@jbrowse/plugin-dotplot-view 2.6.2 → 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.
Files changed (7) hide show
  1. package/dist/DotplotView/model.d.ts +64 -40
  2. package/dist/DotplotView/model.js +11 -3
  3. package/dist/DotplotView/svgcomponents/SVGBackground.js +2 -1
  4. package/esm/DotplotView/model.d.ts +64 -40
  5. package/esm/DotplotView/model.js +11 -3
  6. package/esm/DotplotView/svgcomponents/SVGBackground.js +2 -1
  7. package/package.json +3 -2
package/dist/DotplotView/model.d.ts CHANGED
@@ -58,15 +58,15 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
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  readonly width: number;
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  readonly assemblyNames: string[];
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  readonly displayedRegionsTotalPx: number;
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- readonly maxOffset: number; /**
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- * #property
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+ readonly maxOffset: number;
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+ readonly minOffset: number; /**
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+ * #stateModel DotplotView
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+ * #category view
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+ * extends `BaseViewModel`
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  */
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- readonly minOffset: number;
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  readonly totalBp: number;
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  } & {
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- readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet; /**
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- * #property
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- */
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+ readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
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  readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
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  readonly currBp: number;
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  } & {
@@ -82,14 +82,20 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
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  reversed: boolean;
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  };
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  bpToPx({ refName, coord, regionNumber, }: {
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- refName: string;
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+ refName: string; /**
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+ * #property
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+ */
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  coord: number;
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- regionNumber?: number | undefined;
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+ regionNumber?: number | undefined; /**
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+ * #property
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+ */
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  }): number | undefined;
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  } & {
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  setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
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  showAllRegions(): void;
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- zoomOut(): void;
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+ zoomOut(): void; /**
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+ * #property
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+ */
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  zoomIn(): void;
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  zoomTo(bpPerPx: number, offset?: number | undefined): number;
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  scrollTo(offsetPx: number): number;
@@ -137,15 +143,15 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
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  readonly width: number;
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  readonly assemblyNames: string[];
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  readonly displayedRegionsTotalPx: number;
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- readonly maxOffset: number; /**
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- * #property
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+ readonly maxOffset: number;
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+ readonly minOffset: number; /**
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+ * #stateModel DotplotView
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+ * #category view
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+ * extends `BaseViewModel`
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  */
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- readonly minOffset: number;
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  readonly totalBp: number;
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  } & {
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- readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet; /**
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- * #property
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- */
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+ readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
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  readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
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  readonly currBp: number;
151
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  } & {
@@ -161,14 +167,20 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
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  reversed: boolean;
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  };
163
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  bpToPx({ refName, coord, regionNumber, }: {
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- refName: string;
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+ refName: string; /**
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+ * #property
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+ */
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  coord: number;
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- regionNumber?: number | undefined;
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+ regionNumber?: number | undefined; /**
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+ * #property
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+ */
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  }): number | undefined;
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  } & {
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  setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
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  showAllRegions(): void;
171
- zoomOut(): void;
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+ zoomOut(): void; /**
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+ * #property
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+ */
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  zoomIn(): void;
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  zoomTo(bpPerPx: number, offset?: number | undefined): number;
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  scrollTo(offsetPx: number): number;
@@ -207,7 +219,9 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
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  activateConfigurationUI(): void;
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  showDisplay(displayId: string, initialSnapshot?: {} | undefined): void;
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  hideDisplay(displayId: string): number;
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- replaceDisplay(oldId: string, newId: string, initialSnapshot?: {} | undefined): void;
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+ replaceDisplay(oldId: string, newId: string, initialSnapshot?: {} | undefined): void; /**
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+ * #property
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+ */
211
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  } & {
212
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  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 | {
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  type: string; /**
@@ -216,9 +230,7 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
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  label: string;
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  subMenu: {
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  type: string;
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- label: string; /**
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- * #property
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- */
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+ label: string;
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  checked: boolean;
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  onClick: () => void;
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  }[];
@@ -329,15 +341,15 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
329
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  readonly width: number;
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  readonly assemblyNames: string[];
331
343
  readonly displayedRegionsTotalPx: number;
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- readonly maxOffset: number; /**
333
- * #property
344
+ readonly maxOffset: number;
345
+ readonly minOffset: number; /**
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+ * #stateModel DotplotView
347
+ * #category view
348
+ * extends `BaseViewModel`
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  */
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- readonly minOffset: number;
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  readonly totalBp: number;
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  } & {
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- readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet; /**
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- * #property
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- */
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+ readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
341
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  readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
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  readonly currBp: number;
343
355
  } & {
@@ -353,14 +365,20 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
353
365
  reversed: boolean;
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  };
355
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  bpToPx({ refName, coord, regionNumber, }: {
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- refName: string;
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+ refName: string; /**
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+ * #property
370
+ */
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  coord: number;
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- regionNumber?: number | undefined;
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+ regionNumber?: number | undefined; /**
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+ * #property
374
+ */
359
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  }): number | undefined;
360
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  } & {
361
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  setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
362
378
  showAllRegions(): void;
363
- zoomOut(): void;
379
+ zoomOut(): void; /**
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+ * #property
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+ */
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382
  zoomIn(): void;
365
383
  zoomTo(bpPerPx: number, offset?: number | undefined): number;
366
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  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
- * #property
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
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  readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
420
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  readonly currBp: number;
421
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  } & {
@@ -431,14 +449,20 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
431
449
  reversed: boolean;
432
450
  };
433
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  bpToPx({ refName, coord, regionNumber, }: {
434
- refName: string;
452
+ refName: string; /**
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+ * #property
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+ */
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  coord: number;
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- regionNumber?: number | undefined;
456
+ regionNumber?: number | undefined; /**
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+ * #property
458
+ */
437
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  }): number | undefined;
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  } & {
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  setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
440
462
  showAllRegions(): void;
441
- zoomOut(): void;
463
+ zoomOut(): void; /**
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+ * #property
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+ */
442
466
  zoomIn(): void;
443
467
  zoomTo(bpPerPx: number, offset?: number | undefined): number;
444
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  scrollTo(offsetPx: number): number;
package/dist/DotplotView/model.js CHANGED
@@ -46,6 +46,15 @@ const util_2 = require("./components/util");
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  // lazies
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  const ExportSvgDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ExportSvgDialog'))));
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  const ReturnToImportFormDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@jbrowse/core/ui/ReturnToImportFormDialog'))));
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+ const len = (a) => (0, util_1.measureText)(a.slice(0, 30));
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+ const pxWidthForBlocks = (blocks, hide) => {
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+ return (0, util_1.max)([
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+ ...blocks.filter(b => !hide.has(b.key)).map(b => len(b.refName)),
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+ ...blocks
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+ .filter(b => !hide.has(b.key))
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+ .map(b => len(b.end.toLocaleString('en-us'))),
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+ ]);
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+ };
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  /**
50
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  * #stateModel DotplotView
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  * #category view
@@ -547,9 +556,8 @@ function stateModelFactory(pm) {
547
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  const voffset = vview.offsetPx;
548
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  const vhide = (0, util_2.getBlockLabelKeysToHide)(vblocks, viewHeight, voffset);
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  const hhide = (0, util_2.getBlockLabelKeysToHide)(hblocks, viewWidth, hoffset);
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- const len = (a) => (0, util_1.measureText)(a.slice(0, 30));
551
- const by = (0, util_1.max)(hblocks.filter(b => !hhide.has(b.key)).map(b => len(b.refName)));
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- const bx = (0, util_1.max)(vblocks.filter(b => !vhide.has(b.key)).map(b => len(b.refName)));
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+ const by = pxWidthForBlocks(hblocks, hhide);
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+ const bx = pxWidthForBlocks(vblocks, vhide);
553
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  // these are set via autorun to avoid dependency cycle
554
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  self.setBorderY(Math.max(by + padding, 50));
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  self.setBorderX(Math.max(bx + padding, 50));
package/dist/DotplotView/svgcomponents/SVGBackground.js CHANGED
@@ -4,9 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
4
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  };
5
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  Object.defineProperty(exports, "__esModule", { value: true });
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  const react_1 = __importDefault(require("react"));
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+ const color_1 = __importDefault(require("color"));
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  const material_1 = require("@mui/material");
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  function SVGBackground({ width, height, }) {
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  const theme = (0, material_1.useTheme)();
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- return (react_1.default.createElement("rect", { x: 0, y: 0, width: width, height: height, fill: theme.palette.background.default }));
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+ 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
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  }
12
13
  exports.default = SVGBackground;
package/esm/DotplotView/model.d.ts CHANGED
@@ -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
- * #property
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
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  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
- * #property
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
- * #property
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
- * #property
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;
package/esm/DotplotView/model.js CHANGED
@@ -17,6 +17,15 @@ import { getBlockLabelKeysToHide, makeTicks } from './components/util';
17
17
  // lazies
18
18
  const ExportSvgDialog = lazy(() => import('./components/ExportSvgDialog'));
19
19
  const ReturnToImportFormDialog = lazy(() => import('@jbrowse/core/ui/ReturnToImportFormDialog'));
20
+ const len = (a) => measureText(a.slice(0, 30));
21
+ const pxWidthForBlocks = (blocks, hide) => {
22
+ return max([
23
+ ...blocks.filter(b => !hide.has(b.key)).map(b => len(b.refName)),
24
+ ...blocks
25
+ .filter(b => !hide.has(b.key))
26
+ .map(b => len(b.end.toLocaleString('en-us'))),
27
+ ]);
28
+ };
20
29
  /**
21
30
  * #stateModel DotplotView
22
31
  * #category view
@@ -518,9 +527,8 @@ export default function stateModelFactory(pm) {
518
527
  const voffset = vview.offsetPx;
519
528
  const vhide = getBlockLabelKeysToHide(vblocks, viewHeight, voffset);
520
529
  const hhide = getBlockLabelKeysToHide(hblocks, viewWidth, hoffset);
521
- const len = (a) => measureText(a.slice(0, 30));
522
- const by = max(hblocks.filter(b => !hhide.has(b.key)).map(b => len(b.refName)));
523
- const bx = max(vblocks.filter(b => !vhide.has(b.key)).map(b => len(b.refName)));
530
+ const by = pxWidthForBlocks(hblocks, hhide);
531
+ const bx = pxWidthForBlocks(vblocks, vhide);
524
532
  // these are set via autorun to avoid dependency cycle
525
533
  self.setBorderY(Math.max(by + padding, 50));
526
534
  self.setBorderX(Math.max(bx + padding, 50));
package/esm/DotplotView/svgcomponents/SVGBackground.js CHANGED
@@ -1,6 +1,7 @@
1
1
  import React from 'react';
2
+ import Color from 'color';
2
3
  import { useTheme } from '@mui/material';
3
4
  export default function SVGBackground({ width, height, }) {
4
5
  const theme = useTheme();
5
- return (React.createElement("rect", { x: 0, y: 0, width: width, height: height, fill: theme.palette.background.default }));
6
+ return (React.createElement("rect", { x: 0, y: 0, width: width, height: height, fill: Color(theme.palette.background.default).hex() }));
6
7
  }
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-dotplot-view",
3
- "version": "2.6.2",
3
+ "version": "2.6.3",
4
4
  "description": "JBrowse 2 dotplot view",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -42,6 +42,7 @@
42
42
  "@types/file-saver": "^2.0.1",
43
43
  "@types/normalize-wheel": "^1.0.0",
44
44
  "clone": "^2.1.2",
45
+ "color": "^3.1.3",
45
46
  "file-saver": "^2.0.0",
46
47
  "normalize-wheel": "^1.0.1",
47
48
  "react-popper": "^2.0.0"
@@ -64,5 +65,5 @@
64
65
  "publishConfig": {
65
66
  "access": "public"
66
67
  },
67
- "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
68
+ "gitHead": "ed402c87efb0904858d602c363bd1757d5742129"
68
69
  }