@jbrowse/plugin-dotplot-view 2.6.1 → 2.6.3
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/ComparativeRenderer/index.js +0 -1
- package/dist/DotplotDisplay/components/DotplotDisplay.js +0 -1
- package/dist/DotplotDisplay/index.js +0 -1
- package/dist/DotplotDisplay/renderDotplotBlock.js +0 -1
- package/dist/DotplotDisplay/stateModelFactory.js +0 -1
- package/dist/DotplotReadVsRef/DotplotReadVsRef.js +0 -1
- package/dist/DotplotReadVsRef/index.js +0 -1
- package/dist/DotplotRenderer/ComparativeRenderRpc.js +0 -1
- package/dist/DotplotRenderer/DotplotRenderer.js +0 -1
- package/dist/DotplotRenderer/components/DotplotRendering.js +0 -1
- package/dist/DotplotRenderer/configSchema.js +0 -1
- package/dist/DotplotRenderer/index.js +0 -1
- package/dist/DotplotView/1dview.js +0 -1
- package/dist/DotplotView/blockTypes.js +0 -1
- package/dist/DotplotView/components/Axes.js +0 -1
- package/dist/DotplotView/components/CursorIcon.js +0 -1
- package/dist/DotplotView/components/DotplotTooltip.js +0 -1
- package/dist/DotplotView/components/DotplotView.js +0 -1
- package/dist/DotplotView/components/DotplotWarnings.js +0 -1
- package/dist/DotplotView/components/ExportSvgDialog.js +0 -1
- package/dist/DotplotView/components/Grid.js +0 -1
- package/dist/DotplotView/components/Header.js +0 -1
- package/dist/DotplotView/components/ImportCustomTrack.js +0 -1
- package/dist/DotplotView/components/ImportForm.js +0 -1
- package/dist/DotplotView/components/ImportSyntenyTrackSelector.js +0 -1
- package/dist/DotplotView/components/PanButtons.js +0 -1
- package/dist/DotplotView/components/WarningDialog.js +0 -1
- package/dist/DotplotView/components/util.js +0 -1
- package/dist/DotplotView/index.js +0 -1
- package/dist/DotplotView/model.d.ts +64 -40
- package/dist/DotplotView/model.js +11 -4
- package/dist/DotplotView/svgcomponents/SVGBackground.js +2 -2
- package/dist/DotplotView/svgcomponents/SVGDotplotView.js +0 -1
- package/dist/LaunchDotplotView.js +0 -1
- package/dist/ServerSideRenderedBlockContent.js +0 -1
- package/dist/ServerSideSyntenyRendering.js +0 -1
- package/dist/index.js +0 -1
- package/dist/util.js +0 -1
- package/esm/ComparativeRenderer/index.js +0 -1
- package/esm/DotplotDisplay/components/DotplotDisplay.js +0 -1
- package/esm/DotplotDisplay/index.js +0 -1
- package/esm/DotplotDisplay/renderDotplotBlock.js +0 -1
- package/esm/DotplotDisplay/stateModelFactory.js +0 -1
- package/esm/DotplotReadVsRef/DotplotReadVsRef.js +0 -1
- package/esm/DotplotReadVsRef/index.js +0 -1
- package/esm/DotplotRenderer/ComparativeRenderRpc.js +0 -1
- package/esm/DotplotRenderer/DotplotRenderer.js +0 -1
- package/esm/DotplotRenderer/components/DotplotRendering.js +0 -1
- package/esm/DotplotRenderer/configSchema.js +0 -1
- package/esm/DotplotRenderer/index.js +0 -1
- package/esm/DotplotView/1dview.js +0 -1
- package/esm/DotplotView/blockTypes.js +0 -1
- package/esm/DotplotView/components/Axes.js +0 -1
- package/esm/DotplotView/components/CursorIcon.js +0 -1
- package/esm/DotplotView/components/DotplotTooltip.js +0 -1
- package/esm/DotplotView/components/DotplotView.js +0 -1
- package/esm/DotplotView/components/DotplotWarnings.js +0 -1
- package/esm/DotplotView/components/ExportSvgDialog.js +0 -1
- package/esm/DotplotView/components/Grid.js +0 -1
- package/esm/DotplotView/components/Header.js +0 -1
- package/esm/DotplotView/components/ImportCustomTrack.js +0 -1
- package/esm/DotplotView/components/ImportForm.js +0 -1
- package/esm/DotplotView/components/ImportSyntenyTrackSelector.js +0 -1
- package/esm/DotplotView/components/PanButtons.js +0 -1
- package/esm/DotplotView/components/WarningDialog.js +0 -1
- package/esm/DotplotView/components/util.js +0 -1
- package/esm/DotplotView/index.js +0 -1
- package/esm/DotplotView/model.d.ts +64 -40
- package/esm/DotplotView/model.js +11 -4
- package/esm/DotplotView/svgcomponents/SVGBackground.js +2 -2
- package/esm/DotplotView/svgcomponents/SVGDotplotView.js +0 -1
- package/esm/LaunchDotplotView.js +0 -1
- package/esm/ServerSideRenderedBlockContent.js +0 -1
- package/esm/ServerSideSyntenyRendering.js +0 -1
- package/esm/index.js +0 -1
- package/esm/util.js +0 -1
- package/package.json +4 -4
- package/dist/ComparativeRenderer/index.js.map +0 -1
- package/dist/DotplotDisplay/components/DotplotDisplay.js.map +0 -1
- package/dist/DotplotDisplay/index.js.map +0 -1
- package/dist/DotplotDisplay/renderDotplotBlock.js.map +0 -1
- package/dist/DotplotDisplay/stateModelFactory.js.map +0 -1
- package/dist/DotplotReadVsRef/DotplotReadVsRef.js.map +0 -1
- package/dist/DotplotReadVsRef/index.js.map +0 -1
- package/dist/DotplotRenderer/ComparativeRenderRpc.js.map +0 -1
- package/dist/DotplotRenderer/DotplotRenderer.js.map +0 -1
- package/dist/DotplotRenderer/components/DotplotRendering.js.map +0 -1
- package/dist/DotplotRenderer/configSchema.js.map +0 -1
- package/dist/DotplotRenderer/index.js.map +0 -1
- package/dist/DotplotView/1dview.js.map +0 -1
- package/dist/DotplotView/blockTypes.js.map +0 -1
- package/dist/DotplotView/components/Axes.js.map +0 -1
- package/dist/DotplotView/components/CursorIcon.js.map +0 -1
- package/dist/DotplotView/components/DotplotTooltip.js.map +0 -1
- package/dist/DotplotView/components/DotplotView.js.map +0 -1
- package/dist/DotplotView/components/DotplotWarnings.js.map +0 -1
- package/dist/DotplotView/components/ExportSvgDialog.js.map +0 -1
- package/dist/DotplotView/components/Grid.js.map +0 -1
- package/dist/DotplotView/components/Header.js.map +0 -1
- package/dist/DotplotView/components/ImportCustomTrack.js.map +0 -1
- package/dist/DotplotView/components/ImportForm.js.map +0 -1
- package/dist/DotplotView/components/ImportSyntenyTrackSelector.js.map +0 -1
- package/dist/DotplotView/components/PanButtons.js.map +0 -1
- package/dist/DotplotView/components/WarningDialog.js.map +0 -1
- package/dist/DotplotView/components/util.js.map +0 -1
- package/dist/DotplotView/index.js.map +0 -1
- package/dist/DotplotView/model.js.map +0 -1
- package/dist/DotplotView/svgcomponents/SVGBackground.js.map +0 -1
- package/dist/DotplotView/svgcomponents/SVGDotplotView.js.map +0 -1
- package/dist/LaunchDotplotView.js.map +0 -1
- package/dist/ServerSideRenderedBlockContent.js.map +0 -1
- package/dist/ServerSideSyntenyRendering.js.map +0 -1
- package/dist/index.js.map +0 -1
- package/dist/util.js.map +0 -1
- package/esm/ComparativeRenderer/index.js.map +0 -1
- package/esm/DotplotDisplay/components/DotplotDisplay.js.map +0 -1
- package/esm/DotplotDisplay/index.js.map +0 -1
- package/esm/DotplotDisplay/renderDotplotBlock.js.map +0 -1
- package/esm/DotplotDisplay/stateModelFactory.js.map +0 -1
- package/esm/DotplotReadVsRef/DotplotReadVsRef.js.map +0 -1
- package/esm/DotplotReadVsRef/index.js.map +0 -1
- package/esm/DotplotRenderer/ComparativeRenderRpc.js.map +0 -1
- package/esm/DotplotRenderer/DotplotRenderer.js.map +0 -1
- package/esm/DotplotRenderer/components/DotplotRendering.js.map +0 -1
- package/esm/DotplotRenderer/configSchema.js.map +0 -1
- package/esm/DotplotRenderer/index.js.map +0 -1
- package/esm/DotplotView/1dview.js.map +0 -1
- package/esm/DotplotView/blockTypes.js.map +0 -1
- package/esm/DotplotView/components/Axes.js.map +0 -1
- package/esm/DotplotView/components/CursorIcon.js.map +0 -1
- package/esm/DotplotView/components/DotplotTooltip.js.map +0 -1
- package/esm/DotplotView/components/DotplotView.js.map +0 -1
- package/esm/DotplotView/components/DotplotWarnings.js.map +0 -1
- package/esm/DotplotView/components/ExportSvgDialog.js.map +0 -1
- package/esm/DotplotView/components/Grid.js.map +0 -1
- package/esm/DotplotView/components/Header.js.map +0 -1
- package/esm/DotplotView/components/ImportCustomTrack.js.map +0 -1
- package/esm/DotplotView/components/ImportForm.js.map +0 -1
- package/esm/DotplotView/components/ImportSyntenyTrackSelector.js.map +0 -1
- package/esm/DotplotView/components/PanButtons.js.map +0 -1
- package/esm/DotplotView/components/WarningDialog.js.map +0 -1
- package/esm/DotplotView/components/util.js.map +0 -1
- package/esm/DotplotView/index.js.map +0 -1
- package/esm/DotplotView/model.js.map +0 -1
- package/esm/DotplotView/svgcomponents/SVGBackground.js.map +0 -1
- package/esm/DotplotView/svgcomponents/SVGDotplotView.js.map +0 -1
- package/esm/LaunchDotplotView.js.map +0 -1
- package/esm/ServerSideRenderedBlockContent.js.map +0 -1
- package/esm/ServerSideSyntenyRendering.js.map +0 -1
- package/esm/index.js.map +0 -1
- package/esm/util.js.map +0 -1
- package/src/ComparativeRenderer/index.ts +0 -87
- package/src/DotplotDisplay/components/DotplotDisplay.tsx +0 -34
- package/src/DotplotDisplay/index.ts +0 -48
- package/src/DotplotDisplay/renderDotplotBlock.ts +0 -60
- package/src/DotplotDisplay/stateModelFactory.tsx +0 -196
- package/src/DotplotReadVsRef/DotplotReadVsRef.ts +0 -115
- package/src/DotplotReadVsRef/index.ts +0 -50
- package/src/DotplotRenderer/ComparativeRenderRpc.ts +0 -87
- package/src/DotplotRenderer/DotplotRenderer.ts +0 -328
- package/src/DotplotRenderer/__image_snapshots__/linear-synteny-renderer-test-ts-test-rendering-a-simple-synteny-from-fake-data-1-snap.png +0 -0
- package/src/DotplotRenderer/components/DotplotRendering.tsx +0 -12
- package/src/DotplotRenderer/configSchema.ts +0 -92
- package/src/DotplotRenderer/index.ts +0 -16
- package/src/DotplotView/1dview.ts +0 -98
- package/src/DotplotView/blockTypes.ts +0 -140
- package/src/DotplotView/components/Axes.tsx +0 -246
- package/src/DotplotView/components/CursorIcon.tsx +0 -24
- package/src/DotplotView/components/DotplotTooltip.tsx +0 -163
- package/src/DotplotView/components/DotplotView.tsx +0 -348
- package/src/DotplotView/components/DotplotWarnings.tsx +0 -26
- package/src/DotplotView/components/ExportSvgDialog.tsx +0 -129
- package/src/DotplotView/components/Grid.tsx +0 -112
- package/src/DotplotView/components/Header.tsx +0 -182
- package/src/DotplotView/components/ImportCustomTrack.tsx +0 -262
- package/src/DotplotView/components/ImportForm.tsx +0 -209
- package/src/DotplotView/components/ImportSyntenyTrackSelector.tsx +0 -90
- package/src/DotplotView/components/PanButtons.tsx +0 -93
- package/src/DotplotView/components/WarningDialog.tsx +0 -74
- package/src/DotplotView/components/util.ts +0 -118
- package/src/DotplotView/index.ts +0 -16
- package/src/DotplotView/model.test.ts +0 -17
- package/src/DotplotView/model.ts +0 -719
- package/src/DotplotView/svgcomponents/SVGBackground.tsx +0 -21
- package/src/DotplotView/svgcomponents/SVGDotplotView.tsx +0 -68
- package/src/LaunchDotplotView.ts +0 -63
- package/src/ServerSideRenderedBlockContent.tsx +0 -86
- package/src/ServerSideSyntenyRendering.tsx +0 -54
- package/src/index.ts +0 -41
- package/src/util.ts +0 -14
|
@@ -124,4 +124,3 @@ exports.VerticalAxisRaw = (0, mobx_react_1.observer)(function ({ model, }) {
|
|
|
124
124
|
}),
|
|
125
125
|
react_1.default.createElement("text", { y: (viewHeight - borderY) / 2, x: 12, fill: theme.palette.text.primary, transform: `rotate(-90,12,${(viewHeight - borderY) / 2})`, textAnchor: "middle", fontSize: 11 }, vview.assemblyNames.join(','))));
|
|
126
126
|
});
|
|
127
|
-
//# sourceMappingURL=Axes.js.map
|
|
@@ -16,4 +16,3 @@ function CursorMouse(props) {
|
|
|
16
16
|
react_1.default.createElement("path", { fill: "currentColor", d: "M10.07,14.27C10.57,14.03 11.16,14.25 11.4,14.75L13.7,19.74L15.5,18.89L13.19,13.91C12.95,13.41 13.17,12.81 13.67,12.58L13.95,12.5L16.25,12.05L8,5.12V15.9L9.82,14.43L10.07,14.27M13.64,21.97C13.14,22.21 12.54,22 12.31,21.5L10.13,16.76L7.62,18.78C7.45,18.92 7.24,19 7,19A1,1 0 0,1 6,18V3A1,1 0 0,1 7,2C7.24,2 7.47,2.09 7.64,2.23L7.65,2.22L19.14,11.86C19.57,12.22 19.62,12.85 19.27,13.27C19.12,13.45 18.91,13.57 18.7,13.61L15.54,14.23L17.74,18.96C18,19.46 17.76,20.05 17.26,20.28L13.64,21.97Z" })));
|
|
17
17
|
}
|
|
18
18
|
exports.CursorMouse = CursorMouse;
|
|
19
|
-
//# sourceMappingURL=CursorIcon.js.map
|
|
@@ -37,4 +37,3 @@ exports.default = (0, mobx_react_1.observer)(function ({ model }) {
|
|
|
37
37
|
react_1.default.createElement(material_1.Button, { onClick: () => setShown(true) }, "More info"),
|
|
38
38
|
shown ? (react_1.default.createElement(WarningDialog, { trackWarnings: trackWarnings, handleClose: () => setShown(false) })) : null)) : null;
|
|
39
39
|
});
|
|
40
|
-
//# sourceMappingURL=DotplotWarnings.js.map
|
|
@@ -165,4 +165,3 @@ exports.default = (0, mobx_react_1.observer)(function Header({ model, selection,
|
|
|
165
165
|
react_1.default.createElement(DotplotWarnings_1.default, { model: model }),
|
|
166
166
|
showPanButtons ? react_1.default.createElement(PanButtons_1.default, { model: model }) : null));
|
|
167
167
|
});
|
|
168
|
-
//# sourceMappingURL=Header.js.map
|
|
@@ -177,4 +177,3 @@ const OpenTrack = (0, mobx_react_1.observer)(({ sessionTrackData, assembly1, ass
|
|
|
177
177
|
react_1.default.createElement(ui_1.FileSelector, { name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: loc => setBed2Location(loc) }))))) : (react_1.default.createElement(ui_1.FileSelector, { name: value ? value + ' location' : '', description: "", location: fileLocation, setLocation: loc => setFileLocation(loc) }))))));
|
|
178
178
|
});
|
|
179
179
|
exports.default = OpenTrack;
|
|
180
|
-
//# sourceMappingURL=ImportCustomTrack.js.map
|
|
@@ -118,4 +118,3 @@ const DotplotImportForm = (0, mobx_react_1.observer)(({ model }) => {
|
|
|
118
118
|
react_1.default.createElement(TrackSelector, { setShowTrackId: setShowTrackId, assembly2: assembly2, assembly1: assembly1, setSessionTrackData: setSessionTrackData, sessionTrackData: sessionTrackData, model: model })))));
|
|
119
119
|
});
|
|
120
120
|
exports.default = DotplotImportForm;
|
|
121
|
-
//# sourceMappingURL=ImportForm.js.map
|
|
@@ -66,4 +66,3 @@ const Selector = (0, mobx_react_1.observer)(({ model, assembly1, assembly2, setS
|
|
|
66
66
|
filteredTracks.length ? (react_1.default.createElement(material_1.Select, { value: value, onChange: event => setValue(event.target.value) }, filteredTracks.map(track => (react_1.default.createElement(material_1.MenuItem, { key: track.trackId, value: track.trackId }, (0, tracks_1.getTrackName)(track, session)))))) : (react_1.default.createElement(ui_1.ErrorMessage, { error: `No synteny tracks found for ${assembly1},${assembly2}` }))));
|
|
67
67
|
});
|
|
68
68
|
exports.default = Selector;
|
|
69
|
-
//# sourceMappingURL=ImportSyntenyTrackSelector.js.map
|
|
@@ -38,4 +38,3 @@ exports.default = (0, mobx_react_1.observer)(function WarningDialog({ trackWarni
|
|
|
38
38
|
react_1.default.createElement("div", { style: { height: 600, width: '100%', overflow: 'auto' } },
|
|
39
39
|
react_1.default.createElement(x_data_grid_1.DataGrid, { rows: rows, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, disableColumnMenu: true })))));
|
|
40
40
|
});
|
|
41
|
-
//# sourceMappingURL=WarningDialog.js.map
|
|
@@ -58,15 +58,15 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
|
|
|
58
58
|
readonly width: number;
|
|
59
59
|
readonly assemblyNames: string[];
|
|
60
60
|
readonly displayedRegionsTotalPx: number;
|
|
61
|
-
readonly maxOffset: number;
|
|
62
|
-
|
|
61
|
+
readonly maxOffset: number;
|
|
62
|
+
readonly minOffset: number; /**
|
|
63
|
+
* #stateModel DotplotView
|
|
64
|
+
* #category view
|
|
65
|
+
* extends `BaseViewModel`
|
|
63
66
|
*/
|
|
64
|
-
readonly minOffset: number;
|
|
65
67
|
readonly totalBp: number;
|
|
66
68
|
} & {
|
|
67
|
-
readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
68
|
-
* #property
|
|
69
|
-
*/
|
|
69
|
+
readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
70
70
|
readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
71
71
|
readonly currBp: number;
|
|
72
72
|
} & {
|
|
@@ -82,14 +82,20 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
|
|
|
82
82
|
reversed: boolean;
|
|
83
83
|
};
|
|
84
84
|
bpToPx({ refName, coord, regionNumber, }: {
|
|
85
|
-
refName: string;
|
|
85
|
+
refName: string; /**
|
|
86
|
+
* #property
|
|
87
|
+
*/
|
|
86
88
|
coord: number;
|
|
87
|
-
regionNumber?: number | undefined;
|
|
89
|
+
regionNumber?: number | undefined; /**
|
|
90
|
+
* #property
|
|
91
|
+
*/
|
|
88
92
|
}): number | undefined;
|
|
89
93
|
} & {
|
|
90
94
|
setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
|
|
91
95
|
showAllRegions(): void;
|
|
92
|
-
zoomOut(): void;
|
|
96
|
+
zoomOut(): void; /**
|
|
97
|
+
* #property
|
|
98
|
+
*/
|
|
93
99
|
zoomIn(): void;
|
|
94
100
|
zoomTo(bpPerPx: number, offset?: number | undefined): number;
|
|
95
101
|
scrollTo(offsetPx: number): number;
|
|
@@ -137,15 +143,15 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
|
|
|
137
143
|
readonly width: number;
|
|
138
144
|
readonly assemblyNames: string[];
|
|
139
145
|
readonly displayedRegionsTotalPx: number;
|
|
140
|
-
readonly maxOffset: number;
|
|
141
|
-
|
|
146
|
+
readonly maxOffset: number;
|
|
147
|
+
readonly minOffset: number; /**
|
|
148
|
+
* #stateModel DotplotView
|
|
149
|
+
* #category view
|
|
150
|
+
* extends `BaseViewModel`
|
|
142
151
|
*/
|
|
143
|
-
readonly minOffset: number;
|
|
144
152
|
readonly totalBp: number;
|
|
145
153
|
} & {
|
|
146
|
-
readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
147
|
-
* #property
|
|
148
|
-
*/
|
|
154
|
+
readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
149
155
|
readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
150
156
|
readonly currBp: number;
|
|
151
157
|
} & {
|
|
@@ -161,14 +167,20 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
|
|
|
161
167
|
reversed: boolean;
|
|
162
168
|
};
|
|
163
169
|
bpToPx({ refName, coord, regionNumber, }: {
|
|
164
|
-
refName: string;
|
|
170
|
+
refName: string; /**
|
|
171
|
+
* #property
|
|
172
|
+
*/
|
|
165
173
|
coord: number;
|
|
166
|
-
regionNumber?: number | undefined;
|
|
174
|
+
regionNumber?: number | undefined; /**
|
|
175
|
+
* #property
|
|
176
|
+
*/
|
|
167
177
|
}): number | undefined;
|
|
168
178
|
} & {
|
|
169
179
|
setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
|
|
170
180
|
showAllRegions(): void;
|
|
171
|
-
zoomOut(): void;
|
|
181
|
+
zoomOut(): void; /**
|
|
182
|
+
* #property
|
|
183
|
+
*/
|
|
172
184
|
zoomIn(): void;
|
|
173
185
|
zoomTo(bpPerPx: number, offset?: number | undefined): number;
|
|
174
186
|
scrollTo(offsetPx: number): number;
|
|
@@ -207,7 +219,9 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
|
|
|
207
219
|
activateConfigurationUI(): void;
|
|
208
220
|
showDisplay(displayId: string, initialSnapshot?: {} | undefined): void;
|
|
209
221
|
hideDisplay(displayId: string): number;
|
|
210
|
-
replaceDisplay(oldId: string, newId: string, initialSnapshot?: {} | undefined): void;
|
|
222
|
+
replaceDisplay(oldId: string, newId: string, initialSnapshot?: {} | undefined): void; /**
|
|
223
|
+
* #property
|
|
224
|
+
*/
|
|
211
225
|
} & {
|
|
212
226
|
trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
|
|
213
227
|
type: string; /**
|
|
@@ -216,9 +230,7 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
|
|
|
216
230
|
label: string;
|
|
217
231
|
subMenu: {
|
|
218
232
|
type: string;
|
|
219
|
-
label: string;
|
|
220
|
-
* #property
|
|
221
|
-
*/
|
|
233
|
+
label: string;
|
|
222
234
|
checked: boolean;
|
|
223
235
|
onClick: () => void;
|
|
224
236
|
}[];
|
|
@@ -329,15 +341,15 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
|
|
|
329
341
|
readonly width: number;
|
|
330
342
|
readonly assemblyNames: string[];
|
|
331
343
|
readonly displayedRegionsTotalPx: number;
|
|
332
|
-
readonly maxOffset: number;
|
|
333
|
-
|
|
344
|
+
readonly maxOffset: number;
|
|
345
|
+
readonly minOffset: number; /**
|
|
346
|
+
* #stateModel DotplotView
|
|
347
|
+
* #category view
|
|
348
|
+
* extends `BaseViewModel`
|
|
334
349
|
*/
|
|
335
|
-
readonly minOffset: number;
|
|
336
350
|
readonly totalBp: number;
|
|
337
351
|
} & {
|
|
338
|
-
readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
339
|
-
* #property
|
|
340
|
-
*/
|
|
352
|
+
readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
341
353
|
readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
342
354
|
readonly currBp: number;
|
|
343
355
|
} & {
|
|
@@ -353,14 +365,20 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
|
|
|
353
365
|
reversed: boolean;
|
|
354
366
|
};
|
|
355
367
|
bpToPx({ refName, coord, regionNumber, }: {
|
|
356
|
-
refName: string;
|
|
368
|
+
refName: string; /**
|
|
369
|
+
* #property
|
|
370
|
+
*/
|
|
357
371
|
coord: number;
|
|
358
|
-
regionNumber?: number | undefined;
|
|
372
|
+
regionNumber?: number | undefined; /**
|
|
373
|
+
* #property
|
|
374
|
+
*/
|
|
359
375
|
}): number | undefined;
|
|
360
376
|
} & {
|
|
361
377
|
setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
|
|
362
378
|
showAllRegions(): void;
|
|
363
|
-
zoomOut(): void;
|
|
379
|
+
zoomOut(): void; /**
|
|
380
|
+
* #property
|
|
381
|
+
*/
|
|
364
382
|
zoomIn(): void;
|
|
365
383
|
zoomTo(bpPerPx: number, offset?: number | undefined): number;
|
|
366
384
|
scrollTo(offsetPx: number): number;
|
|
@@ -407,15 +425,15 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
|
|
|
407
425
|
readonly width: number;
|
|
408
426
|
readonly assemblyNames: string[];
|
|
409
427
|
readonly displayedRegionsTotalPx: number;
|
|
410
|
-
readonly maxOffset: number;
|
|
411
|
-
|
|
428
|
+
readonly maxOffset: number;
|
|
429
|
+
readonly minOffset: number; /**
|
|
430
|
+
* #stateModel DotplotView
|
|
431
|
+
* #category view
|
|
432
|
+
* extends `BaseViewModel`
|
|
412
433
|
*/
|
|
413
|
-
readonly minOffset: number;
|
|
414
434
|
readonly totalBp: number;
|
|
415
435
|
} & {
|
|
416
|
-
readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
417
|
-
* #property
|
|
418
|
-
*/
|
|
436
|
+
readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
419
437
|
readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
420
438
|
readonly currBp: number;
|
|
421
439
|
} & {
|
|
@@ -431,14 +449,20 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
|
|
|
431
449
|
reversed: boolean;
|
|
432
450
|
};
|
|
433
451
|
bpToPx({ refName, coord, regionNumber, }: {
|
|
434
|
-
refName: string;
|
|
452
|
+
refName: string; /**
|
|
453
|
+
* #property
|
|
454
|
+
*/
|
|
435
455
|
coord: number;
|
|
436
|
-
regionNumber?: number | undefined;
|
|
456
|
+
regionNumber?: number | undefined; /**
|
|
457
|
+
* #property
|
|
458
|
+
*/
|
|
437
459
|
}): number | undefined;
|
|
438
460
|
} & {
|
|
439
461
|
setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
|
|
440
462
|
showAllRegions(): void;
|
|
441
|
-
zoomOut(): void;
|
|
463
|
+
zoomOut(): void; /**
|
|
464
|
+
* #property
|
|
465
|
+
*/
|
|
442
466
|
zoomIn(): void;
|
|
443
467
|
zoomTo(bpPerPx: number, offset?: number | undefined): number;
|
|
444
468
|
scrollTo(offsetPx: number): number;
|
|
@@ -46,6 +46,15 @@ const util_2 = require("./components/util");
|
|
|
46
46
|
// lazies
|
|
47
47
|
const ExportSvgDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ExportSvgDialog'))));
|
|
48
48
|
const ReturnToImportFormDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@jbrowse/core/ui/ReturnToImportFormDialog'))));
|
|
49
|
+
const len = (a) => (0, util_1.measureText)(a.slice(0, 30));
|
|
50
|
+
const pxWidthForBlocks = (blocks, hide) => {
|
|
51
|
+
return (0, util_1.max)([
|
|
52
|
+
...blocks.filter(b => !hide.has(b.key)).map(b => len(b.refName)),
|
|
53
|
+
...blocks
|
|
54
|
+
.filter(b => !hide.has(b.key))
|
|
55
|
+
.map(b => len(b.end.toLocaleString('en-us'))),
|
|
56
|
+
]);
|
|
57
|
+
};
|
|
49
58
|
/**
|
|
50
59
|
* #stateModel DotplotView
|
|
51
60
|
* #category view
|
|
@@ -547,9 +556,8 @@ function stateModelFactory(pm) {
|
|
|
547
556
|
const voffset = vview.offsetPx;
|
|
548
557
|
const vhide = (0, util_2.getBlockLabelKeysToHide)(vblocks, viewHeight, voffset);
|
|
549
558
|
const hhide = (0, util_2.getBlockLabelKeysToHide)(hblocks, viewWidth, hoffset);
|
|
550
|
-
const
|
|
551
|
-
const
|
|
552
|
-
const bx = (0, util_1.max)(vblocks.filter(b => !vhide.has(b.key)).map(b => len(b.refName)));
|
|
559
|
+
const by = pxWidthForBlocks(hblocks, hhide);
|
|
560
|
+
const bx = pxWidthForBlocks(vblocks, vhide);
|
|
553
561
|
// these are set via autorun to avoid dependency cycle
|
|
554
562
|
self.setBorderY(Math.max(by + padding, 50));
|
|
555
563
|
self.setBorderX(Math.max(bx + padding, 50));
|
|
@@ -644,4 +652,3 @@ function stateModelFactory(pm) {
|
|
|
644
652
|
exports.default = stateModelFactory;
|
|
645
653
|
var _1dview_2 = require("./1dview");
|
|
646
654
|
Object.defineProperty(exports, "Dotplot1DView", { enumerable: true, get: function () { return _1dview_2.Dotplot1DView; } });
|
|
647
|
-
//# sourceMappingURL=model.js.map
|
|
@@ -4,10 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
4
4
|
};
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
6
|
const react_1 = __importDefault(require("react"));
|
|
7
|
+
const color_1 = __importDefault(require("color"));
|
|
7
8
|
const material_1 = require("@mui/material");
|
|
8
9
|
function SVGBackground({ width, height, }) {
|
|
9
10
|
const theme = (0, material_1.useTheme)();
|
|
10
|
-
return (react_1.default.createElement("rect", { x: 0, y: 0, width: width, height: height, fill: theme.palette.background.default }));
|
|
11
|
+
return (react_1.default.createElement("rect", { x: 0, y: 0, width: width, height: height, fill: (0, color_1.default)(theme.palette.background.default).hex() }));
|
|
11
12
|
}
|
|
12
13
|
exports.default = SVGBackground;
|
|
13
|
-
//# sourceMappingURL=SVGBackground.js.map
|
package/dist/index.js
CHANGED
package/dist/util.js
CHANGED
|
@@ -118,4 +118,3 @@ export const VerticalAxisRaw = observer(function ({ model, }) {
|
|
|
118
118
|
}),
|
|
119
119
|
React.createElement("text", { y: (viewHeight - borderY) / 2, x: 12, fill: theme.palette.text.primary, transform: `rotate(-90,12,${(viewHeight - borderY) / 2})`, textAnchor: "middle", fontSize: 11 }, vview.assemblyNames.join(','))));
|
|
120
120
|
});
|
|
121
|
-
//# sourceMappingURL=Axes.js.map
|
|
@@ -8,4 +8,3 @@ export function CursorMouse(props) {
|
|
|
8
8
|
return (React.createElement(SvgIcon, { ...props },
|
|
9
9
|
React.createElement("path", { fill: "currentColor", d: "M10.07,14.27C10.57,14.03 11.16,14.25 11.4,14.75L13.7,19.74L15.5,18.89L13.19,13.91C12.95,13.41 13.17,12.81 13.67,12.58L13.95,12.5L16.25,12.05L8,5.12V15.9L9.82,14.43L10.07,14.27M13.64,21.97C13.14,22.21 12.54,22 12.31,21.5L10.13,16.76L7.62,18.78C7.45,18.92 7.24,19 7,19A1,1 0 0,1 6,18V3A1,1 0 0,1 7,2C7.24,2 7.47,2.09 7.64,2.23L7.65,2.22L19.14,11.86C19.57,12.22 19.62,12.85 19.27,13.27C19.12,13.45 18.91,13.57 18.7,13.61L15.54,14.23L17.74,18.96C18,19.46 17.76,20.05 17.26,20.28L13.64,21.97Z" })));
|
|
10
10
|
}
|
|
11
|
-
//# sourceMappingURL=CursorIcon.js.map
|
|
@@ -12,4 +12,3 @@ export default observer(function ({ model }) {
|
|
|
12
12
|
React.createElement(Button, { onClick: () => setShown(true) }, "More info"),
|
|
13
13
|
shown ? (React.createElement(WarningDialog, { trackWarnings: trackWarnings, handleClose: () => setShown(false) })) : null)) : null;
|
|
14
14
|
});
|
|
15
|
-
//# sourceMappingURL=DotplotWarnings.js.map
|
|
@@ -50,4 +50,3 @@ export default function Grid({ model, children, }) {
|
|
|
50
50
|
return (React.createElement("svg", { width: viewWidth, height: viewHeight, style: { background: 'rgba(0,0,0,0.12)' } },
|
|
51
51
|
React.createElement(GridRaw, { model: model }, children)));
|
|
52
52
|
}
|
|
53
|
-
//# sourceMappingURL=Grid.js.map
|
|
@@ -149,4 +149,3 @@ const OpenTrack = observer(({ sessionTrackData, assembly1, assembly2, setSession
|
|
|
149
149
|
React.createElement(FileSelector, { name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: loc => setBed2Location(loc) }))))) : (React.createElement(FileSelector, { name: value ? value + ' location' : '', description: "", location: fileLocation, setLocation: loc => setFileLocation(loc) }))))));
|
|
150
150
|
});
|
|
151
151
|
export default OpenTrack;
|
|
152
|
-
//# sourceMappingURL=ImportCustomTrack.js.map
|
|
@@ -90,4 +90,3 @@ const DotplotImportForm = observer(({ model }) => {
|
|
|
90
90
|
React.createElement(TrackSelector, { setShowTrackId: setShowTrackId, assembly2: assembly2, assembly1: assembly1, setSessionTrackData: setSessionTrackData, sessionTrackData: sessionTrackData, model: model })))));
|
|
91
91
|
});
|
|
92
92
|
export default DotplotImportForm;
|
|
93
|
-
//# sourceMappingURL=ImportForm.js.map
|