@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/LinearComparativeView/model.d.ts CHANGED
@@ -34,10 +34,10 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
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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>;
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- 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").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
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+ 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]>;
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  colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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- init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined>;
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+ 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;
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  } & {
@@ -53,11 +53,15 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
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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>;
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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").BpOffset;
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- rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").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 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
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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").HighlightType): void;
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- setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
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- removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").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;
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  scrollTo(offsetPx: number): number;
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  zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
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- setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
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+ 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;
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  setNewView(bpPerPx: number, offsetPx: number): void;
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  horizontallyFlip(): void;
@@ -137,7 +144,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
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  setShowCenterLine(b: boolean): void;
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  setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
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  activateTrackSelector(): import("@jbrowse/core/util").Widget;
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- getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
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+ getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view").BpOffset): {
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  assemblyName: string;
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  refName: string;
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  start: number;
@@ -150,9 +157,10 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
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  setDraggingTrackId(idx?: string): void;
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  setLastTrackDragY(y: number): void;
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  setScaleFactor(factor: number): void;
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+ setTargetBpPerPx(target: number | undefined): void;
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  clearView(): void;
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- setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
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- exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
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+ setInit(arg?: import("@jbrowse/plugin-linear-genome-view").InitState): void;
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+ exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view").ExportSvgOptions): Promise<void>;
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  } & {
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  slide: (viewWidths: number) => void;
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  } & {
@@ -171,10 +179,13 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
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  readonly visibleLocStrings: string;
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  readonly coarseVisibleLocStrings: string;
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  readonly coarseTotalBpDisplayStr: string;
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+ readonly effectiveBpPerPx: number;
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+ readonly effectiveTotalBp: number;
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+ readonly effectiveTotalBpDisplayStr: string;
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  } & {
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  setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
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  } & {
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- moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
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+ moveTo(start?: import("@jbrowse/plugin-linear-genome-view").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view").BpOffset): void;
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  navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
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  navToSearchString({ input, assembly, }: {
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  input: string;
@@ -182,8 +193,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
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  }): Promise<void>;
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  navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
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  navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
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- navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
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- navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
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+ navTo(query: import("@jbrowse/plugin-linear-genome-view").NavLocation, grow?: number): void;
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+ navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view").NavLocation[], grow?: number): void;
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  } & {
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  rubberBandMenuItems(): MenuItem[];
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  bpToPx({ refName, coord, regionNumber, }: {
@@ -219,7 +230,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
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  } | undefined;
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  readonly visibleRegions: import("@jbrowse/core/util/blockTypes").BaseBlock[];
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  } & {
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- rubberbandClickMenuItems(clickOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): MenuItem[];
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+ rubberbandClickMenuItems(clickOffset: import("@jbrowse/plugin-linear-genome-view").BpOffset): MenuItem[];
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  } & {
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  afterCreate(): void;
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  afterAttach(): void;
@@ -242,10 +253,10 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
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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>;
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- 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").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
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+ 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]>;
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  colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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- init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined>;
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+ 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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  }>>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
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  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
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  displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -265,10 +276,10 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
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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>;
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- 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").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
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+ 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]>;
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  colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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- init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined>;
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+ 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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  viewTrackConfigs: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
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  }, {
@@ -346,10 +357,10 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
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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>;
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- 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").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
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+ 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]>;
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  colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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- init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined>;
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+ 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;
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  } & {
@@ -365,11 +376,15 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
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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>;
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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").BpOffset;
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- rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").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[];
@@ -423,16 +438,19 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
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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").HighlightType): void;
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- setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
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- removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").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;
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  scrollTo(offsetPx: number): number;
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  zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
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- setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
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+ 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;
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  setNewView(bpPerPx: number, offsetPx: number): void;
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  horizontallyFlip(): void;
@@ -449,7 +467,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
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  setShowCenterLine(b: boolean): void;
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  setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
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  activateTrackSelector(): import("@jbrowse/core/util").Widget;
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- getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
470
+ getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view").BpOffset): {
453
471
  assemblyName: string;
454
472
  refName: string;
455
473
  start: number;
@@ -462,9 +480,10 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
462
480
  setDraggingTrackId(idx?: string): void;
463
481
  setLastTrackDragY(y: number): void;
464
482
  setScaleFactor(factor: number): void;
483
+ setTargetBpPerPx(target: number | undefined): void;
465
484
  clearView(): void;
466
- setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
467
- exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
485
+ setInit(arg?: import("@jbrowse/plugin-linear-genome-view").InitState): void;
486
+ exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view").ExportSvgOptions): Promise<void>;
468
487
  } & {
469
488
  slide: (viewWidths: number) => void;
470
489
  } & {
@@ -483,10 +502,13 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
483
502
  readonly visibleLocStrings: string;
484
503
  readonly coarseVisibleLocStrings: string;
485
504
  readonly coarseTotalBpDisplayStr: string;
505
+ readonly effectiveBpPerPx: number;
506
+ readonly effectiveTotalBp: number;
507
+ readonly effectiveTotalBpDisplayStr: string;
486
508
  } & {
487
509
  setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
488
510
  } & {
489
- moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
511
+ moveTo(start?: import("@jbrowse/plugin-linear-genome-view").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view").BpOffset): void;
490
512
  navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
491
513
  navToSearchString({ input, assembly, }: {
492
514
  input: string;
@@ -494,8 +516,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
494
516
  }): Promise<void>;
495
517
  navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
496
518
  navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
497
- navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
498
- navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
519
+ navTo(query: import("@jbrowse/plugin-linear-genome-view").NavLocation, grow?: number): void;
520
+ navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view").NavLocation[], grow?: number): void;
499
521
  } & {
500
522
  rubberBandMenuItems(): MenuItem[];
501
523
  bpToPx({ refName, coord, regionNumber, }: {
@@ -531,7 +553,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
531
553
  } | undefined;
532
554
  readonly visibleRegions: import("@jbrowse/core/util/blockTypes").BaseBlock[];
533
555
  } & {
534
- rubberbandClickMenuItems(clickOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): MenuItem[];
556
+ rubberbandClickMenuItems(clickOffset: import("@jbrowse/plugin-linear-genome-view").BpOffset): MenuItem[];
535
557
  } & {
536
558
  afterCreate(): void;
537
559
  afterAttach(): void;
@@ -554,10 +576,10 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
554
576
  showCytobandsSetting: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
555
577
  trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
556
578
  showGridlines: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
557
- 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").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
579
+ 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]>;
558
580
  colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
559
581
  showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
560
- init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined>;
582
+ 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>;
561
583
  }>>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
562
584
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
563
585
  displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -577,10 +599,10 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
577
599
  showCytobandsSetting: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
578
600
  trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
579
601
  showGridlines: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
580
- 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").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
602
+ 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]>;
581
603
  colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
582
604
  showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
583
- init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined>;
605
+ 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>;
584
606
  }>>>;
585
607
  viewTrackConfigs: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
586
608
  }>>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
@@ -615,10 +637,10 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
615
637
  showCytobandsSetting: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
616
638
  trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
617
639
  showGridlines: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
618
- 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").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
640
+ 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]>;
619
641
  colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
620
642
  showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
621
- init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined>;
643
+ 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>;
622
644
  }, {
623
645
  width: number;
624
646
  } & {
@@ -634,11 +656,15 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
634
656
  lastTrackDragY: undefined | number;
635
657
  volatileError: unknown;
636
658
  scaleFactor: number;
659
+ targetBpPerPx: number | undefined;
637
660
  trackRefs: Record<string, HTMLDivElement>;
638
661
  coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
639
662
  coarseTotalBp: number;
640
- leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
641
- rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
663
+ leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view").BpOffset;
664
+ rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view").BpOffset;
665
+ isScalebarRefNameMenuOpen: boolean;
666
+ scalebarRefNameClickPending: boolean;
667
+ volatileGuides: import("@jbrowse/plugin-linear-genome-view").VolatileGuide[];
642
668
  } & {
643
669
  readonly pinnedTracks: any[];
644
670
  readonly unpinnedTracks: any[];
@@ -692,16 +718,19 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
692
718
  setShowCytobands(flag: boolean): void;
693
719
  setWidth(newWidth: number): void;
694
720
  setError(error: unknown): void;
721
+ setIsScalebarRefNameMenuOpen(isOpen: boolean): void;
722
+ setScalebarRefNameClickPending(pending: boolean): void;
695
723
  setHideHeader(b: boolean): void;
696
724
  setHideHeaderOverview(b: boolean): void;
697
725
  setHideNoTracksActive(b: boolean): void;
698
726
  setShowGridlines(b: boolean): void;
699
- addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
700
- setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
701
- removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
727
+ addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view").HighlightType): void;
728
+ setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view").HighlightType[]): void;
729
+ removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view").HighlightType): void;
730
+ setVolatileGuides(guides: import("@jbrowse/plugin-linear-genome-view").VolatileGuide[]): void;
702
731
  scrollTo(offsetPx: number): number;
703
732
  zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
704
- setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
733
+ setOffsets(left?: import("@jbrowse/plugin-linear-genome-view").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view").BpOffset): void;
705
734
  setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
706
735
  setNewView(bpPerPx: number, offsetPx: number): void;
707
736
  horizontallyFlip(): void;
@@ -718,7 +747,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
718
747
  setShowCenterLine(b: boolean): void;
719
748
  setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
720
749
  activateTrackSelector(): import("@jbrowse/core/util").Widget;
721
- getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
750
+ getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view").BpOffset): {
722
751
  assemblyName: string;
723
752
  refName: string;
724
753
  start: number;
@@ -731,9 +760,10 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
731
760
  setDraggingTrackId(idx?: string): void;
732
761
  setLastTrackDragY(y: number): void;
733
762
  setScaleFactor(factor: number): void;
763
+ setTargetBpPerPx(target: number | undefined): void;
734
764
  clearView(): void;
735
- setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
736
- exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
765
+ setInit(arg?: import("@jbrowse/plugin-linear-genome-view").InitState): void;
766
+ exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view").ExportSvgOptions): Promise<void>;
737
767
  } & {
738
768
  slide: (viewWidths: number) => void;
739
769
  } & {
@@ -752,10 +782,13 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
752
782
  readonly visibleLocStrings: string;
753
783
  readonly coarseVisibleLocStrings: string;
754
784
  readonly coarseTotalBpDisplayStr: string;
785
+ readonly effectiveBpPerPx: number;
786
+ readonly effectiveTotalBp: number;
787
+ readonly effectiveTotalBpDisplayStr: string;
755
788
  } & {
756
789
  setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
757
790
  } & {
758
- moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
791
+ moveTo(start?: import("@jbrowse/plugin-linear-genome-view").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view").BpOffset): void;
759
792
  navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
760
793
  navToSearchString({ input, assembly, }: {
761
794
  input: string;
@@ -763,8 +796,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
763
796
  }): Promise<void>;
764
797
  navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
765
798
  navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
766
- navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
767
- navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
799
+ navTo(query: import("@jbrowse/plugin-linear-genome-view").NavLocation, grow?: number): void;
800
+ navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view").NavLocation[], grow?: number): void;
768
801
  } & {
769
802
  rubberBandMenuItems(): MenuItem[];
770
803
  bpToPx({ refName, coord, regionNumber, }: {
@@ -800,7 +833,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
800
833
  } | undefined;
801
834
  readonly visibleRegions: import("@jbrowse/core/util/blockTypes").BaseBlock[];
802
835
  } & {
803
- rubberbandClickMenuItems(clickOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): MenuItem[];
836
+ rubberbandClickMenuItems(clickOffset: import("@jbrowse/plugin-linear-genome-view").BpOffset): MenuItem[];
804
837
  } & {
805
838
  afterCreate(): void;
806
839
  afterAttach(): void;
@@ -823,10 +856,10 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
823
856
  showCytobandsSetting: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
824
857
  trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
825
858
  showGridlines: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
826
- 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").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
859
+ 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]>;
827
860
  colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
828
861
  showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
829
- init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined>;
862
+ 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>;
830
863
  }>>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
831
864
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
832
865
  displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -846,10 +879,10 @@ declare function stateModelFactory(pluginManager: PluginManager): import("@jbrow
846
879
  showCytobandsSetting: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
847
880
  trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
848
881
  showGridlines: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
849
- 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").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
882
+ 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]>;
850
883
  colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
851
884
  showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
852
- init: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined>;
885
+ 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>;
853
886
  }>>>;
854
887
  viewTrackConfigs: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
855
888
  }>>;
package/esm/LinearSyntenyDisplay/afterAttach.js CHANGED
@@ -6,6 +6,9 @@ import { autorun, reaction } from 'mobx';
6
6
  import { drawCigarClickMap, drawMouseoverClickMap, drawRef, } from "./drawSynteny.js";
7
7
  export function doAfterAttach(self) {
8
8
  addDisposer(self, autorun(function syntenyDrawAutorun() {
9
+ if (self.isMinimized) {
10
+ return;
11
+ }
9
12
  const view = getContainingView(self);
10
13
  if (!view.initialized ||
11
14
  !view.views.every(a => a.displayedRegions.length > 0 && a.initialized)) {
@@ -24,6 +27,9 @@ export function doAfterAttach(self) {
24
27
  drawCigarClickMap(self, ctx3);
25
28
  }, { name: 'SyntenyDraw' }));
26
29
  addDisposer(self, autorun(function syntenyMouseoverAutorun() {
30
+ if (self.isMinimized) {
31
+ return;
32
+ }
27
33
  const view = getContainingView(self);
28
34
  if (!view.initialized ||
29
35
  !view.views.every(a => a.displayedRegions.length > 0 && a.initialized)) {
@@ -33,6 +39,9 @@ export function doAfterAttach(self) {
33
39
  drawMouseoverClickMap(self);
34
40
  }, { name: 'SyntenyMouseover' }));
35
41
  addDisposer(self, reaction(() => {
42
+ if (self.isMinimized) {
43
+ return { initialized: false };
44
+ }
36
45
  const view = getContainingView(self);
37
46
  return {
38
47
  bpPerPx: view.views.map(v => v.bpPerPx),
package/esm/LinearSyntenyDisplay/components/LinearSyntenyRendering.js CHANGED
@@ -20,7 +20,7 @@ const useStyles = makeStyles()({
20
20
  },
21
21
  mouseoverCanvas: {
22
22
  position: 'absolute',
23
- pointEvents: 'none',
23
+ pointerEvents: 'none',
24
24
  },
25
25
  mainCanvas: {
26
26
  position: 'absolute',
@@ -101,7 +101,7 @@ const LinearSyntenyRendering = observer(function LinearSyntenyRendering({ model,
101
101
  const cigarClickMapCanvasRef = useCallback((ref) => {
102
102
  model.setCigarClickMapCanvasRef(ref);
103
103
  }, [model, height, width]);
104
- return (_jsxs("div", { className: classes.rel, children: [_jsx("canvas", { ref: mouseoverDetectionCanvasRef, width: width, height: height, className: classes.mouseoverCanvas }), _jsx("canvas", { ref: mainSyntenyCanvasRef, onMouseMove: event => {
104
+ return (_jsxs("div", { className: classes.rel, children: [_jsx("canvas", { ref: mainSyntenyCanvasRef, onMouseMove: event => {
105
105
  if (mouseCurrDownX !== undefined) {
106
106
  xOffset.current += mouseCurrDownX - event.clientX;
107
107
  setMouseCurrDownX(event.clientX);
@@ -137,26 +137,26 @@ const LinearSyntenyRendering = observer(function LinearSyntenyRendering({ model,
137
137
  setCurrY(clientY);
138
138
  const [r1, g1, b1] = ctx1.getImageData(x, y, 1, 1).data;
139
139
  const [r2, g2, b2] = ctx2.getImageData(x, y, 1, 1).data;
140
+ if (model.numFeats === 0) {
141
+ setTooltip('');
142
+ return;
143
+ }
140
144
  const unitMultiplier = Math.floor(MAX_COLOR_RANGE / model.numFeats);
141
145
  const id = getId(r1, g1, b1, unitMultiplier);
142
146
  model.setMouseoverId(model.featPositions[id]?.f.id());
143
- if (id === -1) {
147
+ if (id === -1 || !model.featPositions[id]) {
144
148
  setTooltip('');
145
149
  }
146
- else if (model.featPositions[id]) {
150
+ else {
147
151
  const { f, cigar } = model.featPositions[id];
148
152
  const unitMultiplier2 = Math.floor(MAX_COLOR_RANGE / cigar.length);
149
153
  const cigarIdx = getId(r2, g2, b2, unitMultiplier2);
150
- if (cigarIdx % 2 === 0 && (r2 !== 0 || g2 !== 0 || b2 !== 0)) {
151
- setTooltip(getTooltip({
152
- feature: f,
153
- cigarOp: cigar[cigarIdx + 1],
154
- cigarOpLen: cigar[cigarIdx],
155
- }));
156
- }
157
- else {
158
- setTooltip('');
159
- }
154
+ const hasCigarData = cigarIdx % 2 === 0 && (r2 !== 0 || g2 !== 0 || b2 !== 0);
155
+ setTooltip(getTooltip({
156
+ feature: f,
157
+ cigarOp: hasCigarData ? cigar[cigarIdx + 1] : undefined,
158
+ cigarOpLen: hasCigarData ? cigar[cigarIdx] : undefined,
159
+ }));
160
160
  }
161
161
  }
162
162
  }, onMouseLeave: () => {
@@ -174,7 +174,7 @@ const LinearSyntenyRendering = observer(function LinearSyntenyRendering({ model,
174
174
  }
175
175
  }, onContextMenu: evt => {
176
176
  onSynContextClick(evt, model, setAnchorEl);
177
- }, "data-testid": "synteny_canvas", className: classes.mainCanvas, width: width, height: height }), _jsx("canvas", { ref: clickMapCanvasRef, className: classes.pix, width: width, height: height }), _jsx("canvas", { ref: cigarClickMapCanvasRef, className: classes.pix, width: width, height: height }), mouseoverId && tooltip && currX && currY ? (_jsx(SyntenyTooltip, { title: tooltip })) : null, anchorEl ? (_jsx(SyntenyContextMenu, { model: model, anchorEl: anchorEl, onClose: () => {
177
+ }, "data-testid": "synteny_canvas", className: classes.mainCanvas, width: width, height: height }), _jsx("canvas", { ref: mouseoverDetectionCanvasRef, width: width, height: height, className: classes.mouseoverCanvas }), _jsx("canvas", { ref: clickMapCanvasRef, className: classes.pix, width: width, height: height }), _jsx("canvas", { ref: cigarClickMapCanvasRef, className: classes.pix, width: width, height: height }), mouseoverId && tooltip && currX && currY ? (_jsx(SyntenyTooltip, { title: tooltip })) : null, anchorEl ? (_jsx(SyntenyContextMenu, { model: model, anchorEl: anchorEl, onClose: () => {
178
178
  setAnchorEl(undefined);
179
179
  } })) : null] }));
180
180
  });
package/esm/LinearSyntenyDisplay/components/util.d.ts CHANGED
@@ -35,6 +35,7 @@ export declare function draw(ctx: CanvasRenderingContext2D, x1: number, x2: numb
35
35
  export declare function drawLocationMarkers(ctx: CanvasRenderingContext2D, x1: number, x2: number, y1: number, x3: number, x4: number, y2: number, mid: number, bpPerPx1: number, bpPerPx2: number, drawCurves?: boolean): void;
36
36
  export declare function drawBox(ctx: CanvasRenderingContext2D, x1: number, x2: number, y1: number, x3: number, x4: number, y2: number): void;
37
37
  export declare function drawBezierBox(ctx: CanvasRenderingContext2D, x1: number, x2: number, y1: number, x3: number, x4: number, y2: number, mid: number): void;
38
+ export declare function getFeatureAtClick(event: React.MouseEvent, model: LinearSyntenyDisplayModel): import("../model.ts").FeatPos | undefined;
38
39
  export declare function onSynClick(event: React.MouseEvent, model: LinearSyntenyDisplayModel): import("../model.ts").FeatPos | undefined;
39
40
  export declare function onSynContextClick(event: React.MouseEvent, model: LinearSyntenyDisplayModel, setAnchorEl: (arg: ClickCoord) => void): void;
40
41
  export declare function getTooltip({ feature, cigarOp, cigarOpLen, }: {