@jbrowse/plugin-linear-genome-view 5.0.0-beta.2 → 5.0.0-beta.20

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (177) hide show
  1. package/esm/LinearGenomeView/afterAttach.d.ts +22 -5
  2. package/esm/LinearGenomeView/afterAttach.js +129 -106
  3. package/esm/LinearGenomeView/axisConfigSchema.d.ts +18 -0
  4. package/esm/LinearGenomeView/axisConfigSchema.js +22 -0
  5. package/esm/LinearGenomeView/components/CenterLine.js +10 -5
  6. package/esm/LinearGenomeView/components/ConnectedHoverHighlight.js +2 -3
  7. package/esm/LinearGenomeView/components/CrisprGuidePanel.js +3 -5
  8. package/esm/LinearGenomeView/components/ExportSvgDialog.d.ts +9 -4
  9. package/esm/LinearGenomeView/components/ExportSvgDialog.js +45 -8
  10. package/esm/LinearGenomeView/components/GetSequenceDialog.js +2 -2
  11. package/esm/LinearGenomeView/components/Header.js +11 -1
  12. package/esm/LinearGenomeView/components/HeaderClearHighlightButton.js +2 -2
  13. package/esm/LinearGenomeView/components/HeaderPanControls.d.ts +3 -3
  14. package/esm/LinearGenomeView/components/HeaderPanControls.js +6 -3
  15. package/esm/LinearGenomeView/components/HeaderSearchBoxes.js +4 -1
  16. package/esm/LinearGenomeView/components/HeaderZoomControls.js +6 -35
  17. package/esm/LinearGenomeView/components/Highlight.js +27 -11
  18. package/esm/LinearGenomeView/components/HighlightBand.d.ts +11 -2
  19. package/esm/LinearGenomeView/components/HighlightBand.js +32 -13
  20. package/esm/LinearGenomeView/components/HighlightChip.d.ts +3 -3
  21. package/esm/LinearGenomeView/components/HighlightChip.js +13 -8
  22. package/esm/LinearGenomeView/components/HighlightLabelDialog.d.ts +6 -0
  23. package/esm/LinearGenomeView/components/HighlightLabelDialog.js +18 -0
  24. package/esm/LinearGenomeView/components/HoverPositionHighlight.js +3 -3
  25. package/esm/LinearGenomeView/components/ImportForm.js +7 -9
  26. package/esm/LinearGenomeView/components/LinearGenomeView.js +5 -12
  27. package/esm/LinearGenomeView/components/LinearGenomeViewContainer.js +13 -14
  28. package/esm/LinearGenomeView/components/MiniControls.js +11 -5
  29. package/esm/LinearGenomeView/components/OverviewHighlight.js +3 -3
  30. package/esm/LinearGenomeView/components/OverviewHighlightBand.d.ts +3 -2
  31. package/esm/LinearGenomeView/components/OverviewHighlightBand.js +6 -5
  32. package/esm/LinearGenomeView/components/OverviewRubberband.js +25 -48
  33. package/esm/LinearGenomeView/components/OverviewScalebar.js +4 -5
  34. package/esm/LinearGenomeView/components/OverviewScalebarPolygon.js +5 -3
  35. package/esm/LinearGenomeView/components/PaddingBlocks.js +3 -8
  36. package/esm/LinearGenomeView/components/RangeSelectOverlay.js +5 -6
  37. package/esm/LinearGenomeView/components/RegionWidthEditorDialog.d.ts +3 -2
  38. package/esm/LinearGenomeView/components/RegionWidthEditorDialog.js +4 -4
  39. package/esm/LinearGenomeView/components/ResizeAllTracksHandle.d.ts +5 -0
  40. package/esm/LinearGenomeView/components/ResizeAllTracksHandle.js +74 -0
  41. package/esm/LinearGenomeView/components/Rubberband.d.ts +1 -2
  42. package/esm/LinearGenomeView/components/Rubberband.js +3 -2
  43. package/esm/LinearGenomeView/components/SVGHighlightBand.d.ts +10 -1
  44. package/esm/LinearGenomeView/components/SVGHighlightBand.js +16 -5
  45. package/esm/LinearGenomeView/components/Scalebar.d.ts +2 -6
  46. package/esm/LinearGenomeView/components/Scalebar.js +8 -5
  47. package/esm/LinearGenomeView/components/ScalebarRefNameLabels.js +51 -36
  48. package/esm/LinearGenomeView/components/SearchBox.js +10 -16
  49. package/esm/LinearGenomeView/components/SearchPanelForm.d.ts +3 -2
  50. package/esm/LinearGenomeView/components/SearchPanelForm.js +4 -2
  51. package/esm/LinearGenomeView/components/SearchResultsDialog.d.ts +4 -8
  52. package/esm/LinearGenomeView/components/SearchResultsDialog.js +7 -4
  53. package/esm/LinearGenomeView/components/SearchResultsTable.d.ts +4 -7
  54. package/esm/LinearGenomeView/components/SearchResultsTable.js +25 -53
  55. package/esm/LinearGenomeView/components/SequenceFeatureHoverHighlight.js +2 -3
  56. package/esm/LinearGenomeView/components/SequenceSearchDialog.d.ts +2 -4
  57. package/esm/LinearGenomeView/components/StrandCheckboxes.d.ts +3 -2
  58. package/esm/LinearGenomeView/components/StrandCheckboxes.js +4 -2
  59. package/esm/LinearGenomeView/components/TrackContainer.d.ts +2 -3
  60. package/esm/LinearGenomeView/components/TrackContainer.js +63 -10
  61. package/esm/LinearGenomeView/components/TrackLabel.js +14 -4
  62. package/esm/LinearGenomeView/components/TrackLabelButtons.js +2 -2
  63. package/esm/LinearGenomeView/components/TrackLabelDragHandle.js +4 -5
  64. package/esm/LinearGenomeView/components/TrackLabelMenu.js +11 -14
  65. package/esm/LinearGenomeView/components/TrackLabelRefNameWarning.d.ts +3 -4
  66. package/esm/LinearGenomeView/components/TrackLabelRefNameWarning.js +23 -10
  67. package/esm/LinearGenomeView/components/TrackRenderingContainer.d.ts +6 -4
  68. package/esm/LinearGenomeView/components/TrackRenderingContainer.js +12 -24
  69. package/esm/LinearGenomeView/components/TracksContainer.js +11 -23
  70. package/esm/LinearGenomeView/components/VerticalGuide.d.ts +1 -2
  71. package/esm/LinearGenomeView/components/VerticalGuide.js +3 -16
  72. package/esm/LinearGenomeView/components/fetchSequence.d.ts +1 -2
  73. package/esm/LinearGenomeView/components/fetchSequence.js +15 -7
  74. package/esm/LinearGenomeView/components/recentLocationsMenu.js +10 -0
  75. package/esm/LinearGenomeView/components/useRangeSelect.d.ts +0 -3
  76. package/esm/LinearGenomeView/components/useRangeSelect.js +26 -61
  77. package/esm/LinearGenomeView/components/useSearchBoxPrefs.d.ts +3 -1
  78. package/esm/LinearGenomeView/components/useSearchBoxPrefs.js +4 -2
  79. package/esm/LinearGenomeView/components/useSideScroll.d.ts +17 -2
  80. package/esm/LinearGenomeView/components/useSideScroll.js +156 -102
  81. package/esm/LinearGenomeView/components/util.d.ts +4 -0
  82. package/esm/LinearGenomeView/components/util.js +4 -2
  83. package/esm/LinearGenomeView/consts.d.ts +2 -0
  84. package/esm/LinearGenomeView/consts.js +3 -1
  85. package/esm/LinearGenomeView/containingLgv.d.ts +21 -0
  86. package/esm/LinearGenomeView/containingLgv.js +23 -0
  87. package/esm/LinearGenomeView/headerFit.d.ts +4 -2
  88. package/esm/LinearGenomeView/headerFit.js +20 -7
  89. package/esm/LinearGenomeView/index.d.ts +2 -7
  90. package/esm/LinearGenomeView/index.js +5 -7
  91. package/esm/LinearGenomeView/keyboardHandler.d.ts +8 -7
  92. package/esm/LinearGenomeView/keyboardHandler.js +61 -23
  93. package/esm/LinearGenomeView/launchKeys.d.ts +1 -1
  94. package/esm/LinearGenomeView/launchKeys.js +11 -6
  95. package/esm/LinearGenomeView/lazyDialogs.d.ts +16 -3
  96. package/esm/LinearGenomeView/lazyDialogs.js +1 -0
  97. package/esm/LinearGenomeView/linkedViewSync.d.ts +3 -11
  98. package/esm/LinearGenomeView/linkedViewSync.js +27 -49
  99. package/esm/LinearGenomeView/menuItems.d.ts +16 -18
  100. package/esm/LinearGenomeView/menuItems.js +264 -164
  101. package/esm/LinearGenomeView/model.d.ts +1192 -560
  102. package/esm/LinearGenomeView/model.js +805 -590
  103. package/esm/LinearGenomeView/rExport/exportLinearView.d.ts +17 -0
  104. package/esm/LinearGenomeView/rExport/exportLinearView.js +117 -0
  105. package/esm/LinearGenomeView/rExport/rScript.d.ts +110 -0
  106. package/esm/LinearGenomeView/rExport/rScript.js +524 -0
  107. package/esm/LinearGenomeView/sharedScaleContainer.d.ts +1 -1
  108. package/esm/LinearGenomeView/sharedScaleContainer.js +2 -12
  109. package/esm/LinearGenomeView/showFiles.d.ts +2 -0
  110. package/esm/LinearGenomeView/showFiles.js +19 -0
  111. package/esm/LinearGenomeView/showRegionsWithUndo.d.ts +1 -1
  112. package/esm/LinearGenomeView/showRegionsWithUndo.js +13 -5
  113. package/esm/LinearGenomeView/stickyChrome.d.ts +5 -9
  114. package/esm/LinearGenomeView/stickyChrome.js +5 -9
  115. package/esm/LinearGenomeView/svgcomponents/SVGGridlines.js +4 -4
  116. package/esm/LinearGenomeView/svgcomponents/SVGHeader.d.ts +4 -1
  117. package/esm/LinearGenomeView/svgcomponents/SVGHeader.js +8 -21
  118. package/esm/LinearGenomeView/svgcomponents/SVGHighlights.d.ts +3 -1
  119. package/esm/LinearGenomeView/svgcomponents/SVGHighlights.js +9 -9
  120. package/esm/LinearGenomeView/svgcomponents/SVGHighlightsOverlay.d.ts +3 -1
  121. package/esm/LinearGenomeView/svgcomponents/SVGHighlightsOverlay.js +5 -5
  122. package/esm/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js +13 -18
  123. package/esm/LinearGenomeView/svgcomponents/SVGRegionSeparators.js +2 -5
  124. package/esm/LinearGenomeView/svgcomponents/SVGRowHeader.js +5 -6
  125. package/esm/LinearGenomeView/svgcomponents/SVGRuler.js +9 -10
  126. package/esm/LinearGenomeView/svgcomponents/SVGScalebar.js +3 -3
  127. package/esm/LinearGenomeView/svgcomponents/SVGStackedRow.d.ts +26 -0
  128. package/esm/LinearGenomeView/svgcomponents/SVGStackedRow.js +12 -0
  129. package/esm/LinearGenomeView/svgcomponents/SVGTrackLabel.js +21 -13
  130. package/esm/LinearGenomeView/svgcomponents/SVGTracks.d.ts +4 -5
  131. package/esm/LinearGenomeView/svgcomponents/SVGTracks.js +7 -6
  132. package/esm/LinearGenomeView/svgcomponents/SVGView.d.ts +2 -3
  133. package/esm/LinearGenomeView/svgcomponents/SVGView.js +17 -3
  134. package/esm/LinearGenomeView/svgcomponents/renderViewTracks.d.ts +24 -20
  135. package/esm/LinearGenomeView/svgcomponents/renderViewTracks.js +42 -29
  136. package/esm/LinearGenomeView/svgcomponents/useViewSvgFigure.js +74 -77
  137. package/esm/LinearGenomeView/svgcomponents/util.d.ts +28 -12
  138. package/esm/LinearGenomeView/svgcomponents/util.js +41 -29
  139. package/esm/LinearGenomeView/types.d.ts +13 -10
  140. package/esm/LinearGenomeView/types.js +0 -1
  141. package/esm/LinearGenomeView/util.d.ts +103 -46
  142. package/esm/LinearGenomeView/util.js +222 -170
  143. package/esm/MultiLevelRubberband/MultiLevelRubberband.js +9 -6
  144. package/esm/MultiLevelRubberband/index.d.ts +2 -0
  145. package/esm/MultiLevelRubberband/index.js +2 -0
  146. package/esm/MultiLevelRubberband/menuItems.d.ts +34 -0
  147. package/esm/MultiLevelRubberband/menuItems.js +52 -0
  148. package/esm/MultiLevelRubberband/rowLabel.d.ts +22 -0
  149. package/esm/MultiLevelRubberband/rowLabel.js +27 -0
  150. package/esm/MultiLevelRubberband/types.d.ts +1 -0
  151. package/esm/MultiLevelRubberband/useRangeSelect.d.ts +2 -1
  152. package/esm/MultiLevelRubberband/useRangeSelect.js +45 -59
  153. package/esm/TrackModifiers/index.d.ts +83 -0
  154. package/esm/TrackModifiers/index.js +231 -0
  155. package/esm/displayKitTests/perRegionTestEnv.d.ts +244 -68
  156. package/esm/displayKitTests/perRegionTestEnv.js +30 -26
  157. package/esm/index.d.ts +21 -99
  158. package/esm/index.js +17 -38
  159. package/esm/searchUtils.d.ts +26 -10
  160. package/esm/searchUtils.js +137 -137
  161. package/esm/shared/RubberbandSpan.d.ts +3 -2
  162. package/esm/shared/RubberbandSpan.js +6 -3
  163. package/esm/shared/coordLabels.d.ts +11 -4
  164. package/esm/shared/coordLabels.js +20 -5
  165. package/esm/shared/useWindowDrag.d.ts +18 -0
  166. package/esm/shared/useWindowDrag.js +47 -0
  167. package/package.json +12 -11
  168. package/esm/FeatureTrack/configSchema.d.ts +0 -124
  169. package/esm/FeatureTrack/configSchema.js +0 -54
  170. package/esm/FeatureTrack/index.d.ts +0 -2
  171. package/esm/FeatureTrack/index.js +0 -13
  172. package/esm/LinearGenomeView/initKeys.d.ts +0 -12
  173. package/esm/LinearGenomeView/initKeys.js +0 -68
  174. package/esm/MultiLevelRubberband/VerticalGuide.d.ts +0 -6
  175. package/esm/MultiLevelRubberband/VerticalGuide.js +0 -21
  176. package/esm/lazyPluginExports.d.ts +0 -23
  177. package/esm/lazyPluginExports.js +0 -36
@@ -1,4 +1,5 @@
1
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  import type { ExportSvgOptions, TrackLabelMode } from '../types.ts';
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+ import type { LgvSvgExportable } from '@jbrowse/display-kit/renderDisplaySvg';
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  import type { ExportSvgDisplayOptions } from '@jbrowse/display-kit/types';
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  import type { ThemeOptions } from '@mui/material';
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  import type { ReactNode } from 'react';
@@ -6,7 +7,8 @@ export interface SvgExportTrack {
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  minimized: boolean;
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  displays: {
8
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  height: number;
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- svgLegendWidth?: () => number;
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+ regionTooLarge?: boolean;
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+ svgSidebarWidth?: LgvSvgExportable['svgSidebarWidth'];
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  /**
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  * Optional, and the option is the point: SVG export is a substantial extra
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  * implementation for a display type, and a third-party plugin that has not
@@ -21,13 +23,18 @@ export interface SvgExportTrack {
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  export interface ViewTracksSvg<T> {
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  /** the tracks that were rendered, in the order they were laid out */
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  tracks: T[];
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+ /**
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+ * `legendHeight` is the room a track's key has in the gutter, absent for a
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+ * track with no key to draw
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+ */
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  displayResults: {
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  track: T;
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  result: ReactNode;
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+ legendHeight?: number;
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  }[];
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  /** total height of the stack, valid only because the renders above resolved */
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  tracksHeight: number;
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- /** 0 unless `reserveLegendWidth` was asked for */
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+ /** px the caller widens its canvas by for the keys right of the plot */
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  legendWidth: number;
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  /**
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  * Visible tracks left out because their display implements no `renderSvg`.
@@ -40,30 +47,28 @@ export interface ViewTracksSvg<T> {
40
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  * One view's worth of exported track bodies: which tracks are in, their
41
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  * rendered SVG, and how tall the stack ends up.
42
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  *
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- * It exists to own the two orderings that each of the three view exports got
44
- * wrong at least once, because neither is visible at a call site that merely
45
- * lists the same statements in some order:
50
+ * It exists to own an ordering that each of the three view exports got wrong at
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+ * least once, because it is not visible at a call site that merely lists the
52
+ * same statements in some order: the geometry is measured **after** the
53
+ * awaits.
46
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  *
47
- * - `legendWidth` is measured **before** the awaits, because it is an input to
48
- * them: a display draws its legend beside its body or floating over it
49
- * depending on whether the container reserved room. That is why
50
- * `svgLegendWidth` is specified as a function of the *settings* and not of
51
- * the loaded data — see LinearHicDisplay's implementation.
52
- * - `tracksHeight` is measured **after** them. A display whose height follows
53
- * its data (grow mode; `LinearMultiRowFeatureDisplay` is `nrow *
54
- * effectiveRowHeight`) only reaches its final height once `renderSvg`'s
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- * readiness wait resolves, and `SVGTracks` re-reads `displays[0].height`
56
- * later still. Measuring up front sized the canvas for the pre-fetch height
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- * and the taller bodies ran off the bottom of the export — and in the
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- * breakpoint-split export it also desynced the overlay anchors, resolved
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- * after, from the view tops, which weren't.
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+ * - `tracksHeight`: a display whose height follows its data (grow mode;
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+ * `LinearMultiRowFeatureDisplay` is `nrow * effectiveRowHeight`) only reaches
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+ * its final height once `renderSvg`'s readiness wait resolves, and
58
+ * `SVGTracks` re-reads `displays[0].height` later still. Measuring up front
59
+ * sized the canvas for the pre-fetch height and the taller bodies ran off the
60
+ * bottom of the export — and in the breakpoint-split export it also desynced
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+ * the overlay anchors, resolved after, from the view tops, which weren't.
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+ * - `legendWidth`: most keys list what was loaded, and on a headless export
63
+ * (jbrowse-img) nothing has loaded before the waits. Measured after, a track
64
+ * with no key reserves nothing and the figure has no empty strip.
60
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  *
61
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  * The minimized filter and the track order are here for the same reason: the
62
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  * reserved height, the rendered bodies, the label gutter and (breakpoint-split)
63
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  * the ribbon anchors must all be derived from one list, and pinned tracks are
64
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  * drawn at the top of a view on screen.
65
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  */
66
- export declare function renderViewTracks<T extends SvgExportTrack>({ view, opts, theme, textHeight, trackLabels, reserveLegendWidth, }: {
71
+ export declare function renderViewTracks<T extends SvgExportTrack>({ view, opts, theme, textHeight, trackLabels, }: {
67
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  view: {
68
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  pinnedTracks: T[];
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  unpinnedTracks: T[];
@@ -72,5 +77,4 @@ export declare function renderViewTracks<T extends SvgExportTrack>({ view, opts,
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  theme: ThemeOptions | undefined;
73
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  textHeight: number;
74
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  trackLabels: TrackLabelMode;
75
- reserveLegendWidth?: boolean;
76
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  }): Promise<ViewTracksSvg<T>>;
@@ -1,34 +1,33 @@
1
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  import { awaitSvgRenders } from '@jbrowse/core/svg/svgReady';
2
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  import { max } from '@jbrowse/core/util';
3
- import { totalHeight } from './util.js';
3
+ import { svgLegendGutterWidth } from '@jbrowse/display-kit/renderDisplaySvg';
4
+ import { labelOffset, totalHeight, trackBoxOffsets } from './util.js';
4
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  /**
5
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  * One view's worth of exported track bodies: which tracks are in, their
6
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  * rendered SVG, and how tall the stack ends up.
7
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  *
8
- * It exists to own the two orderings that each of the three view exports got
9
- * wrong at least once, because neither is visible at a call site that merely
10
- * lists the same statements in some order:
9
+ * It exists to own an ordering that each of the three view exports got wrong at
10
+ * least once, because it is not visible at a call site that merely lists the
11
+ * same statements in some order: the geometry is measured **after** the
12
+ * awaits.
11
13
  *
12
- * - `legendWidth` is measured **before** the awaits, because it is an input to
13
- * them: a display draws its legend beside its body or floating over it
14
- * depending on whether the container reserved room. That is why
15
- * `svgLegendWidth` is specified as a function of the *settings* and not of
16
- * the loaded data — see LinearHicDisplay's implementation.
17
- * - `tracksHeight` is measured **after** them. A display whose height follows
18
- * its data (grow mode; `LinearMultiRowFeatureDisplay` is `nrow *
19
- * effectiveRowHeight`) only reaches its final height once `renderSvg`'s
20
- * readiness wait resolves, and `SVGTracks` re-reads `displays[0].height`
21
- * later still. Measuring up front sized the canvas for the pre-fetch height
22
- * and the taller bodies ran off the bottom of the export — and in the
23
- * breakpoint-split export it also desynced the overlay anchors, resolved
24
- * after, from the view tops, which weren't.
14
+ * - `tracksHeight`: a display whose height follows its data (grow mode;
15
+ * `LinearMultiRowFeatureDisplay` is `nrow * effectiveRowHeight`) only reaches
16
+ * its final height once `renderSvg`'s readiness wait resolves, and
17
+ * `SVGTracks` re-reads `displays[0].height` later still. Measuring up front
18
+ * sized the canvas for the pre-fetch height and the taller bodies ran off the
19
+ * bottom of the export — and in the breakpoint-split export it also desynced
20
+ * the overlay anchors, resolved after, from the view tops, which weren't.
21
+ * - `legendWidth`: most keys list what was loaded, and on a headless export
22
+ * (jbrowse-img) nothing has loaded before the waits. Measured after, a track
23
+ * with no key reserves nothing and the figure has no empty strip.
25
24
  *
26
25
  * The minimized filter and the track order are here for the same reason: the
27
26
  * reserved height, the rendered bodies, the label gutter and (breakpoint-split)
28
27
  * the ribbon anchors must all be derived from one list, and pinned tracks are
29
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  * drawn at the top of a view on screen.
30
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  */
31
- export async function renderViewTracks({ view, opts, theme, textHeight, trackLabels, reserveLegendWidth = false, }) {
30
+ export async function renderViewTracks({ view, opts, theme, textHeight, trackLabels, }) {
32
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  // Partitioned before anything is measured, so a skipped track reserves no
33
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  // height and takes no place in the label gutter — the alternative is a figure
34
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  // with a labelled empty band where the track would have been. One pass, so
@@ -42,25 +41,39 @@ export async function renderViewTracks({ view, opts, theme, textHeight, trackLab
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  (track.displays[0]?.renderSvg ? tracks : skippedTracks).push(track);
43
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  }
44
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  }
45
- const legendWidth = reserveLegendWidth
46
- ? max(tracks.map(track => track.displays[0].svgLegendWidth?.() ?? 0), 0)
47
- : 0;
48
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  // `awaitSvgRenders` over `Promise.all`: a track whose data won't load fails
49
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  // the export, and a view with three broken tracks should say so once rather
50
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  // than name whichever rejected first
51
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  const displayResults = await awaitSvgRenders(tracks.map(async (track) => ({
52
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  track,
53
- result: await track.displays[0].renderSvg({
54
- ...opts,
55
- theme,
56
- legendWidth,
57
- }),
49
+ result: await track.displays[0].renderSvg({ ...opts, theme }),
58
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  })));
51
+ const tracksHeight = totalHeight(tracks, trackLabels, textHeight);
52
+ const keyed = tracks.map(track => !track.displays[0].regionTooLarge &&
53
+ svgLegendGutterWidth(track.displays[0], theme, Infinity) > 0);
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+ const bodyTops = trackBoxOffsets(tracks, trackLabels, textHeight).map((top, i) => top + labelOffset(tracks[i], trackLabels, textHeight));
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+ // A key runs from its body's top to the next keyed body's, or to the foot of
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+ // the stack, so a long key beside a short track carries on past the unkeyed
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+ // tracks below it before it cuts to "+N more".
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+ const legendHeights = keyed.map((isKeyed, i) => {
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+ const next = keyed.findIndex((k, j) => k && j > i);
60
+ return isKeyed
61
+ ? (next === -1 ? tracksHeight : bodyTops[next]) - bodyTops[i]
62
+ : undefined;
63
+ });
59
64
  return {
60
65
  tracks,
61
- displayResults,
62
- tracksHeight: totalHeight(tracks, textHeight, trackLabels),
63
- legendWidth,
66
+ displayResults: displayResults.map((r, i) => ({
67
+ ...r,
68
+ legendHeight: legendHeights[i],
69
+ })),
70
+ tracksHeight,
71
+ legendWidth: max(tracks.map((track, i) => {
72
+ const height = legendHeights[i];
73
+ return height === undefined
74
+ ? 0
75
+ : svgLegendGutterWidth(track.displays[0], theme, height);
76
+ }), 0),
64
77
  skippedTracks,
65
78
  };
66
79
  }
@@ -1,17 +1,14 @@
1
1
  import { jsx as _jsx } from "react/jsx-runtime";
2
2
  import { memo, useCallback, useEffect, useRef, useSyncExternalStore, } from 'react';
3
+ import { SvgThemeProviders } from '@jbrowse/core/svg/SvgThemeProviders';
3
4
  import { exportMargin } from '@jbrowse/core/svg/constants';
5
+ import { svgNodeId } from '@jbrowse/core/svg/svgId';
4
6
  import { svgTrackName } from '@jbrowse/core/svg/trackNames';
5
- import { StyleThemeProvider } from '@jbrowse/core/ui/PaletteContext';
6
- import { resolveStyleTheme } from '@jbrowse/core/ui/styleTheme';
7
- import { createJBrowseTheme } from '@jbrowse/core/ui/theme';
8
7
  import { getSession } from '@jbrowse/core/util';
9
8
  import { useFetch } from '@jbrowse/core/util/useFetch';
10
- import { isAlive } from '@jbrowse/mobx-state-tree';
11
- import { ThemeProvider } from '@mui/material';
9
+ import { getSnapshot, isAlive } from '@jbrowse/mobx-state-tree';
12
10
  import { reaction } from 'mobx';
13
- import SVGRowHeader from './SVGRowHeader.js';
14
- import SVGView from './SVGView.js';
11
+ import SVGStackedRow from './SVGStackedRow.js';
15
12
  import { useFrozenFigureContract, useOneFigurePerView, } from './figureContract.js';
16
13
  import { renderViewTracks } from './renderViewTracks.js';
17
14
  import { defaultTextHeight, getRowHeaderLayout, trackLabelLeftOffset, } from './util.js';
@@ -19,12 +16,11 @@ import { defaultTextHeight, getRowHeaderLayout, trackLabelLeftOffset, } from './
19
16
  * One figure: every visible track rendered to SVG elements, and the geometry
20
17
  * that lays them out.
21
18
  *
22
- * `renderViewTracks` owns the two orderings this cannot state for itself — the
23
- * legend gutter measured before the renders (a display draws its key beside the
24
- * plot or floating over it depending on whether the container reserved room),
25
- * the stack height after them (a display whose height follows its data only
26
- * reaches its final height once its readiness wait resolves). Everything read
27
- * below is read after the awaits for the same reason.
19
+ * `renderViewTracks` owns the ordering this cannot state for itself: the stack
20
+ * height and the legend gutter are measured after the renders, since a
21
+ * display's height and its key follow data that lands only once its readiness
22
+ * wait resolves. Everything read below is read after the awaits for the same
23
+ * reason.
28
24
  */
29
25
  async function renderFigure(view, opts) {
30
26
  const { fontSize, rulerHeight, trackLabels, rasterizeLayers, showScalebar } = opts;
@@ -42,9 +38,6 @@ async function renderFigure(view, opts) {
42
38
  theme,
43
39
  textHeight,
44
40
  trackLabels,
45
- // an inline figure has room to give: a legend sits beside the plot rather
46
- // than over it
47
- reserveLegendWidth: true,
48
41
  });
49
42
  // the room the row header needs *above* its own origin — it draws the assembly
50
43
  // name and the scalebar at negative y, so the caller reserves the band and
@@ -64,7 +57,6 @@ async function renderFigure(view, opts) {
64
57
  height: bandHeight + rulerHeight + tracksHeight + opts.margin,
65
58
  bandHeight,
66
59
  tracksHeight,
67
- legendWidth,
68
60
  trackLabelOffset,
69
61
  textHeight,
70
62
  locstring: view.visibleLocStrings,
@@ -87,17 +79,16 @@ async function renderFigure(view, opts) {
87
79
  * render. Where it matters, this line is the only thing holding the two halves
88
80
  * together.
89
81
  *
90
- * Both providers, as `wrapSvgExport` mounts for the file path, and for the same
91
- * reason: the chrome takes its colors from the Material UI theme and a
92
- * `makeStyles` component would take its own from the style theme, so a figure
93
- * mounted in a host that installs neither would otherwise draw itself in
94
- * JBrowse's *default light* theme whatever the session is set to.
82
+ * The export's theme providers, as the file path mounts them: a host that
83
+ * installs neither would otherwise get JBrowse's default light theme whatever
84
+ * the session is set to.
95
85
  *
96
86
  * No background rect, unlike a file — that has nothing behind it, and a figure
97
- * in a page has the page. No `resetSvgClipIds` either, and that is the opposite
98
- * decision from the file path on purpose: the counter is document-global, so
99
- * resetting it here would renumber ids that a figure already on the page is
100
- * pointing at. Letting it run is what makes several live figures unique.
87
+ * in a page has the page. No `withFreshSvgClipIds` either, and that is the
88
+ * opposite decision from the file path on purpose: the counter is
89
+ * document-global, so restarting it here would reuse ids that a figure already
90
+ * on the page is pointing at. Letting it run is what makes several live figures
91
+ * unique.
101
92
  */
102
93
  const FrozenSvgFigure = memo(function FrozenSvgFigure({ view, snapshot, }) {
103
94
  const { width, height, margin, theme } = snapshot;
@@ -105,20 +96,14 @@ const FrozenSvgFigure = memo(function FrozenSvgFigure({ view, snapshot, }) {
105
96
  // INSIDE the tree, which the memo above is not between
106
97
  const ref = useRef(null);
107
98
  useFrozenFigureContract(ref, snapshot);
108
- return (_jsx(ThemeProvider, { theme: createJBrowseTheme(theme), children: _jsx(StyleThemeProvider, { theme: resolveStyleTheme({ configTheme: theme }), children: _jsx("svg", { ref: ref, width: width, height: height, viewBox: `0 0 ${width} ${height}`,
109
- // It is a vector, so a narrower container scales it rather than
110
- // clipping it; the height attribute stays, so a box reserved for it
111
- // does not change size when that happens. Deliberately not a prop:
112
- // anything passed per-render would have to reach past the memo above,
113
- // which is the one thing holding the figure's two halves together. A
114
- // host that wants other sizing wraps this in a box of its own.
115
- style: { display: 'block', maxWidth: '100%' }, children: _jsx("g", { transform: `translate(${margin} ${snapshot.bandHeight})`, children: _jsx(SVGView, { view: view, displayResults: snapshot.displayResults, header: _jsx(SVGRowHeader, { view: view, fontSize: snapshot.fontSize, rulerHeight: snapshot.rulerHeight, showScalebar: snapshot.showScalebar }), fontSize: snapshot.fontSize, textHeight: snapshot.textHeight, trackLabels: snapshot.trackLabels, trackLabelOffset: snapshot.trackLabelOffset,
116
- // the row header is exactly the ruler, so the bodies start at its
117
- // height
118
- contentTop: snapshot.rulerHeight, tracksHeight: snapshot.tracksHeight, showGridlines: snapshot.showGridlines,
119
- // the left gutter the per-track clip may bleed into, so content
120
- // drawn left of zero — a wiggle's y-axis — survives
121
- leftBuffer: snapshot.margin, legendWidth: snapshot.legendWidth }) }) }) }) }));
99
+ return (_jsx(SvgThemeProviders, { theme: theme, children: _jsx("svg", { ref: ref, width: width, height: height, viewBox: `0 0 ${width} ${height}`,
100
+ // It is a vector, so a narrower container scales it rather than
101
+ // clipping it; the height attribute stays, so a box reserved for it
102
+ // does not change size when that happens. Deliberately not a prop:
103
+ // anything passed per-render would have to reach past the memo above,
104
+ // which is the one thing holding the figure's two halves together. A
105
+ // host that wants other sizing wraps this in a box of its own.
106
+ style: { display: 'block', maxWidth: '100%' }, children: _jsx(SVGStackedRow, { view: view, rendered: snapshot, top: snapshot.bandHeight, margin: margin, fontSize: snapshot.fontSize, textHeight: snapshot.textHeight, rulerHeight: snapshot.rulerHeight, trackLabels: snapshot.trackLabels, trackLabelOffset: snapshot.trackLabelOffset, showGridlines: snapshot.showGridlines, showScalebar: snapshot.showScalebar }) }) }));
122
107
  });
123
108
  /**
124
109
  * What "the figure is out of date" means, as a string.
@@ -135,17 +120,26 @@ const FrozenSvgFigure = memo(function FrozenSvgFigure({ view, snapshot, }) {
135
120
  * question about regions and is true before a track is instantiated (the first
136
121
  * figure then draws a header over nothing, and nothing else ever changes to
137
122
  * correct it); **their heights and minimized flags**, since the geometry is
138
- * derived from them; **the width**, since a resize can widen the canvas without
123
+ * derived from them; **their configs**, since a display's settings are slots on
124
+ * the track config and a shown track's snapshot spells that config as its id;
125
+ * **the legend sections a reader dismissed** and **the per-group state**
126
+ * (hidden sections, collapses, height overrides: `groupStateKey`), which are
127
+ * volatile and in no snapshot; **the reload counter**, since a Retry or a Force
128
+ * load leaves every snapshot as it was while the figure has an error or a
129
+ * too-large note to replace; **the view's coloring toggles** (`colorByFrame`,
130
+ * `showAminoAcids`), named one by one because the view's own snapshot moves
131
+ * every pan frame; **the width**, since a resize can widen the canvas without
139
132
  * moving the locus; **the theme**, since each display bakes colors into its own
140
133
  * bodies, so a figure from the other mode is not stale but unreadable; and **the
141
134
  * highlight bands**, which are drawn in the figure and are the one thing in it a
142
135
  * reader adds without navigating anywhere.
143
136
  *
144
- * A plugin's own overlay (grid-bookmark's bookmarks, through
145
- * `LinearGenomeView-HighlightSVGComponent`) is state this cannot see, so a
146
- * bookmark added under a drawn figure shows up at its next redraw rather than at
147
- * once. Subscribing from inside the figure is the thing that must not happen —
148
- * see the note at the top of the file.
137
+ * A plugin's own overlay, through `LinearGenomeView-HighlightSVGComponent`, is
138
+ * state this cannot see, so a change to it shows up at the figure's next
139
+ * redraw rather than at once. So does a track's vertical scroll, which moves
140
+ * every wheel frame and has no settled copy to key on. Subscribing from inside
141
+ * the figure is the thing that must not happen — see the note at the top of
142
+ * the file.
149
143
  */
150
144
  function figureKey(view, themeName) {
151
145
  // A closed view is not an error, it is a host doing an ordinary thing in an
@@ -156,10 +150,10 @@ function figureKey(view, themeName) {
156
150
  // throw a TypeError inside the reaction, where MobX swallows it. No key means
157
151
  // no figure, which is what a host that closed the view wanted anyway.
158
152
  //
159
- // `view.width` throws by design before the view has been measured, and
160
- // `ready` is the gate that says it has been — and that there are regions to
161
- // draw, which is the second async step `initialized` does not cover
162
- if (!isAlive(view) || !view.ready) {
153
+ // `view.width` throws by design before the view has been measured. `status`
154
+ // is ready only once it has been AND there are regions to draw — `ready` is
155
+ // also true for a view nothing has told where to look, measured or not
156
+ if (!isAlive(view) || view.status.type !== 'ready') {
163
157
  return '';
164
158
  }
165
159
  const session = getSession(view);
@@ -167,14 +161,22 @@ function figureKey(view, themeName) {
167
161
  view.coarseVisibleLocStrings,
168
162
  view.coarseBpPerPx,
169
163
  view.width,
170
- view.tracks.map(track => [
171
- track.configuration.trackId,
172
- track.minimized,
173
- track.displays[0]?.height,
174
- ]),
164
+ view.tracks.map(track => {
165
+ const display = track.displays[0];
166
+ return [
167
+ getSnapshot(track),
168
+ getSnapshot(track.configuration),
169
+ display?.height,
170
+ display?.dismissedLegendSections,
171
+ display?.groupStateKey,
172
+ display?.reloadCounter,
173
+ ];
174
+ }),
175
+ view.colorByFrame,
176
+ view.showAminoAcids,
175
177
  session.getActiveThemeOptions?.(themeName),
176
- session.highlightsVisible ? view.highlight : false,
177
- view.labelsVisible,
178
+ session.highlightsVisible ? view.highlights : false,
179
+ session.highlightLabelsVisible,
178
180
  ]);
179
181
  }
180
182
  /**
@@ -212,25 +214,7 @@ function useFigureKey(view, themeName) {
212
214
  export function useViewSvgFigure(view, { fontSize = 12, rulerHeight = 30, trackLabels = 'offset', showGridlines = true, showScalebar = true, rasterizeLayers = false, margin = exportMargin, themeName, } = {}) {
213
215
  const key = useFigureKey(view, themeName);
214
216
  useOneFigurePerView(view);
215
- const { data: snapshot, error, isLoading, } = useFetch(
216
- // Every option is in the key by value, so an inline options object costs
217
- // nothing and a changed option redraws. A null key is `useFetch`'s own "not
218
- // yet", which is what an unready view reports.
219
- key
220
- ? [
221
- 'lgv-svg-figure',
222
- key,
223
- JSON.stringify([
224
- fontSize,
225
- rulerHeight,
226
- trackLabels,
227
- showGridlines,
228
- showScalebar,
229
- rasterizeLayers,
230
- margin,
231
- ]),
232
- ]
233
- : null, () => renderFigure(view, {
217
+ const opts = {
234
218
  fontSize,
235
219
  rulerHeight,
236
220
  trackLabels,
@@ -239,7 +223,20 @@ export function useViewSvgFigure(view, { fontSize = 12, rulerHeight = 30, trackL
239
223
  rasterizeLayers,
240
224
  margin,
241
225
  themeName,
242
- }));
226
+ };
227
+ const { data: snapshot, error, isLoading, } = useFetch(
228
+ // Every option is in the key by value, so an inline options object costs
229
+ // nothing and a changed option redraws. The view's id too: two views can
230
+ // share every other term. A null key is `useFetch`'s own "not yet", which
231
+ // is what an unready view reports.
232
+ key
233
+ ? [
234
+ 'lgv-svg-figure',
235
+ svgNodeId(view),
236
+ key,
237
+ JSON.stringify(opts),
238
+ ]
239
+ : null, () => renderFigure(view, opts));
243
240
  // Written in an effect and read during render, which is the order that makes
244
241
  // it work: a key change clears `data` on the render where the ref still holds
245
242
  // the previous commit's size, so the host's box keeps the height it had rather
@@ -1,20 +1,28 @@
1
1
  import type { TrackLabelMode } from '../types.ts';
2
2
  import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
3
3
  import type { TrackCatalog } from '@jbrowse/core/util';
4
+ import type { LgvSvgExportable } from '@jbrowse/display-kit/renderDisplaySvg';
5
+ import type { ExportTextStyle } from '@jbrowse/display-kit/types';
4
6
  import type { ReactNode } from 'react';
7
+ type SidebarDisplay = Pick<LgvSvgExportable, 'svgSidebarWidth'>;
5
8
  interface TrackHeights {
6
- displays: {
9
+ displays: ({
7
10
  height: number;
8
- }[];
11
+ prefersOffset?: boolean;
12
+ } & SidebarDisplay)[];
9
13
  }
10
14
  export interface SvgDisplayResult {
11
15
  track: {
12
16
  configuration: AnyConfigurationModel;
13
- displays: {
17
+ displays: ({
14
18
  height: number;
15
- }[];
19
+ regionTooLarge?: boolean;
20
+ drawsGenomicCoordinates?: boolean;
21
+ } & SidebarDisplay)[];
16
22
  };
17
23
  result: ReactNode;
24
+ /** the room its key has in the export's legend gutter, absent for no key */
25
+ legendHeight?: number;
18
26
  }
19
27
  export declare const trackSpacing = 2;
20
28
  export declare function gridlineTickXs(model: {
@@ -58,6 +66,7 @@ export declare function getRowHeaderLayout({ fontSize, showScalebar, }: {
58
66
  assemblyLabelBaselineY: number;
59
67
  bandHeight: number;
60
68
  };
69
+ export type HeaderLayout = ReturnType<typeof getHeaderLayout>;
61
70
  export declare function getHeaderLayout({ fontSize, showCytobands, rulerHeight, }: {
62
71
  fontSize: number;
63
72
  showCytobands: boolean;
@@ -71,25 +80,32 @@ export declare function getHeaderLayout({ fontSize, showCytobands, rulerHeight,
71
80
  };
72
81
  export declare const RULER_MAJOR_TICK = 5;
73
82
  export declare const RULER_MINOR_TICK = 3;
74
- export declare const RULER_TICK_FONT_SIZE = 11;
75
83
  export declare function getRulerLayout(rulerHeight: number): {
76
84
  tickTopY: number;
77
85
  numbersBaselineY: number;
78
86
  };
79
87
  export declare const refNameLabelBoxHeight: number;
80
88
  export declare const refNameLabelBaselineY: number;
81
- export declare function labelOffset(trackLabels: TrackLabelMode, textHeight: number): number;
89
+ export declare function trackLabelMode(track: {
90
+ displays: ({
91
+ prefersOffset?: boolean;
92
+ } & SidebarDisplay)[];
93
+ }, trackLabels: TrackLabelMode): TrackLabelMode;
94
+ export declare function labelOffset(track: TrackHeights, trackLabels: TrackLabelMode, textHeight: number): number;
95
+ interface SidebarTrack {
96
+ configuration: AnyConfigurationModel;
97
+ displays: SidebarDisplay[];
98
+ }
82
99
  export declare const TRACK_LABEL_GAP = 40;
83
100
  export declare function trackLabelLeftOffset({ tracks, trackLabels, fontSize, fontFamily, session, }: {
84
- tracks: {
85
- configuration: AnyConfigurationModel;
86
- }[];
101
+ tracks: SidebarTrack[];
87
102
  trackLabels: TrackLabelMode;
88
103
  fontSize: number;
89
104
  fontFamily?: string;
90
105
  session: TrackCatalog;
91
106
  }): number;
92
- export declare function trackBoxHeight(track: TrackHeights, textOffset: number): number;
93
- export declare function trackBoxOffsets(tracks: TrackHeights[], textOffset: number): number[];
94
- export declare function totalHeight(tracks: TrackHeights[], textHeight: number, trackLabels: TrackLabelMode): number;
107
+ export declare function trackSidebarWidth(track: Pick<SidebarTrack, 'displays'>, text?: ExportTextStyle): number;
108
+ export declare function trackBoxHeight(track: TrackHeights, trackLabels: TrackLabelMode, textHeight: number): number;
109
+ export declare function trackBoxOffsets(tracks: TrackHeights[], trackLabels: TrackLabelMode, textHeight: number): number[];
110
+ export declare function totalHeight(tracks: TrackHeights[], trackLabels: TrackLabelMode, textHeight: number): number;
95
111
  export {};