@jbrowse/plugin-dotplot-view 3.1.0 → 3.3.0

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.
Files changed (13) 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 +3 -3
  5. package/dist/DotplotView/model.js +7 -5
  6. package/dist/LaunchDotplotView.js +2 -2
  7. package/esm/DotplotRenderer/DotplotRenderer.d.ts +12 -0
  8. package/esm/DotplotView/components/ImportForm/ImportSyntenyOpenCustomTrack.js +3 -3
  9. package/esm/DotplotView/components/ImportForm/index.js +2 -2
  10. package/esm/DotplotView/components/WarningDialog.js +3 -3
  11. package/esm/DotplotView/model.js +7 -5
  12. package/esm/LaunchDotplotView.js +2 -2
  13. 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
@@ -15,8 +15,8 @@ const useStyles = (0, mui_1.makeStyles)()({
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  });
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  function getTrackWarnings({ trackWarnings, }) {
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  const rows = [];
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- for (let i = 0; i < trackWarnings.length; i++) {
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- const track = trackWarnings[i];
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+ for (const [i, trackWarning] of trackWarnings.entries()) {
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+ const track = trackWarning;
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  const name = (0, configuration_1.getConf)(track, 'name');
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  const d = track.displays[0];
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  for (let j = 0; j < d.warnings.length; j++) {
@@ -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/dist/DotplotView/model.js CHANGED
@@ -246,11 +246,13 @@ function stateModelFactory(pm) {
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  hideTrack(trackId) {
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  const schema = pm.pluggableConfigSchemaType('track');
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  const conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
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- const t = self.tracks.filter(t => t.configuration === conf);
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+ const tracks = self.tracks.filter(t => t.configuration === conf);
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  (0, mobx_1.transaction)(() => {
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- t.forEach(t => self.tracks.remove(t));
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+ for (const track of tracks) {
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+ self.tracks.remove(track);
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+ }
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  });
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- return t.length;
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+ return tracks.length;
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  },
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  toggleTrack(trackId) {
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  const hiddenCount = this.hideTrack(trackId);
@@ -387,11 +389,11 @@ function stateModelFactory(pm) {
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  }
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  const views = [self.hview, self.vview];
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  (0, mobx_1.transaction)(() => {
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- self.assemblyNames.forEach((name, index) => {
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+ for (const [index, name] of self.assemblyNames.entries()) {
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  const assembly = session.assemblyManager.get(name);
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  const view = views[index];
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  view.setDisplayedRegions((assembly === null || assembly === void 0 ? void 0 : assembly.regions) || []);
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- });
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+ }
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  self.showAllRegions();
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  });
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  }, { delay: 1000 }));
package/dist/LaunchDotplotView.js CHANGED
@@ -15,9 +15,9 @@ function LaunchDotplotView(pluginManager) {
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  model.setAssemblyNames(assemblyNames[0], assemblyNames[1]);
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  });
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  const idsNotFound = [];
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- tracks.forEach(track => {
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+ for (const track of tracks) {
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  tryTrack(model, track, idsNotFound);
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- });
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+ }
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  if (idsNotFound.length) {
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  throw new Error(`Could not resolve identifiers: ${idsNotFound.join(',')}`);
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  }
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();
48
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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 => {
49
+ 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 => {
50
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  setAssembly2(val);
51
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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
@@ -13,8 +13,8 @@ const useStyles = makeStyles()({
13
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  });
14
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  function getTrackWarnings({ trackWarnings, }) {
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  const rows = [];
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- for (let i = 0; i < trackWarnings.length; i++) {
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- const track = trackWarnings[i];
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+ for (const [i, trackWarning] of trackWarnings.entries()) {
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+ const track = trackWarning;
18
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  const name = getConf(track, 'name');
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  const d = track.displays[0];
20
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  for (let j = 0; j < d.warnings.length; j++) {
@@ -32,6 +32,6 @@ const WarningDialog = observer(function WarningDialog({ trackWarnings, handleClo
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  { field: 'message', width: measureGridWidth(rows.map(r => r.message)) },
33
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  { field: 'effect', width: measureGridWidth(rows.map(r => r.effect)) },
34
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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 }) })] }) }));
35
+ 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 }) })] }) }));
36
36
  });
37
37
  export default WarningDialog;
package/esm/DotplotView/model.js CHANGED
@@ -206,11 +206,13 @@ export default function stateModelFactory(pm) {
206
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  hideTrack(trackId) {
207
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  const schema = pm.pluggableConfigSchemaType('track');
208
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  const conf = resolveIdentifier(schema, getRoot(self), trackId);
209
- const t = self.tracks.filter(t => t.configuration === conf);
209
+ const tracks = self.tracks.filter(t => t.configuration === conf);
210
210
  transaction(() => {
211
- t.forEach(t => self.tracks.remove(t));
211
+ for (const track of tracks) {
212
+ self.tracks.remove(track);
213
+ }
212
214
  });
213
- return t.length;
215
+ return tracks.length;
214
216
  },
215
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  toggleTrack(trackId) {
216
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  const hiddenCount = this.hideTrack(trackId);
@@ -347,11 +349,11 @@ export default function stateModelFactory(pm) {
347
349
  }
348
350
  const views = [self.hview, self.vview];
349
351
  transaction(() => {
350
- self.assemblyNames.forEach((name, index) => {
352
+ for (const [index, name] of self.assemblyNames.entries()) {
351
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  const assembly = session.assemblyManager.get(name);
352
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  const view = views[index];
353
355
  view.setDisplayedRegions((assembly === null || assembly === void 0 ? void 0 : assembly.regions) || []);
354
- });
356
+ }
355
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  self.showAllRegions();
356
358
  });
357
359
  }, { delay: 1000 }));
package/esm/LaunchDotplotView.js CHANGED
@@ -12,9 +12,9 @@ export default function LaunchDotplotView(pluginManager) {
12
12
  model.setAssemblyNames(assemblyNames[0], assemblyNames[1]);
13
13
  });
14
14
  const idsNotFound = [];
15
- tracks.forEach(track => {
15
+ for (const track of tracks) {
16
16
  tryTrack(model, track, idsNotFound);
17
- });
17
+ }
18
18
  if (idsNotFound.length) {
19
19
  throw new Error(`Could not resolve identifiers: ${idsNotFound.join(',')}`);
20
20
  }
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-dotplot-view",
3
- "version": "3.1.0",
3
+ "version": "3.3.0",
4
4
  "description": "JBrowse 2 dotplot view",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -36,11 +36,11 @@
36
36
  "clean": "rimraf dist esm *.tsbuildinfo"
37
37
  },
38
38
  "dependencies": {
39
- "@jbrowse/core": "^3.1.0",
40
- "@jbrowse/plugin-alignments": "^3.1.0",
41
- "@mui/icons-material": "^6.0.0",
42
- "@mui/material": "^6.0.0",
43
- "@mui/x-data-grid": "^7.0.0",
39
+ "@jbrowse/core": "^3.3.0",
40
+ "@jbrowse/plugin-alignments": "^3.3.0",
41
+ "@mui/icons-material": "^7.0.0",
42
+ "@mui/material": "^7.0.0",
43
+ "@mui/x-data-grid": "^8.0.0",
44
44
  "@types/file-saver": "^2.0.1",
45
45
  "file-saver": "^2.0.0",
46
46
  "mobx": "^6.0.0",
@@ -59,5 +59,5 @@
59
59
  "publishConfig": {
60
60
  "access": "public"
61
61
  },
62
- "gitHead": "91492049ddea0aed90eb24d3c066c2d9f5a6b189"
62
+ "gitHead": "0bb64d8cc7ecdd167515308b31eec3d9acbc59e4"
63
63
  }