@jbrowse/plugin-variants 2.2.1 → 2.2.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
@@ -61,12 +61,8 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
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  userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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  userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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  } & {
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- type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">; /**
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- * #property
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- */
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- trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>; /**
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- * #property
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- */
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+ type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
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+ trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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  trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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  trackDisplayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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  trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
@@ -22,25 +22,16 @@ var __importStar = (this && this.__importStar) || function (mod) {
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  __setModuleDefault(result, mod);
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  return result;
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  };
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- var __importDefault = (this && this.__importDefault) || function (mod) {
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- return (mod && mod.__esModule) ? mod : { "default": mod };
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- };
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  Object.defineProperty(exports, "__esModule", { value: true });
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  /* eslint-disable @typescript-eslint/no-explicit-any */
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  const react_1 = __importStar(require("react"));
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  const mobx_react_1 = require("mobx-react");
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  const material_1 = require("@mui/material");
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+ const ui_1 = require("@jbrowse/core/ui");
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  const mui_1 = require("tss-react/mui");
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- const Close_1 = __importDefault(require("@mui/icons-material/Close"));
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  const mobx_state_tree_1 = require("mobx-state-tree");
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  const util_1 = require("@jbrowse/core/util");
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  const useStyles = (0, mui_1.makeStyles)()(theme => ({
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- closeButton: {
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- position: 'absolute',
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- right: theme.spacing(1),
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- top: theme.spacing(1),
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- color: theme.palette.grey[500],
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- },
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  block: {
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  display: 'block',
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  },
@@ -49,12 +40,7 @@ function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
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  const { classes } = useStyles();
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  const [copyTracks, setCopyTracks] = (0, react_1.useState)(true);
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  const [mirrorTracks, setMirrorTracks] = (0, react_1.useState)(true);
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- return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose },
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- react_1.default.createElement(material_1.DialogTitle, null,
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- "Breakpoint split view options",
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- handleClose ? (react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: () => handleClose() },
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- react_1.default.createElement(Close_1.default, null))) : null),
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- react_1.default.createElement(material_1.Divider, null),
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+ return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Breakpoint split view options" },
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  react_1.default.createElement(material_1.DialogContent, null,
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  react_1.default.createElement(material_1.FormControlLabel, { className: classes.block, control: react_1.default.createElement(material_1.Checkbox, { checked: copyTracks, onChange: () => setCopyTracks(val => !val) }), label: "Copy tracks into the new view" }),
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  react_1.default.createElement(material_1.FormControlLabel, { className: classes.block, control: react_1.default.createElement(material_1.Checkbox, { checked: mirrorTracks, onChange: () => setMirrorTracks(val => !val) }), label: "Mirror tracks vertically in vertically stacked view" })),
@@ -1 +1 @@
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+ {"version":3,"file":"BreakendOptionDialog.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/BreakendOptionDialog.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uDAAuD;AACvD,+CAAuC;AACvC,2CAAqC;AACrC,4CAMsB;AACtB,yCAAyC;AACzC,uCAA0C;AAC1C,qDAA6C;AAC7C,6CAAwD;AAExD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,OAAO,EAAE,OAAO;KACjB;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,oBAAoB,CAAC,EAC5B,KAAK,EACL,WAAW,EACX,OAAO,EACP,QAAQ,GAMT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,IAAA,gBAAQ,EAAC,IAAI,CAAC,CAAA;IAClD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,IAAA,gBAAQ,EAAC,IAAI,CAAC,CAAA;IAEtD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,+BAA+B;QACtE,8BAAC,wBAAa;YACZ,8BAAC,2BAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,UAAU,EACnB,QAAQ,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC1C,EAEJ,KAAK,EAAC,+BAA+B,GACrC;YAEF,8BAAC,2BAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,YAAY,EACrB,QAAQ,EAAE,GAAG,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC5C,EAEJ,KAAK,EAAC,qDAAqD,GAC3D,CACY;QAChB,8BAAC,wBAAa;YACZ,8BAAC,iBAAM,IACL,OAAO,EAAE,GAAG,EAAE;oBACZ,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;oBACtB,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;oBACjC,IAAI;wBACF,MAAM,YAAY,GAAG,QAAQ,CAAC,2BAA2B,CACvD,OAAO,EACP,IAAI,CACL,CAAA;wBACD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,WAAW,GAAG,OAAO,CAAA;wBAClC,MAAM,UAAU,GAAQ,IAAA,6BAAW,EAAC,IAAI,CAAC,MAAM,CAAC,CAAA;wBAChD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,UAAU,CAAA;wBACzC,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,YAAY;4BACzC,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,CAAC,OAAO,EAAE;4BAC9B,CAAC,CAAC,UAAU,CAAA;wBAEd,OAAO,CAAC,OAAO,CAAC,qBAAqB,EAAE,YAAY,CAAC,CAAA;qBACrD;oBAAC,OAAO,CAAC,EAAE;wBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;qBACvB;oBACD,WAAW,EAAE,CAAA;gBACf,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,SAAS,eAGF;YACT,8BAAC,iBAAM,IACL,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAC5B,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,aAGZ,CACK,CACT,CACV,CAAA;AACH,CAAC;AACD,kBAAe,IAAA,qBAAQ,EAAC,oBAAoB,CAAC,CAAA"}
@@ -61,12 +61,8 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
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  userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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  userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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  } & {
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- type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">; /**
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- * #property
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- */
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- trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>; /**
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- * #property
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- */
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+ type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
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+ trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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  trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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  trackDisplayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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  trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
@@ -1,18 +1,12 @@
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  /* eslint-disable @typescript-eslint/no-explicit-any */
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  import React, { useState } from 'react';
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  import { observer } from 'mobx-react';
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- import { Button, Checkbox, Dialog, DialogActions, DialogContent, DialogTitle, Divider, FormControlLabel, IconButton, } from '@mui/material';
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+ import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, } from '@mui/material';
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+ import { Dialog } from '@jbrowse/core/ui';
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  import { makeStyles } from 'tss-react/mui';
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- import CloseIcon from '@mui/icons-material/Close';
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  import { getSnapshot } from 'mobx-state-tree';
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  import { getSession } from '@jbrowse/core/util';
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  const useStyles = makeStyles()(theme => ({
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- closeButton: {
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- position: 'absolute',
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- right: theme.spacing(1),
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- top: theme.spacing(1),
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- color: theme.palette.grey[500],
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- },
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  block: {
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  display: 'block',
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  },
@@ -21,12 +15,7 @@ function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
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  const { classes } = useStyles();
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  const [copyTracks, setCopyTracks] = useState(true);
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  const [mirrorTracks, setMirrorTracks] = useState(true);
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- return (React.createElement(Dialog, { open: true, onClose: handleClose },
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- React.createElement(DialogTitle, null,
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- "Breakpoint split view options",
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- handleClose ? (React.createElement(IconButton, { className: classes.closeButton, onClick: () => handleClose() },
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- React.createElement(CloseIcon, null))) : null),
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- React.createElement(Divider, null),
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+ return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Breakpoint split view options" },
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  React.createElement(DialogContent, null,
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  React.createElement(FormControlLabel, { className: classes.block, control: React.createElement(Checkbox, { checked: copyTracks, onChange: () => setCopyTracks(val => !val) }), label: "Copy tracks into the new view" }),
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  React.createElement(FormControlLabel, { className: classes.block, control: React.createElement(Checkbox, { checked: mirrorTracks, onChange: () => setMirrorTracks(val => !val) }), label: "Mirror tracks vertically in vertically stacked view" })),
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"BreakendOptionDialog.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/BreakendOptionDialog.tsx"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,QAAQ,EACR,aAAa,EACb,aAAa,EACb,gBAAgB,GACjB,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC7C,OAAO,EAAE,UAAU,EAAW,MAAM,oBAAoB,CAAA;AAExD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,OAAO,EAAE,OAAO;KACjB;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,oBAAoB,CAAC,EAC5B,KAAK,EACL,WAAW,EACX,OAAO,EACP,QAAQ,GAMT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAClD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAEtD,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,+BAA+B;QACtE,oBAAC,aAAa;YACZ,oBAAC,gBAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,UAAU,EACnB,QAAQ,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC1C,EAEJ,KAAK,EAAC,+BAA+B,GACrC;YAEF,oBAAC,gBAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,YAAY,EACrB,QAAQ,EAAE,GAAG,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC5C,EAEJ,KAAK,EAAC,qDAAqD,GAC3D,CACY;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;oBACZ,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;oBACtB,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;oBACjC,IAAI;wBACF,MAAM,YAAY,GAAG,QAAQ,CAAC,2BAA2B,CACvD,OAAO,EACP,IAAI,CACL,CAAA;wBACD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,WAAW,GAAG,OAAO,CAAA;wBAClC,MAAM,UAAU,GAAQ,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;wBAChD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,UAAU,CAAA;wBACzC,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,YAAY;4BACzC,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,CAAC,OAAO,EAAE;4BAC9B,CAAC,CAAC,UAAU,CAAA;wBAEd,OAAO,CAAC,OAAO,CAAC,qBAAqB,EAAE,YAAY,CAAC,CAAA;qBACrD;oBAAC,OAAO,CAAC,EAAE;wBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;qBACvB;oBACD,WAAW,EAAE,CAAA;gBACf,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,SAAS,eAGF;YACT,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAC5B,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,aAGZ,CACK,CACT,CACV,CAAA;AACH,CAAC;AACD,eAAe,QAAQ,CAAC,oBAAoB,CAAC,CAAA"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-variants",
3
- "version": "2.2.1",
3
+ "version": "2.2.2",
4
4
  "description": "JBrowse 2 variant adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -27,7 +27,7 @@
27
27
  "build": "npm-run-all build:*",
28
28
  "test": "cd ../..; jest plugins/variants",
29
29
  "prepublishOnly": "yarn test",
30
- "prepack": "yarn build; yarn useDist",
30
+ "prepack": "yarn build && yarn useDist",
31
31
  "postpack": "yarn useSrc",
32
32
  "useDist": "node ../../scripts/useDist.js",
33
33
  "useSrc": "node ../../scripts/useSrc.js",
@@ -40,7 +40,7 @@
40
40
  "@flatten-js/interval-tree": "^1.0.15",
41
41
  "@gmod/bgzf-filehandle": "^1.4.3",
42
42
  "@gmod/tabix": "^1.5.2",
43
- "@gmod/vcf": "^5.0.5",
43
+ "@gmod/vcf": "^5.0.9",
44
44
  "@mui/icons-material": "^5.0.2",
45
45
  "@mui/x-data-grid": "^5.0.1",
46
46
  "generic-filehandle": "^3.0.0"
@@ -65,5 +65,5 @@
65
65
  "distModule": "esm/index.js",
66
66
  "srcModule": "src/index.ts",
67
67
  "module": "esm/index.js",
68
- "gitHead": "896d175c5d9345049faea8e1155f243c912aac42"
68
+ "gitHead": "abbc00e8feedbc58de84a7a3e735ec0224909b29"
69
69
  }
@@ -48,7 +48,7 @@ test('has a viewType attr', () => {
48
48
  )
49
49
  const config = configSchema.create({
50
50
  type: 'LinearVariantDisplay',
51
- displayId: 'diplayId0',
51
+ displayId: 'displayId0',
52
52
  name: 'Zonker Display',
53
53
  })
54
54
  expect(config.type).toEqual('LinearVariantDisplay')
@@ -4,26 +4,16 @@ import { observer } from 'mobx-react'
4
4
  import {
5
5
  Button,
6
6
  Checkbox,
7
- Dialog,
8
7
  DialogActions,
9
8
  DialogContent,
10
- DialogTitle,
11
- Divider,
12
9
  FormControlLabel,
13
- IconButton,
14
10
  } from '@mui/material'
11
+ import { Dialog } from '@jbrowse/core/ui'
15
12
  import { makeStyles } from 'tss-react/mui'
16
- import CloseIcon from '@mui/icons-material/Close'
17
13
  import { getSnapshot } from 'mobx-state-tree'
18
14
  import { getSession, Feature } from '@jbrowse/core/util'
19
15
 
20
16
  const useStyles = makeStyles()(theme => ({
21
- closeButton: {
22
- position: 'absolute',
23
- right: theme.spacing(1),
24
- top: theme.spacing(1),
25
- color: theme.palette.grey[500],
26
- },
27
17
  block: {
28
18
  display: 'block',
29
19
  },
@@ -45,20 +35,7 @@ function BreakendOptionDialog({
45
35
  const [mirrorTracks, setMirrorTracks] = useState(true)
46
36
 
47
37
  return (
48
- <Dialog open onClose={handleClose}>
49
- <DialogTitle>
50
- Breakpoint split view options
51
- {handleClose ? (
52
- <IconButton
53
- className={classes.closeButton}
54
- onClick={() => handleClose()}
55
- >
56
- <CloseIcon />
57
- </IconButton>
58
- ) : null}
59
- </DialogTitle>
60
- <Divider />
61
-
38
+ <Dialog open onClose={handleClose} title="Breakpoint split view options">
62
39
  <DialogContent>
63
40
  <FormControlLabel
64
41
  className={classes.block}