@jbrowse/plugin-alignments 1.6.9 → 1.7.3

package/dist/LinearPileupDisplay/components/FilterByTag.js

@@ -0,0 +1,203 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _typeof = require("@babel/runtime/helpers/typeof");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+var _react = _interopRequireWildcard(require("react"));
+
+var _mobxReact = require("mobx-react");
+
+var _core = require("@material-ui/core");
+
+var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
+
+function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
+
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+
+var useStyles = (0, _core.makeStyles)(function (theme) {
+  return {
+    paper: {
+      padding: theme.spacing(2),
+      margin: theme.spacing(2)
+    },
+    closeButton: {
+      position: 'absolute',
+      right: theme.spacing(1),
+      top: theme.spacing(1),
+      color: theme.palette.grey[500]
+    },
+    field: {
+      margin: theme.spacing(2)
+    }
+  };
+});
+var flagNames = ['read paired', 'read mapped in proper pair', 'read unmapped', 'mate unmapped', 'read reverse strand', 'mate reverse strand', 'first in pair', 'second in pair', 'not primary alignment', 'read fails platform/vendor quality checks', 'read is PCR or optical duplicate', 'supplementary alignment'];
+
+function Bitmask(props) {
+  var _props$flag = props.flag,
+      flag = _props$flag === void 0 ? 0 : _props$flag,
+      setFlag = props.setFlag;
+  return /*#__PURE__*/_react["default"].createElement(_react["default"].Fragment, null, /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+    type: "number",
+    value: flag,
+    onChange: function onChange(event) {
+      return setFlag(+event.target.value);
+    }
+  }), flagNames.map(function (name, index) {
+    var val = flag & 1 << index;
+    var key = "".concat(name, "_").concat(val);
+    return /*#__PURE__*/_react["default"].createElement("div", {
+      key: key
+    }, /*#__PURE__*/_react["default"].createElement("input", {
+      type: "checkbox",
+      checked: Boolean(val),
+      onChange: function onChange(event) {
+        if (event.target.checked) {
+          setFlag(flag | 1 << index);
+        } else {
+          setFlag(flag & ~(1 << index));
+        }
+      }
+    }), /*#__PURE__*/_react["default"].createElement("label", {
+      htmlFor: key
+    }, name));
+  }));
+}
+
+function FilterByTagDlg(props) {
+  var _filterBy$tagFilter, _filterBy$tagFilter2;
+
+  var model = props.model,
+      handleClose = props.handleClose;
+  var classes = useStyles();
+  var filterBy = model.filterBy;
+
+  var _useState = (0, _react.useState)(filterBy === null || filterBy === void 0 ? void 0 : filterBy.flagInclude),
+      _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
+      flagInclude = _useState2[0],
+      setFlagInclude = _useState2[1];
+
+  var _useState3 = (0, _react.useState)(filterBy === null || filterBy === void 0 ? void 0 : filterBy.flagExclude),
+      _useState4 = (0, _slicedToArray2["default"])(_useState3, 2),
+      flagExclude = _useState4[0],
+      setFlagExclude = _useState4[1];
+
+  var _useState5 = (0, _react.useState)((filterBy === null || filterBy === void 0 ? void 0 : (_filterBy$tagFilter = filterBy.tagFilter) === null || _filterBy$tagFilter === void 0 ? void 0 : _filterBy$tagFilter.tag) || ''),
+      _useState6 = (0, _slicedToArray2["default"])(_useState5, 2),
+      tag = _useState6[0],
+      setTag = _useState6[1];
+
+  var _useState7 = (0, _react.useState)((filterBy === null || filterBy === void 0 ? void 0 : (_filterBy$tagFilter2 = filterBy.tagFilter) === null || _filterBy$tagFilter2 === void 0 ? void 0 : _filterBy$tagFilter2.value) || ''),
+      _useState8 = (0, _slicedToArray2["default"])(_useState7, 2),
+      tagValue = _useState8[0],
+      setTagValue = _useState8[1];
+
+  var _useState9 = (0, _react.useState)((filterBy === null || filterBy === void 0 ? void 0 : filterBy.readName) || ''),
+      _useState10 = (0, _slicedToArray2["default"])(_useState9, 2),
+      readName = _useState10[0],
+      setReadName = _useState10[1];
+
+  var validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
+  var site = 'https://broadinstitute.github.io/picard/explain-flags.html';
+  return /*#__PURE__*/_react["default"].createElement(_core.Dialog, {
+    open: true,
+    onClose: handleClose
+  }, /*#__PURE__*/_react["default"].createElement(_core.DialogTitle, null, "Filter options", /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
+    "aria-label": "close",
+    className: classes.closeButton,
+    onClick: handleClose
+  }, /*#__PURE__*/_react["default"].createElement(_Close["default"], null))), /*#__PURE__*/_react["default"].createElement(_core.DialogContent, null, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Set filter bitmask options. Refer to ", /*#__PURE__*/_react["default"].createElement(_core.Link, {
+    href: site
+  }, site), ' ', "for details"), /*#__PURE__*/_react["default"].createElement(_core.Paper, {
+    className: classes.paper,
+    variant: "outlined"
+  }, /*#__PURE__*/_react["default"].createElement("div", {
+    style: {
+      display: 'flex'
+    }
+  }, /*#__PURE__*/_react["default"].createElement("div", null, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Read must have ALL these flags"), /*#__PURE__*/_react["default"].createElement(Bitmask, {
+    flag: flagInclude,
+    setFlag: setFlagInclude
+  })), /*#__PURE__*/_react["default"].createElement("div", null, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Read must have NONE of these flags"), /*#__PURE__*/_react["default"].createElement(Bitmask, {
+    flag: flagExclude,
+    setFlag: setFlagExclude
+  })))), /*#__PURE__*/_react["default"].createElement(_core.Paper, {
+    className: classes.paper,
+    variant: "outlined"
+  }, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Filter by tag name and value. Use * in the value field to get all reads containing any value for that tag. Example: filter tag name SA with value * to get all split/supplementary reads. Other examples include HP for haplotype, or RG for read group"), /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+    className: classes.field,
+    value: tag,
+    onChange: function onChange(event) {
+      setTag(event.target.value);
+    },
+    placeholder: "Enter tag name",
+    inputProps: {
+      maxLength: 2,
+      'data-testid': 'color-tag-name-input'
+    },
+    error: tag.length === 2 && !validTag,
+    helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '',
+    "data-testid": "color-tag-name"
+  }), /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+    className: classes.field,
+    value: tagValue,
+    onChange: function onChange(event) {
+      setTagValue(event.target.value);
+    },
+    placeholder: "Enter tag value",
+    inputProps: {
+      'data-testid': 'color-tag-name-input'
+    },
+    "data-testid": "color-tag-value"
+  })), /*#__PURE__*/_react["default"].createElement(_core.Paper, {
+    className: classes.paper,
+    variant: "outlined"
+  }, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Filter by read name"), /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+    className: classes.field,
+    value: readName,
+    onChange: function onChange(event) {
+      setReadName(event.target.value);
+    },
+    placeholder: "Enter read name",
+    inputProps: {
+      'data-testid': 'color-tag-readname-input'
+    },
+    "data-testid": "color-tag-readname"
+  })), /*#__PURE__*/_react["default"].createElement(_core.DialogActions, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    variant: "contained",
+    color: "primary",
+    autoFocus: true,
+    type: "submit",
+    onClick: function onClick() {
+      model.setFilterBy({
+        flagInclude: flagInclude,
+        flagExclude: flagExclude,
+        readName: readName,
+        tagFilter: tag !== '' ? {
+          tag: tag,
+          value: tagValue
+        } : undefined
+      });
+      handleClose();
+    }
+  }, "Submit"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    variant: "contained",
+    color: "secondary",
+    onClick: function onClick() {
+      return handleClose();
+    }
+  }, "Cancel"))));
+}
+
+var _default = (0, _mobxReact.observer)(FilterByTagDlg);
+
+exports["default"] = _default;

package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.d.ts

@@ -1,13 +1,13 @@
-/// <reference types="react" />
-export interface LinearPileupDisplayBlurbProps {
-    model: {
-        sortedBy?: {
-            pos: number;
-            refName: number;
-            type: string;
-        };
-    };
-}
-declare function LinearPileupDisplayBlurb(props: LinearPileupDisplayBlurbProps): JSX.Element | null;
-declare const _default: typeof LinearPileupDisplayBlurb;
-export default _default;
+/// <reference types="react" />
+export interface LinearPileupDisplayBlurbProps {
+    model: {
+        sortedBy?: {
+            pos: number;
+            refName: number;
+            type: string;
+        };
+    };
+}
+declare function LinearPileupDisplayBlurb(props: LinearPileupDisplayBlurbProps): JSX.Element | null;
+declare const _default: typeof LinearPileupDisplayBlurb;
+export default _default;

package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js

@@ -0,0 +1,32 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _react = _interopRequireDefault(require("react"));
+
+var _mobxReact = require("mobx-react");
+
+var _Typography = _interopRequireDefault(require("@material-ui/core/Typography"));
+
+function LinearPileupDisplayBlurb(props) {
+  var model = props.model;
+  var sortedBy = model.sortedBy;
+  return sortedBy ? /*#__PURE__*/_react["default"].createElement("div", {
+    "data-testid": "blurb-".concat(model.sortedBy),
+    style: {
+      backgroundColor: 'white'
+    }
+  }, /*#__PURE__*/_react["default"].createElement(_Typography["default"], {
+    color: "secondary",
+    variant: "caption"
+  }, model.sortedBy ? "Sorted by ".concat(sortedBy.type.toLowerCase(), " at ").concat(sortedBy.refName, ":").concat(sortedBy.pos) : null)) : null;
+}
+
+var _default = (0, _mobxReact.observer)(LinearPileupDisplayBlurb);
+
+exports["default"] = _default;

package/dist/LinearPileupDisplay/components/SetFeatureHeight.d.ts

@@ -1,16 +1,16 @@
-/// <reference types="react" />
-declare function SetFeatureHeightDlg(props: {
-    model: {
-        minScore: number;
-        maxScore: number;
-        setMinScore: Function;
-        setMaxScore: Function;
-        setFeatureHeight: Function;
-        setNoSpacing: Function;
-        featureHeightSetting: number;
-        noSpacing: boolean;
-    };
-    handleClose: () => void;
-}): JSX.Element;
-declare const _default: typeof SetFeatureHeightDlg;
-export default _default;
+/// <reference types="react" />
+declare function SetFeatureHeightDlg(props: {
+    model: {
+        minScore: number;
+        maxScore: number;
+        setMinScore: Function;
+        setMaxScore: Function;
+        setFeatureHeight: Function;
+        setNoSpacing: Function;
+        featureHeightSetting: number;
+        noSpacing: boolean;
+    };
+    handleClose: () => void;
+}): JSX.Element;
+declare const _default: typeof SetFeatureHeightDlg;
+export default _default;

package/dist/LinearPileupDisplay/components/SetFeatureHeight.js

@@ -0,0 +1,99 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _typeof = require("@babel/runtime/helpers/typeof");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+var _react = _interopRequireWildcard(require("react"));
+
+var _mobxReact = require("mobx-react");
+
+var _core = require("@material-ui/core");
+
+var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
+
+function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
+
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+
+var useStyles = (0, _core.makeStyles)(function (theme) {
+  return {
+    closeButton: {
+      position: 'absolute',
+      right: theme.spacing(1),
+      top: theme.spacing(1),
+      color: theme.palette.grey[500]
+    }
+  };
+});
+
+function SetFeatureHeightDlg(props) {
+  var classes = useStyles();
+  var model = props.model,
+      handleClose = props.handleClose;
+  var featureHeightSetting = model.featureHeightSetting,
+      noSpacingSetting = model.noSpacing;
+
+  var _useState = (0, _react.useState)("".concat(featureHeightSetting)),
+      _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
+      height = _useState2[0],
+      setHeight = _useState2[1];
+
+  var _useState3 = (0, _react.useState)(noSpacingSetting),
+      _useState4 = (0, _slicedToArray2["default"])(_useState3, 2),
+      noSpacing = _useState4[0],
+      setNoSpacing = _useState4[1];
+
+  var ok = height !== '' && !Number.isNaN(+height);
+  return /*#__PURE__*/_react["default"].createElement(_core.Dialog, {
+    open: true,
+    onClose: handleClose
+  }, /*#__PURE__*/_react["default"].createElement(_core.DialogTitle, null, "Set feature height", /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
+    className: classes.closeButton,
+    onClick: handleClose
+  }, /*#__PURE__*/_react["default"].createElement(_Close["default"], null))), /*#__PURE__*/_react["default"].createElement(_core.DialogContent, null, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Adjust the feature height and whether there is any spacing between features. Setting feature height to 1 and removing spacing makes the display very compact."), /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+    value: height,
+    helperText: "Feature height",
+    onChange: function onChange(event) {
+      setHeight(event.target.value);
+    }
+  }), /*#__PURE__*/_react["default"].createElement(_core.FormControlLabel, {
+    control: /*#__PURE__*/_react["default"].createElement(_core.Checkbox, {
+      checked: !!noSpacing,
+      onChange: function onChange() {
+        return setNoSpacing(function (val) {
+          return !val;
+        });
+      }
+    }),
+    label: "Remove spacing between features in y-direction?"
+  }), /*#__PURE__*/_react["default"].createElement(_core.DialogActions, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    variant: "contained",
+    color: "primary",
+    type: "submit",
+    autoFocus: true,
+    disabled: !ok,
+    onClick: function onClick() {
+      model.setFeatureHeight(height !== '' && !Number.isNaN(+height) ? +height : undefined);
+      model.setNoSpacing(noSpacing);
+      handleClose();
+    }
+  }, "Submit"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    variant: "contained",
+    color: "secondary",
+    onClick: function onClick() {
+      return handleClose();
+    }
+  }, "Cancel"))));
+}
+
+var _default = (0, _mobxReact.observer)(SetFeatureHeightDlg);
+
+exports["default"] = _default;

package/dist/LinearPileupDisplay/components/SetMaxHeight.d.ts

@@ -1,10 +1,10 @@
-/// <reference types="react" />
-declare function SetMaxHeightDlg(props: {
-    model: {
-        maxHeight?: number;
-        setMaxHeight: Function;
-    };
-    handleClose: () => void;
-}): JSX.Element;
-declare const _default: typeof SetMaxHeightDlg;
-export default _default;
+/// <reference types="react" />
+declare function SetMaxHeightDlg(props: {
+    model: {
+        maxHeight?: number;
+        setMaxHeight: Function;
+    };
+    handleClose: () => void;
+}): JSX.Element;
+declare const _default: typeof SetMaxHeightDlg;
+export default _default;

package/dist/LinearPileupDisplay/components/SetMaxHeight.js

@@ -0,0 +1,90 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _typeof = require("@babel/runtime/helpers/typeof");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+var _react = _interopRequireWildcard(require("react"));
+
+var _mobxReact = require("mobx-react");
+
+var _core = require("@material-ui/core");
+
+var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
+
+function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
+
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+
+var useStyles = (0, _core.makeStyles)(function (theme) {
+  return {
+    root: {
+      width: 500
+    },
+    closeButton: {
+      position: 'absolute',
+      right: theme.spacing(1),
+      top: theme.spacing(1),
+      color: theme.palette.grey[500]
+    },
+    field: {
+      margin: theme.spacing(2)
+    }
+  };
+});
+
+function SetMaxHeightDlg(props) {
+  var model = props.model,
+      handleClose = props.handleClose;
+  var classes = useStyles();
+  var _model$maxHeight = model.maxHeight,
+      maxHeight = _model$maxHeight === void 0 ? '' : _model$maxHeight;
+
+  var _useState = (0, _react.useState)("".concat(maxHeight)),
+      _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
+      max = _useState2[0],
+      setMax = _useState2[1];
+
+  return /*#__PURE__*/_react["default"].createElement(_core.Dialog, {
+    open: true,
+    onClose: handleClose
+  }, /*#__PURE__*/_react["default"].createElement(_core.DialogTitle, null, "Filter options", /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
+    "aria-label": "close",
+    className: classes.closeButton,
+    onClick: handleClose
+  }, /*#__PURE__*/_react["default"].createElement(_Close["default"], null))), /*#__PURE__*/_react["default"].createElement(_core.DialogContent, {
+    className: classes.root
+  }, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\""), /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+    value: max,
+    onChange: function onChange(event) {
+      setMax(event.target.value);
+    },
+    placeholder: "Enter max height for layout"
+  }), /*#__PURE__*/_react["default"].createElement(_core.DialogActions, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    variant: "contained",
+    color: "primary",
+    type: "submit",
+    autoFocus: true,
+    onClick: function onClick() {
+      model.setMaxHeight(max !== '' && !Number.isNaN(+max) ? +max : undefined);
+      handleClose();
+    }
+  }, "Submit"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    variant: "contained",
+    color: "secondary",
+    onClick: function onClick() {
+      return handleClose();
+    }
+  }, "Cancel"))));
+}
+
+var _default = (0, _mobxReact.observer)(SetMaxHeightDlg);
+
+exports["default"] = _default;

package/dist/LinearPileupDisplay/components/SortByTag.d.ts

@@ -1,9 +1,9 @@
-/// <reference types="react" />
-declare function SortByTagDlg(props: {
-    model: {
-        setSortedBy: Function;
-    };
-    handleClose: () => void;
-}): JSX.Element;
-declare const _default: typeof SortByTagDlg;
-export default _default;
+/// <reference types="react" />
+declare function SortByTagDlg(props: {
+    model: {
+        setSortedBy: Function;
+    };
+    handleClose: () => void;
+}): JSX.Element;
+declare const _default: typeof SortByTagDlg;
+export default _default;

package/dist/LinearPileupDisplay/components/SortByTag.js

@@ -0,0 +1,95 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _typeof = require("@babel/runtime/helpers/typeof");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+var _react = _interopRequireWildcard(require("react"));
+
+var _mobxReact = require("mobx-react");
+
+var _core = require("@material-ui/core");
+
+var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
+
+function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
+
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+
+var useStyles = (0, _core.makeStyles)(function (theme) {
+  return {
+    root: {
+      margin: 0,
+      padding: theme.spacing(2)
+    },
+    closeButton: {
+      position: 'absolute',
+      right: theme.spacing(1),
+      top: theme.spacing(1),
+      color: theme.palette.grey[500]
+    }
+  };
+});
+
+function SortByTagDlg(props) {
+  var classes = useStyles();
+  var model = props.model,
+      handleClose = props.handleClose;
+
+  var _useState = (0, _react.useState)(''),
+      _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
+      tag = _useState2[0],
+      setTag = _useState2[1];
+
+  var validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
+  return /*#__PURE__*/_react["default"].createElement(_core.Dialog, {
+    open: true,
+    onClose: handleClose
+  }, /*#__PURE__*/_react["default"].createElement(_core.DialogTitle, null, "Sort by tag", /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
+    "aria-label": "close",
+    className: classes.closeButton,
+    onClick: handleClose
+  }, /*#__PURE__*/_react["default"].createElement(_Close["default"], null))), /*#__PURE__*/_react["default"].createElement(_core.DialogContent, null, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Set the tag to sort by"), /*#__PURE__*/_react["default"].createElement(_core.Typography, {
+    color: "textSecondary"
+  }, "Examples: HP for haplotype, RG for read group, etc."), /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+    value: tag,
+    onChange: function onChange(event) {
+      return setTag(event.target.value);
+    },
+    placeholder: "Enter tag name",
+    inputProps: {
+      maxLength: 2,
+      'data-testid': 'sort-tag-name-input'
+    },
+    error: tag.length === 2 && !validTag,
+    helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '',
+    autoComplete: "off",
+    "data-testid": "sort-tag-name"
+  }), /*#__PURE__*/_react["default"].createElement(_core.DialogActions, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    variant: "contained",
+    color: "primary",
+    type: "submit",
+    autoFocus: true,
+    onClick: function onClick() {
+      model.setSortedBy('tag', tag);
+      handleClose();
+    }
+  }, "Submit"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    variant: "contained",
+    color: "secondary",
+    onClick: function onClick() {
+      return handleClose();
+    }
+  }, "Cancel"))));
+}
+
+var _default = (0, _mobxReact.observer)(SortByTagDlg);
+
+exports["default"] = _default;

package/dist/LinearPileupDisplay/configSchema.d.ts

@@ -1,6 +1,6 @@
-import { Instance } from 'mobx-state-tree';
-import PluginManager from '@jbrowse/core/PluginManager';
-declare function PileupConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export declare type LinearPileupDisplayConfigModel = ReturnType<typeof PileupConfigFactory>;
-export declare type LinearPileupDisplayConfig = Instance<LinearPileupDisplayConfigModel>;
-export default PileupConfigFactory;
+import { Instance } from 'mobx-state-tree';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare function PileupConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare type LinearPileupDisplayConfigModel = ReturnType<typeof PileupConfigFactory>;
+export declare type LinearPileupDisplayConfig = Instance<LinearPileupDisplayConfigModel>;
+export default PileupConfigFactory;