@jbrowse/plugin-linear-genome-view 2.1.0 → 2.1.3
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/BaseLinearDisplay/components/BaseLinearDisplay.js +27 -54
- package/dist/BaseLinearDisplay/components/BaseLinearDisplay.js.map +1 -1
- package/dist/BaseLinearDisplay/components/Block.js +17 -28
- package/dist/BaseLinearDisplay/components/Block.js.map +1 -1
- package/dist/BaseLinearDisplay/components/LinearBlocks.js +19 -21
- package/dist/BaseLinearDisplay/components/LinearBlocks.js.map +1 -1
- package/dist/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js +27 -48
- package/dist/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js.map +1 -1
- package/dist/BaseLinearDisplay/components/Tooltip.js +29 -58
- package/dist/BaseLinearDisplay/components/Tooltip.js.map +1 -1
- package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js +242 -363
- package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js.map +1 -1
- package/dist/BaseLinearDisplay/models/baseLinearDisplayConfigSchema.js +1 -1
- package/dist/BaseLinearDisplay/models/baseLinearDisplayConfigSchema.js.map +1 -1
- package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.js +77 -129
- package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.js.map +1 -1
- package/dist/LinearBareDisplay/configSchema.js +2 -2
- package/dist/LinearBareDisplay/configSchema.js.map +1 -1
- package/dist/LinearBareDisplay/model.js +13 -19
- package/dist/LinearBareDisplay/model.js.map +1 -1
- package/dist/LinearBasicDisplay/components/SetMaxHeight.js +14 -31
- package/dist/LinearBasicDisplay/components/SetMaxHeight.js.map +1 -1
- package/dist/LinearBasicDisplay/configSchema.js +3 -3
- package/dist/LinearBasicDisplay/configSchema.js.map +1 -1
- package/dist/LinearBasicDisplay/model.js +119 -147
- package/dist/LinearBasicDisplay/model.js.map +1 -1
- package/dist/LinearGenomeView/components/CenterLine.js +11 -12
- package/dist/LinearGenomeView/components/CenterLine.js.map +1 -1
- package/dist/LinearGenomeView/components/ExportSvgDialog.js +30 -96
- package/dist/LinearGenomeView/components/ExportSvgDialog.js.map +1 -1
- package/dist/LinearGenomeView/components/GetSequenceDialog.d.ts +9 -0
- package/dist/LinearGenomeView/components/GetSequenceDialog.js +172 -0
- package/dist/LinearGenomeView/components/GetSequenceDialog.js.map +1 -0
- package/dist/LinearGenomeView/components/Gridlines.js +18 -20
- package/dist/LinearGenomeView/components/Gridlines.js.map +1 -1
- package/dist/LinearGenomeView/components/Header.js +26 -31
- package/dist/LinearGenomeView/components/Header.js.map +1 -1
- package/dist/LinearGenomeView/components/HelpDialog.js +10 -11
- package/dist/LinearGenomeView/components/HelpDialog.js.map +1 -1
- package/dist/LinearGenomeView/components/ImportForm.js +91 -158
- package/dist/LinearGenomeView/components/ImportForm.js.map +1 -1
- package/dist/LinearGenomeView/components/LinearGenomeView.js +20 -21
- package/dist/LinearGenomeView/components/LinearGenomeView.js.map +1 -1
- package/dist/LinearGenomeView/components/LinearGenomeViewSvg.js +87 -157
- package/dist/LinearGenomeView/components/LinearGenomeViewSvg.js.map +1 -1
- package/dist/LinearGenomeView/components/MiniControls.js +16 -32
- package/dist/LinearGenomeView/components/MiniControls.js.map +1 -1
- package/dist/LinearGenomeView/components/OverviewRubberBand.d.ts +0 -11
- package/dist/LinearGenomeView/components/OverviewRubberBand.js +44 -76
- package/dist/LinearGenomeView/components/OverviewRubberBand.js.map +1 -1
- package/dist/LinearGenomeView/components/OverviewScaleBar.d.ts +14 -8
- package/dist/LinearGenomeView/components/OverviewScaleBar.js +94 -117
- package/dist/LinearGenomeView/components/OverviewScaleBar.js.map +1 -1
- package/dist/LinearGenomeView/components/RefNameAutocomplete.js +107 -169
- package/dist/LinearGenomeView/components/RefNameAutocomplete.js.map +1 -1
- package/dist/LinearGenomeView/components/RubberBand.js +51 -71
- package/dist/LinearGenomeView/components/RubberBand.js.map +1 -1
- package/dist/LinearGenomeView/components/Ruler.js +17 -18
- package/dist/LinearGenomeView/components/Ruler.js.map +1 -1
- package/dist/LinearGenomeView/components/ScaleBar.js +37 -58
- package/dist/LinearGenomeView/components/ScaleBar.js.map +1 -1
- package/dist/LinearGenomeView/components/SearchBox.js +73 -133
- package/dist/LinearGenomeView/components/SearchBox.js.map +1 -1
- package/dist/LinearGenomeView/components/SearchResultsDialog.js +38 -36
- package/dist/LinearGenomeView/components/SearchResultsDialog.js.map +1 -1
- package/dist/LinearGenomeView/components/{SequenceDialog.d.ts → SequenceSearchDialog.d.ts} +0 -0
- package/dist/LinearGenomeView/components/SequenceSearchDialog.js +104 -0
- package/dist/LinearGenomeView/components/SequenceSearchDialog.js.map +1 -0
- package/dist/LinearGenomeView/components/TrackContainer.js +28 -30
- package/dist/LinearGenomeView/components/TrackContainer.js.map +1 -1
- package/dist/LinearGenomeView/components/TrackLabel.js +37 -71
- package/dist/LinearGenomeView/components/TrackLabel.js.map +1 -1
- package/dist/LinearGenomeView/components/TracksContainer.js +32 -49
- package/dist/LinearGenomeView/components/TracksContainer.js.map +1 -1
- package/dist/LinearGenomeView/components/ZoomControls.js +15 -32
- package/dist/LinearGenomeView/components/ZoomControls.js.map +1 -1
- package/dist/LinearGenomeView/components/util.d.ts +1 -0
- package/dist/LinearGenomeView/components/util.js +28 -88
- package/dist/LinearGenomeView/components/util.js.map +1 -1
- package/dist/LinearGenomeView/index.d.ts +4 -4
- package/dist/LinearGenomeView/index.js +380 -430
- package/dist/LinearGenomeView/index.js.map +1 -1
- package/dist/LinearGenomeView/util.js +17 -36
- package/dist/LinearGenomeView/util.js.map +1 -1
- package/dist/index.js +75 -146
- package/dist/index.js.map +1 -1
- package/esm/LinearGenomeView/components/GetSequenceDialog.d.ts +9 -0
- package/esm/LinearGenomeView/components/{SequenceDialog.js → GetSequenceDialog.js} +4 -7
- package/esm/LinearGenomeView/components/GetSequenceDialog.js.map +1 -0
- package/esm/LinearGenomeView/components/ImportForm.js +39 -42
- package/esm/LinearGenomeView/components/ImportForm.js.map +1 -1
- package/esm/LinearGenomeView/components/LinearGenomeView.js +2 -2
- package/esm/LinearGenomeView/components/LinearGenomeView.js.map +1 -1
- package/esm/LinearGenomeView/components/LinearGenomeViewSvg.js +2 -1
- package/esm/LinearGenomeView/components/LinearGenomeViewSvg.js.map +1 -1
- package/esm/LinearGenomeView/components/OverviewRubberBand.d.ts +0 -11
- package/esm/LinearGenomeView/components/OverviewRubberBand.js +4 -12
- package/esm/LinearGenomeView/components/OverviewRubberBand.js.map +1 -1
- package/esm/LinearGenomeView/components/OverviewScaleBar.d.ts +14 -8
- package/esm/LinearGenomeView/components/OverviewScaleBar.js +0 -2
- package/esm/LinearGenomeView/components/OverviewScaleBar.js.map +1 -1
- package/esm/LinearGenomeView/components/RefNameAutocomplete.js +26 -6
- package/esm/LinearGenomeView/components/RefNameAutocomplete.js.map +1 -1
- package/esm/LinearGenomeView/components/RubberBand.js +0 -1
- package/esm/LinearGenomeView/components/RubberBand.js.map +1 -1
- package/esm/LinearGenomeView/components/SearchBox.js +37 -33
- package/esm/LinearGenomeView/components/SearchBox.js.map +1 -1
- package/esm/LinearGenomeView/components/SearchResultsDialog.js +7 -4
- package/esm/LinearGenomeView/components/SearchResultsDialog.js.map +1 -1
- package/esm/LinearGenomeView/components/{SequenceDialog.d.ts → SequenceSearchDialog.d.ts} +0 -0
- package/esm/LinearGenomeView/components/SequenceSearchDialog.js +76 -0
- package/esm/LinearGenomeView/components/SequenceSearchDialog.js.map +1 -0
- package/esm/LinearGenomeView/components/TrackLabel.js +1 -1
- package/esm/LinearGenomeView/components/TrackLabel.js.map +1 -1
- package/esm/LinearGenomeView/components/util.d.ts +1 -0
- package/esm/LinearGenomeView/components/util.js +12 -0
- package/esm/LinearGenomeView/components/util.js.map +1 -1
- package/esm/LinearGenomeView/index.d.ts +4 -4
- package/esm/LinearGenomeView/index.js +26 -19
- package/esm/LinearGenomeView/index.js.map +1 -1
- package/package.json +2 -3
- package/src/LinearGenomeView/components/{SequenceDialog.tsx → GetSequenceDialog.tsx} +4 -17
- package/src/LinearGenomeView/components/ImportForm.tsx +40 -42
- package/src/LinearGenomeView/components/LinearGenomeView.tsx +3 -3
- package/src/LinearGenomeView/components/LinearGenomeViewSvg.tsx +4 -4
- package/src/LinearGenomeView/components/OverviewRubberBand.tsx +5 -15
- package/src/LinearGenomeView/components/OverviewScaleBar.tsx +0 -2
- package/src/LinearGenomeView/components/RefNameAutocomplete.tsx +27 -8
- package/src/LinearGenomeView/components/RubberBand.tsx +0 -1
- package/src/LinearGenomeView/components/SearchBox.tsx +39 -36
- package/src/LinearGenomeView/components/SearchResultsDialog.tsx +7 -4
- package/src/LinearGenomeView/components/SequenceSearchDialog.tsx +165 -0
- package/src/LinearGenomeView/components/TrackLabel.tsx +3 -1
- package/src/LinearGenomeView/components/__snapshots__/LinearGenomeView.test.js.snap +16 -16
- package/src/LinearGenomeView/components/util.ts +12 -0
- package/src/LinearGenomeView/index.tsx +32 -25
- package/dist/LinearGenomeView/components/SequenceDialog.js +0 -242
- package/dist/LinearGenomeView/components/SequenceDialog.js.map +0 -1
- package/esm/LinearGenomeView/components/SequenceDialog.js.map +0 -1
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71
|
+
const block = overview.dynamicBlocks.contentBlocks[0];
|
|
72
|
+
const first = visibleRegions[0];
|
|
73
|
+
const firstOverviewPx = overview.bpToPx({
|
|
74
|
+
...first,
|
|
75
|
+
coord: first.reversed ? first.end : first.start,
|
|
76
|
+
}) || 0;
|
|
77
|
+
const last = visibleRegions[visibleRegions.length - 1];
|
|
78
|
+
const lastOverviewPx = overview.bpToPx({
|
|
79
|
+
...last,
|
|
80
|
+
coord: last.reversed ? last.start : last.end,
|
|
81
|
+
}) || 0;
|
|
82
|
+
const cytobandHeight = showCytobands ? cytobandHeightIfExists : 0;
|
|
127
83
|
return (react_1.default.createElement("g", { id: "header" },
|
|
128
84
|
react_1.default.createElement("text", { x: 0, y: fontSize, fontSize: fontSize }, assemblyName),
|
|
129
|
-
showCytobands ? (react_1.default.createElement("g", { transform:
|
|
85
|
+
showCytobands ? (react_1.default.createElement("g", { transform: `translate(0 ${rulerHeight})` },
|
|
130
86
|
react_1.default.createElement(OverviewScaleBar_1.Cytobands, { overview: overview, assembly: assembly, block: block }),
|
|
131
87
|
react_1.default.createElement("rect", { stroke: "red", fill: "rgb(255,0,0,0.1)", width: Math.max(lastOverviewPx - firstOverviewPx, 0.5), height: __1.HEADER_OVERVIEW_HEIGHT - 1, x: firstOverviewPx, y: 0.5 }),
|
|
132
|
-
react_1.default.createElement("g", { transform:
|
|
88
|
+
react_1.default.createElement("g", { transform: `translate(0,${__1.HEADER_OVERVIEW_HEIGHT})` },
|
|
133
89
|
react_1.default.createElement(OverviewScaleBar_1.Polygon, { overview: overview, model: model, useOffset: false })))) : null,
|
|
134
|
-
react_1.default.createElement("g", { transform:
|
|
90
|
+
react_1.default.createElement("g", { transform: `translate(0 ${fontSize + cytobandHeight})` },
|
|
135
91
|
react_1.default.createElement(ScaleBar, { model: model, fontSize: fontSize })),
|
|
136
|
-
react_1.default.createElement("g", { transform:
|
|
92
|
+
react_1.default.createElement("g", { transform: `translate(0 ${rulerHeight + cytobandHeight})` },
|
|
137
93
|
react_1.default.createElement(SVGRuler, { model: model, fontSize: fontSize, width: width }))));
|
|
138
94
|
};
|
|
139
95
|
// SVG component, region separator
|
|
140
|
-
|
|
141
|
-
|
|
142
|
-
|
|
143
|
-
return (react_1.default.createElement(react_1.default.Fragment, null, dynamicBlocks.contentBlocks.slice(1).map(function (block) { return (react_1.default.createElement("rect", { key: block.key, x: block.offsetPx - offsetPx - interRegionPaddingWidth, width: interRegionPaddingWidth, y: 0, height: height, stroke: "none", fill: "grey" })); })));
|
|
96
|
+
const SVGRegionSeparators = ({ model, height, }) => {
|
|
97
|
+
const { dynamicBlocks, offsetPx, interRegionPaddingWidth } = model;
|
|
98
|
+
return (react_1.default.createElement(react_1.default.Fragment, null, dynamicBlocks.contentBlocks.slice(1).map(block => (react_1.default.createElement("rect", { key: block.key, x: block.offsetPx - offsetPx - interRegionPaddingWidth, width: interRegionPaddingWidth, y: 0, height: height, stroke: "none", fill: "grey" })))));
|
|
144
99
|
};
|
|
145
100
|
// SVG component, tracks
|
|
146
|
-
function SVGTracks(
|
|
147
|
-
|
|
148
|
-
|
|
149
|
-
|
|
150
|
-
|
|
151
|
-
|
|
152
|
-
|
|
153
|
-
var display = track.displays[0];
|
|
101
|
+
function SVGTracks({ displayResults, model, offset, }) {
|
|
102
|
+
return (react_1.default.createElement(react_1.default.Fragment, null, displayResults.map(({ track, result }) => {
|
|
103
|
+
const current = offset;
|
|
104
|
+
const trackName = (0, configuration_1.getConf)(track, 'name') ||
|
|
105
|
+
`Reference sequence (${(0, configuration_1.readConfObject)((0, mobx_state_tree_1.getParent)(track.configuration), 'displayName') ||
|
|
106
|
+
(0, configuration_1.readConfObject)((0, mobx_state_tree_1.getParent)(track.configuration), 'name')})`;
|
|
107
|
+
const display = track.displays[0];
|
|
154
108
|
offset += display.height + paddingHeight + textHeight;
|
|
155
|
-
return (react_1.default.createElement("g", { key: track.configuration.trackId, transform:
|
|
109
|
+
return (react_1.default.createElement("g", { key: track.configuration.trackId, transform: `translate(0 ${current})` },
|
|
156
110
|
react_1.default.createElement("text", { fontSize: fontSize, x: Math.max(-model.offsetPx, 0) }, trackName),
|
|
157
|
-
react_1.default.createElement("g", { transform:
|
|
111
|
+
react_1.default.createElement("g", { transform: `translate(0 ${textHeight})` },
|
|
158
112
|
result,
|
|
159
113
|
react_1.default.createElement(SVGRegionSeparators, { model: model, height: display.height }))));
|
|
160
114
|
})));
|
|
161
115
|
}
|
|
162
116
|
// render LGV to SVG
|
|
163
|
-
function renderToSvg(model, opts) {
|
|
164
|
-
|
|
165
|
-
|
|
166
|
-
|
|
167
|
-
|
|
168
|
-
|
|
169
|
-
|
|
170
|
-
|
|
171
|
-
|
|
172
|
-
|
|
173
|
-
|
|
174
|
-
|
|
175
|
-
|
|
176
|
-
|
|
177
|
-
|
|
178
|
-
|
|
179
|
-
|
|
180
|
-
|
|
181
|
-
|
|
182
|
-
|
|
183
|
-
|
|
184
|
-
display = track.displays[0];
|
|
185
|
-
return [4 /*yield*/, (0, mobx_1.when)(function () { return (display.ready !== undefined ? display.ready : true); })];
|
|
186
|
-
case 1:
|
|
187
|
-
_a.sent();
|
|
188
|
-
return [4 /*yield*/, display.renderSvg(opts)];
|
|
189
|
-
case 2:
|
|
190
|
-
result = _a.sent();
|
|
191
|
-
return [2 /*return*/, { track: track, result: result }];
|
|
192
|
-
}
|
|
193
|
-
});
|
|
194
|
-
}); }))
|
|
195
|
-
// the xlink namespace is used for rendering <image> tag
|
|
196
|
-
];
|
|
197
|
-
case 2:
|
|
198
|
-
displayResults = _a.sent();
|
|
199
|
-
// the xlink namespace is used for rendering <image> tag
|
|
200
|
-
return [2 /*return*/, (0, server_1.renderToStaticMarkup)(react_1.default.createElement("svg", { width: width, height: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, width + shift * 2, height].toString() },
|
|
201
|
-
react_1.default.createElement("rect", { width: width + shift * 2, height: height, fill: "white" }),
|
|
202
|
-
react_1.default.createElement("g", { stroke: "none", transform: "translate(".concat(shift, " ").concat(fontSize, ")") },
|
|
203
|
-
react_1.default.createElement(SVGHeader, { model: model }),
|
|
204
|
-
react_1.default.createElement(SVGTracks, { model: model, displayResults: displayResults, offset: offset }))))];
|
|
205
|
-
}
|
|
206
|
-
});
|
|
207
|
-
});
|
|
117
|
+
async function renderToSvg(model, opts) {
|
|
118
|
+
await (0, mobx_1.when)(() => model.initialized);
|
|
119
|
+
const { width, tracks, showCytobands } = model;
|
|
120
|
+
const shift = 50;
|
|
121
|
+
const offset = headerHeight +
|
|
122
|
+
rulerHeight +
|
|
123
|
+
(showCytobands ? cytobandHeightIfExists : 0) +
|
|
124
|
+
20;
|
|
125
|
+
const height = totalHeight(tracks) + offset;
|
|
126
|
+
const displayResults = await Promise.all(tracks.map(async (track) => {
|
|
127
|
+
const display = track.displays[0];
|
|
128
|
+
await (0, mobx_1.when)(() => (display.ready !== undefined ? display.ready : true));
|
|
129
|
+
const result = await display.renderSvg(opts);
|
|
130
|
+
return { track, result };
|
|
131
|
+
}));
|
|
132
|
+
// the xlink namespace is used for rendering <image> tag
|
|
133
|
+
return (0, server_1.renderToStaticMarkup)(react_1.default.createElement("svg", { width: width, height: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, width + shift * 2, height].toString() },
|
|
134
|
+
react_1.default.createElement("rect", { width: width + shift * 2, height: height, fill: "white" }),
|
|
135
|
+
react_1.default.createElement("g", { stroke: "none", transform: `translate(${shift} ${fontSize})` },
|
|
136
|
+
react_1.default.createElement(SVGHeader, { model: model }),
|
|
137
|
+
react_1.default.createElement(SVGTracks, { model: model, displayResults: displayResults, offset: offset }))));
|
|
208
138
|
}
|
|
209
139
|
exports.renderToSvg = renderToSvg;
|
|
210
140
|
//# sourceMappingURL=LinearGenomeViewSvg.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"LinearGenomeViewSvg.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/LinearGenomeViewSvg.tsx"],"names":[],"mappings":"
|
|
1
|
+
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{"version":3,"file":"MiniControls.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/MiniControls.tsx"],"names":[],"mappings":"
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@@ -1,5 +1,4 @@
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1
1
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import React from 'react';
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2
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-
import ReactPropTypes from 'prop-types';
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3
2
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import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
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4
3
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import { LinearGenomeViewModel } from '..';
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5
4
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declare type LGV = LinearGenomeViewModel;
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@@ -8,15 +7,5 @@ declare function OverviewRubberBand({ model, overview, ControlComponent, }: {
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8
7
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overview: Base1DViewModel;
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9
8
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ControlComponent?: React.ReactElement;
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10
9
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}): JSX.Element;
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11
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-
declare namespace OverviewRubberBand {
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12
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-
var propTypes: {
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13
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-
model: ReactPropTypes.Validator<any>;
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14
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-
overview: ReactPropTypes.Validator<any>;
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15
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-
ControlComponent: ReactPropTypes.Requireable<ReactPropTypes.ReactNodeLike>;
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16
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-
};
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17
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-
var defaultProps: {
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18
|
-
ControlComponent: JSX.Element;
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19
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-
};
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20
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-
}
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21
10
|
declare const _default: typeof OverviewRubberBand;
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22
11
|
export default _default;
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