@jbrowse/plugin-wiggle 1.6.8 → 1.7.1

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/BigWigAdapter/BigWigAdapter.d.ts +24 -24
  2. package/dist/BigWigAdapter/BigWigAdapter.js +288 -0
  3. package/dist/BigWigAdapter/BigWigAdapter.test.js +157 -0
  4. package/dist/BigWigAdapter/configSchema.d.ts +2 -2
  5. package/dist/BigWigAdapter/configSchema.js +22 -0
  6. package/dist/BigWigAdapter/index.d.ts +1 -1
  7. package/dist/BigWigAdapter/index.js +15 -0
  8. package/dist/DensityRenderer/DensityRenderer.test.js +84 -0
  9. package/dist/DensityRenderer/index.d.ts +6 -6
  10. package/dist/DensityRenderer/index.js +137 -0
  11. package/dist/LinePlotRenderer/LinePlotRenderer.d.ts +4 -9
  12. package/dist/LinePlotRenderer/LinePlotRenderer.js +171 -0
  13. package/dist/LinePlotRenderer/configSchema.d.ts +2 -2
  14. package/dist/LinePlotRenderer/configSchema.js +70 -0
  15. package/dist/LinePlotRenderer/index.d.ts +3 -3
  16. package/dist/LinePlotRenderer/index.js +34 -0
  17. package/dist/LinearWiggleDisplay/components/SetColorDialog.d.ts +10 -10
  18. package/dist/LinearWiggleDisplay/components/SetColorDialog.js +111 -0
  19. package/dist/LinearWiggleDisplay/components/SetMinMaxDialog.d.ts +11 -11
  20. package/dist/LinearWiggleDisplay/components/SetMinMaxDialog.js +112 -0
  21. package/dist/LinearWiggleDisplay/components/Tooltip.d.ts +24 -24
  22. package/dist/LinearWiggleDisplay/components/Tooltip.js +167 -0
  23. package/dist/LinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +8 -8
  24. package/dist/LinearWiggleDisplay/components/WiggleDisplayComponent.js +52 -0
  25. package/dist/LinearWiggleDisplay/components/YScaleBar.d.ts +7 -7
  26. package/dist/LinearWiggleDisplay/components/YScaleBar.js +33 -0
  27. package/dist/LinearWiggleDisplay/index.d.ts +3 -3
  28. package/dist/LinearWiggleDisplay/index.js +43 -0
  29. package/dist/LinearWiggleDisplay/models/configSchema.d.ts +2 -2
  30. package/dist/LinearWiggleDisplay/models/configSchema.js +71 -0
  31. package/dist/LinearWiggleDisplay/models/model.d.ts +288 -288
  32. package/dist/LinearWiggleDisplay/models/model.js +706 -0
  33. package/dist/WiggleBaseRenderer.d.ts +44 -42
  34. package/dist/WiggleBaseRenderer.js +131 -0
  35. package/dist/WiggleRPC/rpcMethods.d.ts +31 -31
  36. package/dist/WiggleRPC/rpcMethods.js +295 -0
  37. package/dist/WiggleRendering.d.ts +16 -16
  38. package/dist/WiggleRendering.js +109 -0
  39. package/dist/WiggleRendering.test.js +52 -0
  40. package/dist/XYPlotRenderer/XYPlotRenderer.d.ts +4 -4
  41. package/dist/XYPlotRenderer/XYPlotRenderer.js +199 -0
  42. package/dist/XYPlotRenderer/XYPlotRenderer.test.js +83 -0
  43. package/dist/XYPlotRenderer/index.d.ts +3 -3
  44. package/dist/XYPlotRenderer/index.js +34 -0
  45. package/dist/configSchema.d.ts +2 -2
  46. package/dist/configSchema.js +75 -0
  47. package/dist/declare.d.js +1 -0
  48. package/dist/index.d.ts +866 -866
  49. package/dist/index.js +251 -6
  50. package/dist/index.test.js +24 -0
  51. package/dist/util.d.ts +41 -41
  52. package/dist/util.js +178 -0
  53. package/dist/util.test.js +66 -0
  54. package/package.json +4 -6
  55. package/src/LinearWiggleDisplay/models/model.tsx +2 -2
  56. package/src/WiggleBaseRenderer.tsx +1 -0
  57. package/dist/DensityRenderer/DensityRenderer.test.d.ts +0 -1
  58. package/dist/WiggleRendering.test.d.ts +0 -1
  59. package/dist/XYPlotRenderer/XYPlotRenderer.test.d.ts +0 -1
  60. package/dist/index.test.d.ts +0 -1
  61. package/dist/plugin-wiggle.cjs.development.js +0 -3556
  62. package/dist/plugin-wiggle.cjs.development.js.map +0 -1
  63. package/dist/plugin-wiggle.cjs.production.min.js +0 -2
  64. package/dist/plugin-wiggle.cjs.production.min.js.map +0 -1
  65. package/dist/plugin-wiggle.esm.js +0 -3541
  66. package/dist/plugin-wiggle.esm.js.map +0 -1
  67. package/dist/util.test.d.ts +0 -1
package/dist/index.js CHANGED
@@ -1,8 +1,253 @@
1
+ "use strict";
1
2
 
2
- 'use strict'
3
+ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
3
4
 
4
- if (process.env.NODE_ENV === 'production') {
5
- module.exports = require('./plugin-wiggle.cjs.production.min.js')
6
- } else {
7
- module.exports = require('./plugin-wiggle.cjs.development.js')
8
- }
5
+ var _typeof = require("@babel/runtime/helpers/typeof");
6
+
7
+ Object.defineProperty(exports, "__esModule", {
8
+ value: true
9
+ });
10
+ var _exportNames = {
11
+ WiggleBaseRenderer: true,
12
+ WiggleRendering: true,
13
+ linearWiggleDisplayModelFactory: true,
14
+ LinearWiggleDisplayReactComponent: true,
15
+ YSCALEBAR_LABEL_OFFSET: true,
16
+ Tooltip: true
17
+ };
18
+ Object.defineProperty(exports, "LinearWiggleDisplayReactComponent", {
19
+ enumerable: true,
20
+ get: function get() {
21
+ return _LinearWiggleDisplay.ReactComponent;
22
+ }
23
+ });
24
+ Object.defineProperty(exports, "Tooltip", {
25
+ enumerable: true,
26
+ get: function get() {
27
+ return _Tooltip.Tooltip;
28
+ }
29
+ });
30
+ Object.defineProperty(exports, "WiggleBaseRenderer", {
31
+ enumerable: true,
32
+ get: function get() {
33
+ return _WiggleBaseRenderer["default"];
34
+ }
35
+ });
36
+ Object.defineProperty(exports, "WiggleRendering", {
37
+ enumerable: true,
38
+ get: function get() {
39
+ return _WiggleRendering["default"];
40
+ }
41
+ });
42
+ Object.defineProperty(exports, "YSCALEBAR_LABEL_OFFSET", {
43
+ enumerable: true,
44
+ get: function get() {
45
+ return _LinearWiggleDisplay.YSCALEBAR_LABEL_OFFSET;
46
+ }
47
+ });
48
+ exports["default"] = void 0;
49
+ Object.defineProperty(exports, "linearWiggleDisplayModelFactory", {
50
+ enumerable: true,
51
+ get: function get() {
52
+ return _LinearWiggleDisplay.modelFactory;
53
+ }
54
+ });
55
+
56
+ var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
57
+
58
+ var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
59
+
60
+ var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
61
+
62
+ var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
63
+
64
+ var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
65
+
66
+ var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
67
+
68
+ var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
69
+
70
+ var _AdapterType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
71
+
72
+ var _TrackType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
73
+
74
+ var _Plugin2 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
75
+
76
+ var _configuration = require("@jbrowse/core/configuration");
77
+
78
+ var _models = require("@jbrowse/core/pluggableElementTypes/models");
79
+
80
+ var _DisplayType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
81
+
82
+ var _WiggleBaseRenderer = _interopRequireDefault(require("./WiggleBaseRenderer"));
83
+
84
+ var _WiggleRendering = _interopRequireDefault(require("./WiggleRendering"));
85
+
86
+ var _BigWigAdapter = require("./BigWigAdapter");
87
+
88
+ var _DensityRenderer = _interopRequireWildcard(require("./DensityRenderer"));
89
+
90
+ var utils = _interopRequireWildcard(require("./util"));
91
+
92
+ Object.keys(utils).forEach(function (key) {
93
+ if (key === "default" || key === "__esModule") return;
94
+ if (Object.prototype.hasOwnProperty.call(_exportNames, key)) return;
95
+ if (key in exports && exports[key] === utils[key]) return;
96
+ Object.defineProperty(exports, key, {
97
+ enumerable: true,
98
+ get: function get() {
99
+ return utils[key];
100
+ }
101
+ });
102
+ });
103
+
104
+ var _LinearWiggleDisplay = require("./LinearWiggleDisplay");
105
+
106
+ var _XYPlotRenderer = _interopRequireWildcard(require("./XYPlotRenderer"));
107
+
108
+ var _LinePlotRenderer = _interopRequireWildcard(require("./LinePlotRenderer"));
109
+
110
+ var _rpcMethods = require("./WiggleRPC/rpcMethods");
111
+
112
+ var _tracks = require("@jbrowse/core/util/tracks");
113
+
114
+ var _Tooltip = require("./LinearWiggleDisplay/components/Tooltip");
115
+
116
+ 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); }
117
+
118
+ 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; }
119
+
120
+ 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); }; }
121
+
122
+ 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; } }
123
+
124
+ var WigglePlugin = /*#__PURE__*/function (_Plugin) {
125
+ (0, _inherits2["default"])(WigglePlugin, _Plugin);
126
+
127
+ var _super = _createSuper(WigglePlugin);
128
+
129
+ function WigglePlugin() {
130
+ var _this;
131
+
132
+ (0, _classCallCheck2["default"])(this, WigglePlugin);
133
+
134
+ for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
135
+ args[_key] = arguments[_key];
136
+ }
137
+
138
+ _this = _super.call.apply(_super, [this].concat(args));
139
+ (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "name", 'WigglePlugin');
140
+ (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "exports", {
141
+ LinearWiggleDisplayReactComponent: _LinearWiggleDisplay.ReactComponent,
142
+ XYPlotRendererReactComponent: _XYPlotRenderer.ReactComponent,
143
+ XYPlotRenderer: _XYPlotRenderer["default"],
144
+ xyPlotRendererConfigSchema: _XYPlotRenderer.configSchema,
145
+ utils: utils,
146
+ WiggleBaseRenderer: _WiggleBaseRenderer["default"],
147
+ linearWiggleDisplayModelFactory: _LinearWiggleDisplay.modelFactory
148
+ });
149
+ return _this;
150
+ }
151
+
152
+ (0, _createClass2["default"])(WigglePlugin, [{
153
+ key: "install",
154
+ value: function install(pluginManager) {
155
+ pluginManager.addTrackType(function () {
156
+ var configSchema = (0, _configuration.ConfigurationSchema)('QuantitativeTrack', {}, {
157
+ baseConfiguration: (0, _models.createBaseTrackConfig)(pluginManager)
158
+ });
159
+ return new _TrackType["default"]({
160
+ name: 'QuantitativeTrack',
161
+ configSchema: configSchema,
162
+ stateModel: (0, _models.createBaseTrackModel)(pluginManager, 'QuantitativeTrack', configSchema)
163
+ });
164
+ });
165
+ pluginManager.addDisplayType(function () {
166
+ var configSchema = (0, _LinearWiggleDisplay.configSchemaFactory)(pluginManager);
167
+ return new _DisplayType["default"]({
168
+ name: 'LinearWiggleDisplay',
169
+ configSchema: configSchema,
170
+ stateModel: (0, _LinearWiggleDisplay.modelFactory)(pluginManager, configSchema),
171
+ trackType: 'QuantitativeTrack',
172
+ viewType: 'LinearGenomeView',
173
+ ReactComponent: _LinearWiggleDisplay.ReactComponent
174
+ });
175
+ });
176
+ pluginManager.addAdapterType(function () {
177
+ return new _AdapterType["default"]({
178
+ name: 'BigWigAdapter',
179
+ configSchema: _BigWigAdapter.configSchema,
180
+ adapterCapabilities: ['hasResolution', 'hasLocalStats', 'hasGlobalStats'],
181
+ getAdapterClass: function getAdapterClass() {
182
+ return Promise.resolve().then(function () {
183
+ return _interopRequireWildcard(require('./BigWigAdapter/BigWigAdapter'));
184
+ }).then(function (r) {
185
+ return r["default"];
186
+ });
187
+ }
188
+ });
189
+ });
190
+ pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
191
+ return function (file, index, adapterHint) {
192
+ var regexGuess = /\.(bw|bigwig)$/i;
193
+ var adapterName = 'BigWigAdapter';
194
+ var fileName = (0, _tracks.getFileName)(file);
195
+ var obj = {
196
+ type: adapterName,
197
+ bigWigLocation: file
198
+ };
199
+
200
+ if (regexGuess.test(fileName) && !adapterHint) {
201
+ return obj;
202
+ } else if (adapterHint === adapterName) {
203
+ return obj;
204
+ }
205
+
206
+ return adapterGuesser(file, index, adapterHint);
207
+ };
208
+ });
209
+ pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
210
+ return function (adapterName) {
211
+ if (adapterName === 'BigWigAdapter') {
212
+ return 'QuantitativeTrack';
213
+ }
214
+
215
+ return trackTypeGuesser(adapterName);
216
+ };
217
+ });
218
+ pluginManager.addRendererType(function () {
219
+ return new _DensityRenderer["default"]({
220
+ name: 'DensityRenderer',
221
+ ReactComponent: _DensityRenderer.ReactComponent,
222
+ configSchema: _DensityRenderer.configSchema,
223
+ pluginManager: pluginManager
224
+ });
225
+ });
226
+ pluginManager.addRendererType(function () {
227
+ return new _LinePlotRenderer["default"]({
228
+ name: 'LinePlotRenderer',
229
+ ReactComponent: _LinePlotRenderer.ReactComponent,
230
+ configSchema: _LinePlotRenderer.configSchema,
231
+ pluginManager: pluginManager
232
+ });
233
+ });
234
+ pluginManager.addRendererType(function () {
235
+ return new _XYPlotRenderer["default"]({
236
+ name: 'XYPlotRenderer',
237
+ ReactComponent: _XYPlotRenderer.ReactComponent,
238
+ configSchema: _XYPlotRenderer.configSchema,
239
+ pluginManager: pluginManager
240
+ });
241
+ });
242
+ pluginManager.addRpcMethod(function () {
243
+ return new _rpcMethods.WiggleGetGlobalStats(pluginManager);
244
+ });
245
+ pluginManager.addRpcMethod(function () {
246
+ return new _rpcMethods.WiggleGetMultiRegionStats(pluginManager);
247
+ });
248
+ }
249
+ }]);
250
+ return WigglePlugin;
251
+ }(_Plugin2["default"]);
252
+
253
+ exports["default"] = WigglePlugin;
@@ -0,0 +1,24 @@
1
+ "use strict";
2
+
3
+ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
4
+
5
+ var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
6
+
7
+ var _mobxStateTree = require("mobx-state-tree");
8
+
9
+ var _ = _interopRequireDefault(require("."));
10
+
11
+ test('plugin in a stock JBrowse', function () {
12
+ console.warn = jest.fn();
13
+ var pluginManager = new _PluginManager["default"]([new _["default"]()]);
14
+ pluginManager.createPluggableElements();
15
+ pluginManager.configure();
16
+ expect(function () {
17
+ return pluginManager.addPlugin(new _["default"]());
18
+ }).toThrow(/JBrowse already configured, cannot add plugins/);
19
+ var BigWigAdapter = pluginManager.getAdapterType('BigWigAdapter');
20
+ var config = BigWigAdapter.configSchema.create({
21
+ type: 'BigWigAdapter'
22
+ });
23
+ expect((0, _mobxStateTree.getSnapshot)(config)).toMatchSnapshot();
24
+ });
package/dist/util.d.ts CHANGED
@@ -1,41 +1,41 @@
1
- export interface ScaleOpts {
2
- domain: number[];
3
- range: number[];
4
- scaleType: string;
5
- pivotValue?: number;
6
- inverted: boolean;
7
- }
8
- /**
9
- * produces a d3-scale from arguments. applies a "nice domain" adjustment
10
- *
11
- * @param object - containing attributes
12
- * - domain [min,max]
13
- * - range [min,max]
14
- * - bounds [min,max]
15
- * - scaleType (linear or log)
16
- * - pivotValue (number)
17
- * - inverted (boolean)
18
- */
19
- export declare function getScale({ domain, range, scaleType, pivotValue, inverted, }: ScaleOpts): import("d3-scale").ScaleLinear<number, number> | import("d3-scale").ScaleQuantize<number>;
20
- /**
21
- * gets the origin for drawing the graph. for linear this is 0, for log this is arbitrarily set to log(1)==0
22
- *
23
- * @param scaleType -
24
- */
25
- export declare function getOrigin(scaleType: string): 1 | 0;
26
- /**
27
- * produces a "nice" domain that actually rounds down to 0 for the min
28
- * or 0 to the max depending on if all values are positive or negative
29
- *
30
- * @param object - containing attributes
31
- * - domain [min,max]
32
- * - bounds [min,max]
33
- * - mean
34
- * - stddev
35
- * - scaleType (linear or log)
36
- */
37
- export declare function getNiceDomain({ scaleType, domain, bounds, }: {
38
- scaleType: string;
39
- domain: number[];
40
- bounds: number[];
41
- }): [number, number];
1
+ export interface ScaleOpts {
2
+ domain: number[];
3
+ range: number[];
4
+ scaleType: string;
5
+ pivotValue?: number;
6
+ inverted: boolean;
7
+ }
8
+ /**
9
+ * produces a d3-scale from arguments. applies a "nice domain" adjustment
10
+ *
11
+ * @param object - containing attributes
12
+ * - domain [min,max]
13
+ * - range [min,max]
14
+ * - bounds [min,max]
15
+ * - scaleType (linear or log)
16
+ * - pivotValue (number)
17
+ * - inverted (boolean)
18
+ */
19
+ export declare function getScale({ domain, range, scaleType, pivotValue, inverted, }: ScaleOpts): import("d3-scale").ScaleLinear<number, number> | import("d3-scale").ScaleQuantize<number>;
20
+ /**
21
+ * gets the origin for drawing the graph. for linear this is 0, for log this is arbitrarily set to log(1)==0
22
+ *
23
+ * @param scaleType -
24
+ */
25
+ export declare function getOrigin(scaleType: string): 1 | 0;
26
+ /**
27
+ * produces a "nice" domain that actually rounds down to 0 for the min
28
+ * or 0 to the max depending on if all values are positive or negative
29
+ *
30
+ * @param object - containing attributes
31
+ * - domain [min,max]
32
+ * - bounds [min,max]
33
+ * - mean
34
+ * - stddev
35
+ * - scaleType (linear or log)
36
+ */
37
+ export declare function getNiceDomain({ scaleType, domain, bounds, }: {
38
+ scaleType: string;
39
+ domain: number[];
40
+ bounds: number[];
41
+ }): [number, number];
package/dist/util.js ADDED
@@ -0,0 +1,178 @@
1
+ "use strict";
2
+
3
+ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
4
+
5
+ Object.defineProperty(exports, "__esModule", {
6
+ value: true
7
+ });
8
+ exports.getNiceDomain = getNiceDomain;
9
+ exports.getOrigin = getOrigin;
10
+ exports.getScale = getScale;
11
+
12
+ var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
13
+
14
+ var _d3Scale = require("d3-scale");
15
+
16
+ /**
17
+ * produces a d3-scale from arguments. applies a "nice domain" adjustment
18
+ *
19
+ * @param object - containing attributes
20
+ * - domain [min,max]
21
+ * - range [min,max]
22
+ * - bounds [min,max]
23
+ * - scaleType (linear or log)
24
+ * - pivotValue (number)
25
+ * - inverted (boolean)
26
+ */
27
+ function getScale(_ref) {
28
+ var _ref$domain = _ref.domain,
29
+ domain = _ref$domain === void 0 ? [] : _ref$domain,
30
+ _ref$range = _ref.range,
31
+ range = _ref$range === void 0 ? [] : _ref$range,
32
+ scaleType = _ref.scaleType,
33
+ pivotValue = _ref.pivotValue,
34
+ inverted = _ref.inverted;
35
+ var scale;
36
+
37
+ var _domain = (0, _slicedToArray2["default"])(domain, 2),
38
+ min = _domain[0],
39
+ max = _domain[1];
40
+
41
+ if (min === undefined || max === undefined) {
42
+ throw new Error('invalid domain');
43
+ }
44
+
45
+ if (scaleType === 'linear') {
46
+ scale = (0, _d3Scale.scaleLinear)();
47
+ } else if (scaleType === 'log') {
48
+ scale = (0, _d3Scale.scaleLog)();
49
+ scale.base(2);
50
+ } else if (scaleType === 'quantize') {
51
+ scale = (0, _d3Scale.scaleQuantize)();
52
+ } else {
53
+ throw new Error('undefined scaleType');
54
+ }
55
+
56
+ scale.domain(pivotValue !== undefined ? [min, pivotValue, max] : [min, max]);
57
+ scale.nice();
58
+
59
+ var _range = (0, _slicedToArray2["default"])(range, 2),
60
+ rangeMin = _range[0],
61
+ rangeMax = _range[1];
62
+
63
+ if (rangeMin === undefined || rangeMax === undefined) {
64
+ throw new Error('invalid range');
65
+ }
66
+
67
+ scale.range(inverted ? range.slice().reverse() : range);
68
+ return scale;
69
+ }
70
+ /**
71
+ * gets the origin for drawing the graph. for linear this is 0, for log this is arbitrarily set to log(1)==0
72
+ *
73
+ * @param scaleType -
74
+ */
75
+
76
+
77
+ function getOrigin(scaleType) {
78
+ // if (pivot) {
79
+ // if (pivot === 'mean') {
80
+ // return stats.scoreMean || 0
81
+ // }
82
+ // if (pivot === 'zero') {
83
+ // return 0
84
+ // }
85
+ // return parseFloat()
86
+ // }
87
+ // if (scaleType === 'z_score') {
88
+ // return stats.scoreMean || 0
89
+ // }
90
+ if (scaleType === 'log') {
91
+ return 1;
92
+ }
93
+
94
+ return 0;
95
+ }
96
+ /**
97
+ * produces a "nice" domain that actually rounds down to 0 for the min
98
+ * or 0 to the max depending on if all values are positive or negative
99
+ *
100
+ * @param object - containing attributes
101
+ * - domain [min,max]
102
+ * - bounds [min,max]
103
+ * - mean
104
+ * - stddev
105
+ * - scaleType (linear or log)
106
+ */
107
+
108
+
109
+ function getNiceDomain(_ref2) {
110
+ var scaleType = _ref2.scaleType,
111
+ domain = _ref2.domain,
112
+ bounds = _ref2.bounds;
113
+
114
+ var _bounds = (0, _slicedToArray2["default"])(bounds, 2),
115
+ minScore = _bounds[0],
116
+ maxScore = _bounds[1];
117
+
118
+ var _domain2 = (0, _slicedToArray2["default"])(domain, 2),
119
+ min = _domain2[0],
120
+ max = _domain2[1];
121
+
122
+ if (scaleType === 'linear') {
123
+ if (max < 0) {
124
+ max = 0;
125
+ }
126
+
127
+ if (min > 0) {
128
+ min = 0;
129
+ }
130
+ }
131
+
132
+ if (scaleType === 'log') {
133
+ // if the min is 0, assume that it's just something
134
+ // with no read coverage and that we should ignore it in calculations
135
+ // if it's greater than 1 pin to 1 for the full range also
136
+ // otherwise, we may see bigwigs with fractional values
137
+ if (min === 0 || min > 1) {
138
+ min = 1;
139
+ }
140
+ }
141
+
142
+ if (min === undefined || max === undefined) {
143
+ throw new Error('invalid domain supplied to stats function');
144
+ }
145
+
146
+ if (minScore !== undefined && minScore !== Number.MIN_VALUE) {
147
+ min = minScore;
148
+ }
149
+
150
+ if (maxScore !== undefined && maxScore !== Number.MAX_VALUE) {
151
+ max = maxScore;
152
+ }
153
+
154
+ var getScaleType = function getScaleType(type) {
155
+ if (type === 'linear') {
156
+ return (0, _d3Scale.scaleLinear)();
157
+ }
158
+
159
+ if (type === 'log') {
160
+ var _scale = (0, _d3Scale.scaleLog)();
161
+
162
+ _scale.base(2);
163
+
164
+ return _scale;
165
+ }
166
+
167
+ if (type === 'quantize') {
168
+ return (0, _d3Scale.scaleQuantize)();
169
+ }
170
+
171
+ throw new Error("undefined scaleType ".concat(type));
172
+ };
173
+
174
+ var scale = getScaleType(scaleType);
175
+ scale.domain([min, max]);
176
+ scale.nice();
177
+ return scale.domain();
178
+ }
@@ -0,0 +1,66 @@
1
+ "use strict";
2
+
3
+ var _util = require("./util");
4
+
5
+ test('linear scale', function () {
6
+ var scaleType = 'linear';
7
+ var domain = [0, 100];
8
+ var range = [0, 100];
9
+ var scale = (0, _util.getScale)({
10
+ scaleType: scaleType,
11
+ domain: domain,
12
+ range: range
13
+ });
14
+ expect(scale.domain()).toEqual(domain);
15
+ });
16
+ test('log scale', function () {
17
+ var scaleType = 'log';
18
+ var domain = [1, 100];
19
+ var range = [0, 100];
20
+ var scale = (0, _util.getScale)({
21
+ scaleType: scaleType,
22
+ domain: domain,
23
+ range: range
24
+ });
25
+ expect(scale.domain()).toEqual([1, 128]);
26
+ });
27
+ test('test inverted', function () {
28
+ var scaleType = 'log';
29
+ var inverted = true;
30
+ var domain = [1, 100];
31
+ var range = [0, 100];
32
+ var scale = (0, _util.getScale)({
33
+ scaleType: scaleType,
34
+ domain: domain,
35
+ range: range,
36
+ inverted: inverted
37
+ });
38
+ expect(scale.domain()).toEqual([1, 128]);
39
+ expect(scale.range()).toEqual(range.reverse());
40
+ });
41
+ test('test minScore', function () {
42
+ var scaleType = 'linear';
43
+ var domain = [0, 100];
44
+ var range = [0, 100];
45
+ var bounds = [50, undefined];
46
+ var ret = (0, _util.getNiceDomain)({
47
+ scaleType: scaleType,
48
+ domain: domain,
49
+ range: range,
50
+ bounds: bounds
51
+ });
52
+ expect(ret).toEqual([50, 100]);
53
+ });
54
+ test('test min and max score', function () {
55
+ var scaleType = 'linear';
56
+ var domain = [1, 100];
57
+ var range = [0, 100];
58
+ var bounds = [undefined, 70];
59
+ var ret = (0, _util.getNiceDomain)({
60
+ scaleType: scaleType,
61
+ domain: domain,
62
+ range: range,
63
+ bounds: bounds
64
+ });
65
+ expect(ret).toEqual([0, 70]);
66
+ });
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-wiggle",
3
- "version": "1.6.8",
3
+ "version": "1.7.1",
4
4
  "description": "JBrowse 2 wiggle adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -18,15 +18,13 @@
18
18
  "distMain": "dist/index.js",
19
19
  "srcMain": "src/index.ts",
20
20
  "main": "dist/index.js",
21
- "distModule": "dist/plugin-wiggle.esm.js",
22
- "module": "dist/plugin-wiggle.esm.js",
23
21
  "files": [
24
22
  "dist",
25
23
  "src"
26
24
  ],
27
25
  "scripts": {
28
- "start": "tsdx watch --verbose --noClean",
29
- "build": "tsdx build",
26
+ "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
27
+ "postbuild": "tsc --build tsconfig.build.json",
30
28
  "test": "cd ../..; jest plugins/wiggle",
31
29
  "prepublishOnly": "yarn test",
32
30
  "prepack": "yarn build; yarn useDist",
@@ -60,5 +58,5 @@
60
58
  "publishConfig": {
61
59
  "access": "public"
62
60
  },
63
- "gitHead": "585e522096651ef4afb188366bb46d723439dc1b"
61
+ "gitHead": "6da232090c90f22ac96fd464c33082c89b8da14b"
64
62
  }
@@ -558,7 +558,7 @@ const stateModelFactory = (
558
558
  try {
559
559
  stats = await getStats({
560
560
  signal: aborter.signal,
561
- filters: self.filters,
561
+ ...self.renderProps(),
562
562
  })
563
563
  if (isAlive(self)) {
564
564
  self.updateStats(stats)
@@ -591,7 +591,7 @@ const stateModelFactory = (
591
591
 
592
592
  const wiggleStats = await getStats({
593
593
  signal: aborter.signal,
594
- filters: self.filters,
594
+ ...self.renderProps(),
595
595
  })
596
596
 
597
597
  if (isAlive(self)) {
@@ -69,6 +69,7 @@ export default abstract class WiggleBaseRenderer extends FeatureRendererType {
69
69
  ...results,
70
70
  ...res,
71
71
  features,
72
+ containsNoTransferables: true,
72
73
  height,
73
74
  width,
74
75
  }
@@ -1 +0,0 @@
1
- export {};
@@ -1 +0,0 @@
1
- export {};
@@ -1 +0,0 @@
1
- export {};
@@ -1 +0,0 @@
1
- export {};