@jbrowse/plugin-alignments 1.7.3 → 1.7.6

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 (67) hide show
  1. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +26 -26
  2. package/dist/AlignmentsFeatureDetail/index.js +3 -3
  3. package/dist/AlignmentsFeatureDetail/index.test.js +2 -2
  4. package/dist/AlignmentsTrack/index.js +2 -2
  5. package/dist/BamAdapter/BamAdapter.js +31 -31
  6. package/dist/BamAdapter/BamAdapter.test.js +10 -10
  7. package/dist/BamAdapter/BamSlightlyLazyFeature.js +6 -6
  8. package/dist/BamAdapter/MismatchParser.js +6 -6
  9. package/dist/BamAdapter/MismatchParser.test.js +2 -2
  10. package/dist/BamAdapter/configSchema.js +2 -2
  11. package/dist/BamAdapter/index.js +6 -6
  12. package/dist/CramAdapter/CramAdapter.js +31 -31
  13. package/dist/CramAdapter/CramAdapter.test.js +10 -10
  14. package/dist/CramAdapter/CramSlightlyLazyFeature.js +6 -6
  15. package/dist/CramAdapter/CramTestAdapters.js +18 -18
  16. package/dist/CramAdapter/configSchema.js +2 -2
  17. package/dist/CramAdapter/index.js +6 -6
  18. package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js +9 -9
  19. package/dist/HtsgetBamAdapter/configSchema.js +2 -2
  20. package/dist/HtsgetBamAdapter/index.js +6 -6
  21. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +8 -8
  22. package/dist/LinearAlignmentsDisplay/index.js +5 -5
  23. package/dist/LinearAlignmentsDisplay/models/configSchema.js +2 -2
  24. package/dist/LinearAlignmentsDisplay/models/configSchema.test.js +11 -11
  25. package/dist/LinearAlignmentsDisplay/models/model.js +15 -15
  26. package/dist/LinearPileupDisplay/components/ColorByModifications.js +18 -18
  27. package/dist/LinearPileupDisplay/components/ColorByTag.js +11 -11
  28. package/dist/LinearPileupDisplay/components/FilterByTag.js +26 -26
  29. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +4 -4
  30. package/dist/LinearPileupDisplay/components/SetFeatureHeight.js +12 -12
  31. package/dist/LinearPileupDisplay/components/SetMaxHeight.js +10 -10
  32. package/dist/LinearPileupDisplay/components/SortByTag.js +10 -10
  33. package/dist/LinearPileupDisplay/configSchema.js +5 -7
  34. package/dist/LinearPileupDisplay/configSchema.test.js +12 -12
  35. package/dist/LinearPileupDisplay/index.js +4 -4
  36. package/dist/LinearPileupDisplay/model.d.ts +2 -3
  37. package/dist/LinearPileupDisplay/model.js +189 -63
  38. package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +10 -10
  39. package/dist/LinearSNPCoverageDisplay/index.js +4 -4
  40. package/dist/LinearSNPCoverageDisplay/models/configSchema.js +1 -1
  41. package/dist/LinearSNPCoverageDisplay/models/configSchema.test.js +7 -7
  42. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +1 -1
  43. package/dist/LinearSNPCoverageDisplay/models/model.js +11 -11
  44. package/dist/NestedFrequencyTable.js +7 -7
  45. package/dist/PileupRPC/rpcMethods.js +23 -23
  46. package/dist/PileupRenderer/PileupLayoutSession.js +8 -8
  47. package/dist/PileupRenderer/PileupRenderer.d.ts +2 -3
  48. package/dist/PileupRenderer/PileupRenderer.js +40 -40
  49. package/dist/PileupRenderer/components/PileupRendering.js +13 -13
  50. package/dist/PileupRenderer/components/PileupRendering.test.js +2 -2
  51. package/dist/PileupRenderer/configSchema.js +2 -2
  52. package/dist/PileupRenderer/index.js +4 -4
  53. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +22 -22
  54. package/dist/SNPCoverageAdapter/configSchema.js +2 -2
  55. package/dist/SNPCoverageAdapter/index.js +6 -6
  56. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +12 -12
  57. package/dist/SNPCoverageRenderer/configSchema.js +2 -2
  58. package/dist/SNPCoverageRenderer/index.js +3 -3
  59. package/dist/index.js +10 -10
  60. package/dist/index.test.js +2 -2
  61. package/dist/shared.js +5 -5
  62. package/dist/util.d.ts +1 -1
  63. package/dist/util.js +3 -3
  64. package/package.json +4 -5
  65. package/src/LinearPileupDisplay/configSchema.ts +1 -4
  66. package/src/LinearPileupDisplay/model.ts +96 -19
  67. package/src/PileupRenderer/PileupRenderer.tsx +6 -2
@@ -7,7 +7,7 @@ var _typeof = require("@babel/runtime/helpers/typeof");
7
7
  Object.defineProperty(exports, "__esModule", {
8
8
  value: true
9
9
  });
10
- exports["default"] = void 0;
10
+ exports.default = void 0;
11
11
 
12
12
  var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
13
13
 
@@ -21,7 +21,7 @@ var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
21
21
 
22
22
  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); }
23
23
 
24
- 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; }
24
+ 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; }
25
25
 
26
26
  var useStyles = (0, _core.makeStyles)(function (theme) {
27
27
  return {
@@ -42,30 +42,30 @@ function SetFeatureHeightDlg(props) {
42
42
  noSpacingSetting = model.noSpacing;
43
43
 
44
44
  var _useState = (0, _react.useState)("".concat(featureHeightSetting)),
45
- _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
45
+ _useState2 = (0, _slicedToArray2.default)(_useState, 2),
46
46
  height = _useState2[0],
47
47
  setHeight = _useState2[1];
48
48
 
49
49
  var _useState3 = (0, _react.useState)(noSpacingSetting),
50
- _useState4 = (0, _slicedToArray2["default"])(_useState3, 2),
50
+ _useState4 = (0, _slicedToArray2.default)(_useState3, 2),
51
51
  noSpacing = _useState4[0],
52
52
  setNoSpacing = _useState4[1];
53
53
 
54
54
  var ok = height !== '' && !Number.isNaN(+height);
55
- return /*#__PURE__*/_react["default"].createElement(_core.Dialog, {
55
+ return /*#__PURE__*/_react.default.createElement(_core.Dialog, {
56
56
  open: true,
57
57
  onClose: handleClose
58
- }, /*#__PURE__*/_react["default"].createElement(_core.DialogTitle, null, "Set feature height", /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
58
+ }, /*#__PURE__*/_react.default.createElement(_core.DialogTitle, null, "Set feature height", /*#__PURE__*/_react.default.createElement(_core.IconButton, {
59
59
  className: classes.closeButton,
60
60
  onClick: handleClose
61
- }, /*#__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, {
61
+ }, /*#__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, {
62
62
  value: height,
63
63
  helperText: "Feature height",
64
64
  onChange: function onChange(event) {
65
65
  setHeight(event.target.value);
66
66
  }
67
- }), /*#__PURE__*/_react["default"].createElement(_core.FormControlLabel, {
68
- control: /*#__PURE__*/_react["default"].createElement(_core.Checkbox, {
67
+ }), /*#__PURE__*/_react.default.createElement(_core.FormControlLabel, {
68
+ control: /*#__PURE__*/_react.default.createElement(_core.Checkbox, {
69
69
  checked: !!noSpacing,
70
70
  onChange: function onChange() {
71
71
  return setNoSpacing(function (val) {
@@ -74,7 +74,7 @@ function SetFeatureHeightDlg(props) {
74
74
  }
75
75
  }),
76
76
  label: "Remove spacing between features in y-direction?"
77
- }), /*#__PURE__*/_react["default"].createElement(_core.DialogActions, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
77
+ }), /*#__PURE__*/_react.default.createElement(_core.DialogActions, null, /*#__PURE__*/_react.default.createElement(_core.Button, {
78
78
  variant: "contained",
79
79
  color: "primary",
80
80
  type: "submit",
@@ -85,7 +85,7 @@ function SetFeatureHeightDlg(props) {
85
85
  model.setNoSpacing(noSpacing);
86
86
  handleClose();
87
87
  }
88
- }, "Submit"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
88
+ }, "Submit"), /*#__PURE__*/_react.default.createElement(_core.Button, {
89
89
  variant: "contained",
90
90
  color: "secondary",
91
91
  onClick: function onClick() {
@@ -96,4 +96,4 @@ function SetFeatureHeightDlg(props) {
96
96
 
97
97
  var _default = (0, _mobxReact.observer)(SetFeatureHeightDlg);
98
98
 
99
- exports["default"] = _default;
99
+ exports.default = _default;
@@ -7,7 +7,7 @@ var _typeof = require("@babel/runtime/helpers/typeof");
7
7
  Object.defineProperty(exports, "__esModule", {
8
8
  value: true
9
9
  });
10
- exports["default"] = void 0;
10
+ exports.default = void 0;
11
11
 
12
12
  var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
13
13
 
@@ -21,7 +21,7 @@ var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
21
21
 
22
22
  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); }
23
23
 
24
- 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; }
24
+ 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; }
25
25
 
26
26
  var useStyles = (0, _core.makeStyles)(function (theme) {
27
27
  return {
@@ -48,26 +48,26 @@ function SetMaxHeightDlg(props) {
48
48
  maxHeight = _model$maxHeight === void 0 ? '' : _model$maxHeight;
49
49
 
50
50
  var _useState = (0, _react.useState)("".concat(maxHeight)),
51
- _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
51
+ _useState2 = (0, _slicedToArray2.default)(_useState, 2),
52
52
  max = _useState2[0],
53
53
  setMax = _useState2[1];
54
54
 
55
- return /*#__PURE__*/_react["default"].createElement(_core.Dialog, {
55
+ return /*#__PURE__*/_react.default.createElement(_core.Dialog, {
56
56
  open: true,
57
57
  onClose: handleClose
58
- }, /*#__PURE__*/_react["default"].createElement(_core.DialogTitle, null, "Filter options", /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
58
+ }, /*#__PURE__*/_react.default.createElement(_core.DialogTitle, null, "Filter options", /*#__PURE__*/_react.default.createElement(_core.IconButton, {
59
59
  "aria-label": "close",
60
60
  className: classes.closeButton,
61
61
  onClick: handleClose
62
- }, /*#__PURE__*/_react["default"].createElement(_Close["default"], null))), /*#__PURE__*/_react["default"].createElement(_core.DialogContent, {
62
+ }, /*#__PURE__*/_react.default.createElement(_Close.default, null))), /*#__PURE__*/_react.default.createElement(_core.DialogContent, {
63
63
  className: classes.root
64
- }, /*#__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, {
64
+ }, /*#__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, {
65
65
  value: max,
66
66
  onChange: function onChange(event) {
67
67
  setMax(event.target.value);
68
68
  },
69
69
  placeholder: "Enter max height for layout"
70
- }), /*#__PURE__*/_react["default"].createElement(_core.DialogActions, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
70
+ }), /*#__PURE__*/_react.default.createElement(_core.DialogActions, null, /*#__PURE__*/_react.default.createElement(_core.Button, {
71
71
  variant: "contained",
72
72
  color: "primary",
73
73
  type: "submit",
@@ -76,7 +76,7 @@ function SetMaxHeightDlg(props) {
76
76
  model.setMaxHeight(max !== '' && !Number.isNaN(+max) ? +max : undefined);
77
77
  handleClose();
78
78
  }
79
- }, "Submit"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
79
+ }, "Submit"), /*#__PURE__*/_react.default.createElement(_core.Button, {
80
80
  variant: "contained",
81
81
  color: "secondary",
82
82
  onClick: function onClick() {
@@ -87,4 +87,4 @@ function SetMaxHeightDlg(props) {
87
87
 
88
88
  var _default = (0, _mobxReact.observer)(SetMaxHeightDlg);
89
89
 
90
- exports["default"] = _default;
90
+ exports.default = _default;
@@ -7,7 +7,7 @@ var _typeof = require("@babel/runtime/helpers/typeof");
7
7
  Object.defineProperty(exports, "__esModule", {
8
8
  value: true
9
9
  });
10
- exports["default"] = void 0;
10
+ exports.default = void 0;
11
11
 
12
12
  var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
13
13
 
@@ -21,7 +21,7 @@ var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
21
21
 
22
22
  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); }
23
23
 
24
- 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; }
24
+ 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; }
25
25
 
26
26
  var useStyles = (0, _core.makeStyles)(function (theme) {
27
27
  return {
@@ -44,21 +44,21 @@ function SortByTagDlg(props) {
44
44
  handleClose = props.handleClose;
45
45
 
46
46
  var _useState = (0, _react.useState)(''),
47
- _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
47
+ _useState2 = (0, _slicedToArray2.default)(_useState, 2),
48
48
  tag = _useState2[0],
49
49
  setTag = _useState2[1];
50
50
 
51
51
  var validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
52
- return /*#__PURE__*/_react["default"].createElement(_core.Dialog, {
52
+ return /*#__PURE__*/_react.default.createElement(_core.Dialog, {
53
53
  open: true,
54
54
  onClose: handleClose
55
- }, /*#__PURE__*/_react["default"].createElement(_core.DialogTitle, null, "Sort by tag", /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
55
+ }, /*#__PURE__*/_react.default.createElement(_core.DialogTitle, null, "Sort by tag", /*#__PURE__*/_react.default.createElement(_core.IconButton, {
56
56
  "aria-label": "close",
57
57
  className: classes.closeButton,
58
58
  onClick: handleClose
59
- }, /*#__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, {
59
+ }, /*#__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, {
60
60
  color: "textSecondary"
61
- }, "Examples: HP for haplotype, RG for read group, etc."), /*#__PURE__*/_react["default"].createElement(_core.TextField, {
61
+ }, "Examples: HP for haplotype, RG for read group, etc."), /*#__PURE__*/_react.default.createElement(_core.TextField, {
62
62
  value: tag,
63
63
  onChange: function onChange(event) {
64
64
  return setTag(event.target.value);
@@ -72,7 +72,7 @@ function SortByTagDlg(props) {
72
72
  helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '',
73
73
  autoComplete: "off",
74
74
  "data-testid": "sort-tag-name"
75
- }), /*#__PURE__*/_react["default"].createElement(_core.DialogActions, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
75
+ }), /*#__PURE__*/_react.default.createElement(_core.DialogActions, null, /*#__PURE__*/_react.default.createElement(_core.Button, {
76
76
  variant: "contained",
77
77
  color: "primary",
78
78
  type: "submit",
@@ -81,7 +81,7 @@ function SortByTagDlg(props) {
81
81
  model.setSortedBy('tag', tag);
82
82
  handleClose();
83
83
  }
84
- }, "Submit"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
84
+ }, "Submit"), /*#__PURE__*/_react.default.createElement(_core.Button, {
85
85
  variant: "contained",
86
86
  color: "secondary",
87
87
  onClick: function onClick() {
@@ -92,4 +92,4 @@ function SortByTagDlg(props) {
92
92
 
93
93
  var _default = (0, _mobxReact.observer)(SortByTagDlg);
94
94
 
95
- exports["default"] = _default;
95
+ exports.default = _default;
@@ -3,7 +3,7 @@
3
3
  Object.defineProperty(exports, "__esModule", {
4
4
  value: true
5
5
  });
6
- exports["default"] = void 0;
6
+ exports.default = void 0;
7
7
 
8
8
  var _configuration = require("@jbrowse/core/configuration");
9
9
 
@@ -12,18 +12,16 @@ var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
12
12
  var _mobxStateTree = require("mobx-state-tree");
13
13
 
14
14
  function PileupConfigFactory(pluginManager) {
15
- var PileupRendererConfigSchema = pluginManager.getRendererType('PileupRenderer').configSchema;
16
- var SvgFeatureRendererConfigSchema = pluginManager.getRendererType('SvgFeatureRenderer').configSchema; // modify config schema to take in a sub coverage display
15
+ var PileupRendererConfigSchema = pluginManager.getRendererType('PileupRenderer').configSchema; // modify config schema to take in a sub coverage display
17
16
 
18
17
  return (0, _configuration.ConfigurationSchema)('LinearPileupDisplay', {
19
18
  defaultRendering: {
20
19
  type: 'stringEnum',
21
- model: _mobxStateTree.types.enumeration('Rendering', ['pileup', 'svg']),
20
+ model: _mobxStateTree.types.enumeration('Rendering', ['pileup']),
22
21
  defaultValue: 'pileup'
23
22
  },
24
23
  renderers: (0, _configuration.ConfigurationSchema)('RenderersConfiguration', {
25
- PileupRenderer: PileupRendererConfigSchema,
26
- SvgFeatureRenderer: SvgFeatureRendererConfigSchema
24
+ PileupRenderer: PileupRendererConfigSchema
27
25
  }),
28
26
  renderer: '',
29
27
  maxFeatureScreenDensity: {
@@ -44,4 +42,4 @@ function PileupConfigFactory(pluginManager) {
44
42
  }
45
43
 
46
44
  var _default = PileupConfigFactory;
47
- exports["default"] = _default;
45
+ exports.default = _default;
@@ -24,7 +24,7 @@ var _PileupRenderer = _interopRequireDefault(require("../PileupRenderer"));
24
24
 
25
25
  var _configSchema = _interopRequireDefault(require("./configSchema"));
26
26
 
27
- function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2["default"])(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2["default"])(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2["default"])(this, result); }; }
27
+ function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
28
28
 
29
29
  function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
30
30
 
@@ -37,39 +37,39 @@ afterEach(function () {
37
37
  });
38
38
 
39
39
  var PileupRendererPlugin = /*#__PURE__*/function (_Plugin) {
40
- (0, _inherits2["default"])(PileupRendererPlugin, _Plugin);
40
+ (0, _inherits2.default)(PileupRendererPlugin, _Plugin);
41
41
 
42
42
  var _super = _createSuper(PileupRendererPlugin);
43
43
 
44
44
  function PileupRendererPlugin() {
45
- (0, _classCallCheck2["default"])(this, PileupRendererPlugin);
45
+ (0, _classCallCheck2.default)(this, PileupRendererPlugin);
46
46
  return _super.apply(this, arguments);
47
47
  }
48
48
 
49
- (0, _createClass2["default"])(PileupRendererPlugin, [{
49
+ (0, _createClass2.default)(PileupRendererPlugin, [{
50
50
  key: "install",
51
51
  value: function install(pluginManager) {
52
- (0, _PileupRenderer["default"])(pluginManager);
52
+ (0, _PileupRenderer.default)(pluginManager);
53
53
  }
54
54
  }]);
55
55
  return PileupRendererPlugin;
56
- }(_Plugin3["default"]);
56
+ }(_Plugin3.default);
57
57
 
58
58
  var SvgFeatureRendererPlugin = /*#__PURE__*/function (_Plugin2) {
59
- (0, _inherits2["default"])(SvgFeatureRendererPlugin, _Plugin2);
59
+ (0, _inherits2.default)(SvgFeatureRendererPlugin, _Plugin2);
60
60
 
61
61
  var _super2 = _createSuper(SvgFeatureRendererPlugin);
62
62
 
63
63
  function SvgFeatureRendererPlugin() {
64
- (0, _classCallCheck2["default"])(this, SvgFeatureRendererPlugin);
64
+ (0, _classCallCheck2.default)(this, SvgFeatureRendererPlugin);
65
65
  return _super2.apply(this, arguments);
66
66
  }
67
67
 
68
- (0, _createClass2["default"])(SvgFeatureRendererPlugin, [{
68
+ (0, _createClass2.default)(SvgFeatureRendererPlugin, [{
69
69
  key: "install",
70
70
  value: function install(pluginManager) {
71
71
  pluginManager.addRendererType(function () {
72
- return new _BoxRendererType["default"]({
72
+ return new _BoxRendererType.default({
73
73
  name: 'SvgFeatureRenderer',
74
74
  ReactComponent: _pluginSvg.SvgFeatureRendererReactComponent,
75
75
  configSchema: _pluginSvg.svgFeatureRendererConfigSchema,
@@ -79,10 +79,10 @@ var SvgFeatureRendererPlugin = /*#__PURE__*/function (_Plugin2) {
79
79
  }
80
80
  }]);
81
81
  return SvgFeatureRendererPlugin;
82
- }(_Plugin3["default"]);
82
+ }(_Plugin3.default);
83
83
 
84
84
  test('has a type attr', function () {
85
- var configSchema = (0, _configSchema["default"])(new _PluginManager["default"]([new PileupRendererPlugin(), new SvgFeatureRendererPlugin()]).createPluggableElements().configure());
85
+ var configSchema = (0, _configSchema.default)(new _PluginManager.default([new PileupRendererPlugin(), new SvgFeatureRendererPlugin()]).createPluggableElements().configure());
86
86
  var config = configSchema.create({
87
87
  type: 'LinearPileupDisplay',
88
88
  displayId: 'display0',
@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
5
5
  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
7
7
  });
8
- exports["default"] = register;
8
+ exports.default = register;
9
9
 
10
10
  var _configSchema = _interopRequireDefault(require("./configSchema"));
11
11
 
@@ -17,11 +17,11 @@ var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
17
17
 
18
18
  function register(pluginManager) {
19
19
  pluginManager.addDisplayType(function () {
20
- var configSchema = (0, _configSchema["default"])(pluginManager);
21
- return new _DisplayType["default"]({
20
+ var configSchema = (0, _configSchema.default)(pluginManager);
21
+ return new _DisplayType.default({
22
22
  name: 'LinearPileupDisplay',
23
23
  configSchema: configSchema,
24
- stateModel: (0, _model["default"])(configSchema),
24
+ stateModel: (0, _model.default)(configSchema),
25
25
  trackType: 'AlignmentsTrack',
26
26
  viewType: 'LinearGenomeView',
27
27
  ReactComponent: _pluginLinearGenomeView.BaseLinearDisplayComponent
@@ -1,7 +1,6 @@
1
- /// <reference types="react" />
1
+ import { Feature } from '@jbrowse/core/util';
2
2
  import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
3
3
  import { Instance } from 'mobx-state-tree';
4
- import { Feature } from '@jbrowse/core/util/simpleFeature';
5
4
  import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
6
5
  import { LinearPileupDisplayConfigModel } from './configSchema';
7
6
  declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel) => import("mobx-state-tree").IModelType<{
@@ -174,7 +173,7 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
174
173
  headers?: Record<string, string> | undefined;
175
174
  signal?: AbortSignal | undefined;
176
175
  filters?: string[] | undefined;
177
- }): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
176
+ }): Promise<{}>;
178
177
  setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
179
178
  setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
180
179
  clearRegionStats(): void;