`;
+                                session.addTrackConf({
+                                    ...trackConf,
+                                    trackId: t1,
+                                    name: `${trackConf.name} (-)`,
+                                    displays: [
+                                        {
+                                            displayId: `${t1}-LinearAlignmentsDisplay`,
+                                            type: 'LinearAlignmentsDisplay',
+                                            pileupDisplay: {
+                                                displayId: `${t1}-LinearAlignmentsDisplay-LinearPileupDisplay`,
+                                                type: 'LinearPileupDisplay',
+                                                filterBy: util_2.negFlags,
+                                            },
+                                        },
+                                        {
+                                            displayId: `${t1}-LinearSNPCoverageDisplay`,
+                                            type: 'LinearSNPCoverageDisplay',
+                                            filterBy: util_2.negFlags,
+                                        },
+                                    ],
+                                });
+                                session.addTrackConf({
+                                    ...trackConf,
+                                    trackId: t2,
+                                    name: `${trackConf.name} (+)`,
+                                    displays: [
+                                        {
+                                            displayId: `${t2}-LinearAlignmentsDisplay`,
+                                            type: 'LinearAlignmentsDisplay',
+                                            pileupDisplay: {
+                                                displayId: `${t2}-LinearAlignmentsDisplay-LinearPileupDisplay`,
+                                                type: 'LinearPileupDisplay',
+                                                filterBy: util_2.posFlags,
+                                            },
+                                        },
+                                        {
+                                            displayId: `${t2}-LinearSNPCoverageDisplay`,
+                                            type: 'LinearSNPCoverageDisplay',
+                                            filterBy: util_2.posFlags,
+                                        },
+                                    ],
+                                });
+                                view.showTrack(t1);
+                                view.showTrack(t2);
+                            }
+                            handleClose();
+                        }, children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                            handleClose();
+                        }, children: "Cancel" })] })] }));
 });
 exports.default = GroupByTagDialog;

package/dist/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/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js

@@ -1,15 +1,11 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importDefault(require("react"));
-const mobx_react_1 = require("mobx-react");
+const jsx_runtime_1 = require("react/jsx-runtime");
 const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const LinearPileupDisplayBlurb = (0, mobx_react_1.observer)(function ({ model, }) {
     var _a;
     const { sortedBy } = model;
-    return sortedBy ? (react_1.default.createElement("div", { "data-testid": `blurb-${sortedBy}` },
-        react_1.default.createElement(material_1.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 ? ((0, jsx_runtime_1.jsx)("div", { "data-testid": `blurb-${sortedBy}`, children: (0, jsx_runtime_1.jsx)(material_1.Typography, { color: "secondary", variant: "caption", children: `Sorted by ${(_a = sortedBy.tag) !== null && _a !== void 0 ? _a : sortedBy.type} at ${sortedBy.refName}:${sortedBy.pos}` }) })) : null;
 });
 exports.default = LinearPileupDisplayBlurb;

package/dist/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/dist/LinearPileupDisplay/components/SetFeatureHeightDialog.js

@@ -1,55 +1,26 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const SetFeatureHeightDialog = (0, mobx_react_1.observer)(function (props) {
     const { model, handleClose } = props;
     const { featureHeightSetting, noSpacing: noSpacingSetting } = model;
     const [height, setHeight] = (0, react_1.useState)(`${featureHeightSetting}`);
     const [noSpacing, setNoSpacing] = (0, react_1.useState)(noSpacingSetting);
     const ok = height !== '' && !Number.isNaN(+height);
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set feature height" },
-        react_1.default.createElement(material_1.DialogContent, null,
-            react_1.default.createElement(material_1.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_1.default.createElement(material_1.TextField, { value: height, helperText: "Feature height", onChange: event => {
-                    setHeight(event.target.value);
-                } }),
-            react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: !!noSpacing, onChange: () => {
-                        setNoSpacing(val => !val);
-                    } }), label: "Remove spacing between features in y-direction?" }),
-            react_1.default.createElement(material_1.DialogActions, null,
-                react_1.default.createElement(material_1.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_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                        handleClose();
-                    } }, "Cancel")))));
+    return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set feature height", children: (0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsx)(material_1.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." }), (0, jsx_runtime_1.jsx)(material_1.TextField, { value: height, helperText: "Feature height", onChange: event => {
+                        setHeight(event.target.value);
+                    } }), (0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: !!noSpacing, onChange: () => {
+                            setNoSpacing(val => !val);
+                        } }), label: "Remove spacing between features in y-direction?" }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.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" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                                handleClose();
+                            }, children: "Cancel" })] })] }) }));
 });
 exports.default = SetFeatureHeightDialog;

package/dist/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/dist/LinearPileupDisplay/components/SetMaxHeightDialog.js

@@ -1,32 +1,10 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()({
     root: {
@@ -38,19 +16,13 @@ const SetMaxHeightDialog = (0, mobx_react_1.observer)(function (props) {
     const { classes } = useStyles();
     const { maxHeight = '' } = model;
     const [max, setMax] = (0, react_1.useState)(`${maxHeight}`);
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set max height" },
-        react_1.default.createElement(material_1.DialogContent, { className: classes.root },
-            react_1.default.createElement(material_1.Typography, null, "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\""),
-            react_1.default.createElement(material_1.TextField, { value: max, autoFocus: true, onChange: event => {
-                    setMax(event.target.value);
-                }, placeholder: "Enter max height for layout" }),
-            react_1.default.createElement(material_1.DialogActions, null,
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: () => {
-                        model.setMaxHeight(max !== '' && !Number.isNaN(+max) ? +max : undefined);
-                        handleClose();
-                    } }, "Submit"),
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                        handleClose();
-                    } }, "Cancel")))));
+    return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set max height", children: (0, jsx_runtime_1.jsxs)(material_1.DialogContent, { className: classes.root, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\"" }), (0, jsx_runtime_1.jsx)(material_1.TextField, { value: max, autoFocus: true, onChange: event => {
+                        setMax(event.target.value);
+                    }, placeholder: "Enter max height for layout" }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: () => {
+                                model.setMaxHeight(max !== '' && !Number.isNaN(+max) ? +max : undefined);
+                                handleClose();
+                            }, children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                                handleClose();
+                            }, children: "Cancel" })] })] }) }));
 });
 exports.default = SetMaxHeightDialog;

package/dist/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/dist/LinearPileupDisplay/components/SortByTagDialog.js

@@ -1,55 +1,26 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const SortByTagDialog = (0, mobx_react_1.observer)(function (props) {
     const { model, handleClose } = props;
     const [tag, setTag] = (0, react_1.useState)('');
     const validTag = /^[A-Za-z][A-Za-z0-9]$/.exec(tag);
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Sort by tag" },
-        react_1.default.createElement(material_1.DialogContent, null,
-            react_1.default.createElement(material_1.Typography, null, "Set the tag to sort by"),
-            react_1.default.createElement(material_1.Typography, { color: "textSecondary" }, "Examples: HP for haplotype, RG for read group, etc."),
-            react_1.default.createElement(material_1.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_1.default.createElement(material_1.DialogActions, null,
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: () => {
-                        model.setSortedBy('tag', tag);
-                        handleClose();
-                    } }, "Submit"),
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                        handleClose();
-                    } }, "Cancel")))));
+    return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Sort by tag", children: (0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Set the tag to sort by" }), (0, jsx_runtime_1.jsx)(material_1.Typography, { color: "textSecondary", children: "Examples: HP for haplotype, RG for read group, etc." }), (0, jsx_runtime_1.jsx)(material_1.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',
+                        },
+                    } }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: () => {
+                                model.setSortedBy('tag', tag);
+                                handleClose();
+                            }, children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                                handleClose();
+                            }, children: "Cancel" })] })] }) }));
 });
 exports.default = SortByTagDialog;

package/dist/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;