@jbrowse/plugin-linear-comparative-view 4.0.3 → 4.1.1

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Files changed (26) hide show
  1. package/esm/LGVSyntenyDisplay/model.d.ts +20 -1
  2. package/esm/LinearComparativeDisplay/stateModelFactory.d.ts +3 -0
  3. package/esm/LinearComparativeView/components/LinearComparativeRenderArea.js +3 -0
  4. package/esm/LinearComparativeView/components/OpacitySlider.js +7 -3
  5. package/esm/LinearComparativeView/components/useRangeSelect.js +3 -0
  6. package/esm/LinearComparativeView/model.d.ts +90 -57
  7. package/esm/LinearSyntenyDisplay/afterAttach.js +9 -0
  8. package/esm/LinearSyntenyDisplay/components/LinearSyntenyRendering.js +15 -15
  9. package/esm/LinearSyntenyDisplay/components/util.d.ts +1 -0
  10. package/esm/LinearSyntenyDisplay/components/util.js +23 -38
  11. package/esm/LinearSyntenyDisplay/drawCigarClickMap.d.ts +2 -0
  12. package/esm/LinearSyntenyDisplay/drawCigarClickMap.js +88 -0
  13. package/esm/LinearSyntenyDisplay/{drawMouseoverClickMap.js → drawMouseover.js} +9 -11
  14. package/esm/LinearSyntenyDisplay/drawRef.d.ts +2 -0
  15. package/esm/LinearSyntenyDisplay/drawRef.js +190 -0
  16. package/esm/LinearSyntenyDisplay/drawSynteny.d.ts +4 -6
  17. package/esm/LinearSyntenyDisplay/drawSynteny.js +4 -461
  18. package/esm/LinearSyntenyDisplay/drawSyntenyUtils.d.ts +58 -0
  19. package/esm/LinearSyntenyDisplay/drawSyntenyUtils.js +62 -0
  20. package/esm/LinearSyntenyDisplay/model.d.ts +47 -2
  21. package/esm/LinearSyntenyDisplay/model.js +50 -2
  22. package/esm/LinearSyntenyView/model.d.ts +111 -69
  23. package/esm/LinearSyntenyView/model.js +23 -24
  24. package/esm/SyntenyFeatureDetail/LinkToSyntenyView.js +4 -4
  25. package/package.json +8 -7
  26. /package/esm/LinearSyntenyDisplay/{drawMouseoverClickMap.d.ts → drawMouseover.d.ts} +0 -0
package/esm/LinearSyntenyDisplay/model.js CHANGED
@@ -1,5 +1,6 @@
1
1
  import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
2
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  import { types } from '@jbrowse/mobx-state-tree';
3
+ import { applyAlpha, colorSchemes, getQueryColor } from "./drawSyntenyUtils.js";
3
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  import baseModelFactory from "../LinearComparativeDisplay/stateModelFactory.js";
4
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  function stateModelFactory(configSchema) {
5
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  return types
@@ -7,6 +8,8 @@ function stateModelFactory(configSchema) {
7
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  type: types.literal('LinearSyntenyDisplay'),
8
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  configuration: ConfigurationReference(configSchema),
9
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  colorBy: types.optional(types.string, 'default'),
11
+ alpha: types.optional(types.number, 0.2),
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+ minAlignmentLength: types.optional(types.number, 0),
10
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  }))
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  .volatile(() => ({
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  mainCanvas: null,
@@ -17,8 +20,6 @@ function stateModelFactory(configSchema) {
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  mouseoverId: undefined,
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  clickId: undefined,
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  cigarMouseoverId: -1,
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- alpha: 0.2,
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- minAlignmentLength: 0,
22
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  }))
23
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  .actions(self => ({
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  setFeatPositions(arg) {
@@ -75,6 +76,53 @@ function stateModelFactory(configSchema) {
75
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  get featMap() {
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  return Object.fromEntries(self.featPositions.map(f => [f.f.id(), f]));
77
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  },
79
+ get colorSchemeConfig() {
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+ return colorSchemes[self.colorBy] || colorSchemes.default;
81
+ },
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+ get colorMapWithAlpha() {
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+ const { alpha } = self;
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+ const activeColorMap = this.colorSchemeConfig.cigarColors;
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+ return {
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+ I: applyAlpha(activeColorMap.I, alpha),
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+ N: applyAlpha(activeColorMap.N, alpha),
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+ D: applyAlpha(activeColorMap.D, alpha),
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+ X: applyAlpha(activeColorMap.X, alpha),
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+ M: applyAlpha(activeColorMap.M, alpha),
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+ '=': applyAlpha(activeColorMap['='], alpha),
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+ };
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+ },
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+ get posColorWithAlpha() {
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+ const posColor = self.colorBy === 'strand' ? colorSchemes.strand.posColor : 'red';
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+ return applyAlpha(posColor, self.alpha);
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+ },
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+ get negColorWithAlpha() {
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+ const negColor = self.colorBy === 'strand' ? colorSchemes.strand.negColor : 'blue';
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+ return applyAlpha(negColor, self.alpha);
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+ },
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+ get queryColorWithAlphaMap() {
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+ const { alpha } = self;
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+ const cache = new Map();
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+ return (queryName) => {
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+ if (!cache.has(queryName)) {
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+ const color = getQueryColor(queryName);
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+ cache.set(queryName, applyAlpha(color, alpha));
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+ }
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+ return cache.get(queryName);
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+ };
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+ },
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+ get queryTotalLengths() {
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+ if (self.minAlignmentLength <= 0) {
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+ return undefined;
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+ }
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+ const lengths = new Map();
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+ for (const { f } of self.featPositions) {
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+ const queryName = f.get('name') || f.get('id') || f.id();
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+ const alignmentLength = Math.abs(f.get('end') - f.get('start'));
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+ const currentTotal = lengths.get(queryName) || 0;
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+ lengths.set(queryName, currentTotal + alignmentLength);
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+ }
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+ return lengths;
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+ },
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  }))
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  .actions(self => ({
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  afterAttach() {
package/esm/LinearSyntenyView/model.d.ts CHANGED
@@ -34,10 +34,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  showCytobandsSetting: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
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  showGridlines: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
37
- highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType>>, [undefined]>;
37
+ highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view").HighlightType, import("@jbrowse/plugin-linear-genome-view").HighlightType, import("@jbrowse/plugin-linear-genome-view").HighlightType>>, [undefined]>;
38
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  colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
39
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  showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
40
- init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined>;
40
+ init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view").InitState | undefined, import("@jbrowse/plugin-linear-genome-view").InitState | undefined, import("@jbrowse/plugin-linear-genome-view").InitState | undefined>;
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  }, {
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  width: number;
43
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  } & {
@@ -53,11 +53,15 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
53
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  lastTrackDragY: undefined | number;
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  volatileError: unknown;
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  scaleFactor: number;
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+ targetBpPerPx: number | undefined;
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  trackRefs: Record<string, HTMLDivElement>;
57
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  coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
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  coarseTotalBp: number;
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- leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset;
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- rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset;
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+ leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view").BpOffset;
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+ rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view").BpOffset;
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+ isScalebarRefNameMenuOpen: boolean;
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+ scalebarRefNameClickPending: boolean;
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+ volatileGuides: import("@jbrowse/plugin-linear-genome-view").VolatileGuide[];
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  } & {
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  readonly pinnedTracks: any[];
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  readonly unpinnedTracks: any[];
@@ -111,16 +115,19 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  setShowCytobands(flag: boolean): void;
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  setWidth(newWidth: number): void;
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  setError(error: unknown): void;
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+ setIsScalebarRefNameMenuOpen(isOpen: boolean): void;
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+ setScalebarRefNameClickPending(pending: boolean): void;
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  setHideHeader(b: boolean): void;
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  setHideHeaderOverview(b: boolean): void;
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  setHideNoTracksActive(b: boolean): void;
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  setShowGridlines(b: boolean): void;
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- addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType): void;
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- setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType[]): void;
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- removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType): void;
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+ addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view").HighlightType): void;
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+ setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view").HighlightType[]): void;
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+ removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view").HighlightType): void;
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+ setVolatileGuides(guides: import("@jbrowse/plugin-linear-genome-view").VolatileGuide[]): void;
121
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  scrollTo(offsetPx: number): number;
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  zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
123
- setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset): void;
130
+ setOffsets(left?: import("@jbrowse/plugin-linear-genome-view").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view").BpOffset): void;
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  setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
125
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  setNewView(bpPerPx: number, offsetPx: number): void;
126
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  horizontallyFlip(): void;
@@ -137,7 +144,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
137
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  setShowCenterLine(b: boolean): void;
138
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  setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
139
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  activateTrackSelector(): import("@jbrowse/core/util").Widget;
140
- getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset): {
147
+ getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view").BpOffset): {
141
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  assemblyName: string;
142
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  refName: string;
143
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  start: number;
@@ -150,9 +157,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
150
157
  setDraggingTrackId(idx?: string): void;
151
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  setLastTrackDragY(y: number): void;
152
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  setScaleFactor(factor: number): void;
160
+ setTargetBpPerPx(target: number | undefined): void;
153
161
  clearView(): void;
154
- setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState): void;
155
- exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").ExportSvgOptions): Promise<void>;
162
+ setInit(arg?: import("@jbrowse/plugin-linear-genome-view").InitState): void;
163
+ exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view").ExportSvgOptions): Promise<void>;
156
164
  } & {
157
165
  slide: (viewWidths: number) => void;
158
166
  } & {
@@ -171,10 +179,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
171
179
  readonly visibleLocStrings: string;
172
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  readonly coarseVisibleLocStrings: string;
173
181
  readonly coarseTotalBpDisplayStr: string;
182
+ readonly effectiveBpPerPx: number;
183
+ readonly effectiveTotalBp: number;
184
+ readonly effectiveTotalBpDisplayStr: string;
174
185
  } & {
175
186
  setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
176
187
  } & {
177
- moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset): void;
188
+ moveTo(start?: import("@jbrowse/plugin-linear-genome-view").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view").BpOffset): void;
178
189
  navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
179
190
  navToSearchString({ input, assembly, }: {
180
191
  input: string;
@@ -182,8 +193,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
182
193
  }): Promise<void>;
183
194
  navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
184
195
  navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
185
- navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").NavLocation): void;
186
- navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").NavLocation[]): void;
196
+ navTo(query: import("@jbrowse/plugin-linear-genome-view").NavLocation, grow?: number): void;
197
+ navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view").NavLocation[], grow?: number): void;
187
198
  } & {
188
199
  rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
189
200
  bpToPx({ refName, coord, regionNumber, }: {
@@ -219,7 +230,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
219
230
  } | undefined;
220
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  readonly visibleRegions: import("@jbrowse/core/util/blockTypes").BaseBlock[];
221
232
  } & {
222
- rubberbandClickMenuItems(clickOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset): import("@jbrowse/core/ui").MenuItem[];
233
+ rubberbandClickMenuItems(clickOffset: import("@jbrowse/plugin-linear-genome-view").BpOffset): import("@jbrowse/core/ui").MenuItem[];
223
234
  } & {
224
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  afterCreate(): void;
225
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  afterAttach(): void;
@@ -242,10 +253,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
242
253
  showCytobandsSetting: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
243
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  trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
244
255
  showGridlines: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
245
- highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType>>, [undefined]>;
256
+ highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view").HighlightType, import("@jbrowse/plugin-linear-genome-view").HighlightType, import("@jbrowse/plugin-linear-genome-view").HighlightType>>, [undefined]>;
246
257
  colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
247
258
  showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
248
- init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined>;
259
+ init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view").InitState | undefined, import("@jbrowse/plugin-linear-genome-view").InitState | undefined, import("@jbrowse/plugin-linear-genome-view").InitState | undefined>;
249
260
  }>>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
250
261
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
251
262
  displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -265,10 +276,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
265
276
  showCytobandsSetting: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
266
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  trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
267
278
  showGridlines: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
268
- highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType>>, [undefined]>;
279
+ highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view").HighlightType, import("@jbrowse/plugin-linear-genome-view").HighlightType, import("@jbrowse/plugin-linear-genome-view").HighlightType>>, [undefined]>;
269
280
  colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
270
281
  showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
271
- init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined>;
282
+ init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view").InitState | undefined, import("@jbrowse/plugin-linear-genome-view").InitState | undefined, import("@jbrowse/plugin-linear-genome-view").InitState | undefined>;
272
283
  }>>>;
273
284
  viewTrackConfigs: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
274
285
  } & {
@@ -349,21 +360,30 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
349
360
  muiName: string;
350
361
  };
351
362
  helpText: string;
363
+ subMenu?: undefined;
352
364
  type?: undefined;
353
365
  checked?: undefined;
354
- subMenu?: undefined;
355
- } | {
356
- label: string;
357
- type: string;
358
- checked: boolean;
359
- onClick: () => void;
360
- helpText: string;
361
- description?: undefined;
362
- icon?: undefined;
363
- subMenu?: undefined;
364
366
  } | {
365
367
  label: string;
366
368
  subMenu: ({
369
+ label: string;
370
+ onClick: () => void;
371
+ description: string;
372
+ icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
373
+ muiName: string;
374
+ };
375
+ helpText: string;
376
+ type?: undefined;
377
+ checked?: undefined;
378
+ } | {
379
+ label: string;
380
+ type: string;
381
+ checked: boolean;
382
+ onClick: () => void;
383
+ helpText: string;
384
+ description?: undefined;
385
+ icon?: undefined;
386
+ } | {
367
387
  label: string;
368
388
  checked: boolean;
369
389
  type: string;
@@ -403,11 +423,11 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
403
423
  muiName: string;
404
424
  };
405
425
  onClick: () => void;
406
- helpText: string;
407
426
  description?: undefined;
427
+ helpText?: undefined;
428
+ subMenu?: undefined;
408
429
  type?: undefined;
409
430
  checked?: undefined;
410
- subMenu?: undefined;
411
431
  })[];
412
432
  menuItems(): (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 | {
413
433
  label: string;
@@ -452,10 +472,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
452
472
  showCytobandsSetting: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
453
473
  trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
454
474
  showGridlines: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
455
- highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType>>, [undefined]>;
475
+ highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view").HighlightType, import("@jbrowse/plugin-linear-genome-view").HighlightType, import("@jbrowse/plugin-linear-genome-view").HighlightType>>, [undefined]>;
456
476
  colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
457
477
  showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
458
- init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined>;
478
+ init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view").InitState | undefined, import("@jbrowse/plugin-linear-genome-view").InitState | undefined, import("@jbrowse/plugin-linear-genome-view").InitState | undefined>;
459
479
  }, {
460
480
  width: number;
461
481
  } & {
@@ -471,11 +491,15 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
471
491
  lastTrackDragY: undefined | number;
472
492
  volatileError: unknown;
473
493
  scaleFactor: number;
494
+ targetBpPerPx: number | undefined;
474
495
  trackRefs: Record<string, HTMLDivElement>;
475
496
  coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
476
497
  coarseTotalBp: number;
477
- leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset;
478
- rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset;
498
+ leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view").BpOffset;
499
+ rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view").BpOffset;
500
+ isScalebarRefNameMenuOpen: boolean;
501
+ scalebarRefNameClickPending: boolean;
502
+ volatileGuides: import("@jbrowse/plugin-linear-genome-view").VolatileGuide[];
479
503
  } & {
480
504
  readonly pinnedTracks: any[];
481
505
  readonly unpinnedTracks: any[];
@@ -529,16 +553,19 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
529
553
  setShowCytobands(flag: boolean): void;
530
554
  setWidth(newWidth: number): void;
531
555
  setError(error: unknown): void;
556
+ setIsScalebarRefNameMenuOpen(isOpen: boolean): void;
557
+ setScalebarRefNameClickPending(pending: boolean): void;
532
558
  setHideHeader(b: boolean): void;
533
559
  setHideHeaderOverview(b: boolean): void;
534
560
  setHideNoTracksActive(b: boolean): void;
535
561
  setShowGridlines(b: boolean): void;
536
- addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType): void;
537
- setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType[]): void;
538
- removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType): void;
562
+ addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view").HighlightType): void;
563
+ setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view").HighlightType[]): void;
564
+ removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view").HighlightType): void;
565
+ setVolatileGuides(guides: import("@jbrowse/plugin-linear-genome-view").VolatileGuide[]): void;
539
566
  scrollTo(offsetPx: number): number;
540
567
  zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
541
- setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset): void;
568
+ setOffsets(left?: import("@jbrowse/plugin-linear-genome-view").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view").BpOffset): void;
542
569
  setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
543
570
  setNewView(bpPerPx: number, offsetPx: number): void;
544
571
  horizontallyFlip(): void;
@@ -555,7 +582,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
555
582
  setShowCenterLine(b: boolean): void;
556
583
  setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
557
584
  activateTrackSelector(): import("@jbrowse/core/util").Widget;
558
- getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset): {
585
+ getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view").BpOffset): {
559
586
  assemblyName: string;
560
587
  refName: string;
561
588
  start: number;
@@ -568,9 +595,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
568
595
  setDraggingTrackId(idx?: string): void;
569
596
  setLastTrackDragY(y: number): void;
570
597
  setScaleFactor(factor: number): void;
598
+ setTargetBpPerPx(target: number | undefined): void;
571
599
  clearView(): void;
572
- setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState): void;
573
- exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").ExportSvgOptions): Promise<void>;
600
+ setInit(arg?: import("@jbrowse/plugin-linear-genome-view").InitState): void;
601
+ exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view").ExportSvgOptions): Promise<void>;
574
602
  } & {
575
603
  slide: (viewWidths: number) => void;
576
604
  } & {
@@ -589,10 +617,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
589
617
  readonly visibleLocStrings: string;
590
618
  readonly coarseVisibleLocStrings: string;
591
619
  readonly coarseTotalBpDisplayStr: string;
620
+ readonly effectiveBpPerPx: number;
621
+ readonly effectiveTotalBp: number;
622
+ readonly effectiveTotalBpDisplayStr: string;
592
623
  } & {
593
624
  setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
594
625
  } & {
595
- moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset): void;
626
+ moveTo(start?: import("@jbrowse/plugin-linear-genome-view").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view").BpOffset): void;
596
627
  navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
597
628
  navToSearchString({ input, assembly, }: {
598
629
  input: string;
@@ -600,8 +631,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
600
631
  }): Promise<void>;
601
632
  navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
602
633
  navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
603
- navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").NavLocation): void;
604
- navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").NavLocation[]): void;
634
+ navTo(query: import("@jbrowse/plugin-linear-genome-view").NavLocation, grow?: number): void;
635
+ navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view").NavLocation[], grow?: number): void;
605
636
  } & {
606
637
  rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
607
638
  bpToPx({ refName, coord, regionNumber, }: {
@@ -637,7 +668,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
637
668
  } | undefined;
638
669
  readonly visibleRegions: import("@jbrowse/core/util/blockTypes").BaseBlock[];
639
670
  } & {
640
- rubberbandClickMenuItems(clickOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset): import("@jbrowse/core/ui").MenuItem[];
671
+ rubberbandClickMenuItems(clickOffset: import("@jbrowse/plugin-linear-genome-view").BpOffset): import("@jbrowse/core/ui").MenuItem[];
641
672
  } & {
642
673
  afterCreate(): void;
643
674
  afterAttach(): void;
@@ -660,10 +691,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
660
691
  showCytobandsSetting: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
661
692
  trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
662
693
  showGridlines: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
663
- highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType>>, [undefined]>;
694
+ highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view").HighlightType, import("@jbrowse/plugin-linear-genome-view").HighlightType, import("@jbrowse/plugin-linear-genome-view").HighlightType>>, [undefined]>;
664
695
  colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
665
696
  showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
666
- init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined>;
697
+ init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view").InitState | undefined, import("@jbrowse/plugin-linear-genome-view").InitState | undefined, import("@jbrowse/plugin-linear-genome-view").InitState | undefined>;
667
698
  }>>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
668
699
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
669
700
  displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -683,10 +714,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
683
714
  showCytobandsSetting: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
684
715
  trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
685
716
  showGridlines: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
686
- highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType>>, [undefined]>;
717
+ highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view").HighlightType, import("@jbrowse/plugin-linear-genome-view").HighlightType, import("@jbrowse/plugin-linear-genome-view").HighlightType>>, [undefined]>;
687
718
  colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
688
719
  showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
689
- init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined>;
720
+ init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view").InitState | undefined, import("@jbrowse/plugin-linear-genome-view").InitState | undefined, import("@jbrowse/plugin-linear-genome-view").InitState | undefined>;
690
721
  }>>>;
691
722
  viewTrackConfigs: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
692
723
  }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
@@ -721,10 +752,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
721
752
  showCytobandsSetting: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
722
753
  trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
723
754
  showGridlines: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
724
- highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType>>, [undefined]>;
755
+ highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view").HighlightType, import("@jbrowse/plugin-linear-genome-view").HighlightType, import("@jbrowse/plugin-linear-genome-view").HighlightType>>, [undefined]>;
725
756
  colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
726
757
  showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
727
- init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined>;
758
+ init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view").InitState | undefined, import("@jbrowse/plugin-linear-genome-view").InitState | undefined, import("@jbrowse/plugin-linear-genome-view").InitState | undefined>;
728
759
  }, {
729
760
  width: number;
730
761
  } & {
@@ -740,11 +771,15 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
740
771
  lastTrackDragY: undefined | number;
741
772
  volatileError: unknown;
742
773
  scaleFactor: number;
774
+ targetBpPerPx: number | undefined;
743
775
  trackRefs: Record<string, HTMLDivElement>;
744
776
  coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
745
777
  coarseTotalBp: number;
746
- leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset;
747
- rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset;
778
+ leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view").BpOffset;
779
+ rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view").BpOffset;
780
+ isScalebarRefNameMenuOpen: boolean;
781
+ scalebarRefNameClickPending: boolean;
782
+ volatileGuides: import("@jbrowse/plugin-linear-genome-view").VolatileGuide[];
748
783
  } & {
749
784
  readonly pinnedTracks: any[];
750
785
  readonly unpinnedTracks: any[];
@@ -798,16 +833,19 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
798
833
  setShowCytobands(flag: boolean): void;
799
834
  setWidth(newWidth: number): void;
800
835
  setError(error: unknown): void;
836
+ setIsScalebarRefNameMenuOpen(isOpen: boolean): void;
837
+ setScalebarRefNameClickPending(pending: boolean): void;
801
838
  setHideHeader(b: boolean): void;
802
839
  setHideHeaderOverview(b: boolean): void;
803
840
  setHideNoTracksActive(b: boolean): void;
804
841
  setShowGridlines(b: boolean): void;
805
- addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType): void;
806
- setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType[]): void;
807
- removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType): void;
842
+ addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view").HighlightType): void;
843
+ setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view").HighlightType[]): void;
844
+ removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view").HighlightType): void;
845
+ setVolatileGuides(guides: import("@jbrowse/plugin-linear-genome-view").VolatileGuide[]): void;
808
846
  scrollTo(offsetPx: number): number;
809
847
  zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
810
- setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset): void;
848
+ setOffsets(left?: import("@jbrowse/plugin-linear-genome-view").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view").BpOffset): void;
811
849
  setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
812
850
  setNewView(bpPerPx: number, offsetPx: number): void;
813
851
  horizontallyFlip(): void;
@@ -824,7 +862,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
824
862
  setShowCenterLine(b: boolean): void;
825
863
  setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
826
864
  activateTrackSelector(): import("@jbrowse/core/util").Widget;
827
- getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset): {
865
+ getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view").BpOffset): {
828
866
  assemblyName: string;
829
867
  refName: string;
830
868
  start: number;
@@ -837,9 +875,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
837
875
  setDraggingTrackId(idx?: string): void;
838
876
  setLastTrackDragY(y: number): void;
839
877
  setScaleFactor(factor: number): void;
878
+ setTargetBpPerPx(target: number | undefined): void;
840
879
  clearView(): void;
841
- setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState): void;
842
- exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").ExportSvgOptions): Promise<void>;
880
+ setInit(arg?: import("@jbrowse/plugin-linear-genome-view").InitState): void;
881
+ exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view").ExportSvgOptions): Promise<void>;
843
882
  } & {
844
883
  slide: (viewWidths: number) => void;
845
884
  } & {
@@ -858,10 +897,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
858
897
  readonly visibleLocStrings: string;
859
898
  readonly coarseVisibleLocStrings: string;
860
899
  readonly coarseTotalBpDisplayStr: string;
900
+ readonly effectiveBpPerPx: number;
901
+ readonly effectiveTotalBp: number;
902
+ readonly effectiveTotalBpDisplayStr: string;
861
903
  } & {
862
904
  setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
863
905
  } & {
864
- moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset): void;
906
+ moveTo(start?: import("@jbrowse/plugin-linear-genome-view").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view").BpOffset): void;
865
907
  navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
866
908
  navToSearchString({ input, assembly, }: {
867
909
  input: string;
@@ -869,8 +911,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
869
911
  }): Promise<void>;
870
912
  navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
871
913
  navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
872
- navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").NavLocation): void;
873
- navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").NavLocation[]): void;
914
+ navTo(query: import("@jbrowse/plugin-linear-genome-view").NavLocation, grow?: number): void;
915
+ navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view").NavLocation[], grow?: number): void;
874
916
  } & {
875
917
  rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
876
918
  bpToPx({ refName, coord, regionNumber, }: {
@@ -906,7 +948,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
906
948
  } | undefined;
907
949
  readonly visibleRegions: import("@jbrowse/core/util/blockTypes").BaseBlock[];
908
950
  } & {
909
- rubberbandClickMenuItems(clickOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").BpOffset): import("@jbrowse/core/ui").MenuItem[];
951
+ rubberbandClickMenuItems(clickOffset: import("@jbrowse/plugin-linear-genome-view").BpOffset): import("@jbrowse/core/ui").MenuItem[];
910
952
  } & {
911
953
  afterCreate(): void;
912
954
  afterAttach(): void;
@@ -929,10 +971,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
929
971
  showCytobandsSetting: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
930
972
  trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
931
973
  showGridlines: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
932
- highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType>>, [undefined]>;
974
+ highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view").HighlightType, import("@jbrowse/plugin-linear-genome-view").HighlightType, import("@jbrowse/plugin-linear-genome-view").HighlightType>>, [undefined]>;
933
975
  colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
934
976
  showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
935
- init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined>;
977
+ init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view").InitState | undefined, import("@jbrowse/plugin-linear-genome-view").InitState | undefined, import("@jbrowse/plugin-linear-genome-view").InitState | undefined>;
936
978
  }>>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
937
979
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
938
980
  displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -952,10 +994,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
952
994
  showCytobandsSetting: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
953
995
  trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
954
996
  showGridlines: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
955
- highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").HighlightType>>, [undefined]>;
997
+ highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view").HighlightType, import("@jbrowse/plugin-linear-genome-view").HighlightType, import("@jbrowse/plugin-linear-genome-view").HighlightType>>, [undefined]>;
956
998
  colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
957
999
  showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
958
- init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types.ts").InitState | undefined>;
1000
+ init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view").InitState | undefined, import("@jbrowse/plugin-linear-genome-view").InitState | undefined, import("@jbrowse/plugin-linear-genome-view").InitState | undefined>;
959
1001
  }>>>;
960
1002
  viewTrackConfigs: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
961
1003
  } & {