@jbrowse/plugin-linear-comparative-view 2.15.1 → 2.15.3

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Files changed (5) hide show
  1. package/dist/LinearSyntenyView/components/ImportForm/ImportCustomTrack.d.ts +2 -2
  2. package/dist/LinearSyntenyView/components/ImportForm/ImportCustomTrack.js +27 -6
  3. package/esm/LinearSyntenyView/components/ImportForm/ImportCustomTrack.d.ts +2 -2
  4. package/esm/LinearSyntenyView/components/ImportForm/ImportCustomTrack.js +28 -7
  5. package/package.json +2 -2
package/dist/LinearSyntenyView/components/ImportForm/ImportCustomTrack.d.ts CHANGED
@@ -2,10 +2,10 @@ import React from 'react';
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  import { SnapshotIn } from 'mobx-state-tree';
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  import { AnyConfigurationModel } from '@jbrowse/core/configuration';
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  type Conf = SnapshotIn<AnyConfigurationModel>;
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- declare const OpenTrack: ({ assembly1, assembly2, setSessionTrackData, }: {
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+ declare const ImportCustomTrack: ({ assembly1, assembly2, setSessionTrackData, }: {
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  sessionTrackData: Conf;
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  assembly1: string;
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  assembly2: string;
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  setSessionTrackData: (arg: Conf) => void;
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  }) => React.JSX.Element;
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- export default OpenTrack;
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+ export default ImportCustomTrack;
package/dist/LinearSyntenyView/components/ImportForm/ImportCustomTrack.js CHANGED
@@ -28,7 +28,7 @@ const material_1 = require("@mui/material");
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  const ui_1 = require("@jbrowse/core/ui");
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  const mobx_react_1 = require("mobx-react");
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  const util_1 = require("./util");
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- function getAdapter({ radioOption, assembly1, assembly2, fileLocation, bed1Location, bed2Location, }) {
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+ function getAdapter({ radioOption, assembly1, assembly2, fileLocation, indexFileLocation, bed1Location, bed2Location, }) {
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  if (radioOption === '.paf') {
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  return {
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  type: 'PAFAdapter',
@@ -79,14 +79,23 @@ function getAdapter({ radioOption, assembly1, assembly2, fileLocation, bed1Locat
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  assemblyNames: [assembly1, assembly2],
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  };
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  }
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+ else if (radioOption === '.pif.gz') {
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+ return {
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+ type: 'PairwiseIndexedPAFAdapter',
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+ pifGzLocation: fileLocation,
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+ index: { location: indexFileLocation },
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+ assemblyNames: [assembly1, assembly2],
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+ };
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+ }
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  else {
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  throw new Error(`Unknown to detect type ${radioOption} from filename (select radio button to clarify)`);
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  }
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  }
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- const OpenTrack = (0, mobx_react_1.observer)(({ assembly1, assembly2, setSessionTrackData, }) => {
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+ const ImportCustomTrack = (0, mobx_react_1.observer)(function ({ assembly1, assembly2, setSessionTrackData, }) {
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  const [bed2Location, setBed2Location] = (0, react_1.useState)();
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  const [bed1Location, setBed1Location] = (0, react_1.useState)();
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  const [fileLocation, setFileLocation] = (0, react_1.useState)();
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+ const [indexFileLocation, setIndexFileLocation] = (0, react_1.useState)();
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  const [value, setValue] = (0, react_1.useState)('');
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  const [error, setError] = (0, react_1.useState)();
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  const fileName = (0, util_1.getName)(fileLocation);
@@ -107,6 +116,7 @@ const OpenTrack = (0, mobx_react_1.observer)(({ assembly1, assembly2, setSession
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  assembly1,
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  assembly2,
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  fileLocation,
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+ indexFileLocation,
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  bed1Location,
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  bed2Location,
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  }),
@@ -124,12 +134,13 @@ const OpenTrack = (0, mobx_react_1.observer)(({ assembly1, assembly2, setSession
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  bed1Location,
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  bed2Location,
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  fileLocation,
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+ indexFileLocation,
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  radioOption,
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  setSessionTrackData,
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  ]);
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  return (react_1.default.createElement(material_1.Paper, { style: { padding: 12 } },
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  error ? react_1.default.createElement(ui_1.ErrorMessage, { error: error }) : null,
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- react_1.default.createElement(material_1.Typography, { style: { textAlign: 'center' } }, "Add a .paf, .out (MashMap), .delta (Mummer), .chain, .anchors or .anchors.simple (MCScan) file to view in the dotplot. These file types can also be gzipped. The first assembly should be the query sequence (e.g. left column of the PAF) and the second assembly should be the target sequence (e.g. right column of the PAF)"),
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+ react_1.default.createElement(material_1.Typography, { style: { textAlign: 'center' } }, "Add a .paf, .out (MashMap), .delta (Mummer), .chain, .anchors or .anchors.simple (MCScan) file to view. These file types can also be gzipped. The first assembly should be the query sequence (e.g. left column of the PAF) and the second assembly should be the target sequence (e.g. right column of the PAF)"),
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  react_1.default.createElement(material_1.RadioGroup, { value: radioOption, onChange: event => {
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  setValue(event.target.value);
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  } },
@@ -145,7 +156,9 @@ const OpenTrack = (0, mobx_react_1.observer)(({ assembly1, assembly2, setSession
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  react_1.default.createElement(material_1.Grid, { item: true },
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  react_1.default.createElement(material_1.FormControlLabel, { value: ".anchors", control: react_1.default.createElement(material_1.Radio, null), label: ".anchors" })),
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  react_1.default.createElement(material_1.Grid, { item: true },
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- react_1.default.createElement(material_1.FormControlLabel, { value: ".anchors.simple", control: react_1.default.createElement(material_1.Radio, null), label: ".anchors.simple" })))),
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+ react_1.default.createElement(material_1.FormControlLabel, { value: ".anchors.simple", control: react_1.default.createElement(material_1.Radio, null), label: ".anchors.simple" })),
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+ react_1.default.createElement(material_1.Grid, { item: true },
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+ react_1.default.createElement(material_1.FormControlLabel, { value: ".pif.gz", control: react_1.default.createElement(material_1.Radio, null), label: ".pif.gz" })))),
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  react_1.default.createElement(material_1.Grid, { container: true, justifyContent: "center" },
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  react_1.default.createElement(material_1.Grid, { item: true }, value === '.anchors' || value === '.anchors.simple' ? (react_1.default.createElement("div", null,
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  react_1.default.createElement("div", { style: { margin: 20 } },
@@ -166,8 +179,16 @@ const OpenTrack = (0, mobx_react_1.observer)(({ assembly1, assembly2, setSession
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  react_1.default.createElement("div", null,
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  react_1.default.createElement(ui_1.FileSelector, { name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: loc => {
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  setBed2Location(loc);
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- } }))))) : (react_1.default.createElement(ui_1.FileSelector, { name: value ? `${value} location` : '', description: "", location: fileLocation, setLocation: loc => {
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+ } }))))) : value === '.pif.gz' ? (react_1.default.createElement("div", { style: { display: 'flex' } },
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+ react_1.default.createElement("div", null,
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+ react_1.default.createElement(ui_1.FileSelector, { name: `${value} location`, description: "", location: fileLocation, setLocation: loc => {
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+ setFileLocation(loc);
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+ } })),
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+ react_1.default.createElement("div", null,
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+ react_1.default.createElement(ui_1.FileSelector, { name: `${value} index location`, description: "", location: indexFileLocation, setLocation: loc => {
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+ setIndexFileLocation(loc);
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+ } })))) : (react_1.default.createElement(ui_1.FileSelector, { name: value ? `${value} location` : '', description: "", location: fileLocation, setLocation: loc => {
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  setFileLocation(loc);
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  } }))))));
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  });
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- exports.default = OpenTrack;
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+ exports.default = ImportCustomTrack;
package/esm/LinearSyntenyView/components/ImportForm/ImportCustomTrack.d.ts CHANGED
@@ -2,10 +2,10 @@ import React from 'react';
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  import { SnapshotIn } from 'mobx-state-tree';
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  import { AnyConfigurationModel } from '@jbrowse/core/configuration';
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  type Conf = SnapshotIn<AnyConfigurationModel>;
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- declare const OpenTrack: ({ assembly1, assembly2, setSessionTrackData, }: {
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+ declare const ImportCustomTrack: ({ assembly1, assembly2, setSessionTrackData, }: {
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  sessionTrackData: Conf;
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  assembly1: string;
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  assembly2: string;
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  setSessionTrackData: (arg: Conf) => void;
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  }) => React.JSX.Element;
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- export default OpenTrack;
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+ export default ImportCustomTrack;
package/esm/LinearSyntenyView/components/ImportForm/ImportCustomTrack.js CHANGED
@@ -2,8 +2,8 @@ import React, { useState, useEffect } from 'react';
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  import { FormControlLabel, Grid, Paper, Radio, RadioGroup, Typography, } from '@mui/material';
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  import { ErrorMessage, FileSelector } from '@jbrowse/core/ui';
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  import { observer } from 'mobx-react';
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- import { extName, getName, stripGz, basename } from './util';
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- function getAdapter({ radioOption, assembly1, assembly2, fileLocation, bed1Location, bed2Location, }) {
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+ import { basename, extName, getName, stripGz } from './util';
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+ function getAdapter({ radioOption, assembly1, assembly2, fileLocation, indexFileLocation, bed1Location, bed2Location, }) {
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  if (radioOption === '.paf') {
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  return {
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  type: 'PAFAdapter',
@@ -54,14 +54,23 @@ function getAdapter({ radioOption, assembly1, assembly2, fileLocation, bed1Locat
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  assemblyNames: [assembly1, assembly2],
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  };
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  }
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+ else if (radioOption === '.pif.gz') {
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+ return {
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+ type: 'PairwiseIndexedPAFAdapter',
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+ pifGzLocation: fileLocation,
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+ index: { location: indexFileLocation },
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+ assemblyNames: [assembly1, assembly2],
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+ };
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+ }
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  else {
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  throw new Error(`Unknown to detect type ${radioOption} from filename (select radio button to clarify)`);
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  }
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  }
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- const OpenTrack = observer(({ assembly1, assembly2, setSessionTrackData, }) => {
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+ const ImportCustomTrack = observer(function ({ assembly1, assembly2, setSessionTrackData, }) {
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  const [bed2Location, setBed2Location] = useState();
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  const [bed1Location, setBed1Location] = useState();
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  const [fileLocation, setFileLocation] = useState();
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+ const [indexFileLocation, setIndexFileLocation] = useState();
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  const [value, setValue] = useState('');
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  const [error, setError] = useState();
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  const fileName = getName(fileLocation);
@@ -82,6 +91,7 @@ const OpenTrack = observer(({ assembly1, assembly2, setSessionTrackData, }) => {
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  assembly1,
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  assembly2,
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  fileLocation,
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+ indexFileLocation,
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  bed1Location,
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  bed2Location,
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  }),
@@ -99,12 +109,13 @@ const OpenTrack = observer(({ assembly1, assembly2, setSessionTrackData, }) => {
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  bed1Location,
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  bed2Location,
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  fileLocation,
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+ indexFileLocation,
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  radioOption,
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  setSessionTrackData,
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  ]);
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  return (React.createElement(Paper, { style: { padding: 12 } },
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  error ? React.createElement(ErrorMessage, { error: error }) : null,
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- React.createElement(Typography, { style: { textAlign: 'center' } }, "Add a .paf, .out (MashMap), .delta (Mummer), .chain, .anchors or .anchors.simple (MCScan) file to view in the dotplot. These file types can also be gzipped. The first assembly should be the query sequence (e.g. left column of the PAF) and the second assembly should be the target sequence (e.g. right column of the PAF)"),
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+ React.createElement(Typography, { style: { textAlign: 'center' } }, "Add a .paf, .out (MashMap), .delta (Mummer), .chain, .anchors or .anchors.simple (MCScan) file to view. These file types can also be gzipped. The first assembly should be the query sequence (e.g. left column of the PAF) and the second assembly should be the target sequence (e.g. right column of the PAF)"),
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  React.createElement(RadioGroup, { value: radioOption, onChange: event => {
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  setValue(event.target.value);
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  } },
@@ -120,7 +131,9 @@ const OpenTrack = observer(({ assembly1, assembly2, setSessionTrackData, }) => {
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  React.createElement(Grid, { item: true },
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  React.createElement(FormControlLabel, { value: ".anchors", control: React.createElement(Radio, null), label: ".anchors" })),
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  React.createElement(Grid, { item: true },
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- React.createElement(FormControlLabel, { value: ".anchors.simple", control: React.createElement(Radio, null), label: ".anchors.simple" })))),
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+ React.createElement(FormControlLabel, { value: ".anchors.simple", control: React.createElement(Radio, null), label: ".anchors.simple" })),
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+ React.createElement(Grid, { item: true },
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+ React.createElement(FormControlLabel, { value: ".pif.gz", control: React.createElement(Radio, null), label: ".pif.gz" })))),
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  React.createElement(Grid, { container: true, justifyContent: "center" },
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  React.createElement(Grid, { item: true }, value === '.anchors' || value === '.anchors.simple' ? (React.createElement("div", null,
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  React.createElement("div", { style: { margin: 20 } },
@@ -141,8 +154,16 @@ const OpenTrack = observer(({ assembly1, assembly2, setSessionTrackData, }) => {
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  React.createElement("div", null,
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  React.createElement(FileSelector, { name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: loc => {
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  setBed2Location(loc);
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- } }))))) : (React.createElement(FileSelector, { name: value ? `${value} location` : '', description: "", location: fileLocation, setLocation: loc => {
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+ } }))))) : value === '.pif.gz' ? (React.createElement("div", { style: { display: 'flex' } },
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+ React.createElement("div", null,
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+ React.createElement(FileSelector, { name: `${value} location`, description: "", location: fileLocation, setLocation: loc => {
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+ setFileLocation(loc);
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+ } })),
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+ React.createElement("div", null,
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+ React.createElement(FileSelector, { name: `${value} index location`, description: "", location: indexFileLocation, setLocation: loc => {
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+ setIndexFileLocation(loc);
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+ } })))) : (React.createElement(FileSelector, { name: value ? `${value} location` : '', description: "", location: fileLocation, setLocation: loc => {
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  setFileLocation(loc);
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  } }))))));
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  });
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- export default OpenTrack;
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+ export default ImportCustomTrack;
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-linear-comparative-view",
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- "version": "2.15.1",
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+ "version": "2.15.3",
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  "description": "JBrowse 2 linear comparative view",
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  "keywords": [
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  "jbrowse",
@@ -61,5 +61,5 @@
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  "publishConfig": {
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  "access": "public"
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  },
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- "gitHead": "86ed70124fc5a0b1161266659d1ca9f8796bf3fe"
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+ "gitHead": "c0f82fe7b210622dd462e702641cc6da01109c6e"
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  }