@jbrowse/plugin-sequence 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.
- package/dist/BgzipFastaAdapter/BgzipFastaAdapter.js +7 -7
- package/dist/BgzipFastaAdapter/BgzipFastaAdapter.test.js +3 -3
- package/dist/BgzipFastaAdapter/configSchema.js +2 -2
- package/dist/BgzipFastaAdapter/index.js +1 -1
- package/dist/ChromSizesAdapter/ChromSizesAdapter.js +13 -13
- package/dist/ChromSizesAdapter/ChromSizesAdapter.test.js +3 -3
- package/dist/ChromSizesAdapter/configSchema.js +2 -2
- package/dist/ChromSizesAdapter/index.js +1 -1
- package/dist/DivSequenceRenderer/components/DivSequenceRendering.js +22 -22
- package/dist/DivSequenceRenderer/components/DivSequenceRendering.test.js +27 -27
- package/dist/DivSequenceRenderer/configSchema.js +2 -2
- package/dist/DivSequenceRenderer/index.js +2 -2
- package/dist/GCContentAdapter/GCContentAdapter.js +18 -18
- package/dist/GCContentAdapter/configSchema.js +2 -2
- package/dist/GCContentAdapter/index.js +5 -5
- package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js +17 -17
- package/dist/IndexedFastaAdapter/IndexedFastaAdapter.test.js +3 -3
- package/dist/IndexedFastaAdapter/configSchema.js +2 -2
- package/dist/IndexedFastaAdapter/index.js +1 -1
- package/dist/LinearReferenceSequenceDisplay/model.d.ts +1 -1
- package/dist/LinearReferenceSequenceDisplay/model.js +4 -4
- package/dist/TwoBitAdapter/TwoBitAdapter.js +18 -18
- package/dist/TwoBitAdapter/TwoBitAdapter.test.js +6 -6
- package/dist/TwoBitAdapter/configSchema.js +2 -2
- package/dist/TwoBitAdapter/index.js +1 -1
- package/dist/index.js +26 -26
- package/dist/index.test.js +2 -2
- package/dist/referenceSeqTrackConfig.js +6 -1
- package/package.json +3 -3
- package/src/referenceSeqTrackConfig.ts +5 -0
|
@@ -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
|
|
8
|
+
exports.default = void 0;
|
|
9
9
|
|
|
10
10
|
var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
|
|
11
11
|
|
|
@@ -25,19 +25,19 @@ var _configuration = require("@jbrowse/core/configuration");
|
|
|
25
25
|
|
|
26
26
|
var _IndexedFastaAdapter = _interopRequireDefault(require("../IndexedFastaAdapter/IndexedFastaAdapter"));
|
|
27
27
|
|
|
28
|
-
function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2
|
|
28
|
+
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); }; }
|
|
29
29
|
|
|
30
30
|
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; } }
|
|
31
31
|
|
|
32
32
|
var _default = /*#__PURE__*/function (_IndexedFasta) {
|
|
33
|
-
(0, _inherits2
|
|
33
|
+
(0, _inherits2.default)(_default, _IndexedFasta);
|
|
34
34
|
|
|
35
35
|
var _super = _createSuper(_default);
|
|
36
36
|
|
|
37
37
|
function _default(config, getSubAdapter, pluginManager) {
|
|
38
38
|
var _this;
|
|
39
39
|
|
|
40
|
-
(0, _classCallCheck2
|
|
40
|
+
(0, _classCallCheck2.default)(this, _default);
|
|
41
41
|
_this = _super.call(this, config, getSubAdapter, pluginManager);
|
|
42
42
|
var fastaLocation = (0, _configuration.readConfObject)(config, 'fastaLocation');
|
|
43
43
|
var faiLocation = (0, _configuration.readConfObject)(config, 'faiLocation');
|
|
@@ -64,7 +64,7 @@ var _default = /*#__PURE__*/function (_IndexedFasta) {
|
|
|
64
64
|
return _this;
|
|
65
65
|
}
|
|
66
66
|
|
|
67
|
-
return (0, _createClass2
|
|
68
|
-
}(_IndexedFastaAdapter
|
|
67
|
+
return (0, _createClass2.default)(_default);
|
|
68
|
+
}(_IndexedFastaAdapter.default);
|
|
69
69
|
|
|
70
|
-
exports
|
|
70
|
+
exports.default = _default;
|
|
@@ -12,13 +12,13 @@ var _BgzipFastaAdapter = _interopRequireDefault(require("./BgzipFastaAdapter"));
|
|
|
12
12
|
|
|
13
13
|
var _configSchema = _interopRequireDefault(require("./configSchema"));
|
|
14
14
|
|
|
15
|
-
test('can use a indexed fasta with gzi', /*#__PURE__*/(0, _asyncToGenerator2
|
|
15
|
+
test('can use a indexed fasta with gzi', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
|
|
16
16
|
var adapter, features, featuresArray, features2, featuresArray2;
|
|
17
|
-
return _regenerator
|
|
17
|
+
return _regenerator.default.wrap(function _callee$(_context) {
|
|
18
18
|
while (1) {
|
|
19
19
|
switch (_context.prev = _context.next) {
|
|
20
20
|
case 0:
|
|
21
|
-
adapter = new _BgzipFastaAdapter
|
|
21
|
+
adapter = new _BgzipFastaAdapter.default(_configSchema.default.create({
|
|
22
22
|
fastaLocation: {
|
|
23
23
|
localPath: require.resolve('../../test_data/volvox.fa.gz'),
|
|
24
24
|
locationType: 'LocalPathLocation'
|
|
@@ -3,7 +3,7 @@
|
|
|
3
3
|
Object.defineProperty(exports, "__esModule", {
|
|
4
4
|
value: true
|
|
5
5
|
});
|
|
6
|
-
exports
|
|
6
|
+
exports.default = void 0;
|
|
7
7
|
|
|
8
8
|
var _configuration = require("@jbrowse/core/configuration");
|
|
9
9
|
|
|
@@ -33,4 +33,4 @@ var _default = (0, _configuration.ConfigurationSchema)('BgzipFastaAdapter', {
|
|
|
33
33
|
explicitlyTyped: true
|
|
34
34
|
});
|
|
35
35
|
|
|
36
|
-
exports
|
|
36
|
+
exports.default = _default;
|
|
@@ -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
|
|
8
|
+
exports.default = void 0;
|
|
9
9
|
|
|
10
10
|
var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
|
|
11
11
|
|
|
@@ -33,12 +33,12 @@ var _io = require("@jbrowse/core/util/io");
|
|
|
33
33
|
|
|
34
34
|
var _configuration = require("@jbrowse/core/configuration");
|
|
35
35
|
|
|
36
|
-
function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2
|
|
36
|
+
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); }; }
|
|
37
37
|
|
|
38
38
|
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; } }
|
|
39
39
|
|
|
40
40
|
var _default = /*#__PURE__*/function (_BaseAdapter) {
|
|
41
|
-
(0, _inherits2
|
|
41
|
+
(0, _inherits2.default)(_default, _BaseAdapter);
|
|
42
42
|
|
|
43
43
|
var _super = _createSuper(_default);
|
|
44
44
|
|
|
@@ -46,10 +46,10 @@ var _default = /*#__PURE__*/function (_BaseAdapter) {
|
|
|
46
46
|
function _default(config, getSubAdapter, pluginManager) {
|
|
47
47
|
var _this;
|
|
48
48
|
|
|
49
|
-
(0, _classCallCheck2
|
|
49
|
+
(0, _classCallCheck2.default)(this, _default);
|
|
50
50
|
_this = _super.call(this, config, getSubAdapter, pluginManager);
|
|
51
|
-
(0, _defineProperty2
|
|
52
|
-
(0, _defineProperty2
|
|
51
|
+
(0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "refSeqs", void 0);
|
|
52
|
+
(0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "source", void 0);
|
|
53
53
|
var chromSizesLocation = (0, _configuration.readConfObject)(config, 'chromSizesLocation');
|
|
54
54
|
|
|
55
55
|
if (!chromSizesLocation) {
|
|
@@ -62,12 +62,12 @@ var _default = /*#__PURE__*/function (_BaseAdapter) {
|
|
|
62
62
|
return _this;
|
|
63
63
|
}
|
|
64
64
|
|
|
65
|
-
(0, _createClass2
|
|
65
|
+
(0, _createClass2.default)(_default, [{
|
|
66
66
|
key: "init",
|
|
67
67
|
value: function () {
|
|
68
|
-
var _init = (0, _asyncToGenerator2
|
|
68
|
+
var _init = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(file) {
|
|
69
69
|
var data, refSeqs;
|
|
70
|
-
return _regenerator
|
|
70
|
+
return _regenerator.default.wrap(function _callee$(_context) {
|
|
71
71
|
while (1) {
|
|
72
72
|
switch (_context.prev = _context.next) {
|
|
73
73
|
case 0:
|
|
@@ -89,7 +89,7 @@ var _default = /*#__PURE__*/function (_BaseAdapter) {
|
|
|
89
89
|
data.split('\n').forEach(function (line) {
|
|
90
90
|
if (line.length) {
|
|
91
91
|
var _line$split = line.split('\t'),
|
|
92
|
-
_line$split2 = (0, _slicedToArray2
|
|
92
|
+
_line$split2 = (0, _slicedToArray2.default)(_line$split, 2),
|
|
93
93
|
name = _line$split2[0],
|
|
94
94
|
length = _line$split2[1];
|
|
95
95
|
|
|
@@ -115,9 +115,9 @@ var _default = /*#__PURE__*/function (_BaseAdapter) {
|
|
|
115
115
|
}, {
|
|
116
116
|
key: "getRegions",
|
|
117
117
|
value: function () {
|
|
118
|
-
var _getRegions = (0, _asyncToGenerator2
|
|
118
|
+
var _getRegions = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
|
|
119
119
|
var refSeqs;
|
|
120
|
-
return _regenerator
|
|
120
|
+
return _regenerator.default.wrap(function _callee2$(_context2) {
|
|
121
121
|
while (1) {
|
|
122
122
|
switch (_context2.prev = _context2.next) {
|
|
123
123
|
case 0:
|
|
@@ -167,4 +167,4 @@ var _default = /*#__PURE__*/function (_BaseAdapter) {
|
|
|
167
167
|
return _default;
|
|
168
168
|
}(_BaseAdapter2.BaseAdapter);
|
|
169
169
|
|
|
170
|
-
exports
|
|
170
|
+
exports.default = _default;
|
|
@@ -10,13 +10,13 @@ var _ChromSizesAdapter = _interopRequireDefault(require("./ChromSizesAdapter"));
|
|
|
10
10
|
|
|
11
11
|
var _configSchema = _interopRequireDefault(require("./configSchema"));
|
|
12
12
|
|
|
13
|
-
test('adapter can fetch sequence from volvox.chrom.sizes', /*#__PURE__*/(0, _asyncToGenerator2
|
|
13
|
+
test('adapter can fetch sequence from volvox.chrom.sizes', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
|
|
14
14
|
var adapter, regions;
|
|
15
|
-
return _regenerator
|
|
15
|
+
return _regenerator.default.wrap(function _callee$(_context) {
|
|
16
16
|
while (1) {
|
|
17
17
|
switch (_context.prev = _context.next) {
|
|
18
18
|
case 0:
|
|
19
|
-
adapter = new _ChromSizesAdapter
|
|
19
|
+
adapter = new _ChromSizesAdapter.default(_configSchema.default.create({
|
|
20
20
|
chromSizesLocation: {
|
|
21
21
|
localPath: require.resolve('./test_data/volvox.chrom.sizes'),
|
|
22
22
|
locationType: 'LocalPathLocation'
|
|
@@ -3,7 +3,7 @@
|
|
|
3
3
|
Object.defineProperty(exports, "__esModule", {
|
|
4
4
|
value: true
|
|
5
5
|
});
|
|
6
|
-
exports
|
|
6
|
+
exports.default = void 0;
|
|
7
7
|
|
|
8
8
|
var _configuration = require("@jbrowse/core/configuration");
|
|
9
9
|
|
|
@@ -19,4 +19,4 @@ var _default = (0, _configuration.ConfigurationSchema)('ChromSizesAdapter', {
|
|
|
19
19
|
explicitlyTyped: true
|
|
20
20
|
});
|
|
21
21
|
|
|
22
|
-
exports
|
|
22
|
+
exports.default = _default;
|
|
@@ -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
|
|
8
|
+
exports.default = void 0;
|
|
9
9
|
|
|
10
10
|
var _extends2 = _interopRequireDefault(require("@babel/runtime/helpers/extends"));
|
|
11
11
|
|
|
@@ -61,13 +61,13 @@ function Translation(props) {
|
|
|
61
61
|
var render = 1 / bpPerPx >= 12;
|
|
62
62
|
var width = (region.end - region.start) / bpPerPx;
|
|
63
63
|
var map = ['#d8d8d8', '#adadad', '#8f8f8f'].reverse();
|
|
64
|
-
return /*#__PURE__*/_react
|
|
64
|
+
return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, translated.map(function (element, index) {
|
|
65
65
|
var x = region.reversed ? width - (w * (index + 1) + effectiveFrame / scale - drop) : w * index + effectiveFrame / scale - drop;
|
|
66
66
|
var letter = element.letter,
|
|
67
67
|
codon = element.codon;
|
|
68
|
-
return /*#__PURE__*/_react
|
|
68
|
+
return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, {
|
|
69
69
|
key: "".concat(index, "-").concat(letter)
|
|
70
|
-
}, /*#__PURE__*/_react
|
|
70
|
+
}, /*#__PURE__*/_react.default.createElement("rect", {
|
|
71
71
|
x: x,
|
|
72
72
|
y: y,
|
|
73
73
|
width: render ? w : w + 0.7
|
|
@@ -76,7 +76,7 @@ function Translation(props) {
|
|
|
76
76
|
height: height,
|
|
77
77
|
stroke: render ? '#555' : 'none',
|
|
78
78
|
fill: _util.defaultStarts.includes(codon) ? theme.palette.startCodon : _util.defaultStops.includes(codon) ? theme.palette.stopCodon : map[Math.abs(frame)]
|
|
79
|
-
}), render ? /*#__PURE__*/_react
|
|
79
|
+
}), render ? /*#__PURE__*/_react.default.createElement("text", {
|
|
80
80
|
x: x + w / 2,
|
|
81
81
|
y: y + height / 2,
|
|
82
82
|
dominantBaseline: "middle",
|
|
@@ -96,26 +96,26 @@ function DNA(props) {
|
|
|
96
96
|
var render = 1 / bpPerPx >= 12;
|
|
97
97
|
|
|
98
98
|
var _bpSpanPx = (0, _util.bpSpanPx)(feature.get('start'), feature.get('end'), region, bpPerPx),
|
|
99
|
-
_bpSpanPx2 = (0, _slicedToArray2
|
|
99
|
+
_bpSpanPx2 = (0, _slicedToArray2.default)(_bpSpanPx, 2),
|
|
100
100
|
leftPx = _bpSpanPx2[0],
|
|
101
101
|
rightPx = _bpSpanPx2[1];
|
|
102
102
|
|
|
103
103
|
var reverse = region.reversed;
|
|
104
104
|
var len = feature.get('end') - feature.get('start');
|
|
105
105
|
var w = Math.max((rightPx - leftPx) / len, 0.8);
|
|
106
|
-
return /*#__PURE__*/_react
|
|
106
|
+
return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, seq.split('').map(function (letter, index) {
|
|
107
107
|
var color = theme.palette.bases[letter.toUpperCase()];
|
|
108
108
|
var x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
|
|
109
|
-
return /*#__PURE__*/_react
|
|
109
|
+
return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, {
|
|
110
110
|
key: index
|
|
111
|
-
}, /*#__PURE__*/_react
|
|
111
|
+
}, /*#__PURE__*/_react.default.createElement("rect", {
|
|
112
112
|
x: x,
|
|
113
113
|
y: y,
|
|
114
114
|
width: w,
|
|
115
115
|
height: height,
|
|
116
116
|
fill: color ? color.main : '#aaa',
|
|
117
117
|
stroke: render ? '#555' : 'none'
|
|
118
|
-
}), render ? /*#__PURE__*/_react
|
|
118
|
+
}), render ? /*#__PURE__*/_react.default.createElement("text", {
|
|
119
119
|
x: x + w / 2,
|
|
120
120
|
y: y + height / 2,
|
|
121
121
|
dominantBaseline: "middle",
|
|
@@ -135,14 +135,14 @@ var SequenceSVG = function SequenceSVG(_ref) {
|
|
|
135
135
|
showTranslation = _ref.showTranslation,
|
|
136
136
|
bpPerPx = _ref.bpPerPx;
|
|
137
137
|
|
|
138
|
-
var _regions = (0, _slicedToArray2
|
|
138
|
+
var _regions = (0, _slicedToArray2.default)(regions, 1),
|
|
139
139
|
region = _regions[0];
|
|
140
140
|
|
|
141
141
|
var theme = (0, _ui.createJBrowseTheme)(configTheme);
|
|
142
142
|
var codonTable = (0, _util.generateCodonTable)(_util.defaultCodonTable);
|
|
143
143
|
var height = 20;
|
|
144
144
|
|
|
145
|
-
var _ref2 = (0, _toConsumableArray2
|
|
145
|
+
var _ref2 = (0, _toConsumableArray2.default)(features.values()),
|
|
146
146
|
feature = _ref2[0];
|
|
147
147
|
|
|
148
148
|
if (!feature) {
|
|
@@ -158,8 +158,8 @@ var SequenceSVG = function SequenceSVG(_ref) {
|
|
|
158
158
|
|
|
159
159
|
|
|
160
160
|
var currY = -20;
|
|
161
|
-
return /*#__PURE__*/_react
|
|
162
|
-
return /*#__PURE__*/_react
|
|
161
|
+
return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, showTranslation && (region.reversed ? showReverse : showForward) ? [2, 1, 0].map(function (index) {
|
|
162
|
+
return /*#__PURE__*/_react.default.createElement(Translation, {
|
|
163
163
|
key: "translation-".concat(index),
|
|
164
164
|
seq: seq,
|
|
165
165
|
y: currY += 20,
|
|
@@ -171,7 +171,7 @@ var SequenceSVG = function SequenceSVG(_ref) {
|
|
|
171
171
|
height: height,
|
|
172
172
|
reverse: region.reversed
|
|
173
173
|
});
|
|
174
|
-
}) : null, showForward ? /*#__PURE__*/_react
|
|
174
|
+
}) : null, showForward ? /*#__PURE__*/_react.default.createElement(DNA, {
|
|
175
175
|
height: height,
|
|
176
176
|
y: currY += 20,
|
|
177
177
|
feature: feature,
|
|
@@ -179,7 +179,7 @@ var SequenceSVG = function SequenceSVG(_ref) {
|
|
|
179
179
|
seq: region.reversed ? (0, _util.complement)(seq) : seq,
|
|
180
180
|
bpPerPx: bpPerPx,
|
|
181
181
|
theme: theme
|
|
182
|
-
}) : null, showReverse ? /*#__PURE__*/_react
|
|
182
|
+
}) : null, showReverse ? /*#__PURE__*/_react.default.createElement(DNA, {
|
|
183
183
|
height: height,
|
|
184
184
|
y: currY += 20,
|
|
185
185
|
feature: feature,
|
|
@@ -188,7 +188,7 @@ var SequenceSVG = function SequenceSVG(_ref) {
|
|
|
188
188
|
bpPerPx: bpPerPx,
|
|
189
189
|
theme: theme
|
|
190
190
|
}) : null, showTranslation && (region.reversed ? showForward : showReverse) ? [0, -1, -2].map(function (index) {
|
|
191
|
-
return /*#__PURE__*/_react
|
|
191
|
+
return /*#__PURE__*/_react.default.createElement(Translation, {
|
|
192
192
|
key: "rev-translation-".concat(index),
|
|
193
193
|
seq: seq,
|
|
194
194
|
y: currY += 20,
|
|
@@ -208,7 +208,7 @@ var Wrapper = function Wrapper(_ref3) {
|
|
|
208
208
|
width = _ref3.width,
|
|
209
209
|
totalHeight = _ref3.totalHeight,
|
|
210
210
|
children = _ref3.children;
|
|
211
|
-
return exportSVG ? /*#__PURE__*/_react
|
|
211
|
+
return exportSVG ? /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, children) : /*#__PURE__*/_react.default.createElement("svg", {
|
|
212
212
|
"data-testid": "sequence_track",
|
|
213
213
|
width: width,
|
|
214
214
|
height: totalHeight,
|
|
@@ -223,17 +223,17 @@ function Sequence(props) {
|
|
|
223
223
|
var regions = props.regions,
|
|
224
224
|
bpPerPx = props.bpPerPx;
|
|
225
225
|
|
|
226
|
-
var _regions2 = (0, _slicedToArray2
|
|
226
|
+
var _regions2 = (0, _slicedToArray2.default)(regions, 1),
|
|
227
227
|
region = _regions2[0];
|
|
228
228
|
|
|
229
229
|
var width = (region.end - region.start) / bpPerPx;
|
|
230
230
|
var totalHeight = 200;
|
|
231
|
-
return /*#__PURE__*/_react
|
|
231
|
+
return /*#__PURE__*/_react.default.createElement(Wrapper, (0, _extends2.default)({}, props, {
|
|
232
232
|
totalHeight: totalHeight,
|
|
233
233
|
width: width
|
|
234
|
-
}), /*#__PURE__*/_react
|
|
234
|
+
}), /*#__PURE__*/_react.default.createElement(SequenceSVG, props));
|
|
235
235
|
}
|
|
236
236
|
|
|
237
237
|
var _default = (0, _mobxReact.observer)(Sequence);
|
|
238
238
|
|
|
239
|
-
exports
|
|
239
|
+
exports.default = _default;
|
|
@@ -30,25 +30,25 @@ var _DivSequenceRendering = _interopRequireDefault(require("./DivSequenceRenderi
|
|
|
30
30
|
|
|
31
31
|
var _configSchema = _interopRequireDefault(require("../configSchema"));
|
|
32
32
|
|
|
33
|
-
function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2
|
|
33
|
+
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); }; }
|
|
34
34
|
|
|
35
35
|
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; } }
|
|
36
36
|
|
|
37
37
|
function Rendering(props) {
|
|
38
|
-
return /*#__PURE__*/_react
|
|
38
|
+
return /*#__PURE__*/_react.default.createElement(_core.ThemeProvider, {
|
|
39
39
|
theme: (0, _ui.createJBrowseTheme)()
|
|
40
|
-
}, /*#__PURE__*/_react
|
|
40
|
+
}, /*#__PURE__*/_react.default.createElement(_DivSequenceRendering.default, props));
|
|
41
41
|
}
|
|
42
42
|
|
|
43
43
|
var ErrorCatcher = /*#__PURE__*/function (_React$Component) {
|
|
44
|
-
(0, _inherits2
|
|
44
|
+
(0, _inherits2.default)(ErrorCatcher, _React$Component);
|
|
45
45
|
|
|
46
46
|
var _super = _createSuper(ErrorCatcher);
|
|
47
47
|
|
|
48
48
|
function ErrorCatcher(props) {
|
|
49
49
|
var _this;
|
|
50
50
|
|
|
51
|
-
(0, _classCallCheck2
|
|
51
|
+
(0, _classCallCheck2.default)(this, ErrorCatcher);
|
|
52
52
|
_this = _super.call(this, props);
|
|
53
53
|
_this.state = {
|
|
54
54
|
hasError: false,
|
|
@@ -57,7 +57,7 @@ var ErrorCatcher = /*#__PURE__*/function (_React$Component) {
|
|
|
57
57
|
return _this;
|
|
58
58
|
}
|
|
59
59
|
|
|
60
|
-
(0, _createClass2
|
|
60
|
+
(0, _createClass2.default)(ErrorCatcher, [{
|
|
61
61
|
key: "render",
|
|
62
62
|
value: function render() {
|
|
63
63
|
var _this$state = this.state,
|
|
@@ -66,7 +66,7 @@ var ErrorCatcher = /*#__PURE__*/function (_React$Component) {
|
|
|
66
66
|
|
|
67
67
|
if (hasError) {
|
|
68
68
|
// You can render any custom fallback UI
|
|
69
|
-
return /*#__PURE__*/_react
|
|
69
|
+
return /*#__PURE__*/_react.default.createElement("h1", {
|
|
70
70
|
className: "error"
|
|
71
71
|
}, errorText);
|
|
72
72
|
}
|
|
@@ -85,10 +85,10 @@ var ErrorCatcher = /*#__PURE__*/function (_React$Component) {
|
|
|
85
85
|
}
|
|
86
86
|
}]);
|
|
87
87
|
return ErrorCatcher;
|
|
88
|
-
}(_react
|
|
88
|
+
}(_react.default.Component);
|
|
89
89
|
|
|
90
90
|
ErrorCatcher.propTypes = {
|
|
91
|
-
children: _propTypes
|
|
91
|
+
children: _propTypes.default.node.isRequired
|
|
92
92
|
};
|
|
93
93
|
describe('<DivSequenceRendering />', function () {
|
|
94
94
|
// This just keeps our testing logs clean by not displaying `console.error`s
|
|
@@ -113,7 +113,7 @@ describe('<DivSequenceRendering />', function () {
|
|
|
113
113
|
console.error = originalError;
|
|
114
114
|
});
|
|
115
115
|
it('renders with no features', function () {
|
|
116
|
-
var _render = (0, _react2.render)( /*#__PURE__*/_react
|
|
116
|
+
var _render = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(Rendering, {
|
|
117
117
|
width: 500,
|
|
118
118
|
height: 500,
|
|
119
119
|
regions: [{
|
|
@@ -121,11 +121,11 @@ describe('<DivSequenceRendering />', function () {
|
|
|
121
121
|
start: 0,
|
|
122
122
|
end: 300
|
|
123
123
|
}],
|
|
124
|
-
layout: new _PrecomputedLayout
|
|
124
|
+
layout: new _PrecomputedLayout.default({
|
|
125
125
|
rectangles: {},
|
|
126
126
|
totalHeight: 20
|
|
127
127
|
}),
|
|
128
|
-
config: _configSchema
|
|
128
|
+
config: _configSchema.default.create(),
|
|
129
129
|
bpPerPx: 3
|
|
130
130
|
})),
|
|
131
131
|
container = _render.container;
|
|
@@ -133,7 +133,7 @@ describe('<DivSequenceRendering />', function () {
|
|
|
133
133
|
expect(container).toMatchSnapshot();
|
|
134
134
|
});
|
|
135
135
|
it('renders with one, zoomed way out', function () {
|
|
136
|
-
var _render2 = (0, _react2.render)( /*#__PURE__*/_react
|
|
136
|
+
var _render2 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(Rendering, {
|
|
137
137
|
width: 500,
|
|
138
138
|
height: 500,
|
|
139
139
|
regions: [{
|
|
@@ -141,13 +141,13 @@ describe('<DivSequenceRendering />', function () {
|
|
|
141
141
|
start: 0,
|
|
142
142
|
end: 1000
|
|
143
143
|
}],
|
|
144
|
-
features: new Map([['one', new _simpleFeature
|
|
144
|
+
features: new Map([['one', new _simpleFeature.default({
|
|
145
145
|
uniqueId: 'one',
|
|
146
146
|
start: 1,
|
|
147
147
|
end: 3,
|
|
148
148
|
seq: 'AB'
|
|
149
149
|
})]]),
|
|
150
|
-
config: _configSchema
|
|
150
|
+
config: _configSchema.default.create({}),
|
|
151
151
|
bpPerPx: 3
|
|
152
152
|
})),
|
|
153
153
|
container = _render2.container;
|
|
@@ -155,7 +155,7 @@ describe('<DivSequenceRendering />', function () {
|
|
|
155
155
|
expect(container).toMatchSnapshot();
|
|
156
156
|
});
|
|
157
157
|
it('renders with one feature with no seq, zoomed in, should throw', function () {
|
|
158
|
-
var _render3 = (0, _react2.render)( /*#__PURE__*/_react
|
|
158
|
+
var _render3 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(ErrorCatcher, null, /*#__PURE__*/_react.default.createElement(Rendering, {
|
|
159
159
|
width: 500,
|
|
160
160
|
height: 500,
|
|
161
161
|
regions: [{
|
|
@@ -163,12 +163,12 @@ describe('<DivSequenceRendering />', function () {
|
|
|
163
163
|
start: 0,
|
|
164
164
|
end: 1000
|
|
165
165
|
}],
|
|
166
|
-
features: new Map([['one', new _simpleFeature
|
|
166
|
+
features: new Map([['one', new _simpleFeature.default({
|
|
167
167
|
uniqueId: 'one',
|
|
168
168
|
start: 1,
|
|
169
169
|
end: 3
|
|
170
170
|
})]]),
|
|
171
|
-
config: _configSchema
|
|
171
|
+
config: _configSchema.default.create({}),
|
|
172
172
|
bpPerPx: 0.05
|
|
173
173
|
}))),
|
|
174
174
|
container = _render3.container;
|
|
@@ -176,7 +176,7 @@ describe('<DivSequenceRendering />', function () {
|
|
|
176
176
|
expect(container).toMatchSnapshot();
|
|
177
177
|
});
|
|
178
178
|
it('renders with one feature with an incorrect seq, zoomed in, should throw', function () {
|
|
179
|
-
var _render4 = (0, _react2.render)( /*#__PURE__*/_react
|
|
179
|
+
var _render4 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(ErrorCatcher, null, /*#__PURE__*/_react.default.createElement(Rendering, {
|
|
180
180
|
width: 500,
|
|
181
181
|
height: 500,
|
|
182
182
|
regions: [{
|
|
@@ -184,13 +184,13 @@ describe('<DivSequenceRendering />', function () {
|
|
|
184
184
|
start: 0,
|
|
185
185
|
end: 1000
|
|
186
186
|
}],
|
|
187
|
-
features: new Map([['one', new _simpleFeature
|
|
187
|
+
features: new Map([['one', new _simpleFeature.default({
|
|
188
188
|
uniqueId: 'one',
|
|
189
189
|
start: 1,
|
|
190
190
|
end: 3,
|
|
191
191
|
seq: 'ABC'
|
|
192
192
|
})]]),
|
|
193
|
-
config: _configSchema
|
|
193
|
+
config: _configSchema.default.create({}),
|
|
194
194
|
bpPerPx: 0.05
|
|
195
195
|
}))),
|
|
196
196
|
container = _render4.container;
|
|
@@ -198,7 +198,7 @@ describe('<DivSequenceRendering />', function () {
|
|
|
198
198
|
expect(container).toMatchSnapshot();
|
|
199
199
|
});
|
|
200
200
|
it('renders with one feature with a correct seq, zoomed in, should render nicely', function () {
|
|
201
|
-
var _render5 = (0, _react2.render)( /*#__PURE__*/_react
|
|
201
|
+
var _render5 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(Rendering, {
|
|
202
202
|
width: 500,
|
|
203
203
|
height: 500,
|
|
204
204
|
regions: [{
|
|
@@ -206,13 +206,13 @@ describe('<DivSequenceRendering />', function () {
|
|
|
206
206
|
start: 0,
|
|
207
207
|
end: 1000
|
|
208
208
|
}],
|
|
209
|
-
features: new Map([['one', new _simpleFeature
|
|
209
|
+
features: new Map([['one', new _simpleFeature.default({
|
|
210
210
|
uniqueId: 'one',
|
|
211
211
|
start: 1,
|
|
212
212
|
end: 10,
|
|
213
213
|
seq: 'ABCDEFGHI'
|
|
214
214
|
})]]),
|
|
215
|
-
config: _configSchema
|
|
215
|
+
config: _configSchema.default.create({}),
|
|
216
216
|
bpPerPx: 0.05
|
|
217
217
|
})),
|
|
218
218
|
container = _render5.container;
|
|
@@ -220,7 +220,7 @@ describe('<DivSequenceRendering />', function () {
|
|
|
220
220
|
expect(container).toMatchSnapshot();
|
|
221
221
|
});
|
|
222
222
|
it('renders with one feature reversed with a correct seq, zoomed in, should render nicely', function () {
|
|
223
|
-
var _render6 = (0, _react2.render)( /*#__PURE__*/_react
|
|
223
|
+
var _render6 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(Rendering, {
|
|
224
224
|
width: 500,
|
|
225
225
|
height: 500,
|
|
226
226
|
regions: [{
|
|
@@ -229,13 +229,13 @@ describe('<DivSequenceRendering />', function () {
|
|
|
229
229
|
end: 1000,
|
|
230
230
|
reversed: true
|
|
231
231
|
}],
|
|
232
|
-
features: new Map([['one', new _simpleFeature
|
|
232
|
+
features: new Map([['one', new _simpleFeature.default({
|
|
233
233
|
uniqueId: 'one',
|
|
234
234
|
start: 1,
|
|
235
235
|
end: 10,
|
|
236
236
|
seq: 'ABCDEFGHI'
|
|
237
237
|
})]]),
|
|
238
|
-
config: _configSchema
|
|
238
|
+
config: _configSchema.default.create({}),
|
|
239
239
|
bpPerPx: 0.05
|
|
240
240
|
})),
|
|
241
241
|
container = _render6.container;
|
|
@@ -3,7 +3,7 @@
|
|
|
3
3
|
Object.defineProperty(exports, "__esModule", {
|
|
4
4
|
value: true
|
|
5
5
|
});
|
|
6
|
-
exports
|
|
6
|
+
exports.default = void 0;
|
|
7
7
|
|
|
8
8
|
var _configuration = require("@jbrowse/core/configuration");
|
|
9
9
|
|
|
@@ -17,4 +17,4 @@ var _default = (0, _configuration.ConfigurationSchema)('DivSequenceRenderer', {
|
|
|
17
17
|
explicitlyTyped: true
|
|
18
18
|
});
|
|
19
19
|
|
|
20
|
-
exports
|
|
20
|
+
exports.default = _default;
|
|
@@ -8,13 +8,13 @@ Object.defineProperty(exports, "__esModule", {
|
|
|
8
8
|
Object.defineProperty(exports, "ReactComponent", {
|
|
9
9
|
enumerable: true,
|
|
10
10
|
get: function get() {
|
|
11
|
-
return _DivSequenceRendering
|
|
11
|
+
return _DivSequenceRendering.default;
|
|
12
12
|
}
|
|
13
13
|
});
|
|
14
14
|
Object.defineProperty(exports, "configSchema", {
|
|
15
15
|
enumerable: true,
|
|
16
16
|
get: function get() {
|
|
17
|
-
return _configSchema
|
|
17
|
+
return _configSchema.default;
|
|
18
18
|
}
|
|
19
19
|
});
|
|
20
20
|
|