@jbrowse/plugin-dotplot-view 3.2.0 → 3.3.0

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Files changed (9) hide show
  1. package/dist/DotplotRenderer/DotplotRenderer.d.ts +12 -0
  2. package/dist/DotplotView/components/ImportForm/ImportSyntenyOpenCustomTrack.js +2 -2
  3. package/dist/DotplotView/components/ImportForm/index.js +1 -1
  4. package/dist/DotplotView/components/WarningDialog.js +1 -1
  5. package/esm/DotplotRenderer/DotplotRenderer.d.ts +12 -0
  6. package/esm/DotplotView/components/ImportForm/ImportSyntenyOpenCustomTrack.js +3 -3
  7. package/esm/DotplotView/components/ImportForm/index.js +2 -2
  8. package/esm/DotplotView/components/WarningDialog.js +1 -1
  9. package/package.json +7 -7
package/dist/DotplotRenderer/DotplotRenderer.d.ts CHANGED
@@ -35,6 +35,10 @@ export default class DotplotRenderer extends ComparativeRenderer {
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  offsetY: number;
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  bpPerPxX: number;
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  bpPerPxY: number;
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+ warnings: {
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+ message: string;
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+ effect: string;
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+ }[];
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  canvasRecordedData: any;
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  reactElement?: React.ReactElement;
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  html?: string;
@@ -45,6 +49,10 @@ export default class DotplotRenderer extends ComparativeRenderer {
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  offsetY: number;
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  bpPerPxX: number;
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  bpPerPxY: number;
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+ warnings: {
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+ message: string;
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+ effect: string;
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+ }[];
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  reactElement: import("react/jsx-runtime").JSX.Element;
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  html?: string;
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  } | {
@@ -54,6 +62,10 @@ export default class DotplotRenderer extends ComparativeRenderer {
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  offsetY: number;
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  bpPerPxX: number;
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  bpPerPxY: number;
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+ warnings: {
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+ message: string;
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+ effect: string;
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+ }[];
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  imageData: any;
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  reactElement?: React.ReactElement;
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  html?: string;
package/dist/DotplotView/components/ImportForm/ImportSyntenyOpenCustomTrack.js CHANGED
@@ -72,7 +72,7 @@ const ImportSyntenyOpenCustomTrack = (0, mobx_react_1.observer)(function ({ mode
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  };
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  return ((0, jsx_runtime_1.jsxs)(material_1.Paper, { style: { padding: 12 }, children: [error ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error }) : null, (0, jsx_runtime_1.jsx)(material_1.Typography, { style: { textAlign: 'center' }, children: "Add a .paf (minimap2), .delta (Mummer), .chain (UCSC liftover), .anchors or .anchors.simple (MCScan), or .pif.gz (jbrowse CLI make-pif) file to view. These file types can also be gzipped." }), (0, jsx_runtime_1.jsx)(material_1.RadioGroup, { value: radioOption, onChange: event => {
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  setValue(event.target.value);
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- }, children: (0, jsx_runtime_1.jsx)(material_1.Grid2, { container: true, justifyContent: "center", children: [
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+ }, children: (0, jsx_runtime_1.jsx)(material_1.Grid, { container: true, justifyContent: "center", children: [
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  '.paf',
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  '.delta',
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  '.out',
@@ -80,7 +80,7 @@ const ImportSyntenyOpenCustomTrack = (0, mobx_react_1.observer)(function ({ mode
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  '.anchors',
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  '.anchors.simple',
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  '.pif.gz',
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- ].map(extension => ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { value: extension, control: (0, jsx_runtime_1.jsx)(material_1.Radio, {}), label: extension }, extension))) }) }), (0, jsx_runtime_1.jsx)(material_1.Grid2, { container: true, justifyContent: "center", children: radioOption === '.paf' ||
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+ ].map(extension => ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { value: extension, control: (0, jsx_runtime_1.jsx)(material_1.Radio, {}), label: extension }, extension))) }) }), (0, jsx_runtime_1.jsx)(material_1.Grid, { container: true, justifyContent: "center", children: radioOption === '.paf' ||
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  radioOption === '.out' ||
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  radioOption === '.delta' ||
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  radioOption === '.chain' ||
package/dist/DotplotView/components/ImportForm/index.js CHANGED
@@ -51,7 +51,7 @@ const DotplotImportForm = (0, mobx_react_1.observer)(function ({ model, }) {
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  const [assembly1, setAssembly1] = (0, react_1.useState)(assemblyNames[0] || '');
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  const [error, setError] = (0, react_1.useState)();
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  const displayError = error || model.error;
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- return ((0, jsx_runtime_1.jsxs)(material_1.Container, { className: classes.importFormContainer, children: [displayError ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: displayError }) : null, (0, jsx_runtime_1.jsxs)(material_1.Paper, { style: { padding: 12 }, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { style: { textAlign: 'center' }, children: "Select assemblies for dotplot view" }), (0, jsx_runtime_1.jsxs)(material_1.Grid2, { container: true, spacing: 1, justifyContent: "center", alignItems: "center", children: [(0, jsx_runtime_1.jsx)(ui_1.AssemblySelector, { helperText: "x-axis assembly", selected: assembly2, session: session, onChange: val => {
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+ return ((0, jsx_runtime_1.jsxs)(material_1.Container, { className: classes.importFormContainer, children: [displayError ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: displayError }) : null, (0, jsx_runtime_1.jsxs)(material_1.Paper, { style: { padding: 12 }, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { style: { textAlign: 'center' }, children: "Select assemblies for dotplot view" }), (0, jsx_runtime_1.jsxs)(material_1.Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center", children: [(0, jsx_runtime_1.jsx)(ui_1.AssemblySelector, { helperText: "x-axis assembly", selected: assembly2, session: session, onChange: val => {
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  setAssembly2(val);
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  } }), (0, jsx_runtime_1.jsx)(ui_1.AssemblySelector, { helperText: "y-axis assembly", selected: assembly1, session: session, onChange: val => {
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  setAssembly1(val);
package/dist/DotplotView/components/WarningDialog.js CHANGED
@@ -34,6 +34,6 @@ const WarningDialog = (0, mobx_react_1.observer)(function WarningDialog({ trackW
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  { field: 'message', width: (0, util_1.measureGridWidth)(rows.map(r => r.message)) },
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  { field: 'effect', width: (0, util_1.measureGridWidth)(rows.map(r => r.effect)) },
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  ];
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- return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, onClose: handleClose, maxWidth: "xl", title: "Dotplot rendered with warnings", children: (0, jsx_runtime_1.jsxs)(material_1.DialogContent, { className: classes.content, children: [(0, jsx_runtime_1.jsx)(material_1.DialogContentText, { children: "Found warnings while rendering the dotplot. This is often due to out-of-bound features that may indicate the wrong assemblies are being used. Check that the query and target are configured correctly, and that the right assemblies are being compared." }), (0, jsx_runtime_1.jsx)("div", { style: { height: 600, width: '100%', overflow: 'auto' }, children: (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { rows: rows, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, disableColumnMenu: true }) })] }) }));
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+ return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, onClose: handleClose, maxWidth: "xl", title: "Dotplot rendered with warnings", children: (0, jsx_runtime_1.jsxs)(material_1.DialogContent, { className: classes.content, children: [(0, jsx_runtime_1.jsx)(material_1.DialogContentText, { children: "Found warnings while rendering the dotplot. This is often due to out-of-bound features that may indicate the wrong assemblies are being used. Check that the query and target are configured correctly, and that the right assemblies are being compared." }), (0, jsx_runtime_1.jsx)("div", { style: { height: 600, width: '100%', overflow: 'auto' }, children: (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { rows: rows, columns: columns, rowHeight: 25, disableColumnMenu: true }) })] }) }));
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  });
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  exports.default = WarningDialog;
package/esm/DotplotRenderer/DotplotRenderer.d.ts CHANGED
@@ -35,6 +35,10 @@ export default class DotplotRenderer extends ComparativeRenderer {
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  offsetY: number;
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  bpPerPxX: number;
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  bpPerPxY: number;
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+ warnings: {
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+ message: string;
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+ effect: string;
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+ }[];
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  canvasRecordedData: any;
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  reactElement?: React.ReactElement;
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  html?: string;
@@ -45,6 +49,10 @@ export default class DotplotRenderer extends ComparativeRenderer {
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  offsetY: number;
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  bpPerPxX: number;
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  bpPerPxY: number;
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+ warnings: {
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+ message: string;
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+ effect: string;
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+ }[];
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  reactElement: import("react/jsx-runtime").JSX.Element;
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  html?: string;
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  } | {
@@ -54,6 +62,10 @@ export default class DotplotRenderer extends ComparativeRenderer {
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  offsetY: number;
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  bpPerPxX: number;
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  bpPerPxY: number;
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+ warnings: {
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+ message: string;
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+ effect: string;
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+ }[];
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  imageData: any;
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  reactElement?: React.ReactElement;
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  html?: string;
package/esm/DotplotView/components/ImportForm/ImportSyntenyOpenCustomTrack.js CHANGED
@@ -2,7 +2,7 @@ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
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  import { useEffect, useState } from 'react';
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  import { ErrorMessage, FileSelector } from '@jbrowse/core/ui';
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  import HelpIcon from '@mui/icons-material/Help';
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- import { Button, FormControlLabel, Grid2, Paper, Radio, RadioGroup, Tooltip, Typography, } from '@mui/material';
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+ import { Button, FormControlLabel, Grid, Paper, Radio, RadioGroup, Tooltip, Typography, } from '@mui/material';
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  import { observer } from 'mobx-react';
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  import { getAdapter } from './getAdapter';
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  import { basename, extName, getName, stripGz } from './util';
@@ -67,7 +67,7 @@ const ImportSyntenyOpenCustomTrack = observer(function ({ model, assembly1, asse
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  };
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  return (_jsxs(Paper, { style: { padding: 12 }, children: [error ? _jsx(ErrorMessage, { error: error }) : null, _jsx(Typography, { style: { textAlign: 'center' }, children: "Add a .paf (minimap2), .delta (Mummer), .chain (UCSC liftover), .anchors or .anchors.simple (MCScan), or .pif.gz (jbrowse CLI make-pif) file to view. These file types can also be gzipped." }), _jsx(RadioGroup, { value: radioOption, onChange: event => {
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  setValue(event.target.value);
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- }, children: _jsx(Grid2, { container: true, justifyContent: "center", children: [
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+ }, children: _jsx(Grid, { container: true, justifyContent: "center", children: [
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  '.paf',
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  '.delta',
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  '.out',
@@ -75,7 +75,7 @@ const ImportSyntenyOpenCustomTrack = observer(function ({ model, assembly1, asse
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  '.anchors',
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  '.anchors.simple',
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  '.pif.gz',
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- ].map(extension => (_jsx(FormControlLabel, { value: extension, control: _jsx(Radio, {}), label: extension }, extension))) }) }), _jsx(Grid2, { container: true, justifyContent: "center", children: radioOption === '.paf' ||
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+ ].map(extension => (_jsx(FormControlLabel, { value: extension, control: _jsx(Radio, {}), label: extension }, extension))) }) }), _jsx(Grid, { container: true, justifyContent: "center", children: radioOption === '.paf' ||
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  radioOption === '.out' ||
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  radioOption === '.delta' ||
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  radioOption === '.chain' ||
package/esm/DotplotView/components/ImportForm/index.js CHANGED
@@ -2,7 +2,7 @@ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
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  import { useState } from 'react';
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  import { AssemblySelector, ErrorMessage } from '@jbrowse/core/ui';
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  import { getSession, isSessionWithAddTracks } from '@jbrowse/core/util';
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- import { Button, Container, FormControl, Grid2, Paper, Typography, } from '@mui/material';
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+ import { Button, Container, FormControl, Grid, Paper, Typography, } from '@mui/material';
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  import { toJS, transaction } from 'mobx';
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  import { observer } from 'mobx-react';
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  import { makeStyles } from 'tss-react/mui';
@@ -46,7 +46,7 @@ const DotplotImportForm = observer(function ({ model, }) {
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  const [assembly1, setAssembly1] = useState(assemblyNames[0] || '');
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  const [error, setError] = useState();
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  const displayError = error || model.error;
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- return (_jsxs(Container, { className: classes.importFormContainer, children: [displayError ? _jsx(ErrorMessage, { error: displayError }) : null, _jsxs(Paper, { style: { padding: 12 }, children: [_jsx(Typography, { style: { textAlign: 'center' }, children: "Select assemblies for dotplot view" }), _jsxs(Grid2, { container: true, spacing: 1, justifyContent: "center", alignItems: "center", children: [_jsx(AssemblySelector, { helperText: "x-axis assembly", selected: assembly2, session: session, onChange: val => {
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+ return (_jsxs(Container, { className: classes.importFormContainer, children: [displayError ? _jsx(ErrorMessage, { error: displayError }) : null, _jsxs(Paper, { style: { padding: 12 }, children: [_jsx(Typography, { style: { textAlign: 'center' }, children: "Select assemblies for dotplot view" }), _jsxs(Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center", children: [_jsx(AssemblySelector, { helperText: "x-axis assembly", selected: assembly2, session: session, onChange: val => {
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  setAssembly2(val);
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  } }), _jsx(AssemblySelector, { helperText: "y-axis assembly", selected: assembly1, session: session, onChange: val => {
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  setAssembly1(val);
package/esm/DotplotView/components/WarningDialog.js CHANGED
@@ -32,6 +32,6 @@ const WarningDialog = observer(function WarningDialog({ trackWarnings, handleClo
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  { field: 'message', width: measureGridWidth(rows.map(r => r.message)) },
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  { field: 'effect', width: measureGridWidth(rows.map(r => r.effect)) },
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  ];
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- return (_jsx(Dialog, { open: true, onClose: handleClose, maxWidth: "xl", title: "Dotplot rendered with warnings", children: _jsxs(DialogContent, { className: classes.content, children: [_jsx(DialogContentText, { children: "Found warnings while rendering the dotplot. This is often due to out-of-bound features that may indicate the wrong assemblies are being used. Check that the query and target are configured correctly, and that the right assemblies are being compared." }), _jsx("div", { style: { height: 600, width: '100%', overflow: 'auto' }, children: _jsx(DataGrid, { rows: rows, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, disableColumnMenu: true }) })] }) }));
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+ return (_jsx(Dialog, { open: true, onClose: handleClose, maxWidth: "xl", title: "Dotplot rendered with warnings", children: _jsxs(DialogContent, { className: classes.content, children: [_jsx(DialogContentText, { children: "Found warnings while rendering the dotplot. This is often due to out-of-bound features that may indicate the wrong assemblies are being used. Check that the query and target are configured correctly, and that the right assemblies are being compared." }), _jsx("div", { style: { height: 600, width: '100%', overflow: 'auto' }, children: _jsx(DataGrid, { rows: rows, columns: columns, rowHeight: 25, disableColumnMenu: true }) })] }) }));
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  });
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  export default WarningDialog;
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-dotplot-view",
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- "version": "3.2.0",
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+ "version": "3.3.0",
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  "description": "JBrowse 2 dotplot view",
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  "keywords": [
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  "jbrowse",
@@ -36,11 +36,11 @@
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  "clean": "rimraf dist esm *.tsbuildinfo"
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  },
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  "dependencies": {
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- "@jbrowse/core": "^3.2.0",
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- "@jbrowse/plugin-alignments": "^3.2.0",
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- "@mui/icons-material": "^6.0.0",
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- "@mui/material": "^6.0.0",
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- "@mui/x-data-grid": "^7.0.0",
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+ "@jbrowse/core": "^3.3.0",
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+ "@jbrowse/plugin-alignments": "^3.3.0",
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+ "@mui/icons-material": "^7.0.0",
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+ "@mui/material": "^7.0.0",
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+ "@mui/x-data-grid": "^8.0.0",
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  "@types/file-saver": "^2.0.1",
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  "file-saver": "^2.0.0",
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  "mobx": "^6.0.0",
@@ -59,5 +59,5 @@
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  "publishConfig": {
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  "access": "public"
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  },
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- "gitHead": "c750e3f56706a490c19ba75abd807fec5e38aebf"
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+ "gitHead": "0bb64d8cc7ecdd167515308b31eec3d9acbc59e4"
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  }